diff --git a/data/1000genomes/1000genomesbioschemas.jsonld b/data/1000genomes/1000genomesbioschemas.jsonld index dcd80bab4ad29..9e508b36bf0ae 100644 --- a/data/1000genomes/1000genomesbioschemas.jsonld +++ b/data/1000genomes/1000genomesbioschemas.jsonld @@ -37,16 +37,16 @@ "@id": "edam:operation_3202" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_3196" } ], "sc:name": "1000Genomes", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.internationalgenome.org" diff --git a/data/1000genomes_assembly_converter/1000genomes_assembly_converterbioschemas.jsonld b/data/1000genomes_assembly_converter/1000genomes_assembly_converterbioschemas.jsonld index c5c96d7a8541f..34f80c26457ef 100644 --- a/data/1000genomes_assembly_converter/1000genomes_assembly_converterbioschemas.jsonld +++ b/data/1000genomes_assembly_converter/1000genomes_assembly_converterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Map your data to the current assembly.", "sc:name": "1000Genomes assembly converter", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://browser.1000genomes.org/tools.html", diff --git a/data/1000genomes_data_slicer/1000genomes_data_slicerbioschemas.jsonld b/data/1000genomes_data_slicer/1000genomes_data_slicerbioschemas.jsonld index 79a9b188209b9..3179208bde53f 100644 --- a/data/1000genomes_data_slicer/1000genomes_data_slicerbioschemas.jsonld +++ b/data/1000genomes_data_slicer/1000genomes_data_slicerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Get a subset of data from a BAM or VCF file.", "sc:name": "1000Genomes data slicer", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://browser.1000genomes.org/tools.html", diff --git a/data/1000genomes_id_history_converter/1000genomes_id_history_converterbioschemas.jsonld b/data/1000genomes_id_history_converter/1000genomes_id_history_converterbioschemas.jsonld index 4d30e976e11d6..553dba3710070 100644 --- a/data/1000genomes_id_history_converter/1000genomes_id_history_converterbioschemas.jsonld +++ b/data/1000genomes_id_history_converter/1000genomes_id_history_converterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Convert a set of Ensembl IDs from a previous release into their current equivalents.", "sc:name": "1000Genomes ID history converter", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "EMBL-EBI", diff --git a/data/1000genomes_variation_pattern_finder/1000genomes_variation_pattern_finderbioschemas.jsonld b/data/1000genomes_variation_pattern_finder/1000genomes_variation_pattern_finderbioschemas.jsonld index 574aa93b09d27..8412709e1e90c 100644 --- a/data/1000genomes_variation_pattern_finder/1000genomes_variation_pattern_finderbioschemas.jsonld +++ b/data/1000genomes_variation_pattern_finder/1000genomes_variation_pattern_finderbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:description": "Identify variation patterns in a chromosomal region of interest for different individuals.", "sc:name": "1000Genomes Variation Pattern Finder", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://browser.1000genomes.org/tools.html", diff --git a/data/13check_rna/13check_rnabioschemas.jsonld b/data/13check_rna/13check_rnabioschemas.jsonld index 4d48c7375c9e9..5a88ab0fc492f 100644 --- a/data/13check_rna/13check_rnabioschemas.jsonld +++ b/data/13check_rna/13check_rnabioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/13Check_RNA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "J. A. Vila", - "A. A. Icazatti" + "A. A. Icazatti", + "J. A. Vila" ], "sc:additionalType": "Library", "sc:description": "Tool to evaluate 13C chemical shift assignments of RNA.", "sc:license": "MIT", "sc:name": "13Check_RNA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/BIOS-IMASL/13Check_RNA" } \ No newline at end of file diff --git a/data/2d-mh/2d-mhbioschemas.jsonld b/data/2d-mh/2d-mhbioschemas.jsonld index 416e3a1837da6..5762a76bca095 100644 --- a/data/2d-mh/2d-mhbioschemas.jsonld +++ b/data/2d-mh/2d-mhbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/2d-mh", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Xiao Lab", - "Xuan Xiao" + "Xuan Xiao", + "Xiao Lab" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:20696175", @@ -20,8 +20,8 @@ "sc:name": "2D-MH", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.jci-bioinfo.cn/pplot/2D-MH" } \ No newline at end of file diff --git a/data/2d-page/2d-pagebioschemas.jsonld b/data/2d-page/2d-pagebioschemas.jsonld index f76840832ab3d..7ad572deec58c 100644 --- a/data/2d-page/2d-pagebioschemas.jsonld +++ b/data/2d-page/2d-pagebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "2D-PAGE database.", "sc:name": "2D-PAGE", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "University of Siena, Italy", "sc:url": "http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi" diff --git a/data/2dprot/2dprotbioschemas.jsonld b/data/2dprot/2dprotbioschemas.jsonld index 68cb962f2bdc0..1549d9da792d0 100644 --- a/data/2dprot/2dprotbioschemas.jsonld +++ b/data/2dprot/2dprotbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Visualization of protein secondary structure via 2D diagrams. The 2D diagrams are based on whole protein family and they take into account 2D structure of the protein family members.", "sc:name": "2DProt", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://78.128.250.85/2DProt/" } \ No newline at end of file diff --git a/data/2dss/2dssbioschemas.jsonld b/data/2dss/2dssbioschemas.jsonld index 02409dc0a3dc9..6c458256e5183 100644 --- a/data/2dss/2dssbioschemas.jsonld +++ b/data/2dss/2dssbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Juliana S.. Bernardes", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:description": "Web server for protein secondary structure visualization.", "sc:license": "Unlicense", "sc:name": "2dSS", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genome.lcqb.upmc.fr/2dss/" } \ No newline at end of file diff --git a/data/2struccompare/2struccomparebioschemas.jsonld b/data/2struccompare/2struccomparebioschemas.jsonld index 3c41556183171..bcb3ab3db25ae 100644 --- a/data/2struccompare/2struccomparebioschemas.jsonld +++ b/data/2struccompare/2struccomparebioschemas.jsonld @@ -13,27 +13,27 @@ "@id": "https://bio.tools/2StrucCompare", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Robert W. Janes", - "Elliot Drew" + "Elliot Drew", + "Robert W. Janes" ], "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:citation": [ - "pmcid:PMC6602421", "pubmed:31114904", { "@id": "https://doi.org/10.1093/NAR/GKZ456" - } + }, + "pmcid:PMC6602421" ], "sc:description": "Webserver for the comparison of secondary structure algorithms and the secondary structure of protein structures.", "sc:featureList": [ { - "@id": "edam:operation_2488" + "@id": "edam:operation_0319" }, { - "@id": "edam:operation_0319" + "@id": "edam:operation_2488" }, { "@id": "edam:operation_0267" @@ -42,9 +42,9 @@ "sc:license": "Unlicense", "sc:name": "2StrucCompare", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://2struccompare.cryst.bbk.ac.uk/index.php" }, diff --git a/data/3d-blast/3d-blastbioschemas.jsonld b/data/3d-blast/3d-blastbioschemas.jsonld index 388e1ddb10bf4..82ef4b797807f 100644 --- a/data/3d-blast/3d-blastbioschemas.jsonld +++ b/data/3d-blast/3d-blastbioschemas.jsonld @@ -17,11 +17,11 @@ "Web application" ], "sc:citation": [ + "pmcid:PMC1868941", + "pubmed:17335583", { "@id": "https://doi.org/10.1186/gb-2007-8-3-r31" - }, - "pmcid:PMC1868941", - "pubmed:17335583" + } ], "sc:description": "3D-BLAST is a very fast and accurate method for discovering the homologous proteins and evolutionary classifications of a newly determined protein structure.", "sc:featureList": { @@ -29,9 +29,9 @@ }, "sc:name": "3D-BLAST beta", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://3d-blast.life.nctu.edu.tw/", "sc:version": "1.02" diff --git a/data/3d-dart/3d-dartbioschemas.jsonld b/data/3d-dart/3d-dartbioschemas.jsonld index f845409bb55ff..1cbf7dc848857 100644 --- a/data/3d-dart/3d-dartbioschemas.jsonld +++ b/data/3d-dart/3d-dartbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-7369-1322", - "@type": "schema:Organization" - }, { "@id": "https://bio.tools/3d-dart", "@type": "sc:SoftwareApplication", @@ -26,8 +22,8 @@ "sc:description": "A web server for generation of 3D-structural DNA models with a defined conformation by providing control over both ‘global’ and ‘local’ conformational features.", "sc:name": "3D-DART", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": { @@ -35,6 +31,10 @@ }, "sc:url": "https://milou.science.uu.nl/services/3DDART/", "sc:version": "1" + }, + { + "@id": "http://orcid.org/0000-0001-7369-1322", + "@type": "schema:Organization" } ] } \ No newline at end of file diff --git a/data/3d-e-chem/3d-e-chembioschemas.jsonld b/data/3d-e-chem/3d-e-chembioschemas.jsonld index f383bf13bd724..23587fc5b0416 100644 --- a/data/3d-e-chem/3d-e-chembioschemas.jsonld +++ b/data/3d-e-chem/3d-e-chembioschemas.jsonld @@ -13,17 +13,17 @@ "@id": "https://bio.tools/3d-e-chem", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "C. De. Graaf", + "S. Verhoeven", "Ross Mcguire", - "S. Verhoeven" + "C. De. Graaf" ], "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC5342320", "pubmed:28125221", { "@id": "https://doi.org/10.1021/ACS.JCIM.6B00686" - }, - "pmcid:PMC5342320" + } ], "sc:description": "Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.", "sc:featureList": [ @@ -31,17 +31,17 @@ "@id": "edam:operation_2414" }, { - "@id": "edam:operation_2406" + "@id": "edam:operation_3646" }, { - "@id": "edam:operation_3646" + "@id": "edam:operation_2406" } ], "sc:name": "3D-e-Chem-VM", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://3d-e-chem.github.io/3D-e-Chem-VM/" }, diff --git a/data/3d-footprint/3d-footprintbioschemas.jsonld b/data/3d-footprint/3d-footprintbioschemas.jsonld index 3d9dd9a040eaf..a796dca06dcb7 100644 --- a/data/3d-footprint/3d-footprintbioschemas.jsonld +++ b/data/3d-footprint/3d-footprintbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.", "sc:name": "3D-Footprint", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://floresta.eead.csic.es/3dfootprint" } \ No newline at end of file diff --git a/data/3d-partner/3d-partnerbioschemas.jsonld b/data/3d-partner/3d-partnerbioschemas.jsonld index 28c4b25d058a4..a5ca85801da87 100644 --- a/data/3d-partner/3d-partnerbioschemas.jsonld +++ b/data/3d-partner/3d-partnerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/3d-partner", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jinn-Moon Yang", - "Yu-Shu Lo" + "Yu-Shu Lo", + "Jinn-Moon Yang" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:17517763", @@ -20,9 +20,9 @@ "sc:license": "Unlicense", "sc:name": "3D-partner", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://gemdock.life.nctu.edu.tw/3d-partner/" } \ No newline at end of file diff --git a/data/3d-pssm/3d-pssmbioschemas.jsonld b/data/3d-pssm/3d-pssmbioschemas.jsonld index 6299c43ea1c9b..abedaad8a9622 100644 --- a/data/3d-pssm/3d-pssmbioschemas.jsonld +++ b/data/3d-pssm/3d-pssmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.", "sc:name": "3D-pssm", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html" } \ No newline at end of file diff --git a/data/3dbionotes/3dbionotesbioschemas.jsonld b/data/3dbionotes/3dbionotesbioschemas.jsonld index ab16731dc2418..df864b7a00b85 100644 --- a/data/3dbionotes/3dbionotesbioschemas.jsonld +++ b/data/3dbionotes/3dbionotesbioschemas.jsonld @@ -15,14 +15,14 @@ "sc:description": "Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB structures and Uniprot sequences where the protein annotations stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can be explored interactively at sequence and structural level.", "sc:name": "3DBIONOTES", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": [ + "cnb.csic.es", "ELIXIR-ES", - "INB", - "cnb.csic.es" + "INB" ], "sc:url": "http://3dbionotes.cnb.csic.es/ws", "sc:version": "v3" diff --git a/data/3dem_loupe/3dem_loupebioschemas.jsonld b/data/3dem_loupe/3dem_loupebioschemas.jsonld index 8df5fcfed4bb0..b570c192b00d7 100644 --- a/data/3dem_loupe/3dem_loupebioschemas.jsonld +++ b/data/3dem_loupe/3dem_loupebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "3DEM Loupe is a web-server that allows normal mode analysis of any uploaded electron microscopy volume. Results can be explored in 3 dimensions through animations and movies.", "sc:name": "3DEM Loupe", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://3demloupe.cnb.csic.es" diff --git a/data/3dembenchmark/3dembenchmarkbioschemas.jsonld b/data/3dembenchmark/3dembenchmarkbioschemas.jsonld index de3501ed20e6e..a1bb0e5a4d91a 100644 --- a/data/3dembenchmark/3dembenchmarkbioschemas.jsonld +++ b/data/3dembenchmark/3dembenchmarkbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Robust computational infrastructure capable of supporting the automatic and standardised benchmarking of image processing applications for cryoEM.", "sc:name": "3DEMBenchmark", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "cnb.csic.es", "sc:url": "http://i2pc.cnb.csic.es/3dembenchmark/LoadHome.htm" diff --git a/data/3did/3didbioschemas.jsonld b/data/3did/3didbioschemas.jsonld index f3d2b554514ee..13b1524dd73b1 100644 --- a/data/3did/3didbioschemas.jsonld +++ b/data/3did/3didbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The web server visualizes these interfaces along with atomic details of individual interactions using Jmol.", "sc:name": "3DID database of 3D interacting domains", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://3did.irbbarcelona.org/" } \ No newline at end of file diff --git a/data/3dligandsite/3dligandsitebioschemas.jsonld b/data/3dligandsite/3dligandsitebioschemas.jsonld index 4d527551ca892..d481e42746b59 100644 --- a/data/3dligandsite/3dligandsitebioschemas.jsonld +++ b/data/3dligandsite/3dligandsitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.", "sc:name": "3DLigandSite", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.sbg.bio.ic.ac.uk/3dligandsite" diff --git a/data/3dmem-enzyme/3dmem-enzymebioschemas.jsonld b/data/3dmem-enzyme/3dmem-enzymebioschemas.jsonld index ac7ce6524efb2..9c54d66cdb8a6 100644 --- a/data/3dmem-enzyme/3dmem-enzymebioschemas.jsonld +++ b/data/3dmem-enzyme/3dmem-enzymebioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Vassilios Burganos", "sc:additionalType": [ - "Script", - "Workbench" + "Workbench", + "Script" ], "sc:description": "This is an in-house code of the FORTH/ICE-HT Laboratory of Simulation of Advanced Materials and Processes, Patras, Greece, providing a reliable 3D reconstruction and simulation of a membrane bioreactor for lactose hydrolysis with immobilized enzymes. The membrane model is coupled to a macroscopic model of a single membrane fiber unit to produce lactose concentration profiles, lactose consumption predictions, and performance index estimates.", "sc:name": "3DMem-enzyme", diff --git a/data/3dmol/3dmolbioschemas.jsonld b/data/3dmol/3dmolbioschemas.jsonld index b7914ce1ff424..26d2bbeb3a730 100644 --- a/data/3dmol/3dmolbioschemas.jsonld +++ b/data/3dmol/3dmolbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "3Dmol.js", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://3dmol.csb.pitt.edu/" } \ No newline at end of file diff --git a/data/3dmorph/3dmorphbioschemas.jsonld b/data/3dmorph/3dmorphbioschemas.jsonld index a4f762439259d..e311221bbfb0f 100644 --- a/data/3dmorph/3dmorphbioschemas.jsonld +++ b/data/3dmorph/3dmorphbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "3DMorph", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/ElisaYork/3DMorph" } \ No newline at end of file diff --git a/data/3dproin/3dproinbioschemas.jsonld b/data/3dproin/3dproinbioschemas.jsonld index 4f5bb94bb9f27..992fbf8930342 100644 --- a/data/3dproin/3dproinbioschemas.jsonld +++ b/data/3dproin/3dproinbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view.", "sc:name": "3DProIN", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bicompute.appspot.com/" } \ No newline at end of file diff --git a/data/3dscript/3dscriptbioschemas.jsonld b/data/3dscript/3dscriptbioschemas.jsonld index 19dc283821c39..e9d6b78c5d96b 100644 --- a/data/3dscript/3dscriptbioschemas.jsonld +++ b/data/3dscript/3dscriptbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "3Dscript", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://imagej.net/3Dscript" } \ No newline at end of file diff --git a/data/3dss/3dssbioschemas.jsonld b/data/3dss/3dssbioschemas.jsonld index 1a7e207e05f3c..2b9629cebb060 100644 --- a/data/3dss/3dssbioschemas.jsonld +++ b/data/3dss/3dssbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for superposing two or more protein structures that uses RASMOL for visualization, some browser configuration is necessary.", "sc:name": "3DSS", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cluster.physics.iisc.ernet.in/3dss/options.html" } \ No newline at end of file diff --git a/data/3matrix/3matrixbioschemas.jsonld b/data/3matrix/3matrixbioschemas.jsonld index 9c7bc998a72c0..6e83372d19a51 100644 --- a/data/3matrix/3matrixbioschemas.jsonld +++ b/data/3matrix/3matrixbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.", "sc:name": "3Matrix", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://motif.stanford.edu/distributions/3matrix/" } \ No newline at end of file diff --git a/data/3motif/3motifbioschemas.jsonld b/data/3motif/3motifbioschemas.jsonld index 0fa67c98a56e2..723dc6ce7026f 100644 --- a/data/3motif/3motifbioschemas.jsonld +++ b/data/3motif/3motifbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.", "sc:name": "3Motif", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://motif.stanford.edu/distributions/3motif/" } \ No newline at end of file diff --git a/data/3omics/3omicsbioschemas.jsonld b/data/3omics/3omicsbioschemas.jsonld index cdc91c83ef36b..ecf688a6acba0 100644 --- a/data/3omics/3omicsbioschemas.jsonld +++ b/data/3omics/3omicsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web based systems biology visualization tool for integrating human transcriptomic, proteomic and metabolomic data.", "sc:name": "3Omics", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://3omics.cmdm.tw/" } \ No newline at end of file diff --git a/data/3srp/3srpbioschemas.jsonld b/data/3srp/3srpbioschemas.jsonld index 583a7c00c2c85..d843f657c541b 100644 --- a/data/3srp/3srpbioschemas.jsonld +++ b/data/3srp/3srpbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-3237-7382", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/3SRP", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Eric Charpentier", "sc:additionalType": "Workflow", "sc:author": [ - "Dimitri MEISTERMANN", { "@id": "https://orcid.org/0000-0003-3237-7382" }, - "Eric Charpentier" + "Eric Charpentier", + "Dimitri MEISTERMANN" ], "sc:description": "A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis. This 3’ Digital gene expression sequencing technique allows a precise and low-cost transcriptome profiling.\n\nThe main steps of the pipeline are:\n- Samples demultiplexing transform the raw paired-end fastq files into a single-end fastq file for each sample.\n- Alignment on refseq reference transcriptome is performed using bwa.\n- Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix.\nIf secondary analysis has been asked (providing a comparisons file), the expression matrix is normalized and differentially expressed genes (DEG) are searched using deseq2.\n- If DEG are found, annotation is performed using the database GO and KEGG.\n- A report is provided listing the main quality controls performed and the results found.", "sc:name": "3SRP", @@ -27,10 +31,6 @@ "sc:provider": "BiRD", "sc:url": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline", "sc:version": "1.0" - }, - { - "@id": "https://orcid.org/0000-0003-3237-7382", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/3uss/3ussbioschemas.jsonld b/data/3uss/3ussbioschemas.jsonld index 46c822dbac1c5..afd965fcdfd9a 100644 --- a/data/3uss/3ussbioschemas.jsonld +++ b/data/3uss/3ussbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web-server developed with the aim of retrieving 3’UTR genomic coordinates and nucleotide sequences of the transcripts assembled by standard RNA-seq analysis protocols.", "sc:name": "3USS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://circe.med.uniroma1.it/3uss_server/" diff --git a/data/4dgenome/4dgenomebioschemas.jsonld b/data/4dgenome/4dgenomebioschemas.jsonld index 47a0ee34d1b59..a0a6f4ebb5211 100644 --- a/data/4dgenome/4dgenomebioschemas.jsonld +++ b/data/4dgenome/4dgenomebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btv158", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/4DGenome", "@type": "sc:SoftwareApplication", @@ -17,10 +21,10 @@ "Web application" ], "sc:citation": [ - "pubmed:25788621", { "@id": "https://doi.org/10.1093/bioinformatics/btv158" }, + "pubmed:25788621", "pmcid:PMC4514924" ], "sc:description": "Curated database of chromatin interaction data covering five organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Plasmodium falciparum, and Saccharomyces cerevisiae.", @@ -31,14 +35,10 @@ "sc:name": "4DGenome", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://4dgenome.research.chop.edu" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btv158", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/4dxpress/4dxpressbioschemas.jsonld b/data/4dxpress/4dxpressbioschemas.jsonld index 8e8cf2df8cf46..7ae07424ca1e1 100644 --- a/data/4dxpress/4dxpressbioschemas.jsonld +++ b/data/4dxpress/4dxpressbioschemas.jsonld @@ -32,11 +32,11 @@ "@id": "edam:topic_0623" }, "sc:citation": [ - "pubmed:17916571", - "pmcid:PMC2238840", { "@id": "https://doi.org/10.1093/nar/gkm797" - } + }, + "pmcid:PMC2238840", + "pubmed:17916571" ], "sc:description": "A platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments.", "sc:featureList": { @@ -44,8 +44,8 @@ }, "sc:name": "4DXpress", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "EMBL", diff --git a/data/4mcpred-ifl/4mcpred-iflbioschemas.jsonld b/data/4mcpred-ifl/4mcpred-iflbioschemas.jsonld index 00e9583cdaeb1..1e7e56ecb3206 100644 --- a/data/4mcpred-ifl/4mcpred-iflbioschemas.jsonld +++ b/data/4mcpred-ifl/4mcpred-iflbioschemas.jsonld @@ -15,16 +15,16 @@ "Shasha Luan" ], "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": "pubmed:31099381", "sc:description": "Generic webserver for predicting N4-methylcytosine (4mC) sites.", "sc:license": "Unlicense", "sc:name": "4mcPred-IFL", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://server.malab.cn/4mcPred-IFL" diff --git a/data/4pipe4/4pipe4bioschemas.jsonld b/data/4pipe4/4pipe4bioschemas.jsonld index 10214e2953a74..4d4a0480acc49 100644 --- a/data/4pipe4/4pipe4bioschemas.jsonld +++ b/data/4pipe4/4pipe4bioschemas.jsonld @@ -25,10 +25,10 @@ "@id": "edam:topic_2885" }, { - "@id": "edam:topic_0080" + "@id": "edam:topic_0077" }, { - "@id": "edam:topic_0077" + "@id": "edam:topic_0080" } ], "sc:citation": [ @@ -46,8 +46,8 @@ "sc:license": "GPL-3.0", "sc:name": "4Pipe4", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:softwareHelp": { "@id": "https://github.com/StuntsPT/4Pipe4/" diff --git a/data/4sale/4salebioschemas.jsonld b/data/4sale/4salebioschemas.jsonld index d875161787a98..be5b1ca1c79a7 100644 --- a/data/4sale/4salebioschemas.jsonld +++ b/data/4sale/4salebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "4SALE allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis.", "sc:name": "4SALE", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://4sale.bioapps.biozentrum.uni-wuerzburg.de/index.html", "sc:version": "1.7" diff --git a/data/959_nematode_genomes/959_nematode_genomesbioschemas.jsonld b/data/959_nematode_genomes/959_nematode_genomesbioschemas.jsonld index b5de942f32592..162c3380b7316 100644 --- a/data/959_nematode_genomes/959_nematode_genomesbioschemas.jsonld +++ b/data/959_nematode_genomes/959_nematode_genomesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A community-curated semantic wiki to coordinate the sequencing efforts of individual labs to collectively sequence 959 genomes spanning the phylum Nematoda. The main goal of the wiki is to track sequencing projects that have been proposed, are in progress, or have been completed.", "sc:name": "959 Nematode Genomes", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.nematodes.org/nematodegenomes/index.php/Main_Page" } \ No newline at end of file diff --git a/data/a-madman/a-madmanbioschemas.jsonld b/data/a-madman/a-madmanbioschemas.jsonld index 374c0f87b8ffb..4bf90c63c3f40 100644 --- a/data/a-madman/a-madmanbioschemas.jsonld +++ b/data/a-madman/a-madmanbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/a-madman", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Andrea Bisognin", - "Stefania Bortoluzzi" + "Stefania Bortoluzzi", + "Andrea Bisognin" ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Open source web application and gene chip analysis automation framework for annotation-based meta-analysis of data from public repositories (NCBI GEO). It allows retrieval, annotation, organization and analysis of gene expression data from public repository. It automates several analysis steps to be accomplished to setup a working environment for conducting meta-analyses, without giving up power and flexibility.", "sc:license": "GPL-3.0", "sc:name": "A-MADMAN", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://compgen.bio.unipd.it/bioinfo/amadman/", diff --git a/data/a-o-tool/a-o-toolbioschemas.jsonld b/data/a-o-tool/a-o-toolbioschemas.jsonld index f003d791c6c21..cc976f8f60c43 100644 --- a/data/a-o-tool/a-o-toolbioschemas.jsonld +++ b/data/a-o-tool/a-o-toolbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://orcid.org/0000-0002-2585-3830", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1186/S12920-019-0524-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/a-o-tool", "@type": "sc:SoftwareApplication", @@ -25,19 +21,19 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:31122257", { "@id": "https://doi.org/10.1186/S12920-019-0524-5" }, - "pubmed:31122257", "pmcid:PMC6533699" ], "sc:description": "Exploiting orthology and de novo transcriptome assembly to refine target sequence information.", "sc:featureList": [ { - "@id": "edam:operation_3258" + "@id": "edam:operation_3644" }, { - "@id": "edam:operation_3644" + "@id": "edam:operation_3258" }, { "@id": "edam:operation_0476" @@ -46,11 +42,15 @@ "sc:license": "GPL-3.0", "sc:name": "a-o-tool", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/Julia-F-S/a-o-tool" + }, + { + "@id": "https://doi.org/10.1186/S12920-019-0524-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/a4/a4bioschemas.jsonld b/data/a4/a4bioschemas.jsonld index 17e1197c4ee34..f91ed4dd6b88f 100644 --- a/data/a4/a4bioschemas.jsonld +++ b/data/a4/a4bioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/a4", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Willem Ligtenberg", - "Tobias Verbeke" + "Tobias Verbeke", + "Willem Ligtenberg" ], "sc:additionalType": [ "Library", @@ -23,8 +23,8 @@ "sc:name": "a4", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/a4.html", "sc:version": "1.22.0" diff --git a/data/a4base/a4basebioschemas.jsonld b/data/a4base/a4basebioschemas.jsonld index c5e7fc68b18f1..559429e2464cf 100644 --- a/data/a4base/a4basebioschemas.jsonld +++ b/data/a4base/a4basebioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/a4base", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Willem Ligtenberg", - "Tobias Verbeke" + "Tobias Verbeke", + "Willem Ligtenberg" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An R package of the \"a4\" packages collection. It comprises of basic funtionalities needed to analyse Affymetrix microarray experiment results.", "sc:license": "GPL-3.0", "sc:name": "a4Base", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/a4Base.html", diff --git a/data/a4base/bioconda_a4base.yaml b/data/a4base/bioconda_a4base.yaml index 4e9fa49016ce1..769bacf8fb943 100644 --- a/data/a4base/bioconda_a4base.yaml +++ b/data/a4base/bioconda_a4base.yaml @@ -3,7 +3,6 @@ description: Automated Affymetrix Array Analysis home: https://bioconductor.org/packages/3.10/bioc/html/a4Base.html identifiers: - biotools:a4base -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-a4base diff --git a/data/a4classif/a4classifbioschemas.jsonld b/data/a4classif/a4classifbioschemas.jsonld index 49311076c5c19..c2c996e2af0b1 100644 --- a/data/a4classif/a4classifbioschemas.jsonld +++ b/data/a4classif/a4classifbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/a4classif", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Willem Ligtenberg", - "Tobias Verbeke" + "Tobias Verbeke", + "Willem Ligtenberg" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An R package of the \"a4\" packages collection. It comprises of commands using machine learning algorithms for classification work to analyse Affymetrix microarray experiment results.", "sc:license": "GPL-3.0", "sc:name": "a4Classif", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/a4Classif.html", "sc:version": "1.22.0" diff --git a/data/a4core/a4corebioschemas.jsonld b/data/a4core/a4corebioschemas.jsonld index 716f1574c0b18..340fbee00651c 100644 --- a/data/a4core/a4corebioschemas.jsonld +++ b/data/a4core/a4corebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/a4core", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Tobias Verbeke", - "Willem Ligtenberg" + "Willem Ligtenberg", + "Tobias Verbeke" ], "sc:additionalType": [ "Command-line tool", @@ -22,9 +22,9 @@ "sc:license": "GPL-3.0", "sc:name": "a4Core", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/a4Core.html", "sc:version": "1.22.0" diff --git a/data/a4core/bioconda_a4core.yaml b/data/a4core/bioconda_a4core.yaml index 7d0fd069569c4..1334e26a78163 100644 --- a/data/a4core/bioconda_a4core.yaml +++ b/data/a4core/bioconda_a4core.yaml @@ -3,7 +3,6 @@ description: Automated Affymetrix Array Analysis Core Package home: https://bioconductor.org/packages/3.10/bioc/html/a4Core.html identifiers: - biotools:a4core -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-a4core diff --git a/data/a4preproc/a4preprocbioschemas.jsonld b/data/a4preproc/a4preprocbioschemas.jsonld index 14ca26d797158..b08593479528e 100644 --- a/data/a4preproc/a4preprocbioschemas.jsonld +++ b/data/a4preproc/a4preprocbioschemas.jsonld @@ -15,16 +15,16 @@ "Willem Ligtenberg" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An R package of the \"a4\" packages collection. It is used for microarray data preprocessing where annotation information is added to experimental result data.", "sc:license": "GPL-3.0", "sc:name": "a4Preproc", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/a4Preproc.html", "sc:version": "1.22.0" diff --git a/data/a4preproc/bioconda_a4preproc.yaml b/data/a4preproc/bioconda_a4preproc.yaml index 891c52b9135bb..87e91acf85f16 100644 --- a/data/a4preproc/bioconda_a4preproc.yaml +++ b/data/a4preproc/bioconda_a4preproc.yaml @@ -3,7 +3,6 @@ description: Automated Affymetrix Array Analysis Preprocessing Package home: https://bioconductor.org/packages/3.10/bioc/html/a4Preproc.html identifiers: - biotools:a4preproc -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-a4preproc diff --git a/data/a4reporting/a4reportingbioschemas.jsonld b/data/a4reporting/a4reportingbioschemas.jsonld index cf6fa1a251ee2..7fdd4d7f460fe 100644 --- a/data/a4reporting/a4reportingbioschemas.jsonld +++ b/data/a4reporting/a4reportingbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/a4reporting", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Tobias Verbeke", - "Willem Ligtenberg" + "Willem Ligtenberg", + "Tobias Verbeke" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An R package of the \"a4\" packages collection. It provides reporting functionality.", "sc:license": "GPL-3.0", "sc:name": "a4Reporting", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/a4Reporting.html", "sc:version": "1.22.0" diff --git a/data/a4reporting/bioconda_a4reporting.yaml b/data/a4reporting/bioconda_a4reporting.yaml index 825aec23cd814..cc00205c7675f 100644 --- a/data/a4reporting/bioconda_a4reporting.yaml +++ b/data/a4reporting/bioconda_a4reporting.yaml @@ -3,7 +3,6 @@ description: Automated Affymetrix Array Analysis Reporting Package home: https://bioconductor.org/packages/3.10/bioc/html/a4Reporting.html identifiers: - biotools:a4reporting -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-a4reporting diff --git a/data/a5-miseq/a5-miseqbioschemas.jsonld b/data/a5-miseq/a5-miseqbioschemas.jsonld index 98b153e22edd9..cae7e540ad241 100644 --- a/data/a5-miseq/a5-miseqbioschemas.jsonld +++ b/data/a5-miseq/a5-miseqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "De novo assembly & analysis of Illumina sequence data, including the A5 pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to facilitate data submission to NCBI and the RAST annotation system", "sc:name": "A5-miseq", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sourceforge.net/projects/ngopt/" } \ No newline at end of file diff --git a/data/aacompident/aacompidentbioschemas.jsonld b/data/aacompident/aacompidentbioschemas.jsonld index ce801bf200e50..ab7b09f8a075b 100644 --- a/data/aacompident/aacompidentbioschemas.jsonld +++ b/data/aacompident/aacompidentbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AACompIdent", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://web.expasy.org/aacompident" } \ No newline at end of file diff --git a/data/aacompsim/aacompsimbioschemas.jsonld b/data/aacompsim/aacompsimbioschemas.jsonld index 5c032af7166df..ef2f2dd2a9fe4 100644 --- a/data/aacompsim/aacompsimbioschemas.jsonld +++ b/data/aacompsim/aacompsimbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Compare amino acid composition of a UniProtKB entry with some or all other UniProtKB entries. Several constellations are available, corresponding to various amino acid analysis techniques.", "sc:name": "AACompSim", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://web.expasy.org/aacompsim/" } \ No newline at end of file diff --git a/data/aaindexextract/aaindexextractbioschemas.jsonld b/data/aaindexextract/aaindexextractbioschemas.jsonld index 14a59174818b4..202017a57ffbc 100644 --- a/data/aaindexextract/aaindexextractbioschemas.jsonld +++ b/data/aaindexextract/aaindexextractbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK BBSRC", "EMBOSS Contributors", - "UK MRC" + "UK BBSRC", + "UK MRC", + "Wellcome Trust" ], "sc:description": "Extract amino acid property data from AAINDEX.", "sc:funder": [ - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "aaindexextract", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/aaindexloc/aaindexlocbioschemas.jsonld b/data/aaindexloc/aaindexlocbioschemas.jsonld index b30dbf19798d0..be76174cf0034 100644 --- a/data/aaindexloc/aaindexlocbioschemas.jsonld +++ b/data/aaindexloc/aaindexlocbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Machine-learning-based algorithm that uses amino acid index to predict protein subcellular localization based on its sequence.", "sc:name": "AAIndexLoc", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://aaindexloc.bii.a-star.edu.sg/" diff --git a/data/aascatterplot/aascatterplotbioschemas.jsonld b/data/aascatterplot/aascatterplotbioschemas.jsonld index 362ec33592824..478fdd85c8a8a 100644 --- a/data/aascatterplot/aascatterplotbioschemas.jsonld +++ b/data/aascatterplot/aascatterplotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "AAScatterPlot", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/WhittakerLab/AAScatterPlot", "sc:version": "1.0" diff --git a/data/aassites/aassitesbioschemas.jsonld b/data/aassites/aassitesbioschemas.jsonld index 87011b01d4773..3ec2b673c2c17 100644 --- a/data/aassites/aassitesbioschemas.jsonld +++ b/data/aassites/aassitesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Automated bioinformatics pipeline to analyse SNP containing DNA sequences mainly for finding SNPs which cause a change in the splicing pattern.", "sc:name": "AASsites", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.welcome#aassites" } \ No newline at end of file diff --git a/data/aastretch/aastretchbioschemas.jsonld b/data/aastretch/aastretchbioschemas.jsonld index 31a1fd77d1dd5..c3333d1c36c79 100644 --- a/data/aastretch/aastretchbioschemas.jsonld +++ b/data/aastretch/aastretchbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Matteo Ramazzotti", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:author": "Matteo Ramazzotti - matteo dot ramazzotti at unifi.it", "sc:citation": "pubmed:22312432", diff --git a/data/abaenrichment/abaenrichmentbioschemas.jsonld b/data/abaenrichment/abaenrichmentbioschemas.jsonld index 48efd8fb275ea..2feb143037a96 100644 --- a/data/abaenrichment/abaenrichmentbioschemas.jsonld +++ b/data/abaenrichment/abaenrichmentbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Steffi Grote", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ { "@id": "https://doi.org/10.1093/bioinformatics/btw392" }, - "pubmed:27354695", - "pmcid:PMC5048072" + "pmcid:PMC5048072", + "pubmed:27354695" ], "sc:description": "The package is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function 'aba_enrich' integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment software FUNC to perform the statistical analyses.", "sc:featureList": { @@ -35,8 +35,8 @@ "sc:license": "GPL-2.0", "sc:name": "ABAEnrichment", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ABAEnrichment.html", "sc:version": "1.4.0" diff --git a/data/abarray/abarraybioschemas.jsonld b/data/abarray/abarraybioschemas.jsonld index 51fd701bf7221..b33a2402ea4c5 100644 --- a/data/abarray/abarraybioschemas.jsonld +++ b/data/abarray/abarraybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "ABarray", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ABarray.html", "sc:version": "1.42.0" diff --git a/data/abcd/abcdbioschemas.jsonld b/data/abcd/abcdbioschemas.jsonld index 2c62d974bb068..12072e4d1bdb5 100644 --- a/data/abcd/abcdbioschemas.jsonld +++ b/data/abcd/abcdbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-5643-2668", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btt041", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/abcd", "@type": "sc:SoftwareApplication", @@ -25,10 +17,10 @@ "Desktop application" ], "sc:citation": [ - "pubmed:23357921", { "@id": "https://doi.org/10.1093/bioinformatics/btt041" }, + "pubmed:23357921", "pmcid:PMC3597143" ], "sc:contributor": { @@ -42,10 +34,18 @@ "sc:name": "AbCD", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://yunliweb.its.unc.edu/AbCD.html" + }, + { + "@id": "http://orcid.org/0000-0002-5643-2668", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btt041", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/abcpred/abcpredbioschemas.jsonld b/data/abcpred/abcpredbioschemas.jsonld index 8cc9a4f576d78..0cab448f41352 100644 --- a/data/abcpred/abcpredbioschemas.jsonld +++ b/data/abcpred/abcpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server to predict linear B cell epitope regions in an antigen sequence, using an artificial neural network. This server will assist in locating epitope regions that are useful in selecting synthetic vaccine candidates, disease diagonosis and also in allergy research.", "sc:name": "ABCpred", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://crdd.osdd.net/raghava//abcpred/" } \ No newline at end of file diff --git a/data/abeem_solver/abeem_solverbioschemas.jsonld b/data/abeem_solver/abeem_solverbioschemas.jsonld index 69394a932f84f..b2322c13771ae 100644 --- a/data/abeem_solver/abeem_solverbioschemas.jsonld +++ b/data/abeem_solver/abeem_solverbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ABEEM Solver", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-CZ", "sc:url": "http://ncbr.muni.cz/~svobodova/eem_abeem", diff --git a/data/aber-owl/aber-owlbioschemas.jsonld b/data/aber-owl/aber-owlbioschemas.jsonld index fdb82ad0776c2..6e7c84a2dab37 100644 --- a/data/aber-owl/aber-owlbioschemas.jsonld +++ b/data/aber-owl/aber-owlbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-015-0456-9", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/aber-owl", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Robert Hoehndorf", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:25627673", { "@id": "https://doi.org/10.1186/S12859-015-0456-9" }, - "pmcid:PMC4384359" + "pmcid:PMC4384359", + "pubmed:25627673" ], "sc:description": "Framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "Aber-OWL", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://aber-owl.net/#/" - }, - { - "@id": "https://doi.org/10.1186/S12859-015-0456-9", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/abi2xml/abi2xmlbioschemas.jsonld b/data/abi2xml/abi2xmlbioschemas.jsonld index ffe741ecea58e..cb30c4ce8997d 100644 --- a/data/abi2xml/abi2xmlbioschemas.jsonld +++ b/data/abi2xml/abi2xmlbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "abi2xml", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://abi2xml.sourceforge.net/", "sc:version": "1.2" diff --git a/data/abiview/abiviewbioschemas.jsonld b/data/abiview/abiviewbioschemas.jsonld index bdd4fef1031c1..18540928d79c0 100644 --- a/data/abiview/abiviewbioschemas.jsonld +++ b/data/abiview/abiviewbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "EMBOSS Contributors", "Wellcome Trust", + "EMBOSS Contributors", + "UK BBSRC", "UK MRC" ], "sc:description": "Display the trace in an ABI sequencer file.", "sc:funder": [ - "UK MRC", "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "abiview", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/abiview_ws_husar/abiview_ws_husarbioschemas.jsonld b/data/abiview_ws_husar/abiview_ws_husarbioschemas.jsonld index 64632d38f012c..4f8ca40dd7688 100644 --- a/data/abiview_ws_husar/abiview_ws_husarbioschemas.jsonld +++ b/data/abiview_ws_husar/abiview_ws_husarbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This tool reads in an ABI sequence trace file and graphically displays the results.", "sc:name": "abiview WS (husar)", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/abiview.html", "sc:version": "1" diff --git a/data/abm-tki/abm-tkibioschemas.jsonld b/data/abm-tki/abm-tkibioschemas.jsonld index 4ac7e44fb282a..ea2851b0de28d 100644 --- a/data/abm-tki/abm-tkibioschemas.jsonld +++ b/data/abm-tki/abm-tkibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Employing agent-based model (ABM) tool to simulate brain tumor growth that includes an EGFR signaling pathway together with a related cell-cycle pathway, angiogenesis and tyrosine kinase inhibitors (TKIs) treatment. The users can apply this tool to predict the responses of brain cancer to TKIs, and to reveal the dual role of angiogenesis during TKI treatment.", "sc:name": "ABM-TKI", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://sites.google.com/site/agentbasedtumormodeling/home" diff --git a/data/abmapper/abmapperbioschemas.jsonld b/data/abmapper/abmapperbioschemas.jsonld index a90245d6b2e22..4d30db303b5ec 100644 --- a/data/abmapper/abmapperbioschemas.jsonld +++ b/data/abmapper/abmapperbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping.", "sc:name": "ABMapper", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.hkbic.cuhk.edu.hk/software/abmapper" } \ No newline at end of file diff --git a/data/abps/abpsbioschemas.jsonld b/data/abps/abpsbioschemas.jsonld index b66d396edc0cf..dfcd0840a26d7 100644 --- a/data/abps/abpsbioschemas.jsonld +++ b/data/abps/abpsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3389/fphys.2018.01638", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ABPS", "@type": "sc:SoftwareApplication", @@ -16,24 +20,20 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC6258961", - "pubmed:30519191", { "@id": "https://doi.org/10.3389/fphys.2018.01638" - } + }, + "pubmed:30519191" ], "sc:description": "R Package for Calculating the Abnormal Blood Profile Score.", "sc:license": "GPL-3.0", "sc:name": "ABPS", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://cran.r-project.org/package=ABPS" - }, - { - "@id": "https://doi.org/10.3389/fphys.2018.01638", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/abra/abrabioschemas.jsonld b/data/abra/abrabioschemas.jsonld index 6fdbb0fb5dd95..5ba0dad3249aa 100644 --- a/data/abra/abrabioschemas.jsonld +++ b/data/abra/abrabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).", "sc:name": "ABRA", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/mozack/abra" } \ No newline at end of file diff --git a/data/abs-scan/abs-scanbioschemas.jsonld b/data/abs-scan/abs-scanbioschemas.jsonld index 49b3d430e9f4b..8560ba09b5344 100644 --- a/data/abs-scan/abs-scanbioschemas.jsonld +++ b/data/abs-scan/abs-scanbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ABS-Scan", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://proline.biochem.iisc.ernet.in/abscan/" } \ No newline at end of file diff --git a/data/abs/absbioschemas.jsonld b/data/abs/absbioschemas.jsonld index adb914b40a37f..cb700395e8277 100644 --- a/data/abs/absbioschemas.jsonld +++ b/data/abs/absbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-2.0", "sc:name": "ABS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "Genome BioInformatics Research Lab", "sc:url": "http://genome.imim.es/datasets/abs2005/" diff --git a/data/absseq/absseqbioschemas.jsonld b/data/absseq/absseqbioschemas.jsonld index c7117c7f23aa1..86a0838b48228 100644 --- a/data/absseq/absseqbioschemas.jsonld +++ b/data/absseq/absseqbioschemas.jsonld @@ -22,48 +22,48 @@ }, "edam:has_output": [ { - "@id": "edam:data_2884" + "@id": "edam:data_0950" }, { - "@id": "edam:data_0950" + "@id": "edam:data_2884" } ], "sc:additionalType": [ "Command-line tool", - "Library", - "Plug-in" + "Plug-in", + "Library" ], "sc:applicationSubCategory": [ { "@id": "edam:topic_3170" }, { - "@id": "edam:topic_0203" + "@id": "edam:topic_2269" }, { - "@id": "edam:topic_2269" + "@id": "edam:topic_0203" } ], "sc:citation": [ - "pmcid:PMC4973090", + "pubmed:27488180", { "@id": "https://doi.org/10.1186/s12864-016-2848-2" }, - "pubmed:27488180" + "pmcid:PMC4973090" ], "sc:description": "An R package which provides RNA-Seq analysis based on modelling absolute expression differences.", "sc:featureList": [ { - "@id": "edam:operation_2238" + "@id": "edam:operation_2426" }, { - "@id": "edam:operation_2426" + "@id": "edam:operation_3223" }, { "@id": "edam:operation_0337" }, { - "@id": "edam:operation_3223" + "@id": "edam:operation_2238" }, { "@id": "edam:operation_2495" @@ -72,9 +72,9 @@ "sc:license": "GPL-3.0", "sc:name": "ABSSeq", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ABSSeq.html", "sc:version": "1.10.0" diff --git a/data/abyss/abyssbioschemas.jsonld b/data/abyss/abyssbioschemas.jsonld index 55611115536e5..8f95f673fcbf0 100644 --- a/data/abyss/abyssbioschemas.jsonld +++ b/data/abyss/abyssbioschemas.jsonld @@ -20,8 +20,8 @@ "Mac" ], "sc:provider": [ - "bcgsc.ca", - "BC Cancer Agency Genome Sciences Centre" + "BC Cancer Agency Genome Sciences Centre", + "bcgsc.ca" ], "sc:url": "https://github.com/bcgsc/abyss/", "sc:version": "1.9.0" diff --git a/data/acacia/acaciabioschemas.jsonld b/data/acacia/acaciabioschemas.jsonld index 6081188d46d71..ec827a01408f4 100644 --- a/data/acacia/acaciabioschemas.jsonld +++ b/data/acacia/acaciabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ACACIA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://gitlab.com/psc_santos/ACACIA" } \ No newline at end of file diff --git a/data/acd/acdbioschemas.jsonld b/data/acd/acdbioschemas.jsonld index 534b3084ef805..c05804c7d9b19 100644 --- a/data/acd/acdbioschemas.jsonld +++ b/data/acd/acdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool to search a knowledge base of the most commonly used chromatographic columns to locate those with the properties best-suited to the separation at hand. The Column Selector database contains information for 254 characterized columns, along with results for >4800 systematic experiments.", "sc:name": "ACD", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.acdlabs.com/resources/freeware/colsel/" } \ No newline at end of file diff --git a/data/acdc/acdcbioschemas.jsonld b/data/acdc/acdcbioschemas.jsonld index 5a7a43daea52d..da7842194df8d 100644 --- a/data/acdc/acdcbioschemas.jsonld +++ b/data/acdc/acdcbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "Wellcome Trust", + "UK MRC", "UK BBSRC", "EMBOSS Contributors" ], "sc:description": "Test an application ACD file.", "sc:funder": [ - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "acdc", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ diff --git a/data/acdc_cell/acdc_cellbioschemas.jsonld b/data/acdc_cell/acdc_cellbioschemas.jsonld index 6f6016f190116..cc33b73f211b3 100644 --- a/data/acdc_cell/acdc_cellbioschemas.jsonld +++ b/data/acdc_cell/acdc_cellbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/acdc_cell", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Joel Dudley", - "Brian Kidd" + "Brian Kidd", + "Joel Dudley" ], "sc:additionalType": "Script", "sc:description": "Automated cell type discovery and classification through knowledge transfer.", diff --git a/data/acdc_estimation/acdc_estimationbioschemas.jsonld b/data/acdc_estimation/acdc_estimationbioschemas.jsonld index cecd308c9853a..97e18c8f68e5b 100644 --- a/data/acdc_estimation/acdc_estimationbioschemas.jsonld +++ b/data/acdc_estimation/acdc_estimationbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Markus Lux", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:author": "Markus Lux", "sc:description": "A tool to test next-generation-sequencing (NGS) data from single-cell sequencing for contamination. By using sophisticated dimensionality reduction and clustering methods, it uses tetramer profiles to differentiate between different species in a given sample.", diff --git a/data/acde/acdebioschemas.jsonld b/data/acde/acdebioschemas.jsonld index 3e35706a4e622..c6f68929d580e 100644 --- a/data/acde/acdebioschemas.jsonld +++ b/data/acde/acdebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Juan Pablo Acosta", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides a multivariate inferential analysis method for detecting DE genes. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR).", "sc:license": "GPL-3.0", "sc:name": "acde", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/acde.html", "sc:version": "1.4.0" diff --git a/data/acdpretty/acdprettybioschemas.jsonld b/data/acdpretty/acdprettybioschemas.jsonld index 0fc949a83fc66..b48bcd05d4525 100644 --- a/data/acdpretty/acdprettybioschemas.jsonld +++ b/data/acdpretty/acdprettybioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Correctly reformat an application ACD file.", "sc:funder": [ - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "acdpretty", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/acdtable/acdtablebioschemas.jsonld b/data/acdtable/acdtablebioschemas.jsonld index ea16534c8c615..71481da4cbffe 100644 --- a/data/acdtable/acdtablebioschemas.jsonld +++ b/data/acdtable/acdtablebioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Generate an HTML table of parameters from an application ACD file.", "sc:funder": [ - "Wellcome Trust", + "UK BBSRC", "UK MRC", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "acdtable", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/acdtable.html", "sc:version": "r6" diff --git a/data/acdtrace/acdtracebioschemas.jsonld b/data/acdtrace/acdtracebioschemas.jsonld index cce2f8a7282e0..c527dd0cb20e6 100644 --- a/data/acdtrace/acdtracebioschemas.jsonld +++ b/data/acdtrace/acdtracebioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", - "Wellcome Trust", "EMBOSS Contributors", + "Wellcome Trust", "UK MRC" ], "sc:description": "Trace processing of an application ACD file (for testing).", "sc:funder": [ - "UK BBSRC", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "acdtrace", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/acdtrace.html", "sc:version": "r6" diff --git a/data/acdvalid/acdvalidbioschemas.jsonld b/data/acdvalid/acdvalidbioschemas.jsonld index 8fc9fc4ce1434..8ae1d9a0fd270 100644 --- a/data/acdvalid/acdvalidbioschemas.jsonld +++ b/data/acdvalid/acdvalidbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", + "Wellcome Trust", "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Validate an application ACD file.", "sc:funder": [ - "Wellcome Trust", + "UK BBSRC", "UK MRC", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "acdvalid", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/acdvalid.html", "sc:version": "r6" diff --git a/data/ace/acebioschemas.jsonld b/data/ace/acebioschemas.jsonld index a4c15f5558373..3665808078a84 100644 --- a/data/ace/acebioschemas.jsonld +++ b/data/ace/acebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Corrects substitution errors in an Illumina archive using a k-mer trie.", "sc:name": "ACE", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/sheikhizadeh/ACE/" } \ No newline at end of file diff --git a/data/ace_gene/ace_genebioschemas.jsonld b/data/ace_gene/ace_genebioschemas.jsonld index 3cb5d9b4f6198..1afc7db36d565 100644 --- a/data/ace_gene/ace_genebioschemas.jsonld +++ b/data/ace_gene/ace_genebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It aids gene prediction accuracy evaluation. It uses GFF format to make it easy to convert gene prediction results into an analyzable format. Novel features include isoform accuracy evaluation from either the annotated gene or gene prediction perspective or both at the same time. Masking of genomic sequence which has unknown features allows gene predictions in annotated regions to be analyzed in a genomic context.", "sc:name": "AcE", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bioinformatics.org/project/?group_id=39", "sc:version": "0.5" diff --git a/data/ace_insect/ace_insectbioschemas.jsonld b/data/ace_insect/ace_insectbioschemas.jsonld index eca16b1792139..227b0e9e7fca8 100644 --- a/data/ace_insect/ace_insectbioschemas.jsonld +++ b/data/ace_insect/ace_insectbioschemas.jsonld @@ -17,16 +17,16 @@ "@id": "https://bio.tools/ace_insect", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jiapeng Luo", - "Dianhao Guo" + "Dianhao Guo", + "Jiapeng Luo" ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28693417", - "pmcid:PMC5504734", { "@id": "https://doi.org/10.1186/s12859-017-1741-6" - } + }, + "pmcid:PMC5504734", + "pubmed:28693417" ], "sc:description": "Efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data.", "sc:featureList": { @@ -34,9 +34,9 @@ }, "sc:name": "ACE", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://genome.zju.edu.cn/software/ace/" } diff --git a/data/acela/acelabioschemas.jsonld b/data/acela/acelabioschemas.jsonld index 260ffae69abb4..9bedac21a6b58 100644 --- a/data/acela/acelabioschemas.jsonld +++ b/data/acela/acelabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool that aims to reduce the human effort required to produce a gold standard corpus of named entity (NE) annotations.", "sc:name": "ACELA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.nactem.ac.uk/acela/" diff --git a/data/aceview/aceviewbioschemas.jsonld b/data/aceview/aceviewbioschemas.jsonld index 7faf006d80835..e9bcfa3347e9f 100644 --- a/data/aceview/aceviewbioschemas.jsonld +++ b/data/aceview/aceviewbioschemas.jsonld @@ -17,23 +17,23 @@ "@id": "https://bio.tools/aceview", "@type": "sc:SoftwareApplication", "edam:has_input": [ - { - "@id": "edam:data_2292" - }, { "@id": "edam:data_2803" }, { - "@id": "edam:data_1045" + "@id": "edam:data_2292" }, { - "@id": "edam:data_2704" + "@id": "edam:data_1045" }, { "@id": "edam:data_1027" }, { "@id": "edam:data_1026" + }, + { + "@id": "edam:data_2704" } ], "edam:has_output": [ @@ -41,10 +41,10 @@ "@id": "edam:data_1276" }, { - "@id": "edam:data_0916" + "@id": "edam:data_3134" }, { - "@id": "edam:data_3134" + "@id": "edam:data_0916" } ], "sc:additionalType": "Database portal", @@ -57,11 +57,11 @@ } ], "sc:citation": [ - "pmcid:PMC3272079", "pubmed:20064451", { "@id": "https://doi.org/10.1016/j.immuni.2009.10.008" - } + }, + "pmcid:PMC3272079" ], "sc:description": "A curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace).", "sc:featureList": { @@ -69,9 +69,9 @@ }, "sc:name": "AceView genes database", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "NCBI", "sc:url": "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/" diff --git a/data/acg/acgbioschemas.jsonld b/data/acg/acgbioschemas.jsonld index 5f58a5dcbb4a9..dbd254de9786c 100644 --- a/data/acg/acgbioschemas.jsonld +++ b/data/acg/acgbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ACG", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://arup.utah.edu/acg/" } \ No newline at end of file diff --git a/data/acgh/acghbioschemas.jsonld b/data/acgh/acghbioschemas.jsonld index 26d4bd1be55cc..4ecb212731920 100644 --- a/data/acgh/acghbioschemas.jsonld +++ b/data/acgh/acghbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "aCGH", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/aCGH.html", "sc:version": "1.52.0" diff --git a/data/acme/acmebioschemas.jsonld b/data/acme/acmebioschemas.jsonld index d408e1f674809..8ad471c74b883 100644 --- a/data/acme/acmebioschemas.jsonld +++ b/data/acme/acmebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-8991-6458", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/acme", "@type": "sc:SoftwareApplication", @@ -16,24 +20,20 @@ "@id": "http://orcid.org/0000-0002-8991-6458" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:16939795", "sc:description": "Set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing \"enrichment\". It does not rely on a specific array technology (although the array should be a \"tiling\" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is fast and can be applied on whole-genome tiling array experiments easily with enough memory.", "sc:license": "GPL-2.0", "sc:name": "ACME", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ACME.html", "sc:version": "2.30.0" - }, - { - "@id": "http://orcid.org/0000-0002-8991-6458", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/acpp/acppbioschemas.jsonld b/data/acpp/acppbioschemas.jsonld index 7c470d7185c5d..5adc0f42eb85f 100644 --- a/data/acpp/acppbioschemas.jsonld +++ b/data/acpp/acppbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-5145-0384", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/ACPP", "@type": "sc:SoftwareApplication", @@ -21,10 +25,6 @@ "sc:name": "ACPP", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/brsaran/ACPP" - }, - { - "@id": "https://orcid.org/0000-0001-5145-0384", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/acpred/acpredbioschemas.jsonld b/data/acpred/acpredbioschemas.jsonld index a9bd6d9d942fd..c7d6086f400d2 100644 --- a/data/acpred/acpredbioschemas.jsonld +++ b/data/acpred/acpredbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "ACPred", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://codes.bio/acpred/" diff --git a/data/act/actbioschemas.jsonld b/data/act/actbioschemas.jsonld index 5220bd42d8192..ed11785e8f81c 100644 --- a/data/act/actbioschemas.jsonld +++ b/data/act/actbioschemas.jsonld @@ -14,33 +14,33 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "https://orcid.org/0000-0002-0519-3820" + "@id": "https://orcid.org/0000-0001-8991-8712" }, { - "@id": "https://orcid.org/0000-0001-8991-8712" + "@id": "https://orcid.org/0000-0002-0519-3820" } ], "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC1538833", - "pubmed:16623895", "pubmed:16845059", { "@id": "https://doi.org/10.1093/nar/gkl204" - } + }, + "pubmed:16623895", + "pmcid:PMC1538833" ], "sc:description": "Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis", "sc:name": "Arabidopsis Co-expression Tool (ACT)", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://www.michalopoulos.net/act/", "sc:version": "II" }, { - "@id": "https://orcid.org/0000-0001-8991-8712", + "@id": "https://orcid.org/0000-0002-0519-3820", "@type": "schema:Person" }, { @@ -48,7 +48,7 @@ "@type": "sc:CreativeWork" }, { - "@id": "https://orcid.org/0000-0002-0519-3820", + "@id": "https://orcid.org/0000-0001-8991-8712", "@type": "schema:Person" } ] diff --git a/data/activedriver/activedriverbioschemas.jsonld b/data/activedriver/activedriverbioschemas.jsonld index 6ac6cf55de7fa..60fed18f03efa 100644 --- a/data/activedriver/activedriverbioschemas.jsonld +++ b/data/activedriver/activedriverbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-2299-2309", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/ActiveDriver", "@type": "sc:SoftwareApplication", @@ -31,6 +27,10 @@ ], "sc:url": "http://reimandlab.org/software/activedriver/", "sc:version": "1.0.0" + }, + { + "@id": "https://orcid.org/0000-0002-2299-2309", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/ad-enm/ad-enmbioschemas.jsonld b/data/ad-enm/ad-enmbioschemas.jsonld index b6a4c5eddd1d5..473e2fe6c9187 100644 --- a/data/ad-enm/ad-enmbioschemas.jsonld +++ b/data/ad-enm/ad-enmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.", "sc:name": "AD-ENM", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://enm.lobos.nih.gov" } \ No newline at end of file diff --git a/data/adacgh2/adacgh2bioschemas.jsonld b/data/adacgh2/adacgh2bioschemas.jsonld index aa09939b9b6da..feeb31cce84a9 100644 --- a/data/adacgh2/adacgh2bioschemas.jsonld +++ b/data/adacgh2/adacgh2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6637-9039", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/adacgh2", "@type": "sc:SoftwareApplication", @@ -16,8 +20,8 @@ "@id": "http://orcid.org/0000-0002-6637-9039" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:24532724", "sc:description": "Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.", @@ -29,10 +33,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ADaCGH2.html", "sc:version": "2.14.0" - }, - { - "@id": "http://orcid.org/0000-0002-6637-9039", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/adapter_removal/adapter_removalbioschemas.jsonld b/data/adapter_removal/adapter_removalbioschemas.jsonld index 71e42c881ba81..989768abd7341 100644 --- a/data/adapter_removal/adapter_removalbioschemas.jsonld +++ b/data/adapter_removal/adapter_removalbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format.", "sc:name": "ADAPTER REMOVAL", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://srna-workbench.cmp.uea.ac.uk/tools/helper-tools/adapter-removal" diff --git a/data/adaptest/adaptestbioschemas.jsonld b/data/adaptest/adaptestbioschemas.jsonld index fcc878e55ce49..6cb26abeb0e6f 100644 --- a/data/adaptest/adaptestbioschemas.jsonld +++ b/data/adaptest/adaptestbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "adaptest", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/adaptest.html", diff --git a/data/adaptml/adaptmlbioschemas.jsonld b/data/adaptml/adaptmlbioschemas.jsonld index e873d28635503..c3d7f63e1d1d2 100644 --- a/data/adaptml/adaptmlbioschemas.jsonld +++ b/data/adaptml/adaptmlbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Software package that will automatically partition groups of gene sequences according to both their genetic and ecological similarity.", "sc:name": "AdaptML", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://almlab.mit.edu/adaptml.html" diff --git a/data/adapts/adaptsbioschemas.jsonld b/data/adapts/adaptsbioschemas.jsonld index 3e3c7c6dbfc9f..8f8cfa18d4ece 100644 --- a/data/adapts/adaptsbioschemas.jsonld +++ b/data/adapts/adaptsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "ADAPTS", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/ADAPTS" diff --git a/data/adat/adatbioschemas.jsonld b/data/adat/adatbioschemas.jsonld index 5b6f2fcfc3460..1b2341b854d5e 100644 --- a/data/adat/adatbioschemas.jsonld +++ b/data/adat/adatbioschemas.jsonld @@ -9,42 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.5334/jors.166", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/adat", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Foo Cheung", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": [ - "pubmed:29951204", { "@id": "https://doi.org/10.5334/jors.166" }, - "pmcid:PMC6017986" + "pmcid:PMC6017986", + "pubmed:29951204" ], "sc:description": "Web Tool for Navigating and Plotting SomaLogic ADAT Files.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_2939" }, { - "@id": "edam:operation_2939" + "@id": "edam:operation_2495" } ], "sc:license": "Apache-2.0", "sc:name": "ADAT", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://foocheung.shinyapps.io/adat/" - }, - { - "@id": "https://doi.org/10.5334/jors.166", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/adenosiland/adenosilandbioschemas.jsonld b/data/adenosiland/adenosilandbioschemas.jsonld index b986221f0c98a..75120e9cf5b3e 100644 --- a/data/adenosiland/adenosilandbioschemas.jsonld +++ b/data/adenosiland/adenosilandbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Adenosiland represents the first attempt of an integrated bioinformatics and chemoinformatics web-resource dedicated to adenosine receptors. This informatics platform provides a wide-ranging of structure based and ligand based query functions to facilitate the exploration of adenosine receptor structures from primary sequences to three-dimensional architectures. Here, we present an overview of Adenosiland platform describing the most valuable searching tools and their functionalities.", "sc:name": "Adenosiland", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", diff --git a/data/adepth/adepthbioschemas.jsonld b/data/adepth/adepthbioschemas.jsonld index 2f75be7104455..73a2b7a386db9 100644 --- a/data/adepth/adepthbioschemas.jsonld +++ b/data/adepth/adepthbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Adepth web server provides both depth and height representation of an atom in a macromolecule; it is capable of computing isosurfaces for atomic depths and presenting graphical view of marcomolecular shape at some distance away from the surface.", "sc:name": "Adepth", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://biodev.cea.fr/adepth" } \ No newline at end of file diff --git a/data/adeptus/adeptusbioschemas.jsonld b/data/adeptus/adeptusbioschemas.jsonld index 8548709bf7898..099366b5ca672 100644 --- a/data/adeptus/adeptusbioschemas.jsonld +++ b/data/adeptus/adeptusbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases.", "sc:name": "ADEPTUS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://adeptus.cs.tau.ac.il/home" } \ No newline at end of file diff --git a/data/adhd/adhdbioschemas.jsonld b/data/adhd/adhdbioschemas.jsonld index 563760af6d0df..cd8f5a1504b35 100644 --- a/data/adhd/adhdbioschemas.jsonld +++ b/data/adhd/adhdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "ADHD", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://ufrgs.br/prodah/adhd-calculator/" } \ No newline at end of file diff --git a/data/adherer/adhererbioschemas.jsonld b/data/adherer/adhererbioschemas.jsonld index 6dbc82812984e..74242be194129 100644 --- a/data/adherer/adhererbioschemas.jsonld +++ b/data/adherer/adhererbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computation of adherence to medications from Electronic Healthcare Data.", "sc:name": "AdhereR", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/AdhereR/index.html" } \ No newline at end of file diff --git a/data/adjustpkl/adjustpklbioschemas.jsonld b/data/adjustpkl/adjustpklbioschemas.jsonld index ac667b387f91f..bd24667de034a 100644 --- a/data/adjustpkl/adjustpklbioschemas.jsonld +++ b/data/adjustpkl/adjustpklbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A tool for adjusting mass spectrometry peaks in PKL file. User can decide whether to shift all spectra or just a single one of the file.", "sc:name": "adjustPKL", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://blog.binfalse.de/software/adjustpkl/" } \ No newline at end of file diff --git a/data/adjutant/adjutantbioschemas.jsonld b/data/adjutant/adjutantbioschemas.jsonld index 5be866d91b201..f7e9304fd1b37 100644 --- a/data/adjutant/adjutantbioschemas.jsonld +++ b/data/adjutant/adjutantbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "Adjutant", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/amcrisan/Adjutant" } \ No newline at end of file diff --git a/data/admetlab/admetlabbioschemas.jsonld b/data/admetlab/admetlabbioschemas.jsonld index c088bcfc4608c..6f6ee81641efd 100644 --- a/data/admetlab/admetlabbioschemas.jsonld +++ b/data/admetlab/admetlabbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Provides a user-friendly, freely available web interface for systematic ADMET evaluation of chemical compounds based on a comprehensive database consisting of 288,967 entries.", "sc:name": "ADMETlab", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://admet.scbdd.com/" } \ No newline at end of file diff --git a/data/admixmap/admixmapbioschemas.jsonld b/data/admixmap/admixmapbioschemas.jsonld index abdff38042437..5fbefddff4837 100644 --- a/data/admixmap/admixmapbioschemas.jsonld +++ b/data/admixmap/admixmapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ADMIXMAP", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html" } \ No newline at end of file diff --git a/data/admixr/admixrbioschemas.jsonld b/data/admixr/admixrbioschemas.jsonld index f4d5f473bd1ba..f6ea4502fda37 100644 --- a/data/admixr/admixrbioschemas.jsonld +++ b/data/admixr/admixrbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "admixr", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://bodkan.net/admixr/articles/tutorial.html", diff --git a/data/admixture/admixturebioschemas.jsonld b/data/admixture/admixturebioschemas.jsonld index ffbcca8870f4f..c53c55cc7af86 100644 --- a/data/admixture/admixturebioschemas.jsonld +++ b/data/admixture/admixturebioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC2752134", + "pubmed:19648217", { "@id": "https://doi.org/10.1101/gr.094052.109" }, - "pubmed:19648217" + "pmcid:PMC2752134" ], "sc:description": "Maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates using a fast numerical optimization algorithm.", "sc:featureList": { @@ -27,8 +27,8 @@ "sc:license": "Not licensed", "sc:name": "Admixture", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://software.genetics.ucla.edu/admixture/" }, diff --git a/data/admixturegraph/admixturegraphbioschemas.jsonld b/data/admixturegraph/admixturegraphbioschemas.jsonld index 1c2825fa994a4..f7f7fed21f757 100644 --- a/data/admixturegraph/admixturegraphbioschemas.jsonld +++ b/data/admixturegraph/admixturegraphbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Implements tools for building and visualising admixture graphs and for extracting equations from them. These equations can be compared to f- statistics obtained from data to test the consistency of a graph against data – for example by comparing the sign of f_4-statistics with the signs predicted by the graph – and graph parameters (edge lengths and admixture proportions) can be fitted to observed statistics.", "sc:name": "admixturegraph", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/admixturegraph/" } \ No newline at end of file diff --git a/data/adnuts/adnutsbioschemas.jsonld b/data/adnuts/adnutsbioschemas.jsonld index 7f8234484df18..e2291aca0d943 100644 --- a/data/adnuts/adnutsbioschemas.jsonld +++ b/data/adnuts/adnutsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Bayesian inference using the no-U-turn (NUTS) algorithm.", "sc:name": "adnuts", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/adnuts/index.html" diff --git a/data/ads-hcspark/ads-hcsparkbioschemas.jsonld b/data/ads-hcspark/ads-hcsparkbioschemas.jsonld index ee3ef96561c64..d843835f8a770 100644 --- a/data/ads-hcspark/ads-hcsparkbioschemas.jsonld +++ b/data/ads-hcspark/ads-hcsparkbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "ADS-HCSpark", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/SCUT-CCNL/ADS-HCSpark.git" } \ No newline at end of file diff --git a/data/adsn/adsnbioschemas.jsonld b/data/adsn/adsnbioschemas.jsonld index b6aa6248280f2..24aefceba4690 100644 --- a/data/adsn/adsnbioschemas.jsonld +++ b/data/adsn/adsnbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/adsn", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jose M. Polo", + "Enrico Petretto", "Owen J. L. Rackham", - "Enrico Petretto" + "Jose M. Polo" ], "sc:additionalType": "Web application", "sc:description": "Single Cell Brain Atlas in Human Alzheimer’s Disease.", "sc:license": "Unlicense", "sc:name": "adsn", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://adsn.ddnetbio.com" } \ No newline at end of file diff --git a/data/adsplit/adsplitbioschemas.jsonld b/data/adsplit/adsplitbioschemas.jsonld index 73d56214354ab..21076e7591193 100644 --- a/data/adsplit/adsplitbioschemas.jsonld +++ b/data/adsplit/adsplitbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Claudio Lottaz", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.", "sc:license": "GPL-2.0", "sc:name": "adSplit", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/adSplit.html", "sc:version": "1.44.0" diff --git a/data/adtex/adtexbioschemas.jsonld b/data/adtex/adtexbioschemas.jsonld index e066ae2b92623..65e2bcf0c034c 100644 --- a/data/adtex/adtexbioschemas.jsonld +++ b/data/adtex/adtexbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "ADTEx", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://adtex.sourceforge.net/" } \ No newline at end of file diff --git a/data/advanced_cell_classifier/advanced_cell_classifierbioschemas.jsonld b/data/advanced_cell_classifier/advanced_cell_classifierbioschemas.jsonld index be23502cc2475..5037537bf1634 100644 --- a/data/advanced_cell_classifier/advanced_cell_classifierbioschemas.jsonld +++ b/data/advanced_cell_classifier/advanced_cell_classifierbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-0371-7782", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/advanced_cell_classifier", "@type": "sc:SoftwareApplication", @@ -21,15 +25,11 @@ "sc:license": "GPL-3.0", "sc:name": "Advanced Cell Classifier", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.cellclassifier.org/" - }, - { - "@id": "http://orcid.org/0000-0002-0371-7782", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/aequatus/aequatusbioschemas.jsonld b/data/aequatus/aequatusbioschemas.jsonld index 60bc82cedd23c..a591280615fe4 100644 --- a/data/aequatus/aequatusbioschemas.jsonld +++ b/data/aequatus/aequatusbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Aequatus", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://aequatus.tgac.ac.uk/" } \ No newline at end of file diff --git a/data/aesop/aesopbioschemas.jsonld b/data/aesop/aesopbioschemas.jsonld index 07b3245756259..a69addb08e1bf 100644 --- a/data/aesop/aesopbioschemas.jsonld +++ b/data/aesop/aesopbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1016/j.bpj.2017.04.005", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/aesop", "@type": "sc:SoftwareApplication", @@ -28,15 +32,11 @@ "sc:license": "GPL-3.0", "sc:name": "AESOP", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://aesop.readthedocs.io/en/latest/index.html" - }, - { - "@id": "https://doi.org/10.1016/j.bpj.2017.04.005", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/afal/afalbioschemas.jsonld b/data/afal/afalbioschemas.jsonld index ca78be9928adc..924a51ee20e34 100644 --- a/data/afal/afalbioschemas.jsonld +++ b/data/afal/afalbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Contact form", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4241235", { "@id": "https://doi.org/10.1007/S10822-014-9783-6" }, - "pubmed:25085083" + "pubmed:25085083", + "pmcid:PMC4241235" ], "sc:description": "Web service for profiling amino acids surrounding ligands in proteins.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "AFAL", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://structuralbio.utalca.cl/AFAL/index.html" } diff --git a/data/affxparser/affxparserbioschemas.jsonld b/data/affxparser/affxparserbioschemas.jsonld index 2944ff1f0a904..6107253a617cf 100644 --- a/data/affxparser/affxparserbioschemas.jsonld +++ b/data/affxparser/affxparserbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "affxparser", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affxparser.html", "sc:version": "1.46.0" diff --git a/data/affy/affybioschemas.jsonld b/data/affy/affybioschemas.jsonld index 8dabe06ad25fd..1f5f61c50e5d1 100644 --- a/data/affy/affybioschemas.jsonld +++ b/data/affy/affybioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-5282-3250", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/affy", "@type": "sc:SoftwareApplication", @@ -28,18 +32,18 @@ "@id": "edam:topic_0203" }, { - "@id": "edam:topic_0092" + "@id": "edam:topic_3473" }, { - "@id": "edam:topic_3473" + "@id": "edam:topic_0092" } ], "sc:citation": [ - "pubmed:27605027", "pmcid:PMC5003452", { "@id": "https://doi.org/10.3390/microarrays3010001" - } + }, + "pubmed:27605027" ], "sc:contributor": { "@id": "http://orcid.org/0000-0001-5282-3250" @@ -51,8 +55,8 @@ "sc:license": "GPL-2.0", "sc:name": "affy", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affy.html", @@ -61,10 +65,6 @@ { "@id": "https://doi.org/10.3390/microarrays3010001", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-5282-3250", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/affy6cnv/affy6cnvbioschemas.jsonld b/data/affy6cnv/affy6cnvbioschemas.jsonld index 7bd7f90c4d73a..485f800fe983b 100644 --- a/data/affy6cnv/affy6cnvbioschemas.jsonld +++ b/data/affy6cnv/affy6cnvbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Affy6CNV is a pipeline for calling CNVs from Affymetrix 6.0 genotyping array data.", "sc:name": "Affy6CNV", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sourceforge.net/projects/affy6cnv/", "sc:version": "0.0.1" diff --git a/data/affycomp/affycompbioschemas.jsonld b/data/affycomp/affycompbioschemas.jsonld index ae82b37f6f114..7239cb9c6c789 100644 --- a/data/affycomp/affycompbioschemas.jsonld +++ b/data/affycomp/affycompbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "affycomp", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affycomp.html", diff --git a/data/affycompatible/affycompatiblebioschemas.jsonld b/data/affycompatible/affycompatiblebioschemas.jsonld index ce27916bfb674..e219cf927b19d 100644 --- a/data/affycompatible/affycompatiblebioschemas.jsonld +++ b/data/affycompatible/affycompatiblebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Martin Morgan", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.", "sc:license": "Artistic-2.0", "sc:name": "AffyCompatible", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AffyCompatible.html", "sc:version": "1.34.0" diff --git a/data/affycompatible/bioconda_affycompatible.yaml b/data/affycompatible/bioconda_affycompatible.yaml index b629f83b7643b..4ccf459f14684 100644 --- a/data/affycompatible/bioconda_affycompatible.yaml +++ b/data/affycompatible/bioconda_affycompatible.yaml @@ -7,7 +7,6 @@ description: This package provides an interface to Affymetrix chip annotation an home: https://bioconductor.org/packages/3.10/bioc/html/AffyCompatible.html identifiers: - biotools:affycompatible -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-affycompatible summary: Affymetrix GeneChip software compatibility diff --git a/data/affycontam/affycontambioschemas.jsonld b/data/affycontam/affycontambioschemas.jsonld index 7c390f687d412..633559caf169f 100644 --- a/data/affycontam/affycontambioschemas.jsonld +++ b/data/affycontam/affycontambioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "affyContam", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affyContam.html", "sc:version": "1.32.0" diff --git a/data/affycontam/bioconda_affycontam.yaml b/data/affycontam/bioconda_affycontam.yaml index 08534c2bf6e97..ff97652ed225d 100644 --- a/data/affycontam/bioconda_affycontam.yaml +++ b/data/affycontam/bioconda_affycontam.yaml @@ -3,7 +3,6 @@ description: structured corruption of cel file data to demonstrate QA effectiven home: https://bioconductor.org/packages/3.10/bioc/html/affyContam.html identifiers: - biotools:affycontam -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-affycontam summary: structured corruption of affymetrix cel file data diff --git a/data/affycoretools/affycoretoolsbioschemas.jsonld b/data/affycoretools/affycoretoolsbioschemas.jsonld index ee951b5f9a6ad..334252c0eb6c9 100644 --- a/data/affycoretools/affycoretoolsbioschemas.jsonld +++ b/data/affycoretools/affycoretoolsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "affycoretools", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affycoretools.html", "sc:version": "1.46.2" diff --git a/data/affycoretools/bioconda_affycoretools.yaml b/data/affycoretools/bioconda_affycoretools.yaml index a9283951af825..b43c17a7dde42 100644 --- a/data/affycoretools/bioconda_affycoretools.yaml +++ b/data/affycoretools/bioconda_affycoretools.yaml @@ -4,7 +4,6 @@ description: Various wrapper functions that have been written to streamline the home: https://bioconductor.org/packages/3.10/bioc/html/affycoretools.html identifiers: - biotools:affycoretools -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-affycoretools summary: Functions useful for those doing repetitive analyses with Affymetrix GeneChips diff --git a/data/affyexpress/affyexpressbioschemas.jsonld b/data/affyexpress/affyexpressbioschemas.jsonld index 528035ee2d3a1..5078fd3dd5408 100644 --- a/data/affyexpress/affyexpressbioschemas.jsonld +++ b/data/affyexpress/affyexpressbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "AffyExpress", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AffyExpress.html", "sc:version": "1.40.0" diff --git a/data/affyexpress/bioconda_affyexpress.yaml b/data/affyexpress/bioconda_affyexpress.yaml index cc1060e852d48..aef2fc7724e26 100644 --- a/data/affyexpress/bioconda_affyexpress.yaml +++ b/data/affyexpress/bioconda_affyexpress.yaml @@ -5,7 +5,6 @@ description: The purpose of this package is to provide a comprehensive and easy- home: https://bioconductor.org/packages/3.10/bioc/html/AffyExpress.html identifiers: - biotools:affyexpress -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-affyexpress diff --git a/data/affygcqc/affygcqcbioschemas.jsonld b/data/affygcqc/affygcqcbioschemas.jsonld index dcd5b4ce77d5a..8d77b6299710a 100644 --- a/data/affygcqc/affygcqcbioschemas.jsonld +++ b/data/affygcqc/affygcqcbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool performs an Affymetrix GeneChip Quality Control by implementing a graphical representation of QC metrics recommended by Affymetrix for GeneChip oligonucleotide array technology. Most importantly, it performs extreme studentized deviate statistical tests for the set of arrays being compared in a given experiment, thus providing an objective measure for outlier detection.", "sc:name": "AffyGCQC", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.transcriptome.ens.fr/AffyGCQC/" diff --git a/data/affyilm/affyilmbioschemas.jsonld b/data/affyilm/affyilmbioschemas.jsonld index 5e2d932a51a07..e045772ff594d 100644 --- a/data/affyilm/affyilmbioschemas.jsonld +++ b/data/affyilm/affyilmbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Fabrice Berger", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.", "sc:license": "GPL-3.0", "sc:name": "affyILM", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affyILM.html", "sc:version": "1.26.0" diff --git a/data/affyio/affyiobioschemas.jsonld b/data/affyio/affyiobioschemas.jsonld index de763d560ee4f..e7dd811e21373 100644 --- a/data/affyio/affyiobioschemas.jsonld +++ b/data/affyio/affyiobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Benjamin Milo Bolstad", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.", "sc:license": "GPL-2.0", "sc:name": "affyio", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affyio.html", "sc:version": "1.44.0" diff --git a/data/affyio/bioconda_affyio.yaml b/data/affyio/bioconda_affyio.yaml index 5aebe4b2fb86e..8a9749e5f2121 100644 --- a/data/affyio/bioconda_affyio.yaml +++ b/data/affyio/bioconda_affyio.yaml @@ -4,7 +4,6 @@ description: Routines for parsing Affymetrix data files based upon file format i home: https://bioconductor.org/packages/3.10/bioc/html/affyio.html identifiers: - biotools:affyio -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-affyio diff --git a/data/affylmgui/affylmguibioschemas.jsonld b/data/affylmgui/affylmguibioschemas.jsonld index 19d6154bb9383..6d137826c0525 100644 --- a/data/affylmgui/affylmguibioschemas.jsonld +++ b/data/affylmgui/affylmguibioschemas.jsonld @@ -9,35 +9,35 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-9221-2892", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/affylmgui", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Keith Satterley", { "@id": "http://orcid.org/0000-0001-9221-2892" }, - "Yifang Hu" + "Yifang Hu", + "Keith Satterley" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:16455752", "sc:description": "A Graphical User Interface for analysis of Affymetrix microarray gene expression data using the affy and limma packages.", "sc:license": "GPL-2.0", "sc:name": "affylmGUI", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affylmGUI.html", "sc:version": "1.48.0" - }, - { - "@id": "http://orcid.org/0000-0001-9221-2892", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/affymetrix_netaffx_analysis_center/affymetrix_netaffx_analysis_centerbioschemas.jsonld b/data/affymetrix_netaffx_analysis_center/affymetrix_netaffx_analysis_centerbioschemas.jsonld index 94af5939b6ea7..19dcca7a8ccba 100644 --- a/data/affymetrix_netaffx_analysis_center/affymetrix_netaffx_analysis_centerbioschemas.jsonld +++ b/data/affymetrix_netaffx_analysis_center/affymetrix_netaffx_analysis_centerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.", "sc:name": "Affymetrix NetAffx Analysis Center", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.affymetrix.com/analysis/index.affx" } \ No newline at end of file diff --git a/data/affypara/affyparabioschemas.jsonld b/data/affypara/affyparabioschemas.jsonld index 5466617237ffe..ac042e25206c3 100644 --- a/data/affypara/affyparabioschemas.jsonld +++ b/data/affypara/affyparabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "affyPara", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affyPara.html", diff --git a/data/affyparaebi/affyparaebibioschemas.jsonld b/data/affyparaebi/affyparaebibioschemas.jsonld index 28328957739ca..a949ac8407b16 100644 --- a/data/affyparaebi/affyparaebibioschemas.jsonld +++ b/data/affyparaebi/affyparaebibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Aan R based pipeline for parallel pre-processing of Affymetrix TM chips. The pipeline starts from a directory containing raw CEL files files and produces Bioconductor R objects containing gene expression measurements suitable for further analysis.", "sc:name": "affyParaEBI", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ebi.ac.uk/Tools/rcloud/", "sc:version": "1.0.0" diff --git a/data/affypdnn/affypdnnbioschemas.jsonld b/data/affypdnn/affypdnnbioschemas.jsonld index 1aa3df0326ead..2fdd860f54357 100644 --- a/data/affypdnn/affypdnnbioschemas.jsonld +++ b/data/affypdnn/affypdnnbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laurent Gautier", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:15509605", "sc:description": "The package contains functions to perform the PDNN method described by Li Zhang et al.", "sc:license": "GPL-3.0", "sc:name": "affypdnn", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affypdnn.html", "sc:version": "1.48.0" diff --git a/data/affyplm/affyplmbioschemas.jsonld b/data/affyplm/affyplmbioschemas.jsonld index 1718d37a4b91b..7ad8ef45993b7 100644 --- a/data/affyplm/affyplmbioschemas.jsonld +++ b/data/affyplm/affyplmbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "GPL-2.0", "sc:name": "affyPLM", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affyPLM.html", diff --git a/data/affyqcreport/affyqcreportbioschemas.jsonld b/data/affyqcreport/affyqcreportbioschemas.jsonld index 05f59fb558a69..dd0d10d8a0a19 100644 --- a/data/affyqcreport/affyqcreportbioschemas.jsonld +++ b/data/affyqcreport/affyqcreportbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Craig Parman", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.", "sc:license": "GPL-2.0", "sc:name": "affyQCReport", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/affyQCReport.html", diff --git a/data/affyrnadegradation/affyrnadegradationbioschemas.jsonld b/data/affyrnadegradation/affyrnadegradationbioschemas.jsonld index fbd9209decf74..42ded97319540 100644 --- a/data/affyrnadegradation/affyrnadegradationbioschemas.jsonld +++ b/data/affyrnadegradation/affyrnadegradationbioschemas.jsonld @@ -18,11 +18,11 @@ "Library" ], "sc:citation": [ - "pubmed:23097420", "pmcid:PMC3530908", { "@id": "https://doi.org/10.1093/bioinformatics/bts629" - } + }, + "pubmed:23097420" ], "sc:description": "The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "AffyRNADegradation", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AffyRNADegradation.html", "sc:version": "1.20.0" diff --git a/data/aflpinsilico/aflpinsilicobioschemas.jsonld b/data/aflpinsilico/aflpinsilicobioschemas.jsonld index 806f9a211948c..ea6b66bd53e56 100644 --- a/data/aflpinsilico/aflpinsilicobioschemas.jsonld +++ b/data/aflpinsilico/aflpinsilicobioschemas.jsonld @@ -20,8 +20,8 @@ "sc:description": "Simulating AFLP fingerprints.", "sc:name": "AFLPinSilico", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "ugent.be", diff --git a/data/afnetwork/afnetworkbioschemas.jsonld b/data/afnetwork/afnetworkbioschemas.jsonld index 9c74ff78ebcf0..b885c43a9d390 100644 --- a/data/afnetwork/afnetworkbioschemas.jsonld +++ b/data/afnetwork/afnetworkbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/f1000research.10225.2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/afnetwork", "@type": "sc:SoftwareApplication", @@ -44,8 +40,8 @@ "sc:name": "AFnetwork", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:softwareHelp": { "@id": "http://bioinformatics.org.au/tools/AFnetwork/READ_ME.txt" @@ -55,6 +51,10 @@ { "@id": "http://orcid.org/0000-0002-3729-8176", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.12688/f1000research.10225.2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/afold/afoldbioschemas.jsonld b/data/afold/afoldbioschemas.jsonld index 2f8e7253f930d..63cc7b001c594 100644 --- a/data/afold/afoldbioschemas.jsonld +++ b/data/afold/afoldbioschemas.jsonld @@ -9,22 +9,30 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-1413-913X", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/S12864-019-5686-1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/aFold", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wentao Yang", { "@id": "https://orcid.org/0000-0002-1413-913X" - } + }, + "Wentao Yang" ], "sc:additionalType": "Library", "sc:citation": [ - "pubmed:31077153", - "pmcid:PMC6509820", { "@id": "https://doi.org/10.1186/S12864-019-5686-1" - } + }, + "pmcid:PMC6509820", + "pubmed:31077153" ], "sc:description": "Using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data.", "sc:featureList": [ @@ -41,19 +49,11 @@ "sc:license": "GPL-3.0", "sc:name": "aFold", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/devel/bioc/html/ABSSeq.html" - }, - { - "@id": "https://orcid.org/0000-0002-1413-913X", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/S12864-019-5686-1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/afq-browser/afq-browserbioschemas.jsonld b/data/afq-browser/afq-browserbioschemas.jsonld index 174837987f273..7b9fb89b8d097 100644 --- a/data/afq-browser/afq-browserbioschemas.jsonld +++ b/data/afq-browser/afq-browserbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Browser-based visualization tools for AFQ results.", "sc:name": "AFQ-Browser", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://yeatmanlab.github.io/AFQBrowser-demo/?table[prevSort][count]=2&table[prevSort][order]=ascending&table[prevSort][key]=&table[sort][count]=2&table[sort][order]=ascending&table[sort][key]=" diff --git a/data/aftol/aftolbioschemas.jsonld b/data/aftol/aftolbioschemas.jsonld index 4b2dd975ef2fa..1bd881f987379 100644 --- a/data/aftol/aftolbioschemas.jsonld +++ b/data/aftol/aftolbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Assembling the Fungal Tree of Life (AFTOL)", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.aftol.org/index.php" } \ No newline at end of file diff --git a/data/afumid/afumidbioschemas.jsonld b/data/afumid/afumidbioschemas.jsonld index dc25f3bc0733a..0f51e75bf1a3b 100644 --- a/data/afumid/afumidbioschemas.jsonld +++ b/data/afumid/afumidbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-7239-4817", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/AfumID", "@type": "sc:SoftwareApplication", @@ -21,8 +17,8 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6529631", "pubmed:31113894", + "pmcid:PMC6529631", { "@id": "https://doi.org/10.1128/MBIO.00392-19" } @@ -30,10 +26,10 @@ "sc:description": "framework for the analysis of Aspergillus fumigatus isolates based on their microsatellite profile.", "sc:featureList": [ { - "@id": "edam:operation_3797" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3797" } ], "sc:license": "Unlicense", @@ -48,6 +44,10 @@ { "@id": "https://doi.org/10.1128/MBIO.00392-19", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-7239-4817", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/agdex/agdexbioschemas.jsonld b/data/agdex/agdexbioschemas.jsonld index 65af82ebad4f9..3586d821bdac6 100644 --- a/data/agdex/agdexbioschemas.jsonld +++ b/data/agdex/agdexbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Cuilan lani Gao", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A tool to evaluate agreement of differential expression for cross-species genomics.", "sc:license": "GPL-2.0", "sc:name": "AGDEX", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AGDEX.html", "sc:version": "1.22.0" diff --git a/data/agenda/agendabioschemas.jsonld b/data/agenda/agendabioschemas.jsonld index 8c42857679343..e1c4a2a87741f 100644 --- a/data/agenda/agendabioschemas.jsonld +++ b/data/agenda/agendabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.", "sc:name": "AGenDA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bibiserv.techfak.uni-bielefeld.de/agenda/" } \ No newline at end of file diff --git a/data/agestructure/agestructurebioschemas.jsonld b/data/agestructure/agestructurebioschemas.jsonld index b2cf9bf6e5edb..5b0f720622507 100644 --- a/data/agestructure/agestructurebioschemas.jsonld +++ b/data/agestructure/agestructurebioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "AgeStructure", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.zsl.org/science/software/agestructure" } \ No newline at end of file diff --git a/data/aggloindel/aggloindelbioschemas.jsonld b/data/aggloindel/aggloindelbioschemas.jsonld index ca1a22910fd45..621dd321934df 100644 --- a/data/aggloindel/aggloindelbioschemas.jsonld +++ b/data/aggloindel/aggloindelbioschemas.jsonld @@ -18,14 +18,14 @@ "sc:description": "This tool to detect structural variations is specifically designed to cluster short-read paired-end data into possibly overlapping predictions for deletions and insertions. It does not make any assumptions on the composition of the data, such as the number of samples, heterogeneity or polyploidy. Taking paired ends mapped to a reference genome as input, it merges mappings to clusters based on a similarity score that takes both the putative location and size of an indel into account.", "sc:name": "AggloIndel", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "CeBiTec", - "Bielefeld University", - "BiBiServ" + "BiBiServ", + "Bielefeld University" ], "sc:url": "http://bibiserv.cebitec.uni-bielefeld.de/agglodel", "sc:version": "1" diff --git a/data/aggregate_scores_in_intervals/aggregate_scores_in_intervalsbioschemas.jsonld b/data/aggregate_scores_in_intervals/aggregate_scores_in_intervalsbioschemas.jsonld index e6b5b119fb7e7..07a8b9ac97acc 100644 --- a/data/aggregate_scores_in_intervals/aggregate_scores_in_intervalsbioschemas.jsonld +++ b/data/aggregate_scores_in_intervals/aggregate_scores_in_intervalsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Such as phastCons, GERP, binCons, and others for a set of genomic intervals.", "sc:name": "aggregate_scores_in_intervals", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/bxlab/bx-python", diff --git a/data/aggrescan3d/aggrescan3dbioschemas.jsonld b/data/aggrescan3d/aggrescan3dbioschemas.jsonld index 44aa64109e2b6..313b40d3b40ff 100644 --- a/data/aggrescan3d/aggrescan3dbioschemas.jsonld +++ b/data/aggrescan3d/aggrescan3dbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/Aggrescan3D", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Michal Jamroz", - "Rafael Zambran" + "Rafael Zambran", + "Michal Jamroz" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:30825368", @@ -20,9 +20,9 @@ "sc:license": "MIT", "sc:name": "Aggrescan3D", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://biocomp.chem.uw.edu.pl/A3D/" } \ No newline at end of file diff --git a/data/agilp/agilpbioschemas.jsonld b/data/agilp/agilpbioschemas.jsonld index aabecec314597..086d05fdd24f6 100644 --- a/data/agilp/agilpbioschemas.jsonld +++ b/data/agilp/agilpbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "agilp", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/agilp.html", diff --git a/data/agimicrorna/agimicrornabioschemas.jsonld b/data/agimicrorna/agimicrornabioschemas.jsonld index 59b2d47f6370c..4e24547649693 100644 --- a/data/agimicrorna/agimicrornabioschemas.jsonld +++ b/data/agimicrorna/agimicrornabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "AgiMicroRna", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AgiMicroRna.html", "sc:version": "2.24.0" diff --git a/data/agotool/agotoolbioschemas.jsonld b/data/agotool/agotoolbioschemas.jsonld index 26c5228512785..b0462eccf9749 100644 --- a/data/agotool/agotoolbioschemas.jsonld +++ b/data/agotool/agotoolbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "aGOtool", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://agotool.sund.ku.dk", "sc:version": "0.1" diff --git a/data/agplus/agplusbioschemas.jsonld b/data/agplus/agplusbioschemas.jsonld index 4fea8b187bb00..904f0a44d10a4 100644 --- a/data/agplus/agplusbioschemas.jsonld +++ b/data/agplus/agplusbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Simple command-line tool that enables rapid and flexible production of text tables tailored for aggregation plots from which users can easily design multiple groups based on user-definitions such as regulatory regions or transcription initiation sites.", "sc:name": "agplus", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/kazumits/agplus" } \ No newline at end of file diff --git a/data/agrigo/agrigobioschemas.jsonld b/data/agrigo/agrigobioschemas.jsonld index 0d83c6abbc11b..3d8b31476fdec 100644 --- a/data/agrigo/agrigobioschemas.jsonld +++ b/data/agrigo/agrigobioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/agrigo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Qi You (Bug report)", "Qi You (Administrator)", - "Tian Tian (Administrator)" + "Tian Tian (Administrator)", + "Qi You (Bug report)" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:20435677", "sc:description": "Integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.", "sc:name": "agriGO", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioinfo.cau.edu.cn/agriGO/" } \ No newline at end of file diff --git a/data/agris/agrisbioschemas.jsonld b/data/agris/agrisbioschemas.jsonld index 26336fcce7496..673bc447ab760 100644 --- a/data/agris/agrisbioschemas.jsonld +++ b/data/agris/agrisbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AGRIS", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://arabidopsis.med.ohio-state.edu/" } \ No newline at end of file diff --git a/data/ahtpdb/ahtpdbbioschemas.jsonld b/data/ahtpdb/ahtpdbbioschemas.jsonld index 1ce7a51416d1c..8100266709117 100644 --- a/data/ahtpdb/ahtpdbbioschemas.jsonld +++ b/data/ahtpdb/ahtpdbbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gku1141", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ahtpdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "DR. Gajendra P. S. Raghava", "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:25392419", "pmcid:PMC4383949", { "@id": "https://doi.org/10.1093/nar/gku1141" - }, - "pubmed:25392419" + } ], "sc:description": "Manually curated database of experimentally validated Antihypertensive peptides (AHTPs) with comprehensive information that includes: sequence, inhibitory concentration (IC50), log value of inhibitory concentration (pIC50) and toxicity.", "sc:featureList": { @@ -27,10 +31,6 @@ }, "sc:name": "AHTPDB", "sc:url": "http://crdd.osdd.net/raghava/ahtpdb/index.php" - }, - { - "@id": "https://doi.org/10.1093/nar/gku1141", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ai_ti-rads/ai_ti-radsbioschemas.jsonld b/data/ai_ti-rads/ai_ti-radsbioschemas.jsonld index 95990cc9b2055..1598e4336891b 100644 --- a/data/ai_ti-rads/ai_ti-radsbioschemas.jsonld +++ b/data/ai_ti-rads/ai_ti-radsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "CC-BY-NC-SA-4.0", "sc:name": "AI TI-RADS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://deckard.duhs.duke.edu/~ai-ti-rads" diff --git a/data/aicd/aicdbioschemas.jsonld b/data/aicd/aicdbioschemas.jsonld index 1d5ed48089ff4..3eed704c611b6 100644 --- a/data/aicd/aicdbioschemas.jsonld +++ b/data/aicd/aicdbioschemas.jsonld @@ -23,8 +23,8 @@ ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31123286", "pmcid:PMC6533287", + "pubmed:31123286", { "@id": "https://doi.org/10.1038/S41598-019-44227-X" } @@ -44,9 +44,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "AICD", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://956023.ichengyun.net/AICD/index.php" } diff --git a/data/aims/aimsbioschemas.jsonld b/data/aims/aimsbioschemas.jsonld index a91fb21c91b25..a05299d907215 100644 --- a/data/aims/aimsbioschemas.jsonld +++ b/data/aims/aimsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "AIMS", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AIMS.html", "sc:version": "1.6.0" diff --git a/data/airlab/airlabbioschemas.jsonld b/data/airlab/airlabbioschemas.jsonld index 89c160f7a7c92..77570e6ebd91b 100644 --- a/data/airlab/airlabbioschemas.jsonld +++ b/data/airlab/airlabbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "AirLab", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.airlaboratory.ch/#/" diff --git a/data/aivar/aivarbioschemas.jsonld b/data/aivar/aivarbioschemas.jsonld index 4b941f08ea2f2..c40d479ff126c 100644 --- a/data/aivar/aivarbioschemas.jsonld +++ b/data/aivar/aivarbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/AIVAR", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jiaqi Luo", + "Jianfeng Sang", "Yujian Shi", - "Jianfeng Sang" + "Jiaqi Luo" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:31141141", @@ -21,9 +21,9 @@ "sc:license": "Unlicense", "sc:name": "AIVAR", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/TopGene/AIvar" } \ No newline at end of file diff --git a/data/akid/akidbioschemas.jsonld b/data/akid/akidbioschemas.jsonld index ba09f693659ce..68db5252716dc 100644 --- a/data/akid/akidbioschemas.jsonld +++ b/data/akid/akidbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Luca Parca", "sc:additionalType": [ - "Command-line tool", - "Web service" + "Web service", + "Command-line tool" ], "sc:description": "AKID is a Deep Neural Network-based method that identifies kinase-specific phosphorylation events at single-kinase level in any given Eukaryotic proteome without prior functional annotation. It automatically detects kinase domains, their residues responsible for target specificity and finally their target peptides.", "sc:name": "AKID", diff --git a/data/aksmooth/aksmoothbioschemas.jsonld b/data/aksmooth/aksmoothbioschemas.jsonld index 24c6439612e54..be004e7194cd2 100644 --- a/data/aksmooth/aksmoothbioschemas.jsonld +++ b/data/aksmooth/aksmoothbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Statistical method that can accurately and efficiently reconstruct the single CpG methylation estimate across the entire methylome using low-coverage bisulfite sequencing (Bi-Seq) data.", "sc:name": "AKSmooth", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/Junfang/AKSmooth" } \ No newline at end of file diff --git a/data/aladyn/aladynbioschemas.jsonld b/data/aladyn/aladynbioschemas.jsonld index 31d36a8017e9c..d796a789f1c09 100644 --- a/data/aladyn/aladynbioschemas.jsonld +++ b/data/aladyn/aladynbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.", "sc:name": "ALADYN", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://aladyn.escience-lab.org" } \ No newline at end of file diff --git a/data/alamut/alamutbioschemas.jsonld b/data/alamut/alamutbioschemas.jsonld index cb8140dc34873..f3f5a0ce306d9 100644 --- a/data/alamut/alamutbioschemas.jsonld +++ b/data/alamut/alamutbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "Proprietary", "sc:name": "Alamut", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.interactive-biosoftware.com/products/" } \ No newline at end of file diff --git a/data/alchemy/alchemybioschemas.jsonld b/data/alchemy/alchemybioschemas.jsonld index 06a43084c39ad..47e6950a100fa 100644 --- a/data/alchemy/alchemybioschemas.jsonld +++ b/data/alchemy/alchemybioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods.", "sc:name": "ALCHEMY", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://alchemy.sourceforge.net/", "sc:version": "1.07" diff --git a/data/aldex2/aldex2bioschemas.jsonld b/data/aldex2/aldex2bioschemas.jsonld index 25091f627ed2a..f5f8e8b8c4899 100644 --- a/data/aldex2/aldex2bioschemas.jsonld +++ b/data/aldex2/aldex2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/2049-2618-2-15", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0001-5803-3380", "@type": "schema:Person" @@ -26,8 +30,8 @@ "@id": "edam:data_0951" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { @@ -38,11 +42,11 @@ } ], "sc:citation": [ - "pmcid:PMC4030730", + "pubmed:24910773", { "@id": "https://doi.org/10.1186/2049-2618-2-15" }, - "pubmed:24910773" + "pmcid:PMC4030730" ], "sc:description": "A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.", "sc:featureList": { @@ -50,16 +54,12 @@ }, "sc:name": "ALDEx2", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ALDEx2.html", "sc:version": "1.6.0" - }, - { - "@id": "https://doi.org/10.1186/2049-2618-2-15", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ale/alebioschemas.jsonld b/data/ale/alebioschemas.jsonld index fb7f0ed0df73c..b429e7651117d 100644 --- a/data/ale/alebioschemas.jsonld +++ b/data/ale/alebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Automated label extraction from GEO metadata.", "sc:name": "ALE", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/wrenlab/label-extraction" } \ No newline at end of file diff --git a/data/aleaves/aleavesbioschemas.jsonld b/data/aleaves/aleavesbioschemas.jsonld index 668237e529cab..06975db3e9de6 100644 --- a/data/aleaves/aleavesbioschemas.jsonld +++ b/data/aleaves/aleavesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server supports homolog collection from diverse animal genomes. An input sequence is passed through the server to collect similar sequences for molecular phylogenetic analysis.", "sc:name": "aLeaves", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://aleaves.cdb.riken.jp/" } \ No newline at end of file diff --git a/data/alevin/alevinbioschemas.jsonld b/data/alevin/alevinbioschemas.jsonld index 2f8d0b8f49b85..3dde7baff8788 100644 --- a/data/alevin/alevinbioschemas.jsonld +++ b/data/alevin/alevinbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13059-019-1670-y", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Alevin", "@type": "sc:SoftwareApplication", @@ -27,26 +31,22 @@ "sc:description": "Tool introducing a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_3200" }, { - "@id": "edam:operation_3799" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_3200" + "@id": "edam:operation_3799" } ], "sc:license": "GPL-3.0", "sc:name": "Alevin", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://salmon.readthedocs.io/en/latest/alevin.html#references" - }, - { - "@id": "https://doi.org/10.1186/s13059-019-1670-y", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/alfred-g/alfred-gbioschemas.jsonld b/data/alfred-g/alfred-gbioschemas.jsonld index 9c598cbfaf019..9965b0b263536 100644 --- a/data/alfred-g/alfred-gbioschemas.jsonld +++ b/data/alfred-g/alfred-gbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5471951", - "pubmed:28617225", { "@id": "https://doi.org/10.1186/s12859-017-1658-0" - } + }, + "pubmed:28617225" ], "sc:description": "Distance Estimator for Phylogenetic Inference.", "sc:featureList": { diff --git a/data/alfresco/alfrescobioschemas.jsonld b/data/alfresco/alfrescobioschemas.jsonld index 4ccc8850963d3..e5aee27d14335 100644 --- a/data/alfresco/alfrescobioschemas.jsonld +++ b/data/alfresco/alfrescobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Alfresco‘s (FRont-End for Sequence COmparison) aim is to develop a new visualisation tool that allows effective comparative genome sequence analysis. The program will compare multiple sequences from putitatively homologous regions in different species. Results from various different existing analysis programs, such as gene prediction, protein homology and regulatory sequence prediction programs shall be visualised and used to find corresponding sequence domains.", "sc:name": "Alfresco", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.sanger.ac.uk/science/tools/alfresco" } \ No newline at end of file diff --git a/data/alfy/alfybioschemas.jsonld b/data/alfy/alfybioschemas.jsonld index 2cfe629d5eee7..c1d7e0d5349a8 100644 --- a/data/alfy/alfybioschemas.jsonld +++ b/data/alfy/alfybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Computer program for comparing one or more query DNA sequences to a set of subject sequences. For each query sequence the output consists of a list of intervals indicating the closest homologue among the set of subject sequences.", "sc:name": "alfy", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://guanine.evolbio.mpg.de/alfy/" } \ No newline at end of file diff --git a/data/algaepath/algaepathbioschemas.jsonld b/data/algaepath/algaepathbioschemas.jsonld index f37e4ce545c3c..cb7c251d20030 100644 --- a/data/algaepath/algaepathbioschemas.jsonld +++ b/data/algaepath/algaepathbioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Database portal", "sc:citation": [ "pubmed:24628857", - "pmcid:PMC4028061", { "@id": "https://doi.org/10.1186/1471-2164-15-196" - } + }, + "pmcid:PMC4028061" ], "sc:description": "Comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "AlgaePath", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://algaepath.itps.ncku.edu.tw/" }, diff --git a/data/alggen/alggenbioschemas.jsonld b/data/alggen/alggenbioschemas.jsonld index b69257c8363d5..8754343fd23c9 100644 --- a/data/alggen/alggenbioschemas.jsonld +++ b/data/alggen/alggenbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.", "sc:name": "ALGGEN", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://alggen.lsi.upc.es/" diff --git a/data/algpred/algpredbioschemas.jsonld b/data/algpred/algpredbioschemas.jsonld index e9f4a0ed695bb..5e8bfbb475362 100644 --- a/data/algpred/algpredbioschemas.jsonld +++ b/data/algpred/algpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.", "sc:name": "AlgPred", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.imtech.res.in/raghava/algpred/" } \ No newline at end of file diff --git a/data/align-gvgd/align-gvgdbioschemas.jsonld b/data/align-gvgd/align-gvgdbioschemas.jsonld index 2a96b14b71e00..d5b43c827c0d5 100644 --- a/data/align-gvgd/align-gvgdbioschemas.jsonld +++ b/data/align-gvgd/align-gvgdbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. Align-GVGD is an extension of the original Grantham difference to multiple sequence alignments and true simultaneous multiple comparisons.", "sc:name": "Align-GVGD", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://agvgd.hci.utah.edu/" } \ No newline at end of file diff --git a/data/align-paths/align-pathsbioschemas.jsonld b/data/align-paths/align-pathsbioschemas.jsonld index ad5aa9fd2659e..7eeb5720e6473 100644 --- a/data/align-paths/align-pathsbioschemas.jsonld +++ b/data/align-paths/align-pathsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-0222-4273", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/align-paths", "@type": "sc:SoftwareApplication", @@ -24,6 +20,10 @@ "sc:name": "Align-paths", "sc:url": "https://github.com/BioDAG/align-paths", "sc:version": "1.0" + }, + { + "@id": "https://orcid.org/0000-0002-0222-4273", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/align/alignbioschemas.jsonld b/data/align/alignbioschemas.jsonld index 2fd3a71f12eed..d8694eef59b75 100644 --- a/data/align/alignbioschemas.jsonld +++ b/data/align/alignbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-4525-7793", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/align", "@type": "sc:SoftwareApplication", @@ -24,16 +20,20 @@ "sc:description": "Pairwise alignment tool.", "sc:name": "ALIGN", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "ELIXIR-ITA-PADOVA", - "University of Padua, Department of Biomedical Sciences, BioComputing UP lab" + "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", + "ELIXIR-ITA-PADOVA" ], "sc:url": "http://protein.bio.unipd.it/align2", "sc:version": "2.0" + }, + { + "@id": "http://orcid.org/0000-0003-4525-7793", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/alignace/alignacebioschemas.jsonld b/data/alignace/alignacebioschemas.jsonld index 91db512e96f63..44ebb29f8d45c 100644 --- a/data/alignace/alignacebioschemas.jsonld +++ b/data/alignace/alignacebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/alignace", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Maryanne Fenerjian (HMS Office of Technology Licensing contact)", - "Zhou Zhu (questions or comments)" + "Zhou Zhu (questions or comments)", + "Maryanne Fenerjian (HMS Office of Technology Licensing contact)" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:9788350", "sc:description": "Aligns Nucleic Acid Conserved Elements; uses pattern recognition to find elements conserved in a set of DNA sequences; free for non-commercial use with license agreement.", "sc:name": "AlignACE", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://arep.med.harvard.edu/mrnadata/mrnasoft.html" } \ No newline at end of file diff --git a/data/aligncopy/aligncopybioschemas.jsonld b/data/aligncopy/aligncopybioschemas.jsonld index c5e0e20315a2e..9fb8e5fb6e71e 100644 --- a/data/aligncopy/aligncopybioschemas.jsonld +++ b/data/aligncopy/aligncopybioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "UK MRC", - "EMBOSS Contributors", - "Wellcome Trust" + "UK BBSRC", + "Wellcome Trust", + "EMBOSS Contributors" ], "sc:description": "Read and write alignments.", "sc:funder": [ "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "aligncopy", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/aligncopy.html", "sc:version": "r6" diff --git a/data/aligncopypair/aligncopypairbioschemas.jsonld b/data/aligncopypair/aligncopypairbioschemas.jsonld index 02c0ec7378a70..808bb8e81cdef 100644 --- a/data/aligncopypair/aligncopypairbioschemas.jsonld +++ b/data/aligncopypair/aligncopypairbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK MRC", "UK BBSRC", - "EMBOSS Contributors", "Wellcome Trust", - "UK MRC" + "EMBOSS Contributors" ], "sc:description": "Read and write pairs from alignments.", "sc:funder": [ + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "aligncopypair", diff --git a/data/alignme/alignmebioschemas.jsonld b/data/alignme/alignmebioschemas.jsonld index 1ce3aaee39e8b..358818e4258c5 100644 --- a/data/alignme/alignmebioschemas.jsonld +++ b/data/alignme/alignmebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "AlignMe", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bioinfo.mpg.de/AlignMe" } \ No newline at end of file diff --git a/data/alignment-annotator/alignment-annotatorbioschemas.jsonld b/data/alignment-annotator/alignment-annotatorbioschemas.jsonld index f2f1f68fc591a..1fa0cc200dd81 100644 --- a/data/alignment-annotator/alignment-annotatorbioschemas.jsonld +++ b/data/alignment-annotator/alignment-annotatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Alignment Annotator is a web service which annotates and renders sequence alignments using annotation services and the PDB. The annotated and colorized alignment can be downloaded as an interactive HTML file for web browsers.", "sc:name": "Alignment-Annotator", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.bioinformatics.org/strap/aa/" } \ No newline at end of file diff --git a/data/alignmentcomparator/alignmentcomparatorbioschemas.jsonld b/data/alignmentcomparator/alignmentcomparatorbioschemas.jsonld index 91ba77e193253..6aa7fab7bd90e 100644 --- a/data/alignmentcomparator/alignmentcomparatorbioschemas.jsonld +++ b/data/alignmentcomparator/alignmentcomparatorbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "GPL-3.0", "sc:name": "AlignmentComparator", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfweb.info/AlignmentComparator/", "sc:version": "1.0.0" diff --git a/data/alignsec/alignsecbioschemas.jsonld b/data/alignsec/alignsecbioschemas.jsonld index d34881a060238..be13c0da0a48f 100644 --- a/data/alignsec/alignsecbioschemas.jsonld +++ b/data/alignsec/alignsecbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Viewing protein secondary structure predictions within large multiple sequence alignments. The module is part of the ANTHEPROT package.", "sc:name": "ALIGNSEC", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://antheprot-pbil.ibcp.fr/" diff --git a/data/alignstat/alignstatbioschemas.jsonld b/data/alignstat/alignstatbioschemas.jsonld index fb0ea951b7acc..b18e27228a2aa 100644 --- a/data/alignstat/alignstatbioschemas.jsonld +++ b/data/alignstat/alignstatbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-2298-7593", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/alignstat", "@type": "sc:SoftwareApplication", @@ -16,15 +20,15 @@ "@id": "http://orcid.org/0000-0002-2298-7593" }, "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC5081975", { "@id": "https://doi.org/10.1186/s12859-016-1300-6" }, - "pubmed:27784265" + "pubmed:27784265", + "pmcid:PMC5081975" ], "sc:description": "AlignStat is a web-tool and R package for statistical comparison of alternative multiple sequence alignments.", "sc:featureList": { @@ -33,17 +37,13 @@ "sc:license": "Other", "sc:name": "AlignStat", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://alignstat.science.latrobe.edu.au/", "sc:version": "1.3.2" }, - { - "@id": "http://orcid.org/0000-0002-2298-7593", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-016-1300-6", "@type": "sc:CreativeWork" diff --git a/data/alkemio/alkemiobioschemas.jsonld b/data/alkemio/alkemiobioschemas.jsonld index 724bb7199ae8b..95ebddc671e86 100644 --- a/data/alkemio/alkemiobioschemas.jsonld +++ b/data/alkemio/alkemiobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jean Fred Fontaine", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:description": "Chemicals prioritization for topics of interest using gene-related PubMed abstracts.", "sc:name": "Alkemio", diff --git a/data/all-fit/all-fitbioschemas.jsonld b/data/all-fit/all-fitbioschemas.jsonld index d4d160391d0ad..5f9f8b7a762b7 100644 --- a/data/all-fit/all-fitbioschemas.jsonld +++ b/data/all-fit/all-fitbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "All-FIT", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/KhiabanianLab/All-FIT" diff --git a/data/all-p/all-pbioschemas.jsonld b/data/all-p/all-pbioschemas.jsonld index ab2c857068bc4..cac9298a1cfdf 100644 --- a/data/all-p/all-pbioschemas.jsonld +++ b/data/all-p/all-pbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances. It performs a simultaneous analysis of all the quantified peptides, handling the biological and technical errors as well as the peptide effect.", "sc:name": "ALL-P", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://pappso.inra.fr/bioinfo/all_p/index.php" diff --git a/data/allele_frequency_net/allele_frequency_netbioschemas.jsonld b/data/allele_frequency_net/allele_frequency_netbioschemas.jsonld index 33be183813496..ad8d8e989eba3 100644 --- a/data/allele_frequency_net/allele_frequency_netbioschemas.jsonld +++ b/data/allele_frequency_net/allele_frequency_netbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Allele frequency net", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.allelefrequencies.net" } \ No newline at end of file diff --git a/data/alleleretain/alleleretainbioschemas.jsonld b/data/alleleretain/alleleretainbioschemas.jsonld index ef4457add7efd..32ade5560be2f 100644 --- a/data/alleleretain/alleleretainbioschemas.jsonld +++ b/data/alleleretain/alleleretainbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R package to simulate small populations. Output includes demographic trends and information, probability of retaining a rare allele, and accumulation of inbreeding over the simulated period.", "sc:name": "AlleleRetain", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://sites.google.com/site/alleleretain/" } \ No newline at end of file diff --git a/data/allelicimbalance/allelicimbalancebioschemas.jsonld b/data/allelicimbalance/allelicimbalancebioschemas.jsonld index 37181bb4fc8f3..b821da2c540c7 100644 --- a/data/allelicimbalance/allelicimbalancebioschemas.jsonld +++ b/data/allelicimbalance/allelicimbalancebioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-5635-2692", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/allelicimbalance", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jesper R Gadin", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ { @@ -34,17 +38,13 @@ "sc:license": "GPL-3.0", "sc:name": "AllelicImbalance", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AllelicImbalance.html", "sc:version": "1.12.0" }, - { - "@id": "http://orcid.org/0000-0002-5635-2692", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-015-0620-2", "@type": "sc:CreativeWork" diff --git a/data/allen_brain_atlas-api/allen_brain_atlas-apibioschemas.jsonld b/data/allen_brain_atlas-api/allen_brain_atlas-apibioschemas.jsonld index b74d40c1c9f73..78eff62b6ba22 100644 --- a/data/allen_brain_atlas-api/allen_brain_atlas-apibioschemas.jsonld +++ b/data/allen_brain_atlas-api/allen_brain_atlas-apibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Integration of gene expression data, connectivity data and neuroanatomical information for the adult and developing brain in mouse, human and non-human primate.", "sc:name": "Allen Brain Atlas-API", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://help.brain-map.org/display/api/RESTful+Model+Access+%28RMA%29", diff --git a/data/allen_brain_atlas/allen_brain_atlasbioschemas.jsonld b/data/allen_brain_atlas/allen_brain_atlasbioschemas.jsonld index 523f21dc3d02d..150304b29da34 100644 --- a/data/allen_brain_atlas/allen_brain_atlasbioschemas.jsonld +++ b/data/allen_brain_atlas/allen_brain_atlasbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The Allen Brain Atlas (ABA) project has developed a web-based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in situ hybridization (ISH) images from over 10,000 genes, reference atlases in both the sagittal and coronal planes, gene expression masks capturing the intensity of gene expression or signal, and the ability to search for gene expression by anatomic region.", "sc:name": "Allen Brain Atlas", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.brain-map.org" diff --git a/data/allerdictor/allerdictorbioschemas.jsonld b/data/allerdictor/allerdictorbioschemas.jsonld index a29f55ad8f569..34974490827c6 100644 --- a/data/allerdictor/allerdictorbioschemas.jsonld +++ b/data/allerdictor/allerdictorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Fast and accurate sequence-based allergen prediction tool that models protein sequences as text documents and employs support vector machine in text classification for allergen prediction.", "sc:name": "Allerdictor", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://allerdictor.vbi.vt.edu/" } \ No newline at end of file diff --git a/data/allergenfp/allergenfpbioschemas.jsonld b/data/allergenfp/allergenfpbioschemas.jsonld index 11b440c459b71..9b52c372eb1fc 100644 --- a/data/allergenfp/allergenfpbioschemas.jsonld +++ b/data/allergenfp/allergenfpbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AllergenFP", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ddg-pharmfac.net/AllergenFP/" } \ No newline at end of file diff --git a/data/allergome/allergomebioschemas.jsonld b/data/allergome/allergomebioschemas.jsonld index 9bfb6bd572648..a1e5806b28cc7 100644 --- a/data/allergome/allergomebioschemas.jsonld +++ b/data/allergome/allergomebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A platform for allergen knowledge.", "sc:name": "Allergome", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.allergome.org/" diff --git a/data/allertop/allertopbioschemas.jsonld b/data/allertop/allertopbioschemas.jsonld index cbecc8e8157dc..e5092cbe13e0e 100644 --- a/data/allertop/allertopbioschemas.jsonld +++ b/data/allertop/allertopbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AllerTOP", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ddg-pharmfac.net/AllerTOP/" } \ No newline at end of file diff --git a/data/allim/allimbioschemas.jsonld b/data/allim/allimbioschemas.jsonld index 09d0f1562b1bb..4a8b764d383f4 100644 --- a/data/allim/allimbioschemas.jsonld +++ b/data/allim/allimbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/allim", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ram Vinay Pandey", "Christian Schlötterer", - "Susanne U. Franssen" + "Susanne U. Franssen", + "Ram Vinay Pandey" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:23615333", @@ -21,8 +21,8 @@ "sc:license": "MPL-1.1", "sc:name": "Allim", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://code.google.com/p/allim/" } \ No newline at end of file diff --git a/data/allodriver/allodriverbioschemas.jsonld b/data/allodriver/allodriverbioschemas.jsonld index bc96184f005a2..b3006e03d6ad1 100644 --- a/data/allodriver/allodriverbioschemas.jsonld +++ b/data/allodriver/allodriverbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-6558-791X", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/NAR/GKZ350", "@type": "sc:CreativeWork" @@ -21,19 +25,19 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC6602569", "pubmed:31069394", { "@id": "https://doi.org/10.1093/NAR/GKZ350" - }, - "pmcid:PMC6602569" + } ], "sc:description": "Method for the identification and analysis of cancer driver targets.", "sc:featureList": [ { - "@id": "edam:operation_0331" + "@id": "edam:operation_3227" }, { - "@id": "edam:operation_3227" + "@id": "edam:operation_0331" } ], "sc:license": "Unlicense", @@ -44,10 +48,6 @@ "Mac" ], "sc:url": "http://mdl.shsmu.edu.cn/ALD" - }, - { - "@id": "https://orcid.org/0000-0002-6558-791X", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/allopred/allopredbioschemas.jsonld b/data/allopred/allopredbioschemas.jsonld index 3fde315b60087..29783bb4537e0 100644 --- a/data/allopred/allopredbioschemas.jsonld +++ b/data/allopred/allopredbioschemas.jsonld @@ -20,15 +20,15 @@ "@id": "http://orcid.org/0000-0002-5154-1929" }, "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": [ + "pubmed:26493317", + "pmcid:PMC4619270", { "@id": "https://doi.org/10.1186/s12859-015-0771-1" - }, - "pubmed:26493317", - "pmcid:PMC4619270" + } ], "sc:description": "Web server uses normal mode analysis and pocket features to predict allosteric pockets on proteins.", "sc:featureList": { diff --git a/data/alloscore/alloscorebioschemas.jsonld b/data/alloscore/alloscorebioschemas.jsonld index db41d172f89a8..02124ce36b811 100644 --- a/data/alloscore/alloscorebioschemas.jsonld +++ b/data/alloscore/alloscorebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Alloscore", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mdl.shsmu.edu.cn/alloscore/" } \ No newline at end of file diff --git a/data/allosite/allositebioschemas.jsonld b/data/allosite/allositebioschemas.jsonld index 2d68d2bda202a..c76571862d4fa 100644 --- a/data/allosite/allositebioschemas.jsonld +++ b/data/allosite/allositebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Allosite", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mdl.shsmu.edu.cn/AST/" } \ No newline at end of file diff --git a/data/allpaths-lg/allpaths-lgbioschemas.jsonld b/data/allpaths-lg/allpaths-lgbioschemas.jsonld index eaa48ff500adb..30a91ed812155 100644 --- a/data/allpaths-lg/allpaths-lgbioschemas.jsonld +++ b/data/allpaths-lg/allpaths-lgbioschemas.jsonld @@ -18,16 +18,16 @@ { "@id": "https://doi.org/10.1073/pnas.1017351108" }, - "pubmed:21187386", - "pmcid:PMC3029755" + "pmcid:PMC3029755", + "pubmed:21187386" ], "sc:description": "Short read assembler that works on both small and large (mammalian size) genomes.", "sc:featureList": [ { - "@id": "edam:operation_0310" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_3197" + "@id": "edam:operation_0310" } ], "sc:license": "MIT", diff --git a/data/allpaths/allpathsbioschemas.jsonld b/data/allpaths/allpathsbioschemas.jsonld index ea4b456f5fa6c..afc5a1a1c2801 100644 --- a/data/allpaths/allpathsbioschemas.jsonld +++ b/data/allpaths/allpathsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ALLPATHS", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.broadinstitute.org/computational-rd/computational-research-and-development" } \ No newline at end of file diff --git a/data/almostsignificant/almostsignificantbioschemas.jsonld b/data/almostsignificant/almostsignificantbioschemas.jsonld index 55586b131bb17..88ab10b773e5b 100644 --- a/data/almostsignificant/almostsignificantbioschemas.jsonld +++ b/data/almostsignificant/almostsignificantbioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTW559" }, - "pmcid:PMC5167069", - "pubmed:27559158" + "pubmed:27559158", + "pmcid:PMC5167069" ], "sc:description": "Simplifying quality control of high-throughput sequencing data.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "AlmostSignificant", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/bartongroup/AlmostSignificant" } diff --git a/data/alohomora/alohomorabioschemas.jsonld b/data/alohomora/alohomorabioschemas.jsonld index 1327e1cbb577c..e0178b875d08d 100644 --- a/data/alohomora/alohomorabioschemas.jsonld +++ b/data/alohomora/alohomorabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Alohomora was designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array", "sc:name": "Alohomora", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://gmc.mdc-berlin.de/alohomora/", "sc:version": "0.33" diff --git a/data/alpha/alphabioschemas.jsonld b/data/alpha/alphabioschemas.jsonld index 6c834c5c9d203..517766faa93cd 100644 --- a/data/alpha/alphabioschemas.jsonld +++ b/data/alpha/alphabioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Automated Local PHylogenomic Analyses.", "sc:name": "ALPHA", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/chilleo/ALPHA" } \ No newline at end of file diff --git a/data/alphampsim/alphampsimbioschemas.jsonld b/data/alphampsim/alphampsimbioschemas.jsonld index 312dcdfb1178e..a74e7190abdba 100644 --- a/data/alphampsim/alphampsimbioschemas.jsonld +++ b/data/alphampsim/alphampsimbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Simple software package for simulating data in multi-parent populations.", "sc:name": "AlphaMPSim", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sites.google.com/site/hickeyjohn/workstuff/alphampsim" } \ No newline at end of file diff --git a/data/alphapred/alphapredbioschemas.jsonld b/data/alphapred/alphapredbioschemas.jsonld index ac25cee39e191..057938f68bbc0 100644 --- a/data/alphapred/alphapredbioschemas.jsonld +++ b/data/alphapred/alphapredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.", "sc:name": "AlphaPred", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/alphapred/" } \ No newline at end of file diff --git a/data/alpine/alpinebioschemas.jsonld b/data/alpine/alpinebioschemas.jsonld index 50288337472d3..032e579cedc59 100644 --- a/data/alpine/alpinebioschemas.jsonld +++ b/data/alpine/alpinebioschemas.jsonld @@ -21,10 +21,10 @@ ], "sc:citation": [ "pmcid:PMC5143225", - "pubmed:27669167", { "@id": "https://doi.org/10.1038/nbt.3682" - } + }, + "pubmed:27669167" ], "sc:description": "Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.", "sc:featureList": { @@ -33,9 +33,9 @@ "sc:license": "GPL-2.0", "sc:name": "alpine", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/alpine.html", "sc:version": "1.0.0" diff --git a/data/alsace/alsacebioschemas.jsonld b/data/alsace/alsacebioschemas.jsonld index c9eb9533da5e9..19b022da59c6e 100644 --- a/data/alsace/alsacebioschemas.jsonld +++ b/data/alsace/alsacebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "alsace", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/alsace.html", diff --git a/data/altcdfenvs/altcdfenvsbioschemas.jsonld b/data/altcdfenvs/altcdfenvsbioschemas.jsonld index 729f66ebc30ad..e49383d0fb341 100644 --- a/data/altcdfenvs/altcdfenvsbioschemas.jsonld +++ b/data/altcdfenvs/altcdfenvsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "altcdfenvs", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/altcdfenvs.html", diff --git a/data/alter/alterbioschemas.jsonld b/data/alter/alterbioschemas.jsonld index 14f7fbf2d8f76..cfba2320447ce 100644 --- a/data/alter/alterbioschemas.jsonld +++ b/data/alter/alterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ALTER is a program-oriented web tool for the conversion between DNA and protein alignments.", "sc:name": "ALTER", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sing.ei.uvigo.es/ALTER/" } \ No newline at end of file diff --git a/data/alternative_splicing_gallery/alternative_splicing_gallerybioschemas.jsonld b/data/alternative_splicing_gallery/alternative_splicing_gallerybioschemas.jsonld index 7c6233eab9bb7..bd62507a53627 100644 --- a/data/alternative_splicing_gallery/alternative_splicing_gallerybioschemas.jsonld +++ b/data/alternative_splicing_gallery/alternative_splicing_gallerybioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/alternative_splicing_gallery", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Steffen Heber", - "Jeremy Leipzig" + "Jeremy Leipzig", + "Steffen Heber" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:15292448", "sc:description": "The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer.", "sc:name": "Alternative Splicing Gallery", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://statgen.ncsu.edu/asg/" } \ No newline at end of file diff --git a/data/althapalignr/althapalignrbioschemas.jsonld b/data/althapalignr/althapalignrbioschemas.jsonld index 56526b868ac09..563bd378e931b 100644 --- a/data/althapalignr/althapalignrbioschemas.jsonld +++ b/data/althapalignr/althapalignrbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Method incorporating alternate reference haplotypes to generate gene- and haplotype-level estimates of transcript abundance for any genomic region where such information is available.", "sc:name": "AltHapAlignR", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/jknightlab/AltHapAlignR" } \ No newline at end of file diff --git a/data/altools/altoolsbioschemas.jsonld b/data/altools/altoolsbioschemas.jsonld index 8faca24570e4d..090e21fc32743 100644 --- a/data/altools/altoolsbioschemas.jsonld +++ b/data/altools/altoolsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13062-016-0110-0", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-8874-9993", "@type": "schema:Person" @@ -25,11 +21,11 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:26883204", - "pmcid:PMC4756442", { "@id": "https://doi.org/10.1186/s13062-016-0110-0" - } + }, + "pmcid:PMC4756442", + "pubmed:26883204" ], "sc:description": "Altools is a software package that allows the precise detection of polymorphisms and structural variations.", "sc:featureList": { @@ -39,6 +35,10 @@ "sc:name": "Altools", "sc:operatingSystem": "Linux", "sc:url": "https://sourceforge.net/projects/altools/" + }, + { + "@id": "https://doi.org/10.1186/s13062-016-0110-0", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/aluscancnv2/aluscancnv2bioschemas.jsonld b/data/aluscancnv2/aluscancnv2bioschemas.jsonld index 5c31954bcc389..ffcc7d7cb47eb 100644 --- a/data/aluscancnv2/aluscancnv2bioschemas.jsonld +++ b/data/aluscancnv2/aluscancnv2bioschemas.jsonld @@ -15,18 +15,18 @@ "biotools:primaryContact": "Taobo Hu", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6411622", - "pubmed:30906832", { "@id": "https://doi.org/10.1016/j.gendis.2018.09.001" - } + }, + "pmcid:PMC6411622", + "pubmed:30906832" ], "sc:description": "R package for copy number variation calling and cancer risk prediction with next-generation sequencing data.", "sc:name": "AluScanCNV2", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/hutaobo/AluScanCNV2" }, diff --git a/data/alview/alviewbioschemas.jsonld b/data/alview/alviewbioschemas.jsonld index c77d1ba978719..518a62e20029b 100644 --- a/data/alview/alviewbioschemas.jsonld +++ b/data/alview/alviewbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Fast bam file viewer from the National Cancer Informatics Program.", "sc:name": "Alview", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cbiit.nci.nih.gov/ncip" } \ No newline at end of file diff --git a/data/alvisir/alvisirbioschemas.jsonld b/data/alvisir/alvisirbioschemas.jsonld index ceeaae87bcaae..0e280f8d09ba5 100644 --- a/data/alvisir/alvisirbioschemas.jsonld +++ b/data/alvisir/alvisirbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Apache-2.0", "sc:name": "AlvisIR", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/Bibliome/alvisir" } \ No newline at end of file diff --git a/data/amas/amasbioschemas.jsonld b/data/amas/amasbioschemas.jsonld index 978929e83f787..3764c26a5f5d4 100644 --- a/data/amas/amasbioschemas.jsonld +++ b/data/amas/amasbioschemas.jsonld @@ -9,41 +9,41 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.7717/peerj.1660", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/amas", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Marek L. Borowiec", "sc:additionalType": [ - "Plug-in", - "Command-line tool" + "Command-line tool", + "Plug-in" ], "sc:citation": [ - "pmcid:PMC4734057", - "pubmed:26835189", { "@id": "https://doi.org/10.7717/peerj.1660" - } + }, + "pmcid:PMC4734057", + "pubmed:26835189" ], "sc:description": "AMAS (Alignment Manipulation And Summary), a tool that works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics.", "sc:featureList": [ { - "@id": "edam:operation_2478" + "@id": "edam:operation_2479" }, { - "@id": "edam:operation_2479" + "@id": "edam:operation_2478" } ], "sc:license": "GPL-3.0", "sc:name": "AMAS", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/marekborowiec/AMAS" + }, + { + "@id": "https://doi.org/10.7717/peerj.1660", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/amatreader/amatreaderbioschemas.jsonld b/data/amatreader/amatreaderbioschemas.jsonld index 6db969dd146f5..5807249035fd0 100644 --- a/data/amatreader/amatreaderbioschemas.jsonld +++ b/data/amatreader/amatreaderbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Augments the Cytoscape network readers by adding the ability to read in an adjacency matrix.", "sc:name": "aMatReader", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.cgl.ucsf.edu/cytoscape/utilities3/amatreader.shtml", "sc:version": "1.1.3" diff --git a/data/amber/amberbioschemas.jsonld b/data/amber/amberbioschemas.jsonld index 8ea4efccabba6..73cf49ee33d19 100644 --- a/data/amber/amberbioschemas.jsonld +++ b/data/amber/amberbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The Assisted Model Building with Energy Refinement tool refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.", "sc:name": "AMBER", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://ambermd.org/" diff --git a/data/ambergpumdsimulation/ambergpumdsimulationbioschemas.jsonld b/data/ambergpumdsimulation/ambergpumdsimulationbioschemas.jsonld index 34ebc2859137e..21d2298e374b3 100644 --- a/data/ambergpumdsimulation/ambergpumdsimulationbioschemas.jsonld +++ b/data/ambergpumdsimulation/ambergpumdsimulationbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/j.bpj.2017.04.055", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ambergpumdsimulation", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Rommie E. Amaro", "sc:additionalType": "Plug-in", "sc:citation": [ + "pmcid:PMC5479118", + "pubmed:28636905", { "@id": "https://doi.org/10.1016/j.bpj.2017.04.055" - }, - "pubmed:28636905", - "pmcid:PMC5479118" + } ], "sc:description": "An automated workflow tool for Kepler to perform AMBER GPU molecular dynamics simulations.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "LGPL-2.0", "sc:name": "AmberGPUMDSimulation", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/nbcrrolls/workflows/tree/master/Production/AmberGPUMDSimulation" + }, + { + "@id": "https://doi.org/10.1016/j.bpj.2017.04.055", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ambertools/ambertoolsbioschemas.jsonld b/data/ambertools/ambertoolsbioschemas.jsonld index ac949e4b1b78e..d17fcdbf733e1 100644 --- a/data/ambertools/ambertoolsbioschemas.jsonld +++ b/data/ambertools/ambertoolsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Consists of several independently developed packages that work well by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models.", "sc:name": "AmberTools", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://ambermd.org/#AmberTools" } \ No newline at end of file diff --git a/data/ambit-smirks/ambit-smirksbioschemas.jsonld b/data/ambit-smirks/ambit-smirksbioschemas.jsonld index 8d589d6316589..be8dff15fb0f0 100644 --- a/data/ambit-smirks/ambit-smirksbioschemas.jsonld +++ b/data/ambit-smirks/ambit-smirksbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Apache-2.0", "sc:name": "Ambit-SMIRKS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://ambit.sourceforge.net/smirks/" } \ No newline at end of file diff --git a/data/amda/amdabioschemas.jsonld b/data/amda/amdabioschemas.jsonld index e4e5d412ee9d4..c580f832ec7c6 100644 --- a/data/amda/amdabioschemas.jsonld +++ b/data/amda/amdabioschemas.jsonld @@ -9,39 +9,39 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3389/FGENE.2019.00350", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/AMDA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xiang Zhan", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6491633", - "pubmed:31068967", { "@id": "https://doi.org/10.3389/FGENE.2019.00350" - } + }, + "pmcid:PMC6491633", + "pubmed:31068967" ], "sc:description": "Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis.", "sc:featureList": [ { - "@id": "edam:operation_3677" + "@id": "edam:operation_3741" }, { - "@id": "edam:operation_3741" + "@id": "edam:operation_3677" } ], "sc:license": "GPL-3.0", "sc:name": "AMDA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/xyz5074/AMDA" + }, + { + "@id": "https://doi.org/10.3389/FGENE.2019.00350", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/amen/amenbioschemas.jsonld b/data/amen/amenbioschemas.jsonld index 6f4d1ae7ab44a..a01b3ff3c99fa 100644 --- a/data/amen/amenbioschemas.jsonld +++ b/data/amen/amenbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1186/1471-2105-9-86", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0002-0535-3628", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/amen", "@type": "sc:SoftwareApplication", @@ -26,26 +22,30 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pmcid:PMC18254954", - "pubmed:18254954", { "@id": "https://doi.org/10.1186/1471-2105-9-86" - } + }, + "pubmed:18254954" ], "sc:description": "The Annotation, Mapping, Expression and Network (AMEN) software is a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i) uploading and pre-processing data from microarray expression profiling experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human.", "sc:featureList": [ { - "@id": "edam:operation_3083" + "@id": "edam:operation_2495" }, { "@id": "edam:operation_3501" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3083" } ], "sc:name": "AMEN", "sc:url": "https://sourceforge.net/projects/amen/", "sc:version": "1.5.4" + }, + { + "@id": "http://orcid.org/0000-0002-0535-3628", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/amica/amicabioschemas.jsonld b/data/amica/amicabioschemas.jsonld index f5276252740f8..df7b9d8214e39 100644 --- a/data/amica/amicabioschemas.jsonld +++ b/data/amica/amicabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web application which provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualized by heat maps and downloaded as a standard clustered data file for further analysis.", "sc:name": "AMICa", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioalgo.iit.cnr.it/amica" diff --git a/data/amigene/amigenebioschemas.jsonld b/data/amigene/amigenebioschemas.jsonld index dd5f5a9e27bc9..535dab773fc08 100644 --- a/data/amigene/amigenebioschemas.jsonld +++ b/data/amigene/amigenebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Gene prediction server that can identify coding sequences in microbes.", "sc:name": "AMIGene", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php" } \ No newline at end of file diff --git a/data/amigo_2/amigo_2bioschemas.jsonld b/data/amigo_2/amigo_2bioschemas.jsonld index b69fed4647b70..5b21d94f85710 100644 --- a/data/amigo_2/amigo_2bioschemas.jsonld +++ b/data/amigo_2/amigo_2bioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The GO Consortium GO browser and search engine.", "sc:name": "AmiGO 2", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://amigo.geneontology.org/amigo" } \ No newline at end of file diff --git a/data/ammodels/ammodelsbioschemas.jsonld b/data/ammodels/ammodelsbioschemas.jsonld index e3cb723c95bdf..f81ff7906218f 100644 --- a/data/ammodels/ammodelsbioschemas.jsonld +++ b/data/ammodels/ammodelsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool which helps enable adaptive management by codifying knowledge in the form of models generated from numerous analyses and data sets. Facilitates this process by storing all models and data sets in a single object that can be updated and saved, thus tracking changes in knowledge through time. A shiny application called AM Model Manager (modelMgr()) enables the use of these functions via a GUI.", "sc:name": "AMModels", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/AMModels/index.html" diff --git a/data/amoebadb/amoebadbbioschemas.jsonld b/data/amoebadb/amoebadbbioschemas.jsonld index fda2a3535ed36..f6e079e68447a 100644 --- a/data/amoebadb/amoebadbbioschemas.jsonld +++ b/data/amoebadb/amoebadbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "It is a new functional genomic databases serving the amoebozoa research communities. It contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. Importantly it utilizes the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility.", "sc:name": "AmoebaDB", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://AmoebaDB.org" } \ No newline at end of file diff --git a/data/amordad/amordadbioschemas.jsonld b/data/amordad/amordadbioschemas.jsonld index a98e661c7a67c..2fc978d25cb3b 100644 --- a/data/amordad/amordadbioschemas.jsonld +++ b/data/amordad/amordadbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database engine for comparing metagenomic data at massive scale. It first obtains the sequence signature of metagenomes and organizes them as points in high dimensional space.", "sc:name": "Amordad", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://smithlabresearch.org/software/amordad/" } \ No newline at end of file diff --git a/data/amountain/amountainbioschemas.jsonld b/data/amountain/amountainbioschemas.jsonld index 0be4f8be9a2f4..d03ebada006c8 100644 --- a/data/amountain/amountainbioschemas.jsonld +++ b/data/amountain/amountainbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dong Li", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A pure data-driven gene network, weighted gene co-expression network (WGCN) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. This tool aims to search active modules in multi-layer WGCN using a continuous optimization approach.", "sc:license": "GPL-2.0", "sc:name": "AMOUNTAIN", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AMOUNTAIN.html", diff --git a/data/amped/ampedbioschemas.jsonld b/data/amped/ampedbioschemas.jsonld index 4a2fb0ff5fc65..18efd568eacaa 100644 --- a/data/amped/ampedbioschemas.jsonld +++ b/data/amped/ampedbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lenore M Martin", "sc:additionalType": [ + "Web service", "Suite", - "Database portal", - "Web service" + "Database portal" ], "sc:description": "Annotated collection of normalized data describing antimicrobial peptides, their sources, their 3D structures, and their target organisms. It enables users to perform quick queries and allows the entire peptide community to contribute to the repository.", "sc:license": "Other", diff --git a/data/amphoranet/amphoranetbioschemas.jsonld b/data/amphoranet/amphoranetbioschemas.jsonld index 9d8f8bc3bef4f..de3ed7c8c1520 100644 --- a/data/amphoranet/amphoranetbioschemas.jsonld +++ b/data/amphoranet/amphoranetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AmphoraNet", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://pitgroup.org/amphoranet/" } \ No newline at end of file diff --git a/data/amphoravizu/amphoravizubioschemas.jsonld b/data/amphoravizu/amphoravizubioschemas.jsonld index fec5e6af9a87a..8c463a7fe259c 100644 --- a/data/amphoravizu/amphoravizubioschemas.jsonld +++ b/data/amphoravizu/amphoravizubioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AmphoraVizu", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://pitgroup.org/amphoravizu/" } \ No newline at end of file diff --git a/data/amplimap/amplimapbioschemas.jsonld b/data/amplimap/amplimapbioschemas.jsonld index 4cccb7b1e48b4..e3c717d5c4127 100644 --- a/data/amplimap/amplimapbioschemas.jsonld +++ b/data/amplimap/amplimapbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "amplimap", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/koelling/amplimap" } \ No newline at end of file diff --git a/data/amplimethprofiler/amplimethprofilerbioschemas.jsonld b/data/amplimethprofiler/amplimethprofilerbioschemas.jsonld index ec8a1e0a17394..7d2aea72e2e65 100644 --- a/data/amplimethprofiler/amplimethprofilerbioschemas.jsonld +++ b/data/amplimethprofiler/amplimethprofilerbioschemas.jsonld @@ -16,18 +16,18 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5123276", - "pubmed:27884103", { "@id": "https://doi.org/10.1186/S12859-016-1380-3" - } + }, + "pubmed:27884103" ], "sc:description": "Pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons.", "sc:featureList": [ { - "@id": "edam:operation_3204" + "@id": "edam:operation_3186" }, { - "@id": "edam:operation_3186" + "@id": "edam:operation_3204" } ], "sc:license": "GPL-3.0", diff --git a/data/ampliqueso/ampliquesobioschemas.jsonld b/data/ampliqueso/ampliquesobioschemas.jsonld index 35b6359ca7cf7..f446713294a5d 100644 --- a/data/ampliqueso/ampliquesobioschemas.jsonld +++ b/data/ampliqueso/ampliquesobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michal Okoniewski", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq.", "sc:license": "GPL-2.0", diff --git a/data/ampred/ampredbioschemas.jsonld b/data/ampred/ampredbioschemas.jsonld index d7908635212ae..ac8c6d409d5ea 100644 --- a/data/ampred/ampredbioschemas.jsonld +++ b/data/ampred/ampredbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Ampred server predicts the Antimicrobial activity of given sequence. The activity may be antifungal, antiviral and antibacterial .This server works based on Multidimensional signatures of antimicrobial peptides", "sc:name": "Ampred", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.bioinformatics.org/Antimicrobial/" } \ No newline at end of file diff --git a/data/amps-nmr/amps-nmrbioschemas.jsonld b/data/amps-nmr/amps-nmrbioschemas.jsonld index 92c715f64b24f..f291f76f2f7d8 100644 --- a/data/amps-nmr/amps-nmrbioschemas.jsonld +++ b/data/amps-nmr/amps-nmrbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "NMR protein structure refinement. Amber (acronym to Assisted Model Building with Energy Refinement) is a suite of programs 1N3L that allow users to perform molecular dynamics (MD) simulations on biological systems. This web portal makes available the entire functionality of AMBER, in particular (but not only) using NMR-derived information as restraints for MD.", "sc:name": "AMPS-NMR", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "CERM", diff --git a/data/ams/amsbioschemas.jsonld b/data/ams/amsbioschemas.jsonld index 0f1f5c3041194..471c1a782d369 100644 --- a/data/ams/amsbioschemas.jsonld +++ b/data/ams/amsbioschemas.jsonld @@ -9,27 +9,27 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1007/s00726-012-1290-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ams", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC3397139", - "pubmed:22555647", { "@id": "https://doi.org/10.1007/s00726-012-1290-2" }, - "pubmed:20423529" + "pmcid:PMC3397139", + "pubmed:20423529", + "pubmed:22555647" ], "sc:description": "Predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences.", "sc:name": "AMS", "sc:operatingSystem": "Linux", "sc:url": "https://code.google.com/p/automotifserver/", "sc:version": "4.0-1.5" + }, + { + "@id": "https://doi.org/10.1007/s00726-012-1290-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/amt/amtbioschemas.jsonld b/data/amt/amtbioschemas.jsonld index b2a9e88ca9765..b5312ab5b1ed5 100644 --- a/data/amt/amtbioschemas.jsonld +++ b/data/amt/amtbioschemas.jsonld @@ -9,14 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1002/ece3.4823", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/amt", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Johannes Signer", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:30766677", "pmcid:PMC6362447", + "pubmed:30766677", { "@id": "https://doi.org/10.1002/ece3.4823" } @@ -29,15 +33,11 @@ "sc:name": "amt", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://cran.r-project.org/package=amt", "sc:version": "0.0.6" - }, - { - "@id": "https://doi.org/10.1002/ece3.4823", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/amtdb/amtdbbioschemas.jsonld b/data/amtdb/amtdbbioschemas.jsonld index 1ebdc9f24b861..23bb023879172 100644 --- a/data/amtdb/amtdbbioschemas.jsonld +++ b/data/amtdb/amtdbbioschemas.jsonld @@ -9,19 +9,15 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-1774-0091", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/AmtDB", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "https://orcid.org/0000-0003-1774-0091" + "@id": "https://orcid.org/0000-0003-3059-6127" }, { - "@id": "https://orcid.org/0000-0003-3059-6127" + "@id": "https://orcid.org/0000-0003-1774-0091" } ], "edam:has_input": { @@ -38,11 +34,11 @@ "@id": "https://orcid.org/0000-0003-1338-638X" }, "sc:citation": [ + "pmcid:PMC6324066", + "pubmed:30247677", { "@id": "https://doi.org/10.1093/nar/gky843" - }, - "pmcid:PMC6324066", - "pubmed:30247677" + } ], "sc:description": "This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Paleolithic to roughly Iron Age times, focusing on an Euroasian geographical area. We provide both the mtDNA sequences (in FASTA format), and the metadata for the samples (IDs, dates, geolocation, site, culture, mtDNA haplogroup etc., available to download in a tab-delimited text file).", "sc:featureList": { @@ -59,12 +55,16 @@ "sc:url": "https://amtdb.org", "sc:version": "v1.002" }, + { + "@id": "https://orcid.org/0000-0003-3059-6127", + "@type": "schema:Person" + }, { "@id": "https://orcid.org/0000-0003-1338-638X", "@type": "schema:Person" }, { - "@id": "https://orcid.org/0000-0003-3059-6127", + "@id": "https://orcid.org/0000-0003-1774-0091", "@type": "schema:Person" }, { diff --git a/data/amtrak/amtrakbioschemas.jsonld b/data/amtrak/amtrakbioschemas.jsonld index 0dc9b5bc5fae2..f1d9d03dbb121 100644 --- a/data/amtrak/amtrakbioschemas.jsonld +++ b/data/amtrak/amtrakbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0167620", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0002-9506-2153", "@type": "schema:Person" @@ -21,10 +25,10 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:27992448", { "@id": "https://doi.org/10.1371/journal.pone.0167620" }, - "pubmed:27992448", "pmcid:PMC5167257" ], "sc:description": "Automated multi-peak tracking kymography (AMTraK) is a software tool that uses peak information and distance minimization to track and automatically quantify kymographs.", @@ -34,14 +38,10 @@ "sc:license": "GPL-3.0", "sc:name": "AMTraK", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.iiserpune.ac.in/~cathale/SupplementaryMaterial/Amtrak.html" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0167620", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/amylpred/amylpredbioschemas.jsonld b/data/amylpred/amylpredbioschemas.jsonld index c4fe78412c9e2..2cd0beceb10f1 100644 --- a/data/amylpred/amylpredbioschemas.jsonld +++ b/data/amylpred/amylpredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Consensus prediction method for identifying possible amyloidogenic regions in protein sequences.", "sc:name": "AMYLPRED", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://aias.biol.uoa.gr/AMYLPRED/" } \ No newline at end of file diff --git a/data/amylpred2/amylpred2bioschemas.jsonld b/data/amylpred2/amylpred2bioschemas.jsonld index f52b9a4f5778d..5800267fa38af 100644 --- a/data/amylpred2/amylpred2bioschemas.jsonld +++ b/data/amylpred2/amylpred2bioschemas.jsonld @@ -15,10 +15,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:23326595", - "pmcid:PMC3542318", { "@id": "https://doi.org/10.1371/journal.pone.0054175" - } + }, + "pmcid:PMC3542318" ], "sc:contributor": { "@id": "https://orcid.org/0000-0001-7446-4412" @@ -29,9 +29,9 @@ }, "sc:name": "AMYL-PRED 2", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://aias.biol.uoa.gr/AMYLPRED2/" }, diff --git a/data/amypdb/amypdbbioschemas.jsonld b/data/amypdb/amypdbbioschemas.jsonld index 88a3f1fe3befa..301cecaab317a 100644 --- a/data/amypdb/amypdbbioschemas.jsonld +++ b/data/amypdb/amypdbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "An online database dedicated to amyloid precursor families and to their amino acid sequence signatures.", "sc:name": "AMYPdb", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://amypdb.genouest.org" } \ No newline at end of file diff --git a/data/anaconda_cnv/anaconda_cnvbioschemas.jsonld b/data/anaconda_cnv/anaconda_cnvbioschemas.jsonld index 6d319ce9b6221..6a9fcc72ec510 100644 --- a/data/anaconda_cnv/anaconda_cnvbioschemas.jsonld +++ b/data/anaconda_cnv/anaconda_cnvbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/anaconda_cnv", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yuanwei Zhang", - "Xiaohua Jiang" + "Xiaohua Jiang", + "Yuanwei Zhang" ], "sc:additionalType": "Command-line tool", "sc:description": "An automated pipeline for somatic copy number variation detection and annotation from tumor exome sequencing data.", diff --git a/data/analysispageserver/analysispageserverbioschemas.jsonld b/data/analysispageserver/analysispageserverbioschemas.jsonld index 6942ac417ba4a..238038fbf5ad6 100644 --- a/data/analysispageserver/analysispageserverbioschemas.jsonld +++ b/data/analysispageserver/analysispageserverbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Brad Friedman", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Modular system that enables sharing of customizable R analyses via the web.", "sc:license": "Artistic-2.0", "sc:name": "AnalysisPageServer", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AnalysisPageServer.html", "sc:version": "1.8.1" diff --git a/data/analyzer/analyzerbioschemas.jsonld b/data/analyzer/analyzerbioschemas.jsonld index 9cca82b0c2ffe..098fa892217bf 100644 --- a/data/analyzer/analyzerbioschemas.jsonld +++ b/data/analyzer/analyzerbioschemas.jsonld @@ -15,22 +15,22 @@ "biotools:primaryContact": "Dr M.D. Fricker", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC6395764", "pubmed:30816109", { "@id": "https://doi.org/10.1038/s41467-019-08893-9" - } + }, + "pmcid:PMC6395764" ], "sc:description": "Software package for quantitative analysis of plant ER architecture and dynamics.", "sc:featureList": [ { - "@id": "edam:operation_3799" + "@id": "edam:operation_3216" }, { - "@id": "edam:operation_3435" + "@id": "edam:operation_3799" }, { - "@id": "edam:operation_3216" + "@id": "edam:operation_3435" } ], "sc:name": "AnalyzER", diff --git a/data/anamir/anamirbioschemas.jsonld b/data/anamir/anamirbioschemas.jsonld index c72419f846b00..6305fdcea57e1 100644 --- a/data/anamir/anamirbioschemas.jsonld +++ b/data/anamir/anamirbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ti-Tai Wang", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.", "sc:license": "GPL-2.0", "sc:name": "anamiR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/anamiR.html", "sc:version": "1.0.1" diff --git a/data/ananke/anankebioschemas.jsonld b/data/ananke/anankebioschemas.jsonld index b192bbcf10862..0ee3d31a2c1d4 100644 --- a/data/ananke/anankebioschemas.jsonld +++ b/data/ananke/anankebioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.7717/peerj.3812", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ananke", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael W. Hall", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5621509", + "pubmed:28966891", { "@id": "https://doi.org/10.7717/peerj.3812" - }, - "pmcid:PMC5621509", - "pubmed:28966891" + } ], "sc:description": "Clustering marker gene data by time-series patterns.", "sc:featureList": { @@ -36,6 +32,10 @@ "Linux" ], "sc:url": "https://github.com/beiko-lab/ananke" + }, + { + "@id": "https://doi.org/10.7717/peerj.3812", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/anaquin/anaquinbioschemas.jsonld b/data/anaquin/anaquinbioschemas.jsonld index 5ace55b63ac0d..5213a235f295e 100644 --- a/data/anaquin/anaquinbioschemas.jsonld +++ b/data/anaquin/anaquinbioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-2748-5496", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/anaquin", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ted Wong", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:27502218", "sc:contributor": { @@ -25,16 +29,12 @@ "sc:license": "BSD-4-Clause", "sc:name": "Anaquin", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Anaquin.html", "sc:version": "1.0.0" - }, - { - "@id": "http://orcid.org/0000-0002-2748-5496", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/anarci/anarcibioschemas.jsonld b/data/anarci/anarcibioschemas.jsonld index 64810c8ad9f0c..c0c7b44d89cb2 100644 --- a/data/anarci/anarcibioschemas.jsonld +++ b/data/anarci/anarcibioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/anarci", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:citation": "pubmed:26424857", "sc:description": "Tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains.", "sc:name": "ANARCI", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php" diff --git a/data/anastasia/anastasiabioschemas.jsonld b/data/anastasia/anastasiabioschemas.jsonld index 6df574713d8a5..8e6ecd25561aa 100644 --- a/data/anastasia/anastasiabioschemas.jsonld +++ b/data/anastasia/anastasiabioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/anastasia", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Eleftherios Pilalis", "Aristotelis Chatziioannou", - "Theodoros Koutsandreas", - "Eleftherios Pilalis" + "Theodoros Koutsandreas" ], "sc:additionalType": [ "Web application", @@ -22,9 +22,9 @@ "sc:description": "ANASTASIA (Automated Nucleotide Animoacid Sequences Translational plAtform for Synthetic Interpretation and Analysis) is a metagenomics analysis platform and repository.", "sc:name": "ANASTASIA", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://motherbox.chemeng.ntua.gr/anastasia_dev/" } \ No newline at end of file diff --git a/data/anca/ancabioschemas.jsonld b/data/anca/ancabioschemas.jsonld index db7aa5d0c5cf7..dc4fed1dfa345 100644 --- a/data/anca/ancabioschemas.jsonld +++ b/data/anca/ancabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1016/j.bpj.2018.03.021", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/anca", "@type": "sc:SoftwareApplication", @@ -28,15 +32,11 @@ "sc:license": "BSD-3-Clause", "sc:name": "ANCA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://csb.pitt.edu/anca/index.html", "sc:version": "1.0" - }, - { - "@id": "https://doi.org/10.1016/j.bpj.2018.03.021", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/anceshc/anceshcbioschemas.jsonld b/data/anceshc/anceshcbioschemas.jsonld index b7c14146aa92b..23577178676c8 100644 --- a/data/anceshc/anceshcbioschemas.jsonld +++ b/data/anceshc/anceshcbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "AncesHC (ancestral haplotype clustering ) is a program for determining the haplotype structure of a population sample from genotype data, and then testing for association of these haplotypes with either a binary or continous outcome.", "sc:name": "AncesHC", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.imperial.ac.uk/people/l.coin", "sc:version": "2009" diff --git a/data/anchor_expedition_suite/anchor_expedition_suitebioschemas.jsonld b/data/anchor_expedition_suite/anchor_expedition_suitebioschemas.jsonld index 9c389583b2974..8488291732aff 100644 --- a/data/anchor_expedition_suite/anchor_expedition_suitebioschemas.jsonld +++ b/data/anchor_expedition_suite/anchor_expedition_suitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "anchor (Expedition suite)", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/YeoLab/anchor" } \ No newline at end of file diff --git a/data/anchor_tfbs_prediction/anchor_tfbs_predictionbioschemas.jsonld b/data/anchor_tfbs_prediction/anchor_tfbs_predictionbioschemas.jsonld index a2734748a2a42..62cc1a1727f40 100644 --- a/data/anchor_tfbs_prediction/anchor_tfbs_predictionbioschemas.jsonld +++ b/data/anchor_tfbs_prediction/anchor_tfbs_predictionbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Package for trans-cell type prediction of transcription factor binding sites.", "sc:name": "Anchor", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/GuanLab/Anchor" } \ No newline at end of file diff --git a/data/anchored_multiplier_calculator/anchored_multiplier_calculatorbioschemas.jsonld b/data/anchored_multiplier_calculator/anchored_multiplier_calculatorbioschemas.jsonld index 6b7ef1b4b175c..a965186a32ac2 100644 --- a/data/anchored_multiplier_calculator/anchored_multiplier_calculatorbioschemas.jsonld +++ b/data/anchored_multiplier_calculator/anchored_multiplier_calculatorbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Anchored Multiplier Calculator", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://anchoredmultiplier.ucsf.edu/" } \ No newline at end of file diff --git a/data/ancis-pytorch/ancis-pytorchbioschemas.jsonld b/data/ancis-pytorch/ancis-pytorchbioschemas.jsonld index 8253660779d66..dd31b6a436c39 100644 --- a/data/ancis-pytorch/ancis-pytorchbioschemas.jsonld +++ b/data/ancis-pytorch/ancis-pytorchbioschemas.jsonld @@ -11,12 +11,12 @@ "@id": "https://bio.tools/ANCIS-Pytorch", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Daniel J. Hoeppner", "Menglin Jiang", "Pengxiang Wu", - "Daniel J. Hoeppner", - "Qiaoying Huang", "Dimitris N. Metaxas", - "Jingru Yi" + "Jingru Yi", + "Qiaoying Huang" ], "sc:additionalType": "Script", "sc:citation": "pubmed:31103790", diff --git a/data/ancorr/ancorrbioschemas.jsonld b/data/ancorr/ancorrbioschemas.jsonld index 826db8898b59f..dc5920f1e6226 100644 --- a/data/ancorr/ancorrbioschemas.jsonld +++ b/data/ancorr/ancorrbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/ancorr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Youri Kravatsky", "Vladimir Chechetkin", - "Galina Kravatskaya", - "Youri Kravatsky" + "Galina Kravatskaya" ], "sc:additionalType": "Web service", "sc:citation": "pubmed:25627242", diff --git a/data/andi/andibioschemas.jsonld b/data/andi/andibioschemas.jsonld index 3bef7d5619b8c..81ab6ad1f4c1d 100644 --- a/data/andi/andibioschemas.jsonld +++ b/data/andi/andibioschemas.jsonld @@ -22,8 +22,8 @@ "sc:name": "andi", "sc:operatingSystem": "Linux", "sc:provider": [ - "evolbio.mpg.de", - "Max Planck Institute for Evolutionary Biology" + "Max Planck Institute for Evolutionary Biology", + "evolbio.mpg.de" ], "sc:url": "https://github.com/EvolBioInf/andi", "sc:version": "0.11" diff --git a/data/andis/andisbioschemas.jsonld b/data/andis/andisbioschemas.jsonld index f72ccd3a8fdf4..81478cb679272 100644 --- a/data/andis/andisbioschemas.jsonld +++ b/data/andis/andisbioschemas.jsonld @@ -9,41 +9,41 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2898-y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ANDIS", "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:31159742", { "@id": "https://doi.org/10.1186/s12859-019-2898-y" }, - "pmcid:PMC6547486" + "pmcid:PMC6547486", + "pubmed:31159742" ], "sc:description": "Atomic angle- and distance-dependent statistical potential for protein structure quality assessment.", "sc:featureList": [ { - "@id": "edam:operation_0249" + "@id": "edam:operation_0321" }, { "@id": "edam:operation_0476" }, { - "@id": "edam:operation_0321" + "@id": "edam:operation_0249" } ], "sc:license": "Unlicense", "sc:name": "ANDIS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://qbp.hzau.edu.cn/ANDIS/" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2898-y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/andom/andombioschemas.jsonld b/data/andom/andombioschemas.jsonld index dcd7c472b91a6..b0ee082fd6a75 100644 --- a/data/andom/andombioschemas.jsonld +++ b/data/andom/andombioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web tool that helps to assign structural domains to protein sequences and to classify them according to SCOP.", "sc:name": "AnDom", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://andom.bioapps.biozentrum.uni-wuerzburg.de/index_new.html" diff --git a/data/aneufinder/aneufinderbioschemas.jsonld b/data/aneufinder/aneufinderbioschemas.jsonld index 0511345ffa853..3ade8cbab47b3 100644 --- a/data/aneufinder/aneufinderbioschemas.jsonld +++ b/data/aneufinder/aneufinderbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-0989-3127", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s13059-016-0971-7", "@type": "sc:CreativeWork" @@ -21,21 +17,21 @@ "@id": "https://bio.tools/aneufinder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Aaron Taudt", { "@id": "http://orcid.org/0000-0003-0989-3127" - } + }, + "Aaron Taudt" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:27246460", - "pmcid:PMC4888588", { "@id": "https://doi.org/10.1186/s13059-016-0971-7" - } + }, + "pmcid:PMC4888588", + "pubmed:27246460" ], "sc:description": "This package implements functions for CNV calling, plotting, export and analysis from whole-genome single cell sequencing data.", "sc:featureList": { @@ -50,6 +46,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AneuFinder.html", "sc:version": "1.2.1" + }, + { + "@id": "http://orcid.org/0000-0003-0989-3127", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/aneuvis/aneuvisbioschemas.jsonld b/data/aneuvis/aneuvisbioschemas.jsonld index 5610af7d6fc45..122bcb82bcd90 100644 --- a/data/aneuvis/aneuvisbioschemas.jsonld +++ b/data/aneuvis/aneuvisbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2842-1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Aneuvis", "@type": "sc:SoftwareApplication", @@ -18,8 +22,8 @@ { "@id": "https://doi.org/10.1186/s12859-019-2842-1" }, - "pmcid:PMC6580570", - "pubmed:31208319" + "pubmed:31208319", + "pmcid:PMC6580570" ], "sc:description": "Web-based exploration of numerical chromosomal variation in single cells.", "sc:featureList": [ @@ -41,10 +45,6 @@ "Linux" ], "sc:url": "https://dpique.shinyapps.io/aneuvis/" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2842-1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/anf/anfbioschemas.jsonld b/data/anf/anfbioschemas.jsonld index 38db3f7277775..1c86b45a3fbc3 100644 --- a/data/anf/anfbioschemas.jsonld +++ b/data/anf/anfbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "ANF", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ANF.html", "sc:version": "1.2.0" diff --git a/data/anglerfish/anglerfishbioschemas.jsonld b/data/anglerfish/anglerfishbioschemas.jsonld index 8243d53e1ab6a..10788d132c558 100644 --- a/data/anglerfish/anglerfishbioschemas.jsonld +++ b/data/anglerfish/anglerfishbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-9649-5092", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTW781", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/anglerfish", "@type": "sc:SoftwareApplication", @@ -17,11 +25,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC5860525", "pubmed:28035031", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTW781" - }, - "pmcid:PMC5860525" + } ], "sc:description": "Method of determining the orientation of an α-helix relative to a defined axis in a rotationally symmetric protein structure such as a membrane protein channel.", "sc:featureList": [ @@ -34,19 +42,11 @@ ], "sc:name": "AnglerFish", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://anglerfish.cryst.bbk.ac.uk/" - }, - { - "@id": "http://orcid.org/0000-0001-9649-5092", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTW781", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/angsd-wrapper/angsd-wrapperbioschemas.jsonld b/data/angsd-wrapper/angsd-wrapperbioschemas.jsonld index 2a563df5ae442..0f01c612ca82e 100644 --- a/data/angsd-wrapper/angsd-wrapperbioschemas.jsonld +++ b/data/angsd-wrapper/angsd-wrapperbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "ANGSD-wrapper is a utility developed to aid in the analysis of next generation sequencing data.", "sc:name": "angsd-wrapper", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/mojaveazure/angsd-wrapper" } \ No newline at end of file diff --git a/data/angsd/angsdbioschemas.jsonld b/data/angsd/angsdbioschemas.jsonld index bfee740f17270..738d3683939d1 100644 --- a/data/angsd/angsdbioschemas.jsonld +++ b/data/angsd/angsdbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "ANGSD", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "binf.ku.dk", diff --git a/data/angular-ripleys-k/angular-ripleys-kbioschemas.jsonld b/data/angular-ripleys-k/angular-ripleys-kbioschemas.jsonld index 4563ccee08486..d795cb3fbda0f 100644 --- a/data/angular-ripleys-k/angular-ripleys-kbioschemas.jsonld +++ b/data/angular-ripleys-k/angular-ripleys-kbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Quantification of fibrous spatial point patterns from single-molecule localization microscopy data.", "sc:name": "Angular-Ripleys-K", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/RubyPeters/Angular-Ripleys-K" } \ No newline at end of file diff --git a/data/animalnexus/animalnexusbioschemas.jsonld b/data/animalnexus/animalnexusbioschemas.jsonld index 769d150a0f120..9d62099600594 100644 --- a/data/animalnexus/animalnexusbioschemas.jsonld +++ b/data/animalnexus/animalnexusbioschemas.jsonld @@ -27,17 +27,17 @@ "sc:description": "Transforming and visualizing animal movement data from static stations.", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_0335" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_0337" } ], "sc:name": "animalnexus", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://animalnexus.ca/" }, diff --git a/data/aniseed/aniseedbioschemas.jsonld b/data/aniseed/aniseedbioschemas.jsonld index 94d724f19b4dd..55bdb5e485d56 100644 --- a/data/aniseed/aniseedbioschemas.jsonld +++ b/data/aniseed/aniseedbioschemas.jsonld @@ -10,11 +10,11 @@ }, "@graph": [ { - "@id": "https://orcid.org/0000-0003-4925-2009", + "@id": "https://orcid.org/0000-0001-7247-6460", "@type": "schema:Person" }, { - "@id": "https://orcid.org/0000-0001-7247-6460", + "@id": "https://orcid.org/0000-0003-4925-2009", "@type": "schema:Person" }, { @@ -22,16 +22,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "https://orcid.org/0000-0001-7247-6460" + "@id": "https://orcid.org/0000-0003-4925-2009" }, { - "@id": "https://orcid.org/0000-0003-4925-2009" + "@id": "https://orcid.org/0000-0001-7247-6460" } ], "sc:additionalType": [ - "Ontology", "Database portal", "Web application", + "Ontology", "Web API" ], "sc:description": "ANISEED is the main model organism database for the worldwide community of scientists working on tunicates (sister-group of vertebrates). It integrates for each species: \ni) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; \nii) A multispecies genomic browser; \niii) a Genomicus gene synteny browser.", diff --git a/data/anm/anmbioschemas.jsonld b/data/anm/anmbioschemas.jsonld index 76064b617d530..bce5f4763cd85 100644 --- a/data/anm/anmbioschemas.jsonld +++ b/data/anm/anmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Simple NMA tool for analysis of vibrational motions in molecular systems. It uses Elastic Network (EN) methodology and represents the system in the residue level.", "sc:name": "ANM", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://anm.csb.pitt.edu/" } \ No newline at end of file diff --git a/data/ann-glycolysis-flux-prediction/ann-glycolysis-flux-predictionbioschemas.jsonld b/data/ann-glycolysis-flux-prediction/ann-glycolysis-flux-predictionbioschemas.jsonld index 28b0058e9e85b..98666a1714b01 100644 --- a/data/ann-glycolysis-flux-prediction/ann-glycolysis-flux-predictionbioschemas.jsonld +++ b/data/ann-glycolysis-flux-prediction/ann-glycolysis-flux-predictionbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://orcid.org/0000-0002-3568-9595", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216178", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ANN-Glycolysis-Flux-Prediction", "@type": "sc:SoftwareApplication", @@ -25,19 +21,19 @@ }, "sc:additionalType": "Script", "sc:citation": [ - "pubmed:31067238", + "pmcid:PMC6505829", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216178" }, - "pmcid:PMC6505829" + "pubmed:31067238" ], "sc:description": "Flux prediction using artificial neural network (ANN) for the upper part of glycolysis.", "sc:featureList": [ { - "@id": "edam:operation_3439" + "@id": "edam:operation_3715" }, { - "@id": "edam:operation_3715" + "@id": "edam:operation_3439" }, { "@id": "edam:operation_3435" @@ -46,11 +42,15 @@ "sc:license": "MIT", "sc:name": "ANN-Glycolysis-Flux-Prediction", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/DSIMB/ANN-Glycolysis-Flux-Prediction" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216178", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ann-solo/ann-solobioschemas.jsonld b/data/ann-solo/ann-solobioschemas.jsonld index c98c9e6f2b0f8..94173569ac0ea 100644 --- a/data/ann-solo/ann-solobioschemas.jsonld +++ b/data/ann-solo/ann-solobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "ANN-SoLo", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/bittremieux/ANN-SoLo" } \ No newline at end of file diff --git a/data/annaffy/annaffybioschemas.jsonld b/data/annaffy/annaffybioschemas.jsonld index 53a201b3a3c69..dac58114a6885 100644 --- a/data/annaffy/annaffybioschemas.jsonld +++ b/data/annaffy/annaffybioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Colin A. Smith", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Functions for handling data from BioConductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.", "sc:license": "GPL-3.0", diff --git a/data/annaffy/bioconda_annaffy.yaml b/data/annaffy/bioconda_annaffy.yaml index ef2b403fbcebf..4097a325a60c1 100644 --- a/data/annaffy/bioconda_annaffy.yaml +++ b/data/annaffy/bioconda_annaffy.yaml @@ -6,7 +6,6 @@ description: Functions for handling data from Bioconductor Affymetrix annotation home: https://bioconductor.org/packages/3.10/bioc/html/annaffy.html identifiers: - biotools:annaffy -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-annaffy diff --git a/data/anncolvar/anncolvarbioschemas.jsonld b/data/anncolvar/anncolvarbioschemas.jsonld index 5b77fb6d136bf..d0fa666de5a42 100644 --- a/data/anncolvar/anncolvarbioschemas.jsonld +++ b/data/anncolvar/anncolvarbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3389/fmolb.2019.00025", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Anncolvar", "@type": "sc:SoftwareApplication", @@ -24,11 +28,11 @@ "@id": "edam:topic_3892" }, "sc:citation": [ - "pmcid:PMC6482212", - "pubmed:31058167", { "@id": "https://doi.org/10.3389/fmolb.2019.00025" - } + }, + "pmcid:PMC6482212", + "pubmed:31058167" ], "sc:description": "Anncolvar builds a feed-forward neural network for approximation of a collective variable of a molecular system. Molecular simulations are slow due to fact that a studied system tends to stay in local energy minima. Methods such as metadynamics address this problem by application of artificial forces acting on collective variables. Collective variables are some descriptors of the state of the molecular system. For example, when simulation binding of a ligand to protein it is possible to use their distance as a collective variable and by applying force onto this collective variable you can accelerate binding and unbinding. However, some sophisticated collective variables are difficult to calculate. For this purpose we developed Anncolvar to approximate such collective variables using artificial neural network.", "sc:featureList": { @@ -40,24 +44,20 @@ "sc:operatingSystem": "Linux", "sc:softwareHelp": [ { - "@id": "https://github.com/spiwokv/anncolvar/blob/master/README.rst" + "@id": "https://github.com/spiwokv/anncolvar/tree/master/docs/html" }, { - "@id": "https://github.com/spiwokv/anncolvar/tree/master/docs/html" + "@id": "https://github.com/spiwokv/anncolvar/blob/master/README.rst" } ], "sc:url": "https://github.com/spiwokv/anncolvar", "sc:version": [ - "v0.2", "v0.4", + "v0.2", "v0.3", "v0.6", "v0.5" ] - }, - { - "@id": "https://doi.org/10.3389/fmolb.2019.00025", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/annmap/annmapbioschemas.jsonld b/data/annmap/annmapbioschemas.jsonld index 09c690aaa1229..7bc2077385513 100644 --- a/data/annmap/annmapbioschemas.jsonld +++ b/data/annmap/annmapbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chris Wirth", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl.", "sc:license": "GPL-2.0", "sc:name": "annmap", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/annmap.html", "sc:version": "1.16.0" diff --git a/data/anno-j/anno-jbioschemas.jsonld b/data/anno-j/anno-jbioschemas.jsonld index 95611db2cdeb6..461e873e74d8a 100644 --- a/data/anno-j/anno-jbioschemas.jsonld +++ b/data/anno-j/anno-jbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Anno-J", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://dandelion.liveholonics.com/dart/annoj.php" } \ No newline at end of file diff --git a/data/annocript/annocriptbioschemas.jsonld b/data/annocript/annocriptbioschemas.jsonld index 268f5db809716..658f750800cb1 100644 --- a/data/annocript/annocriptbioschemas.jsonld +++ b/data/annocript/annocriptbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission", "sc:name": "Annocript", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/frankMusacchia/Annocript" } \ No newline at end of file diff --git a/data/annokey/annokeybioschemas.jsonld b/data/annokey/annokeybioschemas.jsonld index 323dc862dadb6..d04a730d594f2 100644 --- a/data/annokey/annokeybioschemas.jsonld +++ b/data/annokey/annokeybioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest.", "sc:name": "Annokey", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bjpop.github.io/annokey/" } \ No newline at end of file diff --git a/data/annolnc/annolncbioschemas.jsonld b/data/annolnc/annolncbioschemas.jsonld index 133708f2e7f66..67ff17a7c974e 100644 --- a/data/annolnc/annolncbioschemas.jsonld +++ b/data/annolnc/annolncbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12864-016-3287-9", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/annolnc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5112684", - "pubmed:27852242", { "@id": "https://doi.org/10.1186/s12864-016-3287-9" - } + }, + "pmcid:PMC5112684", + "pubmed:27852242" ], "sc:description": "A web server for systematically annotating novel human lncRNAs.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "AnnoLnc", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://annolnc.cbi.pku.edu.cn/index.jsp" + }, + { + "@id": "https://doi.org/10.1186/s12864-016-3287-9", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/annotate/annotatebioschemas.jsonld b/data/annotate/annotatebioschemas.jsonld index 00013af1f2b6d..72d051ed3b6b6 100644 --- a/data/annotate/annotatebioschemas.jsonld +++ b/data/annotate/annotatebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "annotate", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/annotate.html", diff --git a/data/annotate/bioconda_annotate.yaml b/data/annotate/bioconda_annotate.yaml index 4275538c580be..3f050c1e66cd8 100644 --- a/data/annotate/bioconda_annotate.yaml +++ b/data/annotate/bioconda_annotate.yaml @@ -3,7 +3,6 @@ description: Using R enviroments for annotation. home: https://bioconductor.org/packages/3.10/bioc/html/annotate.html identifiers: - biotools:annotate -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotate summary: Annotation for microarrays diff --git a/data/annotategenes/annotategenesbioschemas.jsonld b/data/annotategenes/annotategenesbioschemas.jsonld index 2040bc46fd98b..7b6b2602efcef 100644 --- a/data/annotategenes/annotategenesbioschemas.jsonld +++ b/data/annotategenes/annotategenesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution.", "sc:name": "annotategenes", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/annotategenes/annotateGenes/1.0", "sc:version": "1.0" diff --git a/data/annotategenomicregions/annotategenomicregionsbioschemas.jsonld b/data/annotategenomicregions/annotategenomicregionsbioschemas.jsonld index aee9e0649fb56..d4124772bc1a1 100644 --- a/data/annotategenomicregions/annotategenomicregionsbioschemas.jsonld +++ b/data/annotategenomicregions/annotategenomicregionsbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Contact form", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:24564446", - "pmcid:PMC4015944", { "@id": "https://doi.org/10.1186/1471-2105-15-S1-S8" - } + }, + "pubmed:24564446", + "pmcid:PMC4015944" ], "sc:description": "Web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations.", "sc:featureList": { diff --git a/data/annotatepeaks/annotatepeaksbioschemas.jsonld b/data/annotatepeaks/annotatepeaksbioschemas.jsonld index 883511930f72a..827b17af69e40 100644 --- a/data/annotatepeaks/annotatepeaksbioschemas.jsonld +++ b/data/annotatepeaks/annotatepeaksbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution.", "sc:name": "annotatepeaks", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/annotatepeaks/annotatePeaks/1.0", "sc:version": "1.0" diff --git a/data/annotationdbi/annotationdbibioschemas.jsonld b/data/annotationdbi/annotationdbibioschemas.jsonld index 107a3ffc6d3d9..09e0cbbe3ba57 100644 --- a/data/annotationdbi/annotationdbibioschemas.jsonld +++ b/data/annotationdbi/annotationdbibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "AnnotationDbi", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html", "sc:version": "1.36.0" diff --git a/data/annotationdbi/bioconda_annotationdbi.yaml b/data/annotationdbi/bioconda_annotationdbi.yaml index e695a0a3cd54f..836b879a72602 100644 --- a/data/annotationdbi/bioconda_annotationdbi.yaml +++ b/data/annotationdbi/bioconda_annotationdbi.yaml @@ -4,7 +4,6 @@ description: Implements a user-friendly interface for querying SQLite-based anno home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationDbi.html identifiers: - biotools:annotationdbi -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotationdbi summary: Manipulation of SQLite-based annotations in Bioconductor diff --git a/data/annotationfilter/annotationfilterbioschemas.jsonld b/data/annotationfilter/annotationfilterbioschemas.jsonld index 45568056d68d2..a342d568513ce 100644 --- a/data/annotationfilter/annotationfilterbioschemas.jsonld +++ b/data/annotationfilter/annotationfilterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "AnnotationFilter", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AnnotationFilter.html", "sc:version": "1.4.0" diff --git a/data/annotationforge/annotationforgebioschemas.jsonld b/data/annotationforge/annotationforgebioschemas.jsonld index e6546ed42d64d..bd1e89cc62650 100644 --- a/data/annotationforge/annotationforgebioschemas.jsonld +++ b/data/annotationforge/annotationforgebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.", "sc:license": "Artistic-2.0", "sc:name": "AnnotationForge", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AnnotationForge.html", diff --git a/data/annotationforge/bioconda_annotationforge.yaml b/data/annotationforge/bioconda_annotationforge.yaml index f3fa58c27243c..5a8d9f6d09148 100644 --- a/data/annotationforge/bioconda_annotationforge.yaml +++ b/data/annotationforge/bioconda_annotationforge.yaml @@ -4,7 +4,6 @@ description: Provides code for generating Annotation packages and their database home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationForge.html identifiers: - biotools:annotationforge -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotationforge summary: Tools for building SQLite-based annotation data packages diff --git a/data/annotationfuncs/annotationfuncsbioschemas.jsonld b/data/annotationfuncs/annotationfuncsbioschemas.jsonld index 6cf5166fb3aa4..b82bf28a69d14 100644 --- a/data/annotationfuncs/annotationfuncsbioschemas.jsonld +++ b/data/annotationfuncs/annotationfuncsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "AnnotationFuncs", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AnnotationFuncs.html", "sc:version": "1.24.0" diff --git a/data/annotationfuncs/bioconda_annotationfuncs.yaml b/data/annotationfuncs/bioconda_annotationfuncs.yaml index ab46c6eca27d6..fa18d91c52787 100644 --- a/data/annotationfuncs/bioconda_annotationfuncs.yaml +++ b/data/annotationfuncs/bioconda_annotationfuncs.yaml @@ -4,7 +4,6 @@ description: Functions for handling translating between different identifieres u home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationFuncs.html identifiers: - biotools:annotationfuncs -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-annotationfuncs diff --git a/data/annotationhub/annotationhubbioschemas.jsonld b/data/annotationhub/annotationhubbioschemas.jsonld index 4de4e25c1a795..93984e252dc7e 100644 --- a/data/annotationhub/annotationhubbioschemas.jsonld +++ b/data/annotationhub/annotationhubbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides a client for the BioConductor corresponding web resource, which provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.", "sc:license": "Artistic-2.0", diff --git a/data/annotationhub/bioconda_annotationhub.yaml b/data/annotationhub/bioconda_annotationhub.yaml index 56213aec16adb..1ae3d1ec9edd4 100644 --- a/data/annotationhub/bioconda_annotationhub.yaml +++ b/data/annotationhub/bioconda_annotationhub.yaml @@ -9,7 +9,6 @@ description: This package provides a client for the Bioconductor AnnotationHub w home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationHub.html identifiers: - biotools:annotationhub -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotationhub summary: Client to access AnnotationHub resources diff --git a/data/annotationhubdata/annotationhubdatabioschemas.jsonld b/data/annotationhubdata/annotationhubdatabioschemas.jsonld index 8927aa13d46dc..0f1b1d9fab0f0 100644 --- a/data/annotationhubdata/annotationhubdatabioschemas.jsonld +++ b/data/annotationhubdata/annotationhubdatabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard BioConductor data structures.", "sc:license": "Artistic-2.0", "sc:name": "AnnotationHubData", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AnnotationHubData.html", "sc:version": "1.4.1" diff --git a/data/annotationhubdata/bioconda_annotationhubdata.yaml b/data/annotationhubdata/bioconda_annotationhubdata.yaml index f1d2d27b71f1a..8e8f23ac5d611 100644 --- a/data/annotationhubdata/bioconda_annotationhubdata.yaml +++ b/data/annotationhubdata/bioconda_annotationhubdata.yaml @@ -4,7 +4,6 @@ description: These recipes convert a wide variety and a growing number of public home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationHubData.html identifiers: - biotools:annotationhubdata -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotationhubdata summary: Transform public data resources into Bioconductor Data Structures diff --git a/data/annotationtools/annotationtoolsbioschemas.jsonld b/data/annotationtools/annotationtoolsbioschemas.jsonld index bddf58edf76ce..4bf2c2fd12bd8 100644 --- a/data/annotationtools/annotationtoolsbioschemas.jsonld +++ b/data/annotationtools/annotationtoolsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-9-26", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/annotationtools", "@type": "sc:SoftwareApplication", @@ -24,8 +20,8 @@ "@id": "edam:data_2080" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { @@ -39,11 +35,11 @@ } ], "sc:citation": [ - "pmcid:PMC2267709", "pubmed:18201381", { "@id": "https://doi.org/10.1186/1471-2105-9-26" - } + }, + "pmcid:PMC2267709" ], "sc:description": "Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).", "sc:featureList": [ @@ -57,12 +53,16 @@ "sc:license": "GPL-3.0", "sc:name": "annotationTools", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/annotationTools.html", "sc:version": "1.48.0" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-9-26", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/annotatr/annotatrbioschemas.jsonld b/data/annotatr/annotatrbioschemas.jsonld index 2bfa0520f7f6d..44f846bdbfd36 100644 --- a/data/annotatr/annotatrbioschemas.jsonld +++ b/data/annotatr/annotatrbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "annotatr", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/annotatr.html", "sc:version": "1.0.2" diff --git a/data/annotqtl/annotqtlbioschemas.jsonld b/data/annotqtl/annotqtlbioschemas.jsonld index d55bbf905f188..3403dcb577880 100644 --- a/data/annotqtl/annotqtlbioschemas.jsonld +++ b/data/annotqtl/annotqtlbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool designed to gather the functional annotation of genes from several institutional databases for a specific chromosomal region.", "sc:name": "AnnotQTL", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "GenOuest", "sc:url": "http://annotqtl.genouest.org/", diff --git a/data/annotree/annotreebioschemas.jsonld b/data/annotree/annotreebioschemas.jsonld index b4dbdf868cb10..e7842e42140ab 100644 --- a/data/annotree/annotreebioschemas.jsonld +++ b/data/annotree/annotreebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "AnnoTree", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://annotree.uwaterloo.ca" } \ No newline at end of file diff --git a/data/annotsv/annotsvbioschemas.jsonld b/data/annotsv/annotsvbioschemas.jsonld index 9af7e9facd78a..d948ba788af12 100644 --- a/data/annotsv/annotsvbioschemas.jsonld +++ b/data/annotsv/annotsvbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-4149-0857", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/AnnotSV", "@type": "sc:SoftwareApplication", @@ -28,6 +24,10 @@ "sc:name": "AnnotSV", "sc:operatingSystem": "Linux", "sc:url": "https://lbgi.fr/AnnotSV/" + }, + { + "@id": "https://orcid.org/0000-0002-4149-0857", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/annovar/annovarbioschemas.jsonld b/data/annovar/annovarbioschemas.jsonld index f5da188ee6dd9..ebdf2940ecc9a 100644 --- a/data/annovar/annovarbioschemas.jsonld +++ b/data/annovar/annovarbioschemas.jsonld @@ -35,9 +35,9 @@ ], "sc:name": "ANNOVAR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://annovar.openbioinformatics.org/en/latest/" }, diff --git a/data/annovar_annotate_variation/annovar_annotate_variationbioschemas.jsonld b/data/annovar_annotate_variation/annovar_annotate_variationbioschemas.jsonld index 422409e2e836f..36661ae26db4a 100644 --- a/data/annovar_annotate_variation/annovar_annotate_variationbioschemas.jsonld +++ b/data/annovar_annotate_variation/annovar_annotate_variationbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "annovar_annotate_variation", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://annovar.openbioinformatics.org/en/latest/", "sc:version": "0.0.2" diff --git a/data/annovar_summarize/annovar_summarizebioschemas.jsonld b/data/annovar_summarize/annovar_summarizebioschemas.jsonld index d1f80ad8edf01..94d334fce2b75 100644 --- a/data/annovar_summarize/annovar_summarizebioschemas.jsonld +++ b/data/annovar_summarize/annovar_summarizebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Annotate genetic variants detected from human genome.", "sc:name": "annovar_summarize", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://annovar.openbioinformatics.org/en/latest/", "sc:version": "1.0.0" diff --git a/data/anocva/anocvabioschemas.jsonld b/data/anocva/anocvabioschemas.jsonld index f13d3265c1a6b..6a440dbe2ab1f 100644 --- a/data/anocva/anocvabioschemas.jsonld +++ b/data/anocva/anocvabioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Maciel C. Vidal", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:28174516", + "pmcid:PMC5258722", { "@id": "https://doi.org/10.3389/fnins.2017.00016" }, - "pmcid:PMC5258722" + "pubmed:28174516" ], "sc:description": "A Non-Parametric Statistical Test to Compare Clustering Structures.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "ANOCVA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/anocva/index.html", "sc:version": "0.1.1" diff --git a/data/anolea/anoleabioschemas.jsonld b/data/anolea/anoleabioschemas.jsonld index fbd5e0ca8f325..5b4f9471a10a0 100644 --- a/data/anolea/anoleabioschemas.jsonld +++ b/data/anolea/anoleabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server to assess the quality of a three dimensional protein structure. It uses a statistical potential at the atomic level and gives an energy profile as ouput. Also, the user can choose to have a molecular graphical output representation of the energy profile.", "sc:name": "ANOLEA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://melolab.org/anolea/index.html" } \ No newline at end of file diff --git a/data/anota/anotabioschemas.jsonld b/data/anota/anotabioschemas.jsonld index 42369bf2538fe..964129845b15e 100644 --- a/data/anota/anotabioschemas.jsonld +++ b/data/anota/anotabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ola Larsson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package allows for genome wide studies of translational control using partial variances and the random variance model, identifying differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels.", "sc:license": "GPL-3.0", "sc:name": "anota", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/anota.html", "sc:version": "1.22.0" diff --git a/data/anota2seq/anota2seqbioschemas.jsonld b/data/anota2seq/anota2seqbioschemas.jsonld index 67c977ae283da..27bff6e3a991b 100644 --- a/data/anota2seq/anota2seqbioschemas.jsonld +++ b/data/anota2seq/anota2seqbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "anota2seq", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/anota2seq.html", "sc:version": "1.2.0" diff --git a/data/anpela/anpelabioschemas.jsonld b/data/anpela/anpelabioschemas.jsonld index 6d7aae30ac2a3..9cff99d300a8e 100644 --- a/data/anpela/anpelabioschemas.jsonld +++ b/data/anpela/anpelabioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/ANPELA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jianbo Fu", - "Jing Tang", "Feng Zhu", - "Yunxia Wang" + "Yunxia Wang", + "Jianbo Fu", + "Jing Tang" ], "sc:additionalType": "Web application", "sc:description": "Analysis and Performance Assessment of Label-free Proteome Quantification.", "sc:license": "Unlicense", "sc:name": "ANPELA", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://idrblab.cn/anpela/" } \ No newline at end of file diff --git a/data/antar/antarbioschemas.jsonld b/data/antar/antarbioschemas.jsonld index e7af242c31cc2..e1b06a74ccc6b 100644 --- a/data/antar/antarbioschemas.jsonld +++ b/data/antar/antarbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Predict miRNA targets for human and mouse using the two predictive models: a model trained from microarry studies following transfection, and a model trained from PAR-CLIP datasets.", "sc:name": "Antar", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "binf.ku.dk", "sc:url": "http://servers.binf.ku.dk/antar/index.php" diff --git a/data/antarna/antarnabioschemas.jsonld b/data/antarna/antarnabioschemas.jsonld index 4371ed7803940..196cc187e6b4b 100644 --- a/data/antarna/antarnabioschemas.jsonld +++ b/data/antarna/antarnabioschemas.jsonld @@ -9,14 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-8231-3323", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/antarna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Robert Kleinkauf", { "@id": "http://orcid.org/0000-0001-8231-3323" - } + }, + "Robert Kleinkauf" ], "edam:has_input": { "@id": "edam:data_0880" @@ -48,8 +52,8 @@ "sc:isAccessibleForFree": true, "sc:name": "AntaRNA", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ @@ -65,10 +69,6 @@ { "@id": "https://doi.org/10.1093/bioinformatics/btv319", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-8231-3323", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/antiangiopred/antiangiopredbioschemas.jsonld b/data/antiangiopred/antiangiopredbioschemas.jsonld index 9c41ff859fefc..a1d3a629c8421 100644 --- a/data/antiangiopred/antiangiopredbioschemas.jsonld +++ b/data/antiangiopred/antiangiopredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "User-friendly web server for the prediction of anti-angiogenic peptides.", "sc:name": "AntiAngioPred", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://crdd.osdd.net/raghava/antiangiopred/" } \ No newline at end of file diff --git a/data/antibp/antibpbioschemas.jsonld b/data/antibp/antibpbioschemas.jsonld index f07775b6cdb0a..2d34f77894be3 100644 --- a/data/antibp/antibpbioschemas.jsonld +++ b/data/antibp/antibpbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Antibp server predicts the antibacterial peptides in a protein sequence.Prediction can be done by using QM,ANN and SVM based methods using binary patterns of peptide sequences and overall accuracy of this server is ~92.11%.This server can help in finding and designing of peptides based antibiotics.", "sc:name": "AntiBP", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.imtech.res.in/raghava/antibp/" diff --git a/data/anticp/anticpbioschemas.jsonld b/data/anticp/anticpbioschemas.jsonld index 0b91a1b3795a6..49cfc99da12ee 100644 --- a/data/anticp/anticpbioschemas.jsonld +++ b/data/anticp/anticpbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web based prediction server for anticancer peptides. SVM models developed are based on amino acid composition and binary profile features. Positive dataset consists of 225 antimicrobial peptides with anticancer properties.", "sc:name": "AntiCP", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://crdd.osdd.net/raghava/anticp/" diff --git a/data/antigendb/antigendbbioschemas.jsonld b/data/antigendb/antigendbbioschemas.jsonld index 9a4d77f176b50..cecd70ea0ace8 100644 --- a/data/antigendb/antigendbbioschemas.jsonld +++ b/data/antigendb/antigendbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Contains 500 antigens to pathogenic species curated from the literature and other immunological resources. In it, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. It also provides links to major internal and external databases.", "sc:name": "AntigenDB", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/antigendb/" diff --git a/data/antigenic/antigenicbioschemas.jsonld b/data/antigenic/antigenicbioschemas.jsonld index 28a7a6e125afd..d150aa3a04644 100644 --- a/data/antigenic/antigenicbioschemas.jsonld +++ b/data/antigenic/antigenicbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK MRC", "UK BBSRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "Wellcome Trust" ], "sc:description": "Find antigenic sites in proteins.", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "antigenic", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/antigenic.html", "sc:version": "r6" diff --git a/data/antiprofiles/antiprofilesbioschemas.jsonld b/data/antiprofiles/antiprofilesbioschemas.jsonld index 11293365bd69f..ff490be14153d 100644 --- a/data/antiprofiles/antiprofilesbioschemas.jsonld +++ b/data/antiprofiles/antiprofilesbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "antiProfiles", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/antiProfiles.html", "sc:version": "1.14.0" diff --git a/data/antismash/antismashbioschemas.jsonld b/data/antismash/antismashbioschemas.jsonld index a82baf5f0fbcb..00d70f3c1259e 100644 --- a/data/antismash/antismashbioschemas.jsonld +++ b/data/antismash/antismashbioschemas.jsonld @@ -17,14 +17,14 @@ "sc:description": "Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.", "sc:name": "antiSMASH", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://antismash.secondarymetabolites.org", "sc:version": [ - "1", + "2.0", "3.0", - "2.0" + "1" ] } \ No newline at end of file diff --git a/data/antmap/antmapbioschemas.jsonld b/data/antmap/antmapbioschemas.jsonld index d0877efbf4831..2393c1c409e81 100644 --- a/data/antmap/antmapbioschemas.jsonld +++ b/data/antmap/antmapbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It is a software for constructing genetic linkage maps using an ant colony optimization algorithm. It seeks the linear order of loci that minimizes the sum of adjacent recombination fractions or that maximizes the log likelihood of locus order. Analyses based on simulated data sets indicated that the algorithm displayed a high efficiency level. The high performance of the algorithm enabled to save time and labor, and also to validate an estimated order by bootstrap tests.", "sc:name": "AntMap", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://lbm.ab.a.u-tokyo.ac.jp/~iwata/antmap/index.html", "sc:version": "1.2" diff --git a/data/anyexpress/anyexpressbioschemas.jsonld b/data/anyexpress/anyexpressbioschemas.jsonld index 281315353d2c6..ee05f242cda3e 100644 --- a/data/anyexpress/anyexpressbioschemas.jsonld +++ b/data/anyexpress/anyexpressbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "AnyExpress is a software package that combines cross-platform gene expression data using a fast interval-matching algorithm.", "sc:name": "AnyExpress", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://anyexpress.sourceforge.net/", "sc:version": "1.0" diff --git a/data/apache_taverna/apache_tavernabioschemas.jsonld b/data/apache_taverna/apache_tavernabioschemas.jsonld index fe925fd450ca2..313d6772424ba 100644 --- a/data/apache_taverna/apache_tavernabioschemas.jsonld +++ b/data/apache_taverna/apache_tavernabioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/apache_taverna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Apache Taverna mailing lists", - "Apache Taverna community" + "Apache Taverna community", + "Apache Taverna mailing lists" ], "sc:additionalType": [ - "Web service", - "Web application", - "Workbench", "Command-line tool", "Desktop application", + "Workbench", + "Web service", + "Web application", "Web API" ], "sc:author": "Apache Taverna community", @@ -27,13 +27,13 @@ "sc:license": "Apache-2.0", "sc:name": "Apache Taverna", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": [ - "Apache Software Foundation", - "cs.manchester.ac.uk" + "cs.manchester.ac.uk", + "Apache Software Foundation" ], "sc:url": "http://taverna.incubator.apache.org/", "sc:version": "3" diff --git a/data/apcomplex/apcomplexbioschemas.jsonld b/data/apcomplex/apcomplexbioschemas.jsonld index efdb02cb975a2..4a953b2994de0 100644 --- a/data/apcomplex/apcomplexbioschemas.jsonld +++ b/data/apcomplex/apcomplexbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "apComplex", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/apComplex.html", diff --git a/data/apecs/apecsbioschemas.jsonld b/data/apecs/apecsbioschemas.jsonld index 434a5c9711723..85bbb12350b1a 100644 --- a/data/apecs/apecsbioschemas.jsonld +++ b/data/apecs/apecsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Proteomics method for intensity-based precursor ion selection, using a MALDI-TOF/TOF instrument, from a complex sample separated by 2D-LC.", "sc:name": "APECS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://trac.nbic.nl/apecs/" } \ No newline at end of file diff --git a/data/apeglm/apeglmbioschemas.jsonld b/data/apeglm/apeglmbioschemas.jsonld index 28e09c8c1c6f5..091682308a46d 100644 --- a/data/apeglm/apeglmbioschemas.jsonld +++ b/data/apeglm/apeglmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "apeglm", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/apeglm.html", "sc:version": "1.2.0" diff --git a/data/apex/apexbioschemas.jsonld b/data/apex/apexbioschemas.jsonld index bc39188824127..0c918bfad9a4a 100644 --- a/data/apex/apexbioschemas.jsonld +++ b/data/apex/apexbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Absolute protein expression Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data. This technique uses machine learning algorithms to help correct for variable peptide detection related to certain peptide physicochemical properties which favor or hinder detection. A sample data set and descriptive tutorial help to acquaint users with the operation of the tool.", "sc:name": "APEX", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://sourceforge.net/projects/apexqpt/", diff --git a/data/apex_r/apex_rbioschemas.jsonld b/data/apex_r/apex_rbioschemas.jsonld index 2ec8fde2209f9..0467885ee1b17 100644 --- a/data/apex_r/apex_rbioschemas.jsonld +++ b/data/apex_r/apex_rbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-2226-8692", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1111/1755-0998.12567", "@type": "sc:CreativeWork" @@ -43,6 +39,10 @@ ], "sc:url": "https://cran.r-project.org/web/packages/apex/index.html", "sc:version": "1.0.3" + }, + { + "@id": "http://orcid.org/0000-0003-2226-8692", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/aphidbase/aphidbasebioschemas.jsonld b/data/aphidbase/aphidbasebioschemas.jsonld index 90a6a5a7002d3..caac7359212cc 100644 --- a/data/aphidbase/aphidbasebioschemas.jsonld +++ b/data/aphidbase/aphidbasebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "AphidBase", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "GenOuest", "sc:url": "http://aphidbase.com/" diff --git a/data/apid/apidbioschemas.jsonld b/data/apid/apidbioschemas.jsonld index 01e9376b593c4..39dec80572474 100644 --- a/data/apid/apidbioschemas.jsonld +++ b/data/apid/apidbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Agile Protein Interaction DataAnalyzer (APID) allows you to query protein-protein interactions using a common platform facilitating comparison across different datasets. Currently supported interaction databases are BIND, HPRD, DIP, IntAct, and MINT.", "sc:name": "APID", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioinfow.dep.usal.es/apid/" diff --git a/data/apollo/apollobioschemas.jsonld b/data/apollo/apollobioschemas.jsonld index dfede186f7b2a..e433992e537c9 100644 --- a/data/apollo/apollobioschemas.jsonld +++ b/data/apollo/apollobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.", "sc:name": "Apollo Genome Annotation and Curation Tool", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://apollo.berkeleybop.org" } \ No newline at end of file diff --git a/data/appa/appabioschemas.jsonld b/data/appa/appabioschemas.jsonld index 18f2b62442bd7..d3c39ccd40e72 100644 --- a/data/appa/appabioschemas.jsonld +++ b/data/appa/appabioschemas.jsonld @@ -9,46 +9,46 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKZ358", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/AppA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Minh N Nguyen", "Chandra S Verma", - "Pingyu Zhong", - "Minh N Nguyen" + "Pingyu Zhong" ], "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31069385", + "pmcid:PMC6602511", { "@id": "https://doi.org/10.1093/NAR/GKZ358" - }, - "pmcid:PMC6602511", - "pubmed:31069385" + } ], "sc:description": "Web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models.", "sc:featureList": [ - { - "@id": "edam:operation_0394" - }, { "@id": "edam:operation_2950" }, { "@id": "edam:operation_0272" + }, + { + "@id": "edam:operation_0394" } ], "sc:license": "Unlicense", "sc:name": "AppA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://mspc.bii.a-star.edu.sg/minhn/appa.html" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ358", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/apparent/apparentbioschemas.jsonld b/data/apparent/apparentbioschemas.jsonld index 307858abc9b56..7a491a71422b6 100644 --- a/data/apparent/apparentbioschemas.jsonld +++ b/data/apparent/apparentbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Arthur Melo", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6396488", + "pubmed:30819089", { "@id": "https://doi.org/10.1186/s12859-019-2662-3" }, - "pubmed:30819089" + "pmcid:PMC6396488" ], "sc:description": "R package for accurate SNP-based parentage analysis in the absence of guiding information.", "sc:featureList": [ @@ -27,18 +27,18 @@ "@id": "edam:operation_3661" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_0484" }, { - "@id": "edam:operation_0484" + "@id": "edam:operation_3196" } ], "sc:license": "GPL-2.0", "sc:name": "apparent", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/package=apparent", "sc:version": "1.1" diff --git a/data/appex/appexbioschemas.jsonld b/data/appex/appexbioschemas.jsonld index 1c7b90f147fbf..033f4dba5e7c9 100644 --- a/data/appex/appexbioschemas.jsonld +++ b/data/appex/appexbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-based platform to perform survival analysis, particularly, to support identifying molecular signatures significantly associated with cancer patients’ outcome. It provides various analysis methods to discover genes or any other molecules associated with survival of cancer patients.", "sc:name": "APPEX", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.appex.kr/appex/" } \ No newline at end of file diff --git a/data/appris/apprisbioschemas.jsonld b/data/appris/apprisbioschemas.jsonld index 1efa93d081b0b..d5012d54093b5 100644 --- a/data/appris/apprisbioschemas.jsonld +++ b/data/appris/apprisbioschemas.jsonld @@ -31,8 +31,8 @@ ], "sc:provider": [ "INB", - "CNIO", - "cnio.es" + "cnio.es", + "CNIO" ], "sc:url": "http://appris.bioinfo.cnio.es/#/database", "sc:version": "23" diff --git a/data/approve/approvebioschemas.jsonld b/data/approve/approvebioschemas.jsonld index 42d1b838f88ae..c348a9c4d8a7f 100644 --- a/data/approve/approvebioschemas.jsonld +++ b/data/approve/approvebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Computational tool that predicts the interaction of a PPR (pentatricopeptide repeat) with its RNA binding site.", "sc:name": "aPPRove", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://www.cs.colostate.edu/~approve/" } \ No newline at end of file diff --git a/data/apricot/apricotbioschemas.jsonld b/data/apricot/apricotbioschemas.jsonld index 2e96b227bcfbd..363b0ff7483d2 100644 --- a/data/apricot/apricotbioschemas.jsonld +++ b/data/apricot/apricotbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKX137", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/apricot", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:28334975", "pmcid:PMC5499795", { "@id": "https://doi.org/10.1093/NAR/GKX137" - }, - "pubmed:28334975" + } ], "sc:description": "Integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins.", "sc:featureList": { @@ -31,6 +27,10 @@ }, "sc:name": "APRICOT", "sc:url": "https://pypi.org/project/bio-apricot/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKX137", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/apse/apsebioschemas.jsonld b/data/apse/apsebioschemas.jsonld index 8fdaa73c95ce2..378d60d600dcc 100644 --- a/data/apse/apsebioschemas.jsonld +++ b/data/apse/apsebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This search engine recommends PubMed articles relevant to a given article. It automatically extracts keywords from the title and abstract indexed in PubMed to generate recommendations. The database contains all PubMed records, providing up to 60 recommendations per searched article. Researchers were invited to annotate degrees of relevance for provided recommendations. All evaluations received will be curated into a benchmark dataset to be made available for free download and redistribution.", "sc:name": "Article-based PubMed Search Engine (APSE)", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://pubmed.ict.griffith.edu.au/" } \ No newline at end of file diff --git a/data/aqua-duct/aqua-ductbioschemas.jsonld b/data/aqua-duct/aqua-ductbioschemas.jsonld index 545ea2b8ee533..c54181e8cda0f 100644 --- a/data/aqua-duct/aqua-ductbioschemas.jsonld +++ b/data/aqua-duct/aqua-ductbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Tool that facilitates analysis of the behaviour of molecules that penetrate any selected region in a protein.", "sc:name": "AQUA-DUCT", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.aquaduct.pl/" } \ No newline at end of file diff --git a/data/aquaria/aquariabioschemas.jsonld b/data/aquaria/aquariabioschemas.jsonld index 7fa9c7154c301..e7cb034980f4a 100644 --- a/data/aquaria/aquariabioschemas.jsonld +++ b/data/aquaria/aquariabioschemas.jsonld @@ -15,34 +15,34 @@ "Web application" ], "sc:author": [ - "Andrea Schafferhans", "Seán I O'Donoghue", - "Kenneth S Sabir", - "Christian Stolte" + "Christian Stolte", + "Andrea Schafferhans", + "Kenneth S Sabir" ], "sc:contributor": [ + "Manfred Roos", + "Benjamin Wellmann", "Fabian A Buske", "Vivian Ho", "Maria Kalemanov", "Julian Heinrich", - "Benjamin Wellmann", "Burkhard Rost", - "Manfred Roos", "Nelson Perdigão" ], "sc:description": "Simplifying the generation of insight from protein structures through structure visualisation, annotated with protein features; loads sequence-to-structure alignments from the PSSH2 database, sequence features from UniProt and Interpro and user defined features on demand from JSON files; there is also a WebAPI (see ...).", "sc:license": "GPL-2.0", "sc:name": "Aquaria", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "School of Molecular Bioscience, The University of Sydney", - "Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney", "Department for Bioinformatics and Computational Biology, Technische Universität München", - "Digital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney" + "Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney", + "Digital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney", + "School of Molecular Bioscience, The University of Sydney" ], "sc:url": "http://aquaria.ws", "sc:version": "1" diff --git a/data/aquasaxs/aquasaxsbioschemas.jsonld b/data/aquasaxs/aquasaxsbioschemas.jsonld index 85f51efd86d82..89583b201d4ba 100644 --- a/data/aquasaxs/aquasaxsbioschemas.jsonld +++ b/data/aquasaxs/aquasaxsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AquaSAXS", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://lorentz.dynstr.pasteur.fr/aquasaxs.php" } \ No newline at end of file diff --git a/data/ar_nhpred/ar_nhpredbioschemas.jsonld b/data/ar_nhpred/ar_nhpredbioschemas.jsonld index 27f79e3f856f4..809be116fe172 100644 --- a/data/ar_nhpred/ar_nhpredbioschemas.jsonld +++ b/data/ar_nhpred/ar_nhpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Predicts the aromatic backbone NH interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups.", "sc:name": "Ar_NHPred", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/ar_nhpred" } \ No newline at end of file diff --git a/data/arabidopsis_efp_browser/arabidopsis_efp_browserbioschemas.jsonld b/data/arabidopsis_efp_browser/arabidopsis_efp_browserbioschemas.jsonld index ac15339f9eb66..08aa7ae582974 100644 --- a/data/arabidopsis_efp_browser/arabidopsis_efp_browserbioschemas.jsonld +++ b/data/arabidopsis_efp_browser/arabidopsis_efp_browserbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "An \"\"Electronic Fluorescent Pictograph\"\" browser for exploring and analyzing large-scale biological data sets (using example of Arabidopsis). Explores microarray and other data for hypothesis generation. eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets.", "sc:name": "Arabidopsis eFP Browser", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpWeb.cgi" diff --git a/data/arabidopsis_growth_regulators_network/arabidopsis_growth_regulators_networkbioschemas.jsonld b/data/arabidopsis_growth_regulators_network/arabidopsis_growth_regulators_networkbioschemas.jsonld index c4af3663232fe..426c74619f582 100644 --- a/data/arabidopsis_growth_regulators_network/arabidopsis_growth_regulators_networkbioschemas.jsonld +++ b/data/arabidopsis_growth_regulators_network/arabidopsis_growth_regulators_networkbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Integrated network of Arabidopsis growth regulators.", "sc:name": "Arabidopsis growth regulators network", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/supplementary_data/ehsab/gene_prioritization/", diff --git a/data/arabidopsis_interactions_viewer/arabidopsis_interactions_viewerbioschemas.jsonld b/data/arabidopsis_interactions_viewer/arabidopsis_interactions_viewerbioschemas.jsonld index a042c69fa55cc..e414ba353cf4b 100644 --- a/data/arabidopsis_interactions_viewer/arabidopsis_interactions_viewerbioschemas.jsonld +++ b/data/arabidopsis_interactions_viewer/arabidopsis_interactions_viewerbioschemas.jsonld @@ -9,25 +9,29 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1104/pp.18.01216", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Arabidopsis_Interactions_Viewer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nicholas Provart", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:30679268", "pmcid:PMC6446796", { "@id": "https://doi.org/10.1104/pp.18.01216" - }, - "pubmed:30679268" + } ], "sc:description": "Proteome-wide structure-based prediction of protein-protein interactions in Arabidopsis.", "sc:featureList": [ { - "@id": "edam:operation_2497" + "@id": "edam:operation_0478" }, { - "@id": "edam:operation_0478" + "@id": "edam:operation_2497" }, { "@id": "edam:operation_2949" @@ -35,15 +39,11 @@ ], "sc:name": "Arabidopsis Interactions Viewer", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bar.utoronto.ca/interactions2/" - }, - { - "@id": "https://doi.org/10.1104/pp.18.01216", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/arachne/arachnebioschemas.jsonld b/data/arachne/arachnebioschemas.jsonld index 2150aac756614..a8504f06f3c93 100644 --- a/data/arachne/arachnebioschemas.jsonld +++ b/data/arachne/arachnebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Program for assembling data from whole genome shotgun sequencing experiments.", "sc:name": "Arachne", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://www.broadinstitute.org/computational-rd/computational-research-and-development" } \ No newline at end of file diff --git a/data/arachnoserver/arachnoserverbioschemas.jsonld b/data/arachnoserver/arachnoserverbioschemas.jsonld index b0980c6ba8897..bf90310411917 100644 --- a/data/arachnoserver/arachnoserverbioschemas.jsonld +++ b/data/arachnoserver/arachnoserverbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ArachnoServer", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.arachnoserver.org" } \ No newline at end of file diff --git a/data/aracne/aracnebioschemas.jsonld b/data/aracne/aracnebioschemas.jsonld index 9ee4dc79e1b4e..de6c737265f79 100644 --- a/data/aracne/aracnebioschemas.jsonld +++ b/data/aracne/aracnebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks), a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.", "sc:name": "ARACNE", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/ARACNE?", "sc:version": "2" diff --git a/data/aramemnon/aramemnonbioschemas.jsonld b/data/aramemnon/aramemnonbioschemas.jsonld index 17b4be1cbd355..3b18a53fdf032 100644 --- a/data/aramemnon/aramemnonbioschemas.jsonld +++ b/data/aramemnon/aramemnonbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1104/pp.011577", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/aramemnon", "@type": "sc:SoftwareApplication", @@ -34,10 +30,10 @@ ], "sc:citation": [ "pubmed:12529511", + "pmcid:PMC166783", { "@id": "https://doi.org/10.1104/pp.011577" - }, - "pmcid:PMC166783" + } ], "sc:description": "Plant membrane proteins.", "sc:featureList": { @@ -46,11 +42,15 @@ "sc:name": "ARAMEMNON database of plant membrane proteins", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Botanical Institute University of Cologne", "sc:url": "http://aramemnon.botanik.uni-koeln.de/" + }, + { + "@id": "https://doi.org/10.1104/pp.011577", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/araport/araportbioschemas.jsonld b/data/araport/araportbioschemas.jsonld index 30f43263d66e1..8fb87a68d32ab 100644 --- a/data/araport/araportbioschemas.jsonld +++ b/data/araport/araportbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Not licensed", "sc:name": "Araport", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://www.araport.org/" diff --git a/data/arc/arcbioschemas.jsonld b/data/arc/arcbioschemas.jsonld index 529ad9be2d656..67c5bb75334ed 100644 --- a/data/arc/arcbioschemas.jsonld +++ b/data/arc/arcbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ARC", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ibest.github.io/ARC/", "sc:version": "1.1.4-beta" diff --git a/data/arcadia/arcadiabioschemas.jsonld b/data/arcadia/arcadiabioschemas.jsonld index 978f1da39b502..1f89598f68836 100644 --- a/data/arcadia/arcadiabioschemas.jsonld +++ b/data/arcadia/arcadiabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.It is a viewer, not an editor: this means a simpler interface, offering multiple perspectives on the same data, with a focus on navigation. It translates text-based descriptions of biological networks into standardized diagrams. Users can view the same model from different perspectives and easily alter the layout to emulate traditional textbook representations.", "sc:name": "Arcadia", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://arcadiapathways.sourceforge.net/", "sc:version": "1.0rc2" diff --git a/data/archaeafun/archaeafunbioschemas.jsonld b/data/archaeafun/archaeafunbioschemas.jsonld index b2e4b5d611145..63325aea1b476 100644 --- a/data/archaeafun/archaeafunbioschemas.jsonld +++ b/data/archaeafun/archaeafunbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://orcid.org/0000-0003-0316-5866", - "@type": "schema:Person" + "@id": "https://doi.org/10.1110/ps.0225102", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/archaeafun", @@ -35,11 +35,11 @@ "@id": "edam:topic_1775" }, "sc:citation": [ - "pmcid:PMC2373754", - "pubmed:12441387", { "@id": "https://doi.org/10.1110/ps.0225102" - } + }, + "pmcid:PMC2373754", + "pubmed:12441387" ], "sc:description": "Ab initio predictions of enzyme class (if any) from sequence.", "sc:featureList": { @@ -49,25 +49,25 @@ "sc:license": "Other", "sc:name": "ArchaeaFun", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "CBS", "sc:softwareHelp": [ { - "@id": "http://www.cbs.dtu.dk/services/ArchaeaFun/instructions.php" + "@id": "http://www.cbs.dtu.dk/services/ArchaeaFun/" }, { - "@id": "http://www.cbs.dtu.dk/services/ArchaeaFun/" + "@id": "http://www.cbs.dtu.dk/services/ArchaeaFun/instructions.php" } ], "sc:url": "http://cbs.dtu.dk/services/ArchaeaFun/", "sc:version": "1.0" }, { - "@id": "https://doi.org/10.1110/ps.0225102", - "@type": "sc:CreativeWork" + "@id": "https://orcid.org/0000-0003-0316-5866", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/archaeopteryx/archaeopteryxbioschemas.jsonld b/data/archaeopteryx/archaeopteryxbioschemas.jsonld index 9e906f0c1ccd6..741eca5a3753c 100644 --- a/data/archaeopteryx/archaeopteryxbioschemas.jsonld +++ b/data/archaeopteryx/archaeopteryxbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Archaeopteryx", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://en.bio-soft.net/tree/ATV.html" } \ No newline at end of file diff --git a/data/archcandy/archcandybioschemas.jsonld b/data/archcandy/archcandybioschemas.jsonld index 4fcf5c0c14a30..d1ede4bdbc096 100644 --- a/data/archcandy/archcandybioschemas.jsonld +++ b/data/archcandy/archcandybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool able to decode protein sequence motifs that have a potential to form amyloids.", "sc:name": "ArchCandy", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinfo.montp.cnrs.fr/?r=ArchCandy" } \ No newline at end of file diff --git a/data/archdb/archdbbioschemas.jsonld b/data/archdb/archdbbioschemas.jsonld index e4f9135f6c7fc..7b38bbd03c1a3 100644 --- a/data/archdb/archdbbioschemas.jsonld +++ b/data/archdb/archdbbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkt1189", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0001-5210-4387", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1093/nar/gkt1189", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/archdb", "@type": "sc:SoftwareApplication", @@ -25,11 +25,11 @@ "@id": "http://orcid.org/0000-0001-5210-4387" }, "sc:citation": [ + "pubmed:24265221", { "@id": "https://doi.org/10.1093/nar/gkt1189" }, - "pmcid:PMC3964960", - "pubmed:24265221" + "pmcid:PMC3964960" ], "sc:description": "Structural classification of loops extracted from known protein structures.", "sc:featureList": { @@ -37,9 +37,9 @@ }, "sc:name": "ArchDB14", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "upf.edu", "sc:url": "http://sbi.imim.es/archdb/" diff --git a/data/archidart/archidartbioschemas.jsonld b/data/archidart/archidartbioschemas.jsonld index 3b72210218184..5321c36e39698 100644 --- a/data/archidart/archidartbioschemas.jsonld +++ b/data/archidart/archidartbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/archidart", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", - "Web application" + "Web application", + "Library" ], "sc:description": "Plant Root System Architecture Analysis Using DART and RSML Files.", "sc:license": "GPL-2.0", "sc:name": "archiDART", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://archidart.github.io", "sc:version": "3.3" diff --git a/data/archip/archipbioschemas.jsonld b/data/archip/archipbioschemas.jsonld index 6203bd119abcb..43219cfde8ffd 100644 --- a/data/archip/archipbioschemas.jsonld +++ b/data/archip/archipbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ArchiP", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=archip" } \ No newline at end of file diff --git a/data/archki/archkibioschemas.jsonld b/data/archki/archkibioschemas.jsonld index 4c28738fc1fc0..7a7b61bcadadf 100644 --- a/data/archki/archkibioschemas.jsonld +++ b/data/archki/archkibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool performs a structural classification of kinase loops with information of functional residues to find relationships between structure and function of classified kinase-loops.", "sc:name": "ArchKI", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioinf.uab.es/cgi-bin/archki/loops.pl?class=all&set=ArchKI" } \ No newline at end of file diff --git a/data/archpred/archpredbioschemas.jsonld b/data/archpred/archpredbioschemas.jsonld index b618a6e679c03..428e8a543e292 100644 --- a/data/archpred/archpredbioschemas.jsonld +++ b/data/archpred/archpredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop.", "sc:name": "ArchPred", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.bioinsilico.org/ARCHPRED/" diff --git a/data/archschema/archschemabioschemas.jsonld b/data/archschema/archschemabioschemas.jsonld index 4405d527eb7e6..95ed5e8beabdc 100644 --- a/data/archschema/archschemabioschemas.jsonld +++ b/data/archschema/archschemabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ArchSchema", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/archschema/", "sc:version": "1.1" diff --git a/data/ard2/ard2bioschemas.jsonld b/data/ard2/ard2bioschemas.jsonld index d291f20b73371..3e9a4ecb15818 100644 --- a/data/ard2/ard2bioschemas.jsonld +++ b/data/ard2/ard2bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ARD2", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cbdm-01.zdv.uni-mainz.de/~fournier/ard2/" } \ No newline at end of file diff --git a/data/ardock/ardockbioschemas.jsonld b/data/ardock/ardockbioschemas.jsonld index cd6a32bca7b08..b7e65154a45ab 100644 --- a/data/ardock/ardockbioschemas.jsonld +++ b/data/ardock/ardockbioschemas.jsonld @@ -23,12 +23,12 @@ "sc:name": "arDock", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "UCBL", - "CNRS" + "CNRS", + "UCBL" ], "sc:url": "http://ardock.ibcp.fr", "sc:version": "0.9" diff --git a/data/aresite/aresitebioschemas.jsonld b/data/aresite/aresitebioschemas.jsonld index f7b1da408dade..a7dd2a153feba 100644 --- a/data/aresite/aresitebioschemas.jsonld +++ b/data/aresite/aresitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "AREsite", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "bioinf.uni-leipzig.de", "sc:url": "http://rna.tbi.univie.ac.at/AREsite", diff --git a/data/arga/argabioschemas.jsonld b/data/arga/argabioschemas.jsonld index b54319037a672..9cc2cba6c68f5 100644 --- a/data/arga/argabioschemas.jsonld +++ b/data/arga/argabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "ARGA", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://mem.rcees.ac.cn:8083/" } \ No newline at end of file diff --git a/data/argonnenatlab/argonnenatlabbioschemas.jsonld b/data/argonnenatlab/argonnenatlabbioschemas.jsonld index 82c9b2ac838f4..30045b90c596d 100644 --- a/data/argonnenatlab/argonnenatlabbioschemas.jsonld +++ b/data/argonnenatlab/argonnenatlabbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available.", "sc:name": "Argonne National Laboratory", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://www.anl.gov/" } \ No newline at end of file diff --git a/data/argot2/argot2bioschemas.jsonld b/data/argot2/argot2bioschemas.jsonld index e4ad47e44cf23..c54957307f4db 100644 --- a/data/argot2/argot2bioschemas.jsonld +++ b/data/argot2/argot2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-0246-3119", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/argot2", "@type": "sc:SoftwareApplication", @@ -17,20 +21,20 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:22536960", { "@id": "https://doi.org/10.1371/journal.pone.0004619" }, "pmcid:PMC2645684", - "pubmed:19247487", - "pubmed:22536960" + "pubmed:19247487" ], "sc:description": "Annotation Retrieval of Gene Ontology Terms", "sc:license": "Other", "sc:name": "Argot2", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://www.medcomp.medicina.unipd.it/Argot2/", @@ -39,10 +43,6 @@ { "@id": "https://doi.org/10.1371/journal.pone.0004619", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-0246-3119", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/argyle/argylebioschemas.jsonld b/data/argyle/argylebioschemas.jsonld index fe342b5f229a4..cc6142f568d64 100644 --- a/data/argyle/argylebioschemas.jsonld +++ b/data/argyle/argylebioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:26684930", - "pmcid:PMC4751548", { "@id": "https://doi.org/10.1534/G3.115.023739" - } + }, + "pmcid:PMC4751548" ], "sc:description": "An R Package for Analysis of Illumina Genotyping Arrays.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "argyle", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/andrewparkermorgan/argyle" } diff --git a/data/aria/ariabioschemas.jsonld b/data/aria/ariabioschemas.jsonld index 279e970ad1062..2140e0471f9f4 100644 --- a/data/aria/ariabioschemas.jsonld +++ b/data/aria/ariabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "MIT", "sc:name": "ARIA", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Institut Pasteur", "sc:url": "http://aria.pasteur.fr/", diff --git a/data/arioc/ariocbioschemas.jsonld b/data/arioc/ariocbioschemas.jsonld index 022ed953b1ef8..644915400f5f4 100644 --- a/data/arioc/ariocbioschemas.jsonld +++ b/data/arioc/ariocbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Set of computer programs that carry out the alignment of short DNA sequences to a comparatively large reference sequence or genome.", "sc:name": "Arioc", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/RWilton/Arioc" } \ No newline at end of file diff --git a/data/arion_4_omics/arion_4_omicsbioschemas.jsonld b/data/arion_4_omics/arion_4_omicsbioschemas.jsonld index af20bd250b911..a758ca0e79ebb 100644 --- a/data/arion_4_omics/arion_4_omicsbioschemas.jsonld +++ b/data/arion_4_omics/arion_4_omicsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Proprietary", "sc:name": "Arion 4 Omics", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://multicoredynamics.com", diff --git a/data/arkmap/arkmapbioschemas.jsonld b/data/arkmap/arkmapbioschemas.jsonld index a4c4e5f5edafd..ef7f7663e472d 100644 --- a/data/arkmap/arkmapbioschemas.jsonld +++ b/data/arkmap/arkmapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Desktop application that allows users to draw and align genetic maps.", "sc:name": "ArkMAP", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bioinformatics.roslin.ed.ac.uk/arkmap/" } \ No newline at end of file diff --git a/data/arks/arksbioschemas.jsonld b/data/arks/arksbioschemas.jsonld index e66482239bd7b..2ea42492858df 100644 --- a/data/arks/arksbioschemas.jsonld +++ b/data/arks/arksbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ARKS", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/bcgsc/arks" } \ No newline at end of file diff --git a/data/arlequin/arlequinbioschemas.jsonld b/data/arlequin/arlequinbioschemas.jsonld index c35c1d123cdbe..9a2682c8afcf3 100644 --- a/data/arlequin/arlequinbioschemas.jsonld +++ b/data/arlequin/arlequinbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/arlequin", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "Large set of basic methods and statistical tests, to extract information on genetic and demographic features of a collection of population samples. The analyses can perform on the data fall into two main categories: intra-population and inter-population methods.", "sc:license": "Not licensed", "sc:name": "Arlequin", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://cmpg.unibe.ch/software/arlequin35/", "sc:version": "3.5" diff --git a/data/armor/armorbioschemas.jsonld b/data/armor/armorbioschemas.jsonld index eb24495942753..0ec5f81efc732 100644 --- a/data/armor/armorbioschemas.jsonld +++ b/data/armor/armorbioschemas.jsonld @@ -9,27 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1534/G3.119.400185", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0002-3048-5518", "@type": "schema:Person" }, - { - "@id": "https://orcid.org/0000-0003-3833-2169", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/ARMOR", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "https://orcid.org/0000-0002-3048-5518" + "@id": "https://orcid.org/0000-0003-3833-2169" }, { - "@id": "https://orcid.org/0000-0003-3833-2169" + "@id": "https://orcid.org/0000-0002-3048-5518" } ], "sc:additionalType": "Command-line tool", @@ -37,29 +29,37 @@ { "@id": "https://doi.org/10.1534/G3.119.400185" }, - "pubmed:31088905", - "pmcid:PMC6643886" + "pmcid:PMC6643886", + "pubmed:31088905" ], "sc:description": "ARMOR (Automated Reproducible MOdular RNA-seq) Workflow for Preprocessing and Differential Analysis of RNA-seq Data.", "sc:featureList": [ { - "@id": "edam:operation_2428" + "@id": "edam:operation_3800" }, { - "@id": "edam:operation_3192" + "@id": "edam:operation_2428" }, { - "@id": "edam:operation_3800" + "@id": "edam:operation_3192" } ], "sc:license": "MIT", "sc:name": "ARMOR", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/csoneson/ARMOR" + }, + { + "@id": "https://doi.org/10.1534/G3.119.400185", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0003-3833-2169", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/arp_warp/arp_warpbioschemas.jsonld b/data/arp_warp/arp_warpbioschemas.jsonld index ad71ad6967252..db1bf70c7ac83 100644 --- a/data/arp_warp/arp_warpbioschemas.jsonld +++ b/data/arp_warp/arp_warpbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A program for building macromolecular models from crystallograpgic data. It builds proteins, RNA/DNA, seqondary structure, side chains, loops, solvent and ligands", "sc:name": "ARP wARP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://www.embl-hamburg.de/ARP/", diff --git a/data/arpeggio/arpeggiobioschemas.jsonld b/data/arpeggio/arpeggiobioschemas.jsonld index e4e18669cbbf4..0d9059d1f4539 100644 --- a/data/arpeggio/arpeggiobioschemas.jsonld +++ b/data/arpeggio/arpeggiobioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1016/J.JMB.2016.12.004", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/arpeggio", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jubb HC", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5282402", - "pubmed:27964945", { "@id": "https://doi.org/10.1016/J.JMB.2016.12.004" - } + }, + "pubmed:27964945", + "pmcid:PMC5282402" ], "sc:description": "A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "Arpeggio", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://structure.bioc.cam.ac.uk/arpeggio/" - }, - { - "@id": "https://doi.org/10.1016/J.JMB.2016.12.004", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/arrayexpress/arrayexpressbioschemas.jsonld b/data/arrayexpress/arrayexpressbioschemas.jsonld index 9bc121dc55f1d..b45c0f45a5550 100644 --- a/data/arrayexpress/arrayexpressbioschemas.jsonld +++ b/data/arrayexpress/arrayexpressbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies.", "sc:name": "ArrayExpress", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.ebi.ac.uk/arrayexpress" } \ No newline at end of file diff --git a/data/arrayexpresshts/arrayexpresshtsbioschemas.jsonld b/data/arrayexpresshts/arrayexpresshtsbioschemas.jsonld index 699f9d6f03899..f315575bed811 100644 --- a/data/arrayexpresshts/arrayexpresshtsbioschemas.jsonld +++ b/data/arrayexpresshts/arrayexpresshtsbioschemas.jsonld @@ -23,9 +23,9 @@ "sc:license": "Artistic-2.0", "sc:name": "ArrayExpressHTS", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ArrayExpressHTS.html", "sc:version": "1.24.0" diff --git a/data/arraylasso/arraylassobioschemas.jsonld b/data/arraylasso/arraylassobioschemas.jsonld index 0973fc46f7817..f43a0968374dc 100644 --- a/data/arraylasso/arraylassobioschemas.jsonld +++ b/data/arraylasso/arraylassobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool implements a set of five open-source R functions that allow the user to acquire data from public sources such as GEO, train a set of Lasso models on that data, and directly map one microarray platform to another. It significantly predicts expression levels with higher fidelity than technical replicates of the same RNA pool, demonstrating its utility in the integration of data sets from different platforms.", "sc:name": "aRrayLasso", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/adam-sam-brown/aRrayLasso" } \ No newline at end of file diff --git a/data/arraymaker/arraymakerbioschemas.jsonld b/data/arraymaker/arraymakerbioschemas.jsonld index e29e2d73fc913..773be67130b31 100644 --- a/data/arraymaker/arraymakerbioschemas.jsonld +++ b/data/arraymaker/arraymakerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms.", "sc:name": "ArrayMaker", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/cw2014/ArrayMaker/" } \ No newline at end of file diff --git a/data/arraymap/arraymapbioschemas.jsonld b/data/arraymap/arraymapbioschemas.jsonld index 9786077f9027f..23968acfcf73d 100644 --- a/data/arraymap/arraymapbioschemas.jsonld +++ b/data/arraymap/arraymapbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides an entry point for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data.", "sc:name": "arrayMap", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://www.arraymap.org" diff --git a/data/arrayminer/arrayminerbioschemas.jsonld b/data/arrayminer/arrayminerbioschemas.jsonld index a274e7b0b1d73..7cfa6597148da 100644 --- a/data/arrayminer/arrayminerbioschemas.jsonld +++ b/data/arrayminer/arrayminerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "ArrayMiner® is a set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data. Its unique graphical interface gives you an intimate understanding of the analysis and an easy publishing of its results.", "sc:name": "ArrayMiner", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm", "sc:version": "5.3" diff --git a/data/arraymvout/arraymvoutbioschemas.jsonld b/data/arraymvout/arraymvoutbioschemas.jsonld index 3c6c150756aac..3841449e2f8e2 100644 --- a/data/arraymvout/arraymvoutbioschemas.jsonld +++ b/data/arraymvout/arraymvoutbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "V. Carey", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.", "sc:license": "Artistic-2.0", "sc:name": "arrayMvout", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/arrayMvout.html", diff --git a/data/arraypipe/arraypipebioschemas.jsonld b/data/arraypipe/arraypipebioschemas.jsonld index 2caef09ee51a1..17290daa817b5 100644 --- a/data/arraypipe/arraypipebioschemas.jsonld +++ b/data/arraypipe/arraypipebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.", "sc:name": "ArrayPipe", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl" } \ No newline at end of file diff --git a/data/arrayquality/arrayqualitybioschemas.jsonld b/data/arrayquality/arrayqualitybioschemas.jsonld index 97cf000fe9382..a318c34787d2f 100644 --- a/data/arrayquality/arrayqualitybioschemas.jsonld +++ b/data/arrayquality/arrayqualitybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "arrayQuality", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/arrayQuality.html", "sc:version": "1.52.0" diff --git a/data/arraystar/arraystarbioschemas.jsonld b/data/arraystar/arraystarbioschemas.jsonld index 02b0e0371ad44..1973145b4f845 100644 --- a/data/arraystar/arraystarbioschemas.jsonld +++ b/data/arraystar/arraystarbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An application for gene expression and variant analysis. It enables analyzing a variety of experimental data.", "sc:name": "ArrayStar", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.dnastar.com/t-sub-products-genomics-arraystar.aspx" } \ No newline at end of file diff --git a/data/arraytools/arraytoolsbioschemas.jsonld b/data/arraytools/arraytoolsbioschemas.jsonld index ee6161f736972..a1e446d9df75c 100644 --- a/data/arraytools/arraytoolsbioschemas.jsonld +++ b/data/arraytools/arraytoolsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Arthur Li", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package is designed to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. It generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.", "sc:license": "GPL-2.0", diff --git a/data/arraytools/bioconda_arraytools.yaml b/data/arraytools/bioconda_arraytools.yaml index e4ce18b9e0f71..3e4eacd67f1fb 100644 --- a/data/arraytools/bioconda_arraytools.yaml +++ b/data/arraytools/bioconda_arraytools.yaml @@ -9,7 +9,6 @@ description: This package is designed to provide solutions for quality assessmen home: https://bioconductor.org/packages/3.10/bioc/html/ArrayTools.html identifiers: - biotools:arraytools -- doi:10.1038/nmeth.3252 license: LGPL (>= 2.0) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-arraytools diff --git a/data/arraytrack/arraytrackbioschemas.jsonld b/data/arraytrack/arraytrackbioschemas.jsonld index 2b237cc4de1ae..90fbec9045c74 100644 --- a/data/arraytrack/arraytrackbioschemas.jsonld +++ b/data/arraytrack/arraytrackbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ArrayTrack", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/" } \ No newline at end of file diff --git a/data/arraytv/arraytvbioschemas.jsonld b/data/arraytv/arraytvbioschemas.jsonld index 25bd17849ec1d..876acb07dfb63 100644 --- a/data/arraytv/arraytvbioschemas.jsonld +++ b/data/arraytv/arraytvbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Eitan Halper-Stromberg", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Wave correction for genotyping and copy number arrays.", "sc:license": "GPL-2.0", "sc:name": "ArrayTV", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ArrayTV.html", "sc:version": "1.12.0" diff --git a/data/arrayxpath/arrayxpathbioschemas.jsonld b/data/arrayxpath/arrayxpathbioschemas.jsonld index 5db8d518124a6..260bcb812e5db 100644 --- a/data/arrayxpath/arrayxpathbioschemas.jsonld +++ b/data/arrayxpath/arrayxpathbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.", "sc:name": "ArrayXPath", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.snubi.org/software/ArrayXPath/" } \ No newline at end of file diff --git a/data/arrest/arrestbioschemas.jsonld b/data/arrest/arrestbioschemas.jsonld index 0811613f8b4ca..6ebc6500efe94 100644 --- a/data/arrest/arrestbioschemas.jsonld +++ b/data/arrest/arrestbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool is designed to enable a deep understanding of antigen receptor sequences with a cascade of algorithms and databases.", "sc:name": "ARResT", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://tools.bat.infspire.org/arrest/assignsubsets/" } \ No newline at end of file diff --git a/data/arrp/arrpbioschemas.jsonld b/data/arrp/arrpbioschemas.jsonld index 354c860123e39..de394278a2014 100644 --- a/data/arrp/arrpbioschemas.jsonld +++ b/data/arrp/arrpbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This software calculates asymptotic and robust regressions corresponding to the constant and linear asymptotic regression models.", "sc:name": "ARRP", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/software/program.html?uid=3" } \ No newline at end of file diff --git a/data/arshift/arshiftbioschemas.jsonld b/data/arshift/arshiftbioschemas.jsonld index 43f048bd6c776..d259955f3e0f4 100644 --- a/data/arshift/arshiftbioschemas.jsonld +++ b/data/arshift/arshiftbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Method of calculating side-chain aromatic chemical shifts from protein structures.", "sc:name": "ArShift", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www-sidechain.ch.cam.ac.uk/ArShift/" } \ No newline at end of file diff --git a/data/artemis/artemisbioschemas.jsonld b/data/artemis/artemisbioschemas.jsonld index 9fc31f96ef276..d63a2f6158355 100644 --- a/data/artemis/artemisbioschemas.jsonld +++ b/data/artemis/artemisbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.", "sc:name": "Artemis", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.sanger.ac.uk/science/tools/artemis" } \ No newline at end of file diff --git a/data/arto/artobioschemas.jsonld b/data/arto/artobioschemas.jsonld index 625b245cc05f2..38e96a7d61277 100644 --- a/data/arto/artobioschemas.jsonld +++ b/data/arto/artobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The Analysis of Replication Timing and Organization tool uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. It takes raw time of replication (ToR) measurement signals as input and outputs for each genomic location an estimate of its ToR and an association to CTR (constant ToR region) or TTR (Temporal Transition Region).", "sc:name": "ARTO", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/" diff --git a/data/artp2/artp2bioschemas.jsonld b/data/artp2/artp2bioschemas.jsonld index 3c05a318676b1..3023e43c6a1a4 100644 --- a/data/artp2/artp2bioschemas.jsonld +++ b/data/artp2/artp2bioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/artp2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kai Yu", "Division of Cancer Epidemiology and Genetics (DCEG), NCI", - "Han Zhang" + "Han Zhang", + "Kai Yu" ], "sc:additionalType": [ "Library", @@ -23,9 +23,9 @@ "sc:description": "Adaptive Rank Truncated Product is an R package for analyzing pre-defined genetic pathway based on a genetic association study.", "sc:name": "ARTP2", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://dceg.cancer.gov/tools/analysis/artp" } \ No newline at end of file diff --git a/data/arts/artsbioschemas.jsonld b/data/arts/artsbioschemas.jsonld index 085997da99ded..9f61adefe2273 100644 --- a/data/arts/artsbioschemas.jsonld +++ b/data/arts/artsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.", "sc:name": "ARTS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/ARTS/" } \ No newline at end of file diff --git a/data/arts_antibiotics/arts_antibioticsbioschemas.jsonld b/data/arts_antibiotics/arts_antibioticsbioschemas.jsonld index 277c68f3b3aa8..280ec3963f27d 100644 --- a/data/arts_antibiotics/arts_antibioticsbioschemas.jsonld +++ b/data/arts_antibiotics/arts_antibioticsbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkx360", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/arts_antibiotics", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5570205", - "pubmed:28472505", { "@id": "https://doi.org/10.1093/nar/gkx360" - } + }, + "pmcid:PMC5570205", + "pubmed:28472505" ], "sc:description": "Antibiotic Resistant Target Seeker. Specific and efficient genome mining for antibiotics with interesting and novel targets. Automate the screening of large amounts of sequence data and to focus on the most promising strains that produce antibiotics with new modes of action. It integrates target directed genome mining methods, antibiotic gene cluster predictions and ‘essential gene screening’ to provide an interactive page for rapid identification of known and putative targets in BGCs.", "sc:featureList": { @@ -31,10 +27,14 @@ "sc:license": "GPL-3.0", "sc:name": "ARTS", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://arts.ziemertlab.com/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkx360", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/as2ts/as2tsbioschemas.jsonld b/data/as2ts/as2tsbioschemas.jsonld index c2bef7c71af2a..e9f1fa5301d4d 100644 --- a/data/as2ts/as2tsbioschemas.jsonld +++ b/data/as2ts/as2tsbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "AS2TS", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://proteinmodel.org/" } \ No newline at end of file diff --git a/data/asaaap/asaaapbioschemas.jsonld b/data/asaaap/asaaapbioschemas.jsonld index 43d00ab85f2f5..08acac94c6b6d 100644 --- a/data/asaaap/asaaapbioschemas.jsonld +++ b/data/asaaap/asaaapbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-4216-2721", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/ASAAAP", "@type": "sc:SoftwareApplication", @@ -29,6 +25,10 @@ "sc:operatingSystem": "Linux", "sc:url": "https://github.com/oschwengers/asap", "sc:version": "1.2.2" + }, + { + "@id": "http://orcid.org/0000-0003-4216-2721", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/asaim/asaimbioschemas.jsonld b/data/asaim/asaimbioschemas.jsonld index 42e85240d9d4e..e9f75d8795bda 100644 --- a/data/asaim/asaimbioschemas.jsonld +++ b/data/asaim/asaimbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "ASaiM", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/ASaiM" } \ No newline at end of file diff --git a/data/asap/asapbioschemas.jsonld b/data/asap/asapbioschemas.jsonld index a7ec1f40e03ea..22b913d661cda 100644 --- a/data/asap/asapbioschemas.jsonld +++ b/data/asap/asapbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Troels T. Marstrand", "sc:additionalType": [ + "Command-line tool", "Web application", - "Desktop application", - "Command-line tool" + "Desktop application" ], "sc:description": "A framework for promoter analysis based on a fast search engine using enhanced suffix arrays. The framework includes several statistics for calculating over-representation of motifs in a set of promoters from co-regulated genes compared to a background set.", "sc:license": "GPL-3.0", "sc:name": "ASAP", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "binf.ku.dk", "sc:url": "http://asap.binf.ku.dk/Asap/Home.html", diff --git a/data/asap_pipeline/asap_pipelinebioschemas.jsonld b/data/asap_pipeline/asap_pipelinebioschemas.jsonld index 92f11b086942a..ee1e62b446734 100644 --- a/data/asap_pipeline/asap_pipelinebioschemas.jsonld +++ b/data/asap_pipeline/asap_pipelinebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Automated Single-cell Analysis Pipeline.", "sc:name": "ASAP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/DeplanckeLab/ASAP" } \ No newline at end of file diff --git a/data/asatura/asaturabioschemas.jsonld b/data/asatura/asaturabioschemas.jsonld index 0a93b258018f0..9b953e117408c 100644 --- a/data/asatura/asaturabioschemas.jsonld +++ b/data/asatura/asaturabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Discriminates aa substitutions with high and low probabilities of occurrence.", "sc:name": "ASaturA", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/ASaturA", diff --git a/data/asc/ascbioschemas.jsonld b/data/asc/ascbioschemas.jsonld index 16e01bf16cca9..fb1e956f6f209 100644 --- a/data/asc/ascbioschemas.jsonld +++ b/data/asc/ascbioschemas.jsonld @@ -11,13 +11,13 @@ "@id": "https://bio.tools/asc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sonya T Dyhrman", "Melissa Mercier", - "Mak A Saito", + "Sonya T Dyhrman", + "Bethany D Jenkins", + "LeAnn P Whitney", "Tatiana A Rynearson", "Zhijin Wu", - "Bethany D Jenkins", - "LeAnn P Whitney" + "Mak A Saito" ], "sc:additionalType": "Library", "sc:citation": "pubmed:21080965", diff --git a/data/ascend/ascendbioschemas.jsonld b/data/ascend/ascendbioschemas.jsonld index e9eaacf77a06a..0cddc33b15433 100644 --- a/data/ascend/ascendbioschemas.jsonld +++ b/data/ascend/ascendbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ascend", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/IMB-Computational-Genomics-Lab/ascend" } \ No newline at end of file diff --git a/data/asd/asdbioschemas.jsonld b/data/asd/asdbioschemas.jsonld index 911c116ea996c..444448ffdb70f 100644 --- a/data/asd/asdbioschemas.jsonld +++ b/data/asd/asdbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/asd", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jian Zhang", - "ASD Support" + "ASD Support", + "Jian Zhang" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:21051350", "sc:description": "AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area.", "sc:name": "ASD", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://mdl.shsmu.edu.cn/ASD/" } \ No newline at end of file diff --git a/data/asgsca/asgscabioschemas.jsonld b/data/asgsca/asgscabioschemas.jsonld index cd347fe26d375..467ccca77d543 100644 --- a/data/asgsca/asgscabioschemas.jsonld +++ b/data/asgsca/asgscabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hela Romdhani", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA).", "sc:license": "GPL-3.0", "sc:name": "ASGSCA", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ASGSCA.html", "sc:version": "1.8.0" diff --git a/data/asics/asicsbioschemas.jsonld b/data/asics/asicsbioschemas.jsonld index 0090dee4f5551..31adad179ff06 100644 --- a/data/asics/asicsbioschemas.jsonld +++ b/data/asics/asicsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "ASICS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ASICS.html", "sc:version": "1.0.0" diff --git a/data/asmvar/asmvarbioschemas.jsonld b/data/asmvar/asmvarbioschemas.jsonld index 063584bf204b2..7e5793e71eb0b 100644 --- a/data/asmvar/asmvarbioschemas.jsonld +++ b/data/asmvar/asmvarbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13742-015-0103-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/asmvar", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:26705468", + "pmcid:PMC4690232", { "@id": "https://doi.org/10.1186/s13742-015-0103-4" - }, - "pmcid:PMC4690232" + } ], "sc:description": "Software for discovery, genotyping and characterization of structural variants.", "sc:featureList": { @@ -35,6 +31,10 @@ "Linux" ], "sc:url": "http://bioinformatics-centre.github.io/AsmVar/" + }, + { + "@id": "https://doi.org/10.1186/s13742-015-0103-4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/asnr/asnrbioschemas.jsonld b/data/asnr/asnrbioschemas.jsonld index bb328e9e62108..5503c8ce7b1cf 100644 --- a/data/asnr/asnrbioschemas.jsonld +++ b/data/asnr/asnrbioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/S41597-019-0056-Z", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ASNR", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Shweta Bansal", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:31036810", "pmcid:PMC6488576", + "pubmed:31036810", { "@id": "https://doi.org/10.1038/S41597-019-0056-Z" } @@ -37,11 +33,15 @@ "sc:license": "GPL-3.0", "sc:name": "ASNR", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://bansallab.github.io/asnr/" + }, + { + "@id": "https://doi.org/10.1038/S41597-019-0056-Z", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/aspgd/aspgdbioschemas.jsonld b/data/aspgd/aspgdbioschemas.jsonld index 3a458d344297e..e62fe86229fc4 100644 --- a/data/aspgd/aspgdbioschemas.jsonld +++ b/data/aspgd/aspgdbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AspGD", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.aspergillusgenome.org/" } \ No newline at end of file diff --git a/data/aspic-geneid/aspic-geneidbioschemas.jsonld b/data/aspic-geneid/aspic-geneidbioschemas.jsonld index b36da73d3e2ba..22c6e5fe5c8f1 100644 --- a/data/aspic-geneid/aspic-geneidbioschemas.jsonld +++ b/data/aspic-geneid/aspic-geneidbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A lightweight pipeline for gene prediction and alternative isoforms detection.", "sc:name": "ASPic-GeneID", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "ELIXIR-ITA-CNR", "sc:url": "http://150.145.82.212/aspic/aspicgeneid.tar.gz", diff --git a/data/aspli/asplibioschemas.jsonld b/data/aspli/asplibioschemas.jsonld index 52389ed14f0bd..0b64bb7d0d6be 100644 --- a/data/aspli/asplibioschemas.jsonld +++ b/data/aspli/asplibioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "ASpli", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ASpli.html", "sc:version": "1.0.0" diff --git a/data/aspli/bioconda_aspli.yaml b/data/aspli/bioconda_aspli.yaml index bcbfc3d7600b5..e64b21095fcc7 100644 --- a/data/aspli/bioconda_aspli.yaml +++ b/data/aspli/bioconda_aspli.yaml @@ -3,7 +3,6 @@ description: Integrative pipeline for the analysis of alternative splicing using home: https://bioconductor.org/packages/3.10/bioc/html/ASpli.html identifiers: - biotools:aspli -- doi:10.1038/nmeth.3252 license: GPL license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-aspli diff --git a/data/aspu/aspubioschemas.jsonld b/data/aspu/aspubioschemas.jsonld index d2fa3f959e693..df1a045201545 100644 --- a/data/aspu/aspubioschemas.jsonld +++ b/data/aspu/aspubioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R package for adaptive sum of powered score test(ASPU) in genetic association studies.", "sc:name": "aSPU", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/aSPU/" } \ No newline at end of file diff --git a/data/aspwood/aspwoodbioschemas.jsonld b/data/aspwood/aspwoodbioschemas.jsonld index 3ec7d130c4e1f..656918bc7b385 100644 --- a/data/aspwood/aspwoodbioschemas.jsonld +++ b/data/aspwood/aspwoodbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "AspWood", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://aspwood.popgenie.org/aspwood-v3.0/" } \ No newline at end of file diff --git a/data/asreml/asremlbioschemas.jsonld b/data/asreml/asremlbioschemas.jsonld index fd89c1826a787..5a7d914b38d7c 100644 --- a/data/asreml/asremlbioschemas.jsonld +++ b/data/asreml/asremlbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Proprietary", "sc:name": "ASReml", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://asreml.org/" } \ No newline at end of file diff --git a/data/assam/assambioschemas.jsonld b/data/assam/assambioschemas.jsonld index 667b61842a281..0a419424cf36c 100644 --- a/data/assam/assambioschemas.jsonld +++ b/data/assam/assambioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ASSAM tool searches for patterns of amino acid side chains in 3D space within PDB structures. Input must be a 3D amino acid pattern, which will be used in based on distances between the amino acid side chains.", "sc:name": "ASSAM", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://mfrlab.org/grafss/assam" } \ No newline at end of file diff --git a/data/assaycorrector/assaycorrectorbioschemas.jsonld b/data/assaycorrector/assaycorrectorbioschemas.jsonld index 687691dfe7633..ba1af18e94c8e 100644 --- a/data/assaycorrector/assaycorrectorbioschemas.jsonld +++ b/data/assaycorrector/assaycorrectorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Detecting and removing multiplicative spatial bias in high-throughput screening technologies.", "sc:name": "AssayCorrector", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/AssayCorrector/index.html" } \ No newline at end of file diff --git a/data/assayr/assayrbioschemas.jsonld b/data/assayr/assayrbioschemas.jsonld index 71bff4245ba63..a3728922f4911 100644 --- a/data/assayr/assayrbioschemas.jsonld +++ b/data/assayr/assayrbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1021/acs.analchem.7b02401", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/assayr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jimi Wills", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:28850215", { "@id": "https://doi.org/10.1021/acs.analchem.7b02401" }, - "pmcid:PMC5628912", - "pubmed:28850215" + "pmcid:PMC5628912" ], "sc:description": "Simple Mass Spectrometry Software Tool for Targeted Metabolic and Stable Isotope Tracer Analyses.", "sc:featureList": { @@ -31,10 +35,6 @@ "Linux" ], "sc:url": "https://gitlab.com/jimiwills/assay.R/" - }, - { - "@id": "https://doi.org/10.1021/acs.analchem.7b02401", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/assembly_converter/assembly_converterbioschemas.jsonld b/data/assembly_converter/assembly_converterbioschemas.jsonld index 3ac9be8b41060..9e2189e9969e4 100644 --- a/data/assembly_converter/assembly_converterbioschemas.jsonld +++ b/data/assembly_converter/assembly_converterbioschemas.jsonld @@ -15,13 +15,13 @@ "sc:description": "Map your data to the current assembly.", "sc:name": "Assembly converter", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ - "Sanger Institute", - "EMBL-EBI" + "EMBL-EBI", + "Sanger Institute" ], "sc:url": "http://www.ensembl.org/Homo_sapiens/UserData/SelectFeatures", "sc:version": "1" diff --git a/data/assembly_pcr_oligo_maker/assembly_pcr_oligo_makerbioschemas.jsonld b/data/assembly_pcr_oligo_maker/assembly_pcr_oligo_makerbioschemas.jsonld index 2041c7dd990cd..703fee8993594 100644 --- a/data/assembly_pcr_oligo_maker/assembly_pcr_oligo_makerbioschemas.jsonld +++ b/data/assembly_pcr_oligo_maker/assembly_pcr_oligo_makerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.", "sc:name": "Assembly PCR Oligo Maker", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.yorku.ca/pjohnson/AssemblyPCRoligomaker.html" } \ No newline at end of file diff --git a/data/assemblyget/assemblygetbioschemas.jsonld b/data/assemblyget/assemblygetbioschemas.jsonld index 57b4af3c414b0..8276d8d335d00 100644 --- a/data/assemblyget/assemblygetbioschemas.jsonld +++ b/data/assemblyget/assemblygetbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "Wellcome Trust", "EMBOSS Contributors", + "UK MRC", "UK BBSRC" ], "sc:description": "An Emboss tool that searches for a sequence assembly and returns the data in one of the EMBOSS assembly formats.", diff --git a/data/assemblymanager/assemblymanagerbioschemas.jsonld b/data/assemblymanager/assemblymanagerbioschemas.jsonld index bb1783c24baa0..fb4d377696830 100644 --- a/data/assemblymanager/assemblymanagerbioschemas.jsonld +++ b/data/assemblymanager/assemblymanagerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "assemblyManager", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://andersonlab.qb3.berkeley.edu/#/software" } \ No newline at end of file diff --git a/data/assemblytics/assemblyticsbioschemas.jsonld b/data/assemblytics/assemblyticsbioschemas.jsonld index b8d59c3198a6e..a2d94eaf6db98 100644 --- a/data/assemblytics/assemblyticsbioschemas.jsonld +++ b/data/assemblytics/assemblyticsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Assemblytics", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://assemblytics.com/" } \ No newline at end of file diff --git a/data/asseq/asseqbioschemas.jsonld b/data/asseq/asseqbioschemas.jsonld index 30e33cbd8e4c7..6141561a89522 100644 --- a/data/asseq/asseqbioschemas.jsonld +++ b/data/asseq/asseqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software of allele specific study of next generation sequencing data, with emphasis on RNA-seq and ChIP-seq data.", "sc:name": "asSeq", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.bios.unc.edu/~weisun/software/asSeq.htm" diff --git a/data/asset/assetbioschemas.jsonld b/data/asset/assetbioschemas.jsonld index bb1dcaf4589b9..3f3f27943321f 100644 --- a/data/asset/assetbioschemas.jsonld +++ b/data/asset/assetbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "ASSET", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ASSET.html", "sc:version": "1.12.0" diff --git a/data/assign/assignbioschemas.jsonld b/data/assign/assignbioschemas.jsonld index 9f9af5a02baf9..d71abb9e170a4 100644 --- a/data/assign/assignbioschemas.jsonld +++ b/data/assign/assignbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ying Shen", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Tool to evaluate the pathway deregulation/activation status in patient samples. It employs a Bayesian factor analysis approach to adapt predetermined pathway signatures derived from knowledge-based literatures or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.", "sc:license": "MIT", "sc:name": "ASSIGN", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ASSIGN.html", "sc:version": "1.10.0" diff --git a/data/assist/assistbioschemas.jsonld b/data/assist/assistbioschemas.jsonld index 083768b92a780..d32dc6cf3de53 100644 --- a/data/assist/assistbioschemas.jsonld +++ b/data/assist/assistbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:funder": "http://www.fruitbreedomics.com/", "sc:name": "ASSIST", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ELIXIR-ITA-MACH", "sc:url": "http://compbiotoolbox.fmach.it/assist/", diff --git a/data/assist_active/assist_activebioschemas.jsonld b/data/assist_active/assist_activebioschemas.jsonld index 8f1908fe8714e..acea46eff02ee 100644 --- a/data/assist_active/assist_activebioschemas.jsonld +++ b/data/assist_active/assist_activebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "ASSIST is an application for the detection of catalytic sites in unknown function proteins.", "sc:name": "ASSIST v1- Active Site Similarity Search Tool", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.computationalbiology.it/software.html" } \ No newline at end of file diff --git a/data/association_viewer/association_viewerbioschemas.jsonld b/data/association_viewer/association_viewerbioschemas.jsonld index a35c25d95c194..c6adaca9f291b 100644 --- a/data/association_viewer/association_viewerbioschemas.jsonld +++ b/data/association_viewer/association_viewerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "AssociationViewer is a Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.", "sc:name": "Association Viewer", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://associationviewer.vital-it.ch/" } \ No newline at end of file diff --git a/data/astalavista/astalavistabioschemas.jsonld b/data/astalavista/astalavistabioschemas.jsonld index dda214e4a99d8..df23d6229f569 100644 --- a/data/astalavista/astalavistabioschemas.jsonld +++ b/data/astalavista/astalavistabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "AStalavista", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ "crg.eu", diff --git a/data/astd/astdbioschemas.jsonld b/data/astd/astdbioschemas.jsonld index 798c005671d1e..766a5cc73b259 100644 --- a/data/astd/astdbioschemas.jsonld +++ b/data/astd/astdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "AltSplice and AltExtron provide information on alternative intron/exons, alternative splice events, and isoform splice patterns. AEdb contains: AEdb-Sequence (sequence and properties of alternatively splice exons), AEdb-Function (data on functional aspects of alternative splicing), AEdb-motif (data and sequence of known splice regulatory motifs), and AEdb-minigene (a collection of known minigene constructs for alternative splice events).", "sc:name": "ASTD", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.ebi.ac.uk/astd/" } \ No newline at end of file diff --git a/data/astral/astralbioschemas.jsonld b/data/astral/astralbioschemas.jsonld index 15649c63db306..32a2e12bca350 100644 --- a/data/astral/astralbioschemas.jsonld +++ b/data/astral/astralbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Java program for estimating a species tree given a set of unrooted gene trees.", "sc:name": "ASTRAL", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/smirarab/ASTRAL" diff --git a/data/astrocyte_quantification_and_analysis_aqua/astrocyte_quantification_and_analysis_aquabioschemas.jsonld b/data/astrocyte_quantification_and_analysis_aqua/astrocyte_quantification_and_analysis_aquabioschemas.jsonld index da824466a4d88..041e7424db0d6 100644 --- a/data/astrocyte_quantification_and_analysis_aqua/astrocyte_quantification_and_analysis_aquabioschemas.jsonld +++ b/data/astrocyte_quantification_and_analysis_aqua/astrocyte_quantification_and_analysis_aquabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "Astrocyte Quantification and Analysis (AQuA)", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/yu-lab-vt/aqua" } \ No newline at end of file diff --git a/data/atac/atacbioschemas.jsonld b/data/atac/atacbioschemas.jsonld index 105800700dd6f..5652216bced3d 100644 --- a/data/atac/atacbioschemas.jsonld +++ b/data/atac/atacbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/atac", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Brian Walenz", - "Liliana Florea" + "Liliana Florea", + "Brian Walenz" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:14769938", diff --git a/data/atacseqqc/atacseqqcbioschemas.jsonld b/data/atacseqqc/atacseqqcbioschemas.jsonld index c81d8960250fb..df04c4dbbb286 100644 --- a/data/atacseqqc/atacseqqcbioschemas.jsonld +++ b/data/atacseqqc/atacseqqcbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ATACseqQC", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ATACseqQC.html", "sc:version": "1.4.1" diff --git a/data/ataris/atarisbioschemas.jsonld b/data/ataris/atarisbioschemas.jsonld index dec35f8b12f39..aa08ddfea4692 100644 --- a/data/ataris/atarisbioschemas.jsonld +++ b/data/ataris/atarisbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Plug-in", "sc:citation": [ "pubmed:23269662", + "pmcid:PMC3613583", { "@id": "https://doi.org/10.1101/GR.143586.112" - }, - "pmcid:PMC3613583" + } ], "sc:description": "Computational quantification of gene suppression phenotypes from multisample RNAi screens.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "ATARiS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.broadinstitute.org/ataris-computational-quantification-gene-suppression-phenotypes-multisample-rnai-screens" } diff --git a/data/atcc/atccbioschemas.jsonld b/data/atcc/atccbioschemas.jsonld index fee1f234e9d9b..f9329d2f571a1 100644 --- a/data/atcc/atccbioschemas.jsonld +++ b/data/atcc/atccbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Global biological materials resource and standards organization whose mission focuses on the acquisition, authentication, production, preservation, development, and distribution of standard reference microorganisms, cell lines, and other materials.", "sc:name": "American Type Culture Collection (ATCC)", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "ATCC", diff --git a/data/atcoecis/atcoecisbioschemas.jsonld b/data/atcoecis/atcoecisbioschemas.jsonld index a66d609adc402..59c1b5963df97 100644 --- a/data/atcoecis/atcoecisbioschemas.jsonld +++ b/data/atcoecis/atcoecisbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ATCOECIS", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "PSB", "sc:url": "http://bioinformatics.psb.ugent.be/ATCOECIS/", diff --git a/data/atfusiondb/atfusiondbbioschemas.jsonld b/data/atfusiondb/atfusiondbbioschemas.jsonld index 179d17388d10d..0cfc321f3ee89 100644 --- a/data/atfusiondb/atfusiondbbioschemas.jsonld +++ b/data/atfusiondb/atfusiondbbioschemas.jsonld @@ -25,8 +25,8 @@ { "@id": "https://doi.org/10.1093/database/bay135" }, - "pmcid:PMC6323297", - "pubmed:30624648" + "pubmed:30624648", + "pmcid:PMC6323297" ], "sc:description": "Database of fusion transcripts in Arabidopsis thaliana.", "sc:featureList": [ @@ -34,10 +34,10 @@ "@id": "edam:operation_2495" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_0495" }, { - "@id": "edam:operation_0495" + "@id": "edam:operation_0224" } ], "sc:name": "AtFusionDB", diff --git a/data/atlasrdf/atlasrdfbioschemas.jsonld b/data/atlasrdf/atlasrdfbioschemas.jsonld index cf0fc5446b5b9..10bbf8eb7fcc3 100644 --- a/data/atlasrdf/atlasrdfbioschemas.jsonld +++ b/data/atlasrdf/atlasrdfbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Apache-2.0", "sc:name": "AtlasRDF", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AtlasRDF.html", "sc:version": "1.10.0" diff --git a/data/atomap/atomapbioschemas.jsonld b/data/atomap/atomapbioschemas.jsonld index 2db3558bb1551..960e8084a3c8b 100644 --- a/data/atomap/atomapbioschemas.jsonld +++ b/data/atomap/atomapbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7981-5293", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/atomap", "@type": "sc:SoftwareApplication", @@ -31,16 +35,12 @@ "sc:name": "Atomap", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://atomap.org/", "sc:version": "0.1.2" }, - { - "@id": "http://orcid.org/0000-0001-7981-5293", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s40679-017-0042-5", "@type": "sc:CreativeWork" diff --git a/data/atomicchargecalculator/atomicchargecalculatorbioschemas.jsonld b/data/atomicchargecalculator/atomicchargecalculatorbioschemas.jsonld index 6caec7e8febf3..675794c940c0a 100644 --- a/data/atomicchargecalculator/atomicchargecalculatorbioschemas.jsonld +++ b/data/atomicchargecalculator/atomicchargecalculatorbioschemas.jsonld @@ -11,21 +11,21 @@ "@id": "https://bio.tools/atomicchargecalculator", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": "David Sehnal", "sc:contributor": [ - "Lukáš Pravda", "Stanislav Geidl", - "Crina Maria Ionescu" + "Crina Maria Ionescu", + "Lukáš Pravda" ], "sc:description": "A web application for the calculation and analysis of atomic charges in both large biomolecular complexes and small drug-like molecules.", "sc:name": "AtomicChargeCalculator", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "Masaryk University, Brno, Czech Republic", "sc:url": "http://ncbr.muni.cz/ACC", diff --git a/data/atpid/atpidbioschemas.jsonld b/data/atpid/atpidbioschemas.jsonld index 13966d009e02a..fc582d9fc67b5 100644 --- a/data/atpid/atpidbioschemas.jsonld +++ b/data/atpid/atpidbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome.", "sc:name": "AtPID", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.megabionet.org/atpid/" } \ No newline at end of file diff --git a/data/atram/atrambioschemas.jsonld b/data/atram/atrambioschemas.jsonld index 17d8a1b0467c5..449c0765cf979 100644 --- a/data/atram/atrambioschemas.jsonld +++ b/data/atram/atrambioschemas.jsonld @@ -9,24 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-1497-1284", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/S12859-015-0515-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/atram", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4380108", "pubmed:25887972", { "@id": "https://doi.org/10.1186/S12859-015-0515-2" - } + }, + "pmcid:PMC4380108" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-1497-1284" @@ -42,6 +34,14 @@ ], "sc:url": "https://github.com/juliema/aTRAM", "sc:version": "1.04" + }, + { + "@id": "http://orcid.org/0000-0002-1497-1284", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/S12859-015-0515-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/atrhunter/atrhunterbioschemas.jsonld b/data/atrhunter/atrhunterbioschemas.jsonld index d55b01d1ed9c0..0bdcfd032504d 100644 --- a/data/atrhunter/atrhunterbioschemas.jsonld +++ b/data/atrhunter/atrhunterbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/atrhunter", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web service", - "Command-line tool" + "Command-line tool", + "Web service" ], "sc:citation": "pubmed:16201913", "sc:description": "Software that finds and displays approximate tandem repeats (ATR) in DNA sequences. An approximate tandem repeat (ATR) in a genomic sequence is a string of nucleotides repeated consecutively at least twice with some small differences between the repeated copies.", "sc:name": "ATRHunter", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.cs.technion.ac.il/labs/cbl/atrhunter/ATRinformation.htm" } \ No newline at end of file diff --git a/data/atsnp/atsnpbioschemas.jsonld b/data/atsnp/atsnpbioschemas.jsonld index 93a5efc807eab..f94543717009d 100644 --- a/data/atsnp/atsnpbioschemas.jsonld +++ b/data/atsnp/atsnpbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "atSNP", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/chandlerzuo/atsnp" } \ No newline at end of file diff --git a/data/atsubp/atsubpbioschemas.jsonld b/data/atsubp/atsubpbioschemas.jsonld index 4acb53226f138..7c6acb5c0103d 100644 --- a/data/atsubp/atsubpbioschemas.jsonld +++ b/data/atsubp/atsubpbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AtSubP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo3.noble.org/AtSubP/" } \ No newline at end of file diff --git a/data/attract/attractbioschemas.jsonld b/data/attract/attractbioschemas.jsonld index 9b59bb1f2a0fb..18b83ac35cf8a 100644 --- a/data/attract/attractbioschemas.jsonld +++ b/data/attract/attractbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Samuel Zimmerman", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression.", "sc:license": "GPL-2.0", "sc:name": "attract", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/attract.html", "sc:version": "1.26.0" diff --git a/data/aucell/aucellbioschemas.jsonld b/data/aucell/aucellbioschemas.jsonld index 65b03d3b888cc..96f2dee254087 100644 --- a/data/aucell/aucellbioschemas.jsonld +++ b/data/aucell/aucellbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AUCell", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/AUCell.html", "sc:version": "1.2.4" diff --git a/data/aurea/aureabioschemas.jsonld b/data/aurea/aureabioschemas.jsonld index 7e289901e1bf9..6417b70619d48 100644 --- a/data/aurea/aureabioschemas.jsonld +++ b/data/aurea/aureabioschemas.jsonld @@ -16,24 +16,24 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:23496976", - "pmcid:PMC3599560", { "@id": "https://doi.org/10.1186/1471-2105-14-78" - } + }, + "pmcid:PMC3599560" ], "sc:description": "Open-source software system for accurate and user-friendly identification of relative expression molecular signatures.", "sc:featureList": [ { - "@id": "edam:operation_0239" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_0239" } ], "sc:name": "AUREA", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://hood-price.systemsbiology.org/research/aurea/" diff --git a/data/aureme/auremebioschemas.jsonld b/data/aureme/auremebioschemas.jsonld index cfad28f7acf29..33d9942bea389 100644 --- a/data/aureme/auremebioschemas.jsonld +++ b/data/aureme/auremebioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/aureme", "@type": "sc:SoftwareApplication", "sc:additionalType": [ + "Command-line tool", "Workbench", - "Workflow", - "Command-line tool" + "Workflow" ], "sc:description": "A unified workspace built around a Python package PADMet (Python library for hAndling metaData of METabolism), to house the reconstruction of genome-scale metabolic models.", "sc:license": "GPL-3.0", diff --git a/data/aureolib/aureolibbioschemas.jsonld b/data/aureolib/aureolibbioschemas.jsonld index 69077b5160ad2..42fcce9a1ef46 100644 --- a/data/aureolib/aureolibbioschemas.jsonld +++ b/data/aureolib/aureolibbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0070669", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/aureolib", "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ + "pmcid:PMC3742771", { "@id": "https://doi.org/10.1371/journal.pone.0070669" }, - "pubmed:23967085", - "pmcid:PMC3742771" + "pubmed:23967085" ], "sc:description": "Proteomic signature library of Staphylococcus aureus Pathophysiology for inter-experimental expression data analyses.", "sc:featureList": { @@ -27,10 +31,6 @@ "sc:name": "Aureolib", "sc:url": "http://www.aureolib.de/index.php", "sc:version": "1.2" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0070669", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/autalasso/autalassobioschemas.jsonld b/data/autalasso/autalassobioschemas.jsonld index bf1a26f091348..182f5a8aaeb35 100644 --- a/data/autalasso/autalassobioschemas.jsonld +++ b/data/autalasso/autalassobioschemas.jsonld @@ -16,27 +16,27 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:30940067", + "pmcid:PMC6444607", { "@id": "https://doi.org/10.1186/s12859-019-2743-3" - }, - "pmcid:PMC6444607" + } ], "sc:description": "Automatic adaptive LASSO for genome-wide prediction.", "sc:featureList": [ { - "@id": "edam:operation_3557" + "@id": "edam:operation_3659" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3557" }, { - "@id": "edam:operation_3659" + "@id": "edam:operation_3196" } ], "sc:name": "AUTALASSO", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/patwa67/AUTALASSO" }, diff --git a/data/autismkb/autismkbbioschemas.jsonld b/data/autismkb/autismkbbioschemas.jsonld index 320bc20e71bd9..0a67459b23f3c 100644 --- a/data/autismkb/autismkbbioschemas.jsonld +++ b/data/autismkb/autismkbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An evidence-based knowledgebase of autism genetics.", "sc:name": "AutismKB", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://autismkb.cbi.pku.edu.cn/" } \ No newline at end of file diff --git a/data/auto-rickshaw/auto-rickshawbioschemas.jsonld b/data/auto-rickshaw/auto-rickshawbioschemas.jsonld index 220e40f4c4f18..45c05c563933a 100644 --- a/data/auto-rickshaw/auto-rickshawbioschemas.jsonld +++ b/data/auto-rickshaw/auto-rickshawbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-6058-7793", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/auto-rickshaw", "@type": "sc:SoftwareApplication", @@ -22,8 +18,8 @@ "sc:additionalType": "Web service", "sc:citation": [ "pmcid:PMC2756167", - "pubmed:15805600", "pubmed:19770506", + "pubmed:15805600", { "@id": "https://doi.org/10.1107/S0907444909029643" } @@ -40,6 +36,10 @@ { "@id": "https://doi.org/10.1107/S0907444909029643", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-6058-7793", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/autoassemblyd/autoassemblydbioschemas.jsonld b/data/autoassemblyd/autoassemblydbioschemas.jsonld index c49d042d3ef66..b0b28090e503b 100644 --- a/data/autoassemblyd/autoassemblydbioschemas.jsonld +++ b/data/autoassemblyd/autoassemblydbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "AutoAssemblyD", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sourceforge.net/projects/autoassemblyd/" } \ No newline at end of file diff --git a/data/autoassign/autoassignbioschemas.jsonld b/data/autoassign/autoassignbioschemas.jsonld index 9b29d4d2b1048..4bee1b35fe31d 100644 --- a/data/autoassign/autoassignbioschemas.jsonld +++ b/data/autoassign/autoassignbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Using this software, complete backbone resonance assignments are now routinely made within hours of completing the final data acquisition.", "sc:name": "AUTOASSIGN", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html", diff --git a/data/autoclass_ijm/autoclass_ijmbioschemas.jsonld b/data/autoclass_ijm/autoclass_ijmbioschemas.jsonld index f9bfbb3c9fb45..c691d72ad090b 100644 --- a/data/autoclass_ijm/autoclass_ijmbioschemas.jsonld +++ b/data/autoclass_ijm/autoclass_ijmbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "AutoClass IJM", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ijm.fr/en/ijm/resources/bioinformatics/" } \ No newline at end of file diff --git a/data/autocsa/autocsabioschemas.jsonld b/data/autocsa/autocsabioschemas.jsonld index ce11e550862a6..fc1261579b4ff 100644 --- a/data/autocsa/autocsabioschemas.jsonld +++ b/data/autocsa/autocsabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "AutoCSA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.sanger.ac.uk/science/tools/autocsa", "sc:version": "1.0" diff --git a/data/autodesk_molecule_viewer/autodesk_molecule_viewerbioschemas.jsonld b/data/autodesk_molecule_viewer/autodesk_molecule_viewerbioschemas.jsonld index 196b68807de72..63ee6074941de 100644 --- a/data/autodesk_molecule_viewer/autodesk_molecule_viewerbioschemas.jsonld +++ b/data/autodesk_molecule_viewer/autodesk_molecule_viewerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Freeware", "sc:name": "Autodesk Molecule Viewer", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://moleculeviewer.lifesciences.autodesk.com/" diff --git a/data/autodock_vina/autodock_vinabioschemas.jsonld b/data/autodock_vina/autodock_vinabioschemas.jsonld index fdeaf7f4f38bb..659f16c49d4f7 100644 --- a/data/autodock_vina/autodock_vinabioschemas.jsonld +++ b/data/autodock_vina/autodock_vinabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.", "sc:name": "AutoDock Vina", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://vina.scripps.edu/", "sc:version": "1.1.2" diff --git a/data/autohd/autohdbioschemas.jsonld b/data/autohd/autohdbioschemas.jsonld index 7b9585e4ba83a..4a15cacd590df 100644 --- a/data/autohd/autohdbioschemas.jsonld +++ b/data/autohd/autohdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "AUTOHD", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.ms-utils.org/autohd.html" } \ No newline at end of file diff --git a/data/autoosc/autooscbioschemas.jsonld b/data/autoosc/autooscbioschemas.jsonld index c0f564c52a333..61d2968e5c5d7 100644 --- a/data/autoosc/autooscbioschemas.jsonld +++ b/data/autoosc/autooscbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Mathematica package for analyzing time-series of oscillatory signals, particularly those originating from biological/chemical systems.", "sc:name": "Autoosc", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://babylone.ulb.ac.be/autoosc/" } \ No newline at end of file diff --git a/data/autopad/autopadbioschemas.jsonld b/data/autopad/autopadbioschemas.jsonld index 033a45b713036..fb095dee87aa9 100644 --- a/data/autopad/autopadbioschemas.jsonld +++ b/data/autopad/autopadbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The paper-based microfluidic device design software.", "sc:name": "AutoPAD", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/MaceLab/AutoPAD" } \ No newline at end of file diff --git a/data/autoroot/autorootbioschemas.jsonld b/data/autoroot/autorootbioschemas.jsonld index 2be58cce8425b..1f2a13da950fb 100644 --- a/data/autoroot/autorootbioschemas.jsonld +++ b/data/autoroot/autorootbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13007-017-0161-y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/autoroot", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael P. Pound", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:28286542", "pmcid:PMC5341458", { "@id": "https://doi.org/10.1186/s13007-017-0161-y" - }, - "pubmed:28286542" + } ], "sc:description": "Open-source software employing a novel image analysis approach to support fully-automated plant phenotyping.", "sc:featureList": { @@ -33,6 +29,10 @@ "sc:name": "AutoRoot", "sc:operatingSystem": "Windows", "sc:url": "https://zenodo.org/record/60433#.W1NXONj7TOQ" + }, + { + "@id": "https://doi.org/10.1186/s13007-017-0161-y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/autoseqman/autoseqmanbioschemas.jsonld b/data/autoseqman/autoseqmanbioschemas.jsonld index 974df3cf34dcc..e6d5e6537167c 100644 --- a/data/autoseqman/autoseqmanbioschemas.jsonld +++ b/data/autoseqman/autoseqmanbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.24272/j.issn.2095-8137.2018.027", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/autoseqman", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pmcid:PMC5885390", - "pubmed:29515094", { "@id": "https://doi.org/10.24272/j.issn.2095-8137.2018.027" - } + }, + "pubmed:29515094" ], "sc:description": "Batch Assembly of Contigs for Sanger Sequences.", "sc:featureList": { @@ -28,10 +32,6 @@ "sc:name": "AutoSeqMan", "sc:operatingSystem": "Windows", "sc:url": "https://github.com/Sun-Yanbo/autoSeqMan" - }, - { - "@id": "https://doi.org/10.24272/j.issn.2095-8137.2018.027", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/autosequin/autosequinbioschemas.jsonld b/data/autosequin/autosequinbioschemas.jsonld index 33337a8f03f99..903a14516ce19 100644 --- a/data/autosequin/autosequinbioschemas.jsonld +++ b/data/autosequin/autosequinbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "AutoSequin is designed to speed up the process of submitting HIV sequences to GenBank via NCBI’s Sequin program. It is ideal for the batch sequence submission. It makes a special formated table required for running NCBI’s tbl2asn program to generate .sqn file for submission to GenBank.", "sc:name": "AutoSequin", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://indra.mullins.microbiol.washington.edu/perlscript/docs/AutoSequin.html" } \ No newline at end of file diff --git a/data/autosite/autositebioschemas.jsonld b/data/autosite/autositebioschemas.jsonld index dae2367e5f840..fcb57bd81bc53 100644 --- a/data/autosite/autositebioschemas.jsonld +++ b/data/autosite/autositebioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Michel F. Sanner", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5048065", - "pubmed:27354702", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTW367" - } + }, + "pmcid:PMC5048065", + "pubmed:27354702" ], "sc:description": "Computational method for identifying and characterizing small molecules binding sites for receptors of known three-dimensional structure. Binding sites are identified using energetic aspects to select high affinity points in space around the receptor, and a clustering technique for segregating these points into clusters called fills and corresponding to potential binding pockets.", "sc:featureList": { @@ -27,8 +27,8 @@ }, "sc:name": "AutoSite", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://adfr.scripps.edu/AutoDockFR/autosite.html" }, diff --git a/data/autosnpdb/autosnpdbbioschemas.jsonld b/data/autosnpdb/autosnpdbbioschemas.jsonld index 142ca0be0dc4d..4d01585184806 100644 --- a/data/autosnpdb/autosnpdbbioschemas.jsonld +++ b/data/autosnpdb/autosnpdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "AutoSNPdb", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://autosnpdb.appliedbioinformatics.com.au/index.jsp?species=" } \ No newline at end of file diff --git a/data/avedissr/avedissrbioschemas.jsonld b/data/avedissr/avedissrbioschemas.jsonld index 16d47e783588c..f429543e1c968 100644 --- a/data/avedissr/avedissrbioschemas.jsonld +++ b/data/avedissr/avedissrbioschemas.jsonld @@ -9,14 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3732/apps.1700018", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/avedissr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yong-Bi Fu", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:28791204", "pmcid:PMC5546164", + "pubmed:28791204", { "@id": "https://doi.org/10.3732/apps.1700018" } @@ -27,15 +31,11 @@ }, "sc:name": "AveDissR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://figshare.com/articles/AveDissR_An_R_function_for_assessing_genetic_distinctness_and_genetic_redundancy/5082451/3" - }, - { - "@id": "https://doi.org/10.3732/apps.1700018", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/avia/aviabioschemas.jsonld b/data/avia/aviabioschemas.jsonld index 377938379158e..f3414b0feff09 100644 --- a/data/avia/aviabioschemas.jsonld +++ b/data/avia/aviabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web based annotation and visualization workflow that allow users with variation data to easily get more information about their specific mutations without having to search multiple websites or databases.", "sc:name": "AVIA", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://avia.abcc.ncifcrf.gov" } \ No newline at end of file diff --git a/data/avpdb/avpdbbioschemas.jsonld b/data/avpdb/avpdbbioschemas.jsonld index 2157b1ae8a93f..8f2a8c496e4cb 100644 --- a/data/avpdb/avpdbbioschemas.jsonld +++ b/data/avpdb/avpdbbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkt1191", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/avpdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr. Manoj Kumar", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:24285301", "pmcid:PMC3964995", { "@id": "https://doi.org/10.1093/nar/gkt1191" - } + }, + "pubmed:24285301" ], "sc:description": "Anti Viral Peptide Database. Experimentally verified AVPs targeting over 60 medically important viruses including Influenza, HCV, HSV, RSV, HBV, DENV, SARS, etc.", "sc:featureList": { @@ -32,6 +28,10 @@ "sc:name": "AVPdb", "sc:operatingSystem": "Linux", "sc:url": "http://crdd.osdd.net/servers/avpdb/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkt1191", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/avppred/avppredbioschemas.jsonld b/data/avppred/avppredbioschemas.jsonld index a15201d31f1fe..664273ae9293e 100644 --- a/data/avppred/avppredbioschemas.jsonld +++ b/data/avppred/avppredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ANPpred webserver is an antiviral peptide prediction server. It contains 1245 peptides which have been experimentally validated for antiviral activity against human viruses.", "sc:name": "AVPpred", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://crdd.osdd.net/servers/avppred" } \ No newline at end of file diff --git a/data/axiom_analysis_suite/axiom_analysis_suitebioschemas.jsonld b/data/axiom_analysis_suite/axiom_analysis_suitebioschemas.jsonld index a6acd5d71e9a5..68808ec944d01 100644 --- a/data/axiom_analysis_suite/axiom_analysis_suitebioschemas.jsonld +++ b/data/axiom_analysis_suite/axiom_analysis_suitebioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12864-019-5712-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0001-9224-056X", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/S12864-019-5712-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Axiom_Analysis_Suite", "@type": "sc:SoftwareApplication", @@ -37,13 +37,13 @@ "sc:description": "Axiom Analysis Suite advances genotyping data analysis with a single-source software package to enable complete genotyping analysis of all Axiom arrays and copy number analysis on select Axiom arrays.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_0308" }, { - "@id": "edam:operation_0484" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_0308" + "@id": "edam:operation_0484" } ], "sc:license": "Unlicense", diff --git a/data/axiome/axiomebioschemas.jsonld b/data/axiome/axiomebioschemas.jsonld index 9e2161d2d0646..bd7f77c8ab731 100644 --- a/data/axiome/axiomebioschemas.jsonld +++ b/data/axiome/axiomebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Automation, eXtension, and Integration Of Microbial Ecology is a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.", "sc:name": "AXIOME", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://neufeld.github.io/AXIOME/" } \ No newline at end of file diff --git a/data/axonpacking/axonpackingbioschemas.jsonld b/data/axonpacking/axonpackingbioschemas.jsonld index 157e692767da9..e5553fd1bbfe8 100644 --- a/data/axonpacking/axonpackingbioschemas.jsonld +++ b/data/axonpacking/axonpackingbioschemas.jsonld @@ -28,8 +28,8 @@ "sc:license": "MIT", "sc:name": "AxonPacking", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/neuropoly/axonpacking" }, diff --git a/data/ayla/aylabioschemas.jsonld b/data/ayla/aylabioschemas.jsonld index 71dfb71bb59b3..ebe4a3def8437 100644 --- a/data/ayla/aylabioschemas.jsonld +++ b/data/ayla/aylabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A free, open source visualization tool for researchers in biochemistry, molecular dynamics, and protein folding.", "sc:name": "Ayla", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.aylasoftware.org/" } \ No newline at end of file diff --git a/data/azahar/azaharbioschemas.jsonld b/data/azahar/azaharbioschemas.jsonld index 58384c0c669f5..34d9357fcf414 100644 --- a/data/azahar/azaharbioschemas.jsonld +++ b/data/azahar/azaharbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PyMOL plugin for construction, visualization and analysis of glycan molecules.", "sc:name": "Azahar", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://pymolwiki.org/index.php/Azahar" } \ No newline at end of file diff --git a/data/azara/azarabioschemas.jsonld b/data/azara/azarabioschemas.jsonld index 9e5c636633fe6..4e196e47d21d9 100644 --- a/data/azara/azarabioschemas.jsonld +++ b/data/azara/azarabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Collection of NMR programs for interactive display and processing of NMR data.", "sc:name": "AZARA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://www.ccpn.ac.uk/azara/", diff --git a/data/b6db/b6dbbioschemas.jsonld b/data/b6db/b6dbbioschemas.jsonld index 90ab321c7a02f..afa0ebab45a87 100644 --- a/data/b6db/b6dbbioschemas.jsonld +++ b/data/b6db/b6dbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "The B6 Database (B6DB)", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ELIXIR-ITA-PARMA", "sc:url": "http://bioinformatics.unipr.it/B6db" diff --git a/data/baalchip/baalchipbioschemas.jsonld b/data/baalchip/baalchipbioschemas.jsonld index 40f526eaa3369..3ad4018244e2e 100644 --- a/data/baalchip/baalchipbioschemas.jsonld +++ b/data/baalchip/baalchipbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "BaalChIP", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BaalChIP.html", "sc:version": "1.0.0" diff --git a/data/babelomics/babelomicsbioschemas.jsonld b/data/babelomics/babelomicsbioschemas.jsonld index 35dfc8fc82118..c7c4d5c3d3bf8 100644 --- a/data/babelomics/babelomicsbioschemas.jsonld +++ b/data/babelomics/babelomicsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Integrative platform for the analysis of Transcriptomics, Proteomics and Genomics data with advanced functional profiling. It integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods.", "sc:name": "Babelomics", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": [ "cipf.es", diff --git a/data/bac/bacbioschemas.jsonld b/data/bac/bacbioschemas.jsonld index 30adee71eddba..2ad5e79de59bb 100644 --- a/data/bac/bacbioschemas.jsonld +++ b/data/bac/bacbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Raphael Gottardo", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.", "sc:license": "Artistic-2.0", diff --git a/data/baca/bacabioschemas.jsonld b/data/baca/bacabioschemas.jsonld index 75bb7ce754ee6..fbfa7bcf1047b 100644 --- a/data/baca/bacabioschemas.jsonld +++ b/data/baca/bacabioschemas.jsonld @@ -19,27 +19,27 @@ "biotools:primaryContact": "Vittorio Fortino", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC4377007", { "@id": "https://doi.org/10.1186/S12859-015-0477-4" }, - "pmcid:PMC4377007", "pubmed:25652236" ], "sc:description": "R-based graphical tool to concisely visualise and compare biological annotations queried from the DAVID web service.", "sc:featureList": [ { - "@id": "edam:operation_0361" + "@id": "edam:operation_2451" }, { - "@id": "edam:operation_2451" + "@id": "edam:operation_0361" } ], "sc:license": "GPL-3.0", "sc:name": "BACA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/BACA/" } diff --git a/data/bacarena/bacarenabioschemas.jsonld b/data/bacarena/bacarenabioschemas.jsonld index 0769fa29b3cf7..adddd237042f6 100644 --- a/data/bacarena/bacarenabioschemas.jsonld +++ b/data/bacarena/bacarenabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "BacArena", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/BacArena/index.html" } \ No newline at end of file diff --git a/data/bacdive/bacdivebioschemas.jsonld b/data/bacdive/bacdivebioschemas.jsonld index 43dfc67473609..4fa7046073b70 100644 --- a/data/bacdive/bacdivebioschemas.jsonld +++ b/data/bacdive/bacdivebioschemas.jsonld @@ -14,13 +14,13 @@ "sc:description": "Provides strain-linked information about bacterial and archaeal biodiversity. The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. The majority of data is manually annotated and curated.", "sc:name": "BacDive", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ - "Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH", - "bacdive" + "bacdive", + "Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" ], "sc:url": "http://bacdive.dsmz.de" } \ No newline at end of file diff --git a/data/bacdive_ws/bacdive_wsbioschemas.jsonld b/data/bacdive_ws/bacdive_wsbioschemas.jsonld index d04f83d4afedd..2c98c6eaff303 100644 --- a/data/bacdive_ws/bacdive_wsbioschemas.jsonld +++ b/data/bacdive_ws/bacdive_wsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/bacdive_ws", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Database portal" + "Database portal", + "Command-line tool" ], "sc:description": "Retrieving contents of BacDive and related information resources in a machine-readable form. BacDive is the Bacterial Diversity Metadatabase and provides strain-linked information about bacterial and archaeal biodiversity. The web-service offers several possibilities to query detailed strain information. It allows the retrieval by genus, species and/or subspecies, a given culture collection number or an INSDC accession number.", "sc:name": "BacDive WS", diff --git a/data/bacdiver/bacdiverbioschemas.jsonld b/data/bacdiver/bacdiverbioschemas.jsonld index 3073d76097076..8a6d1d2b0b6b9 100644 --- a/data/bacdiver/bacdiverbioschemas.jsonld +++ b/data/bacdiver/bacdiverbioschemas.jsonld @@ -16,10 +16,10 @@ "@id": "https://orcid.org/0000-0001-5135-5758" }, "sc:additionalType": [ - "Web service", "Library", - "Script", "Plug-in", + "Web service", + "Script", "Command-line tool" ], "sc:description": "The DSMZ's Bacterial Diversity Metadatabase (BacDive) focuses on providing organism-linked information covering the multifarious aspects of bacterial biodiversity: taxonomic classification, morphology, physiology, cultivation, origin natural habitat and more, both for bacterial and archaeal strains. BacDiveR helps you investigate this data offline, and semi-automatically in R.", diff --git a/data/bacello/bacellobioschemas.jsonld b/data/bacello/bacellobioschemas.jsonld index c3b998ff3112d..91740594e8871 100644 --- a/data/bacello/bacellobioschemas.jsonld +++ b/data/bacello/bacellobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Predictor for the subcellular localization of proteins in eukaryotes.", "sc:name": "BaCelLo", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", diff --git a/data/backclip/backclipbioschemas.jsonld b/data/backclip/backclipbioschemas.jsonld index 5ebc300727142..33c63c3bf362e 100644 --- a/data/backclip/backclipbioschemas.jsonld +++ b/data/backclip/backclipbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool to identify the presence of common RNA background in a PAR-CLIP dataset.", "sc:name": "BackCLIP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/phrh/BackCLIP" } \ No newline at end of file diff --git a/data/backtranambig-ebi/backtranambig-ebibioschemas.jsonld b/data/backtranambig-ebi/backtranambig-ebibioschemas.jsonld index 9e22ad38a316e..7830f6909d73c 100644 --- a/data/backtranambig-ebi/backtranambig-ebibioschemas.jsonld +++ b/data/backtranambig-ebi/backtranambig-ebibioschemas.jsonld @@ -22,9 +22,9 @@ "sc:description": "Back-translate a protein sequence to ambiguous nucleotide sequence. It reads a protein sequence and writes the nucleic acid sequence it could have come from. It does this by using nucleotide ambiguity codes that represent all possible codons for each amino acid.", "sc:name": "backtranambig (EBI)", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/st/emboss_backtranambig/", diff --git a/data/backtranambig/backtranambigbioschemas.jsonld b/data/backtranambig/backtranambigbioschemas.jsonld index 7310a5820e776..5ed29dbfc4d36 100644 --- a/data/backtranambig/backtranambigbioschemas.jsonld +++ b/data/backtranambig/backtranambigbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "EMBOSS Contributors", "UK BBSRC", + "Wellcome Trust", "UK MRC" ], "sc:description": "Back-translate a protein sequence to ambiguous nucleotide sequence.", @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "backtranambig", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/backtranambig.html", "sc:version": "r6" diff --git a/data/backtranseq-ebi/backtranseq-ebibioschemas.jsonld b/data/backtranseq-ebi/backtranseq-ebibioschemas.jsonld index 7c88a4a40919c..9703b64ae734e 100644 --- a/data/backtranseq-ebi/backtranseq-ebibioschemas.jsonld +++ b/data/backtranseq-ebi/backtranseq-ebibioschemas.jsonld @@ -16,15 +16,15 @@ "Web application" ], "sc:author": [ - "EMBOSS", - "Web Production" + "Web Production", + "EMBOSS" ], "sc:description": "Back-translate a protein sequence to a nucleotide sequence, using codon frequency.It reads a protein sequence and writes the nucleic acid sequence it is most likely to have come from.", "sc:name": "backtranseq (EBI)", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/st/emboss_backtranseq/", diff --git a/data/backtranseq/backtranseqbioschemas.jsonld b/data/backtranseq/backtranseqbioschemas.jsonld index deee950718e58..84194496b0314 100644 --- a/data/backtranseq/backtranseqbioschemas.jsonld +++ b/data/backtranseq/backtranseqbioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK MRC", + "UK BBSRC", "EMBOSS Contributors", - "Wellcome Trust", - "UK BBSRC" + "Wellcome Trust" ], "sc:description": "Back-translate a protein sequence to a nucleotide sequence.", "sc:funder": [ "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "backtranseq", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/backtranseq.html", "sc:version": "r6" diff --git a/data/bacmap/bacmapbioschemas.jsonld b/data/bacmap/bacmapbioschemas.jsonld index 8cef315a4c98a..bb1ca6f913765 100644 --- a/data/bacmap/bacmapbioschemas.jsonld +++ b/data/bacmap/bacmapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.", "sc:name": "BacMap", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bacmap.wishartlab.com/" } \ No newline at end of file diff --git a/data/bacoca/bacocabioschemas.jsonld b/data/bacoca/bacocabioschemas.jsonld index 07706ec4b794e..03636777d72b3 100644 --- a/data/bacoca/bacocabioschemas.jsonld +++ b/data/bacoca/bacocabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "BAse COmposition CAlculator is a user-friendly software that combines multiple statistical approaches (like RCFV and C value calculations) to identify biases in aligned sequence data which potentially mislead phylogenetic reconstructions.", "sc:name": "BaCoCa", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://annelida.de/research/bioinformatics/software/index.html" diff --git a/data/bacom/bacombioschemas.jsonld b/data/bacom/bacombioschemas.jsonld index 6825409ca37f3..3607e75bca46c 100644 --- a/data/bacom/bacombioschemas.jsonld +++ b/data/bacom/bacombioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Bayesian Analysis of COpy number Mixtures is a statistically-principled in silico approach to accurately estimate genomic deletions and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We have developed a cross-platform and open source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues and other relevant processing steps. We also provide an R interface, bacomR.", "sc:name": "BACOM", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://code.google.com/p/bacom/" } \ No newline at end of file diff --git a/data/bacon/baconbioschemas.jsonld b/data/bacon/baconbioschemas.jsonld index 5570b9d59b257..56d9000c8492e 100644 --- a/data/bacon/baconbioschemas.jsonld +++ b/data/bacon/baconbioschemas.jsonld @@ -33,8 +33,8 @@ "sc:license": "GPL-2.0", "sc:name": "bacon", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/bacon.html", diff --git a/data/bacpp/bacppbioschemas.jsonld b/data/bacpp/bacppbioschemas.jsonld index de50bec6fafba..16697579db003 100644 --- a/data/bacpp/bacppbioschemas.jsonld +++ b/data/bacpp/bacppbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "BacPP", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bacpp.bioinfoucs.com/home" } \ No newline at end of file diff --git a/data/bactag/bactagbioschemas.jsonld b/data/bactag/bactagbioschemas.jsonld index 96b1321ccc3f5..7aa692aa5e7b5 100644 --- a/data/bactag/bactagbioschemas.jsonld +++ b/data/bactag/bactagbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-0218-9092", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/BacTag", "@type": "sc:SoftwareApplication", @@ -24,8 +20,8 @@ { "@id": "https://doi.org/10.1186/S12864-019-5723-0" }, - "pmcid:PMC6501397", - "pubmed:31060512" + "pubmed:31060512", + "pmcid:PMC6501397" ], "sc:description": "Pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing.", "sc:featureList": [ @@ -42,8 +38,8 @@ "sc:license": "Unlicense", "sc:name": "BacTag", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://git.lumc.nl/l.khachatryan/BacTag" @@ -51,6 +47,10 @@ { "@id": "https://doi.org/10.1186/S12864-019-5723-0", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-0218-9092", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/bactgeneshow/bactgeneshowbioschemas.jsonld b/data/bactgeneshow/bactgeneshowbioschemas.jsonld index 20653299998dc..3d628ac9ad9c5 100644 --- a/data/bactgeneshow/bactgeneshowbioschemas.jsonld +++ b/data/bactgeneshow/bactgeneshowbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool analyses bacterial sequences and detects genes.", "sc:name": "bactgeneSHOW", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "IFB ELIXIR-FR", "sc:url": "http://genome.jouy.inra.fr/ssb/SHOW/", diff --git a/data/bactsnp/bactsnpbioschemas.jsonld b/data/bactsnp/bactsnpbioschemas.jsonld index 032504ebfdf35..4e39fe6c77305 100644 --- a/data/bactsnp/bactsnpbioschemas.jsonld +++ b/data/bactsnp/bactsnpbioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1099/MGEN.0.000261", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/BactSNP", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Takehiko Itoh", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6562250", { "@id": "https://doi.org/10.1099/MGEN.0.000261" }, - "pmcid:PMC6562250", "pubmed:31099741" ], "sc:description": "Tool to identify SNPs among bacterial isolates. BactSNP can detect SNPs and create a simple TSV file with SNP information as well as an alignment FASTA file containing reconstructed pseudo-genomes of the target isolates in a one-step process.", "sc:featureList": [ { - "@id": "edam:operation_3840" + "@id": "edam:operation_0484" }, { "@id": "edam:operation_3216" }, { - "@id": "edam:operation_0484" + "@id": "edam:operation_3840" } ], "sc:license": "GPL-3.0", "sc:name": "BactSNP", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/IEkAdN/BactSNP" - }, - { - "@id": "https://doi.org/10.1099/MGEN.0.000261", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/bader/baderbioschemas.jsonld b/data/bader/baderbioschemas.jsonld index 06d0f1e105fd0..5fe78e84c8932 100644 --- a/data/bader/baderbioschemas.jsonld +++ b/data/bader/baderbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "BADER", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BADER.html", "sc:version": "1.12.0" diff --git a/data/bader/bioconda_bader.yaml b/data/bader/bioconda_bader.yaml index 722b13670258e..e1fb996a19c75 100644 --- a/data/bader/bioconda_bader.yaml +++ b/data/bader/bioconda_bader.yaml @@ -7,7 +7,6 @@ description: For RNA sequencing count data, BADER fits a Bayesian hierarchical m home: https://bioconductor.org/packages/3.10/bioc/html/BADER.html identifiers: - biotools:bader -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-bader diff --git a/data/badregionfinder/badregionfinderbioschemas.jsonld b/data/badregionfinder/badregionfinderbioschemas.jsonld index ed25fcca3c879..9efea2d97f018 100644 --- a/data/badregionfinder/badregionfinderbioschemas.jsonld +++ b/data/badregionfinder/badregionfinderbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sarah Sandmann", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package identifies regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.", "sc:license": "GPL-3.0", "sc:name": "BadRegionFinder", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BadRegionFinder.html", diff --git a/data/badregionfinder/bioconda_badregionfinder.yaml b/data/badregionfinder/bioconda_badregionfinder.yaml index 0669a39c4d15b..c78e5763c66fc 100644 --- a/data/badregionfinder/bioconda_badregionfinder.yaml +++ b/data/badregionfinder/bioconda_badregionfinder.yaml @@ -6,7 +6,6 @@ description: BadRegionFinder is a package for identifying regions with a bad, ac home: https://bioconductor.org/packages/3.10/bioc/html/BadRegionFinder.html identifiers: - biotools:badregionfinder -- doi:10.1038/nmeth.3252 license: LGPL-3 license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-badregionfinder diff --git a/data/badtrip/badtripbioschemas.jsonld b/data/badtrip/badtripbioschemas.jsonld index 03f90034b3cad..b29d49ea024d1 100644 --- a/data/badtrip/badtripbioschemas.jsonld +++ b/data/badtrip/badtripbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "BadTrIP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bitbucket.org/nicofmay/badtrip" } \ No newline at end of file diff --git a/data/bagel/bagelbioschemas.jsonld b/data/bagel/bagelbioschemas.jsonld index 0aca84d933456..f6de1b2a53e40 100644 --- a/data/bagel/bagelbioschemas.jsonld +++ b/data/bagel/bagelbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.", "sc:name": "BAGEL", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bagel.molgenrug.nl/" } \ No newline at end of file diff --git a/data/bagel3/bagel3bioschemas.jsonld b/data/bagel3/bagel3bioschemas.jsonld index bff93c3406c10..8f936c3e7a39f 100644 --- a/data/bagel3/bagel3bioschemas.jsonld +++ b/data/bagel3/bagel3bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Automated identification of genes encoding bacteriocins and (non)-bacteriocidal post-translationally modified peptides using updated bacteriocin and context protein databases. Input is single or multiple FASTA formatted files.", "sc:name": "BAGEL3", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bagel.molgenrug.nl" } \ No newline at end of file diff --git a/data/bagheera/bagheerabioschemas.jsonld b/data/bagheera/bagheerabioschemas.jsonld index c089697ec4364..7b865b2fcc3b9 100644 --- a/data/bagheera/bagheerabioschemas.jsonld +++ b/data/bagheera/bagheerabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Bagheera is a web server of prediction of genes in yeast species by providing the correct CUG decoding scheme , that allows determining the most probable CUG codon translation for a given transcriptome or genome assembly based on extensive reference data.", "sc:name": "Bagheera", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.motorprotein.de/bagheera" } \ No newline at end of file diff --git a/data/bagpipe/bagpipebioschemas.jsonld b/data/bagpipe/bagpipebioschemas.jsonld index 7ee1976c32e64..33872668e0650 100644 --- a/data/bagpipe/bagpipebioschemas.jsonld +++ b/data/bagpipe/bagpipebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Bagpipe is a program for performing genomewide linkage disequilibrium mapping of quantitative trait loci in populations whose genome structure can be accommodated in the happy framework. This includes most diploid crosses where the founders of the individuals have known genotypes.", "sc:name": "Bagpipe", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://valdarlab.unc.edu/software/bagpipe/_build/html/index.html", "sc:version": "0.33" diff --git a/data/bait/baitbioschemas.jsonld b/data/bait/baitbioschemas.jsonld index 640ebc5e357ba..da8d4853dc424 100644 --- a/data/bait/baitbioschemas.jsonld +++ b/data/bait/baitbioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:23042453", - "pmcid:PMC3580294", { "@id": "https://doi.org/10.1038/nmeth.2206" - } + }, + "pmcid:PMC3580294", + "pubmed:23042453" ], "sc:description": "BAIT (Bioinformatic Analysis of Inherited Templates) is a software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.", "sc:featureList": { diff --git a/data/balbes/balbesbioschemas.jsonld b/data/balbes/balbesbioschemas.jsonld index 690247fa488d5..1860a50cb6c4a 100644 --- a/data/balbes/balbesbioschemas.jsonld +++ b/data/balbes/balbesbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A system for solving protein structures using x-ray crystallographic data.", "sc:name": "BALBES", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Instruct", "sc:url": "https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/balbes/balbes.html", diff --git a/data/balboa/balboabioschemas.jsonld b/data/balboa/balboabioschemas.jsonld index 57ffb0fe8c6dd..474a3738d1bb8 100644 --- a/data/balboa/balboabioschemas.jsonld +++ b/data/balboa/balboabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An ORF (Open Reading Frame) annotation approach, in which classifiers are constructed from the class specific expression patterns discovered by bicluster analysis. Firstly a set of bicluster classifiers is build using a labelled training set from the annotated ORFs in the expression data. These biclusters are then used to classify an unlabelled ORF set i.e. the unannotated ORFs from the expression dataset.", "sc:name": "BALBOA", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://mlg.ucd.ie/balboa.html" } \ No newline at end of file diff --git a/data/baldr/baldrbioschemas.jsonld b/data/baldr/baldrbioschemas.jsonld index 73d720615c99b..06ca428c8fe31 100644 --- a/data/baldr/baldrbioschemas.jsonld +++ b/data/baldr/baldrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "BALDR", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.bosingerlab.com/baldr/" } \ No newline at end of file diff --git a/data/bali-phy/bali-phybioschemas.jsonld b/data/bali-phy/bali-phybioschemas.jsonld index e3180cd3c04d3..59b02a342b1f0 100644 --- a/data/bali-phy/bali-phybioschemas.jsonld +++ b/data/bali-phy/bali-phybioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Markov chain Monte Carlo software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling via probabilistic programming.", "sc:name": "BAli-Phy", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.bali-phy.org/" } \ No newline at end of file diff --git a/data/ballgown/ballgownbioschemas.jsonld b/data/ballgown/ballgownbioschemas.jsonld index 5c7cb3c6e0d86..b629709bb2993 100644 --- a/data/ballgown/ballgownbioschemas.jsonld +++ b/data/ballgown/ballgownbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jack Fu", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.", "sc:license": "Artistic-2.0", diff --git a/data/bam2fastq/bam2fastqbioschemas.jsonld b/data/bam2fastq/bam2fastqbioschemas.jsonld index bd5c7443c4429..ad036715f0388 100644 --- a/data/bam2fastq/bam2fastqbioschemas.jsonld +++ b/data/bam2fastq/bam2fastqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Extract reads from a bam file and write them in fastq format.", "sc:name": "bam2fastq", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://gsl.hudsonalpha.org/information/software/bam2fastq", diff --git a/data/bam2roi/bam2roibioschemas.jsonld b/data/bam2roi/bam2roibioschemas.jsonld index e4bb0327c498f..0f3aa4983e4fe 100644 --- a/data/bam2roi/bam2roibioschemas.jsonld +++ b/data/bam2roi/bam2roibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Create ROI from BAM file.", "sc:name": "bam2roi", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/bam2roi/0.2.2", "sc:version": "0.2.2" diff --git a/data/bam_to_bigwig/bam_to_bigwigbioschemas.jsonld b/data/bam_to_bigwig/bam_to_bigwigbioschemas.jsonld index 22747c7e0b31d..ec22dfd5e5fa7 100644 --- a/data/bam_to_bigwig/bam_to_bigwigbioschemas.jsonld +++ b/data/bam_to_bigwig/bam_to_bigwigbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Calculate coverage from a BAM alignment file.", "sc:name": "bam_to_bigwig", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/bam_to_bigwig/bam_to_bigwig/0.1.0", diff --git a/data/bam_to_sam/bam_to_sambioschemas.jsonld b/data/bam_to_sam/bam_to_sambioschemas.jsonld index c579b3989618f..e899d46c48e33 100644 --- a/data/bam_to_sam/bam_to_sambioschemas.jsonld +++ b/data/bam_to_sam/bam_to_sambioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Convert BAM format to SAM format.", "sc:name": "bam_to_sam", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.htslib.org/", "sc:version": "1.0.3" diff --git a/data/bam_to_sam_parallel/bam_to_sam_parallelbioschemas.jsonld b/data/bam_to_sam_parallel/bam_to_sam_parallelbioschemas.jsonld index f30a9e351cb24..a96b7e059cdf3 100644 --- a/data/bam_to_sam_parallel/bam_to_sam_parallelbioschemas.jsonld +++ b/data/bam_to_sam_parallel/bam_to_sam_parallelbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Converts a list of BAM format files to SAM format.", "sc:name": "bam_to_sam_parallel", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.htslib.org/", "sc:version": "1.0.0" diff --git a/data/bambino/bambinobioschemas.jsonld b/data/bambino/bambinobioschemas.jsonld index 70fe56f4ce047..2ed554d7a70b4 100644 --- a/data/bambino/bambinobioschemas.jsonld +++ b/data/bambino/bambinobioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "Bambino", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/NCIP/cgr-bambino" } \ No newline at end of file diff --git a/data/bamm-sc/bamm-scbioschemas.jsonld b/data/bamm-sc/bamm-scbioschemas.jsonld index 47c00c3517369..66b7377af4361 100644 --- a/data/bamm-sc/bamm-scbioschemas.jsonld +++ b/data/bamm-sc/bamm-scbioschemas.jsonld @@ -17,12 +17,12 @@ "@id": "https://bio.tools/BAMM-SC", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Zhe Sun", - "Li Chen" + "Li Chen", + "Zhe Sun" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pubmed:30967541", @@ -34,10 +34,10 @@ "sc:description": "Bayesian mixture model for single-cell sequencing (BAMM-SC) method for clustering droplet-based single cell transcriptomic data from population studies.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_3216" }, { - "@id": "edam:operation_3216" + "@id": "edam:operation_3431" } ], "sc:license": "GPL-2.0", diff --git a/data/bamseek/bamseekbioschemas.jsonld b/data/bamseek/bamseekbioschemas.jsonld index d572dd7cb8348..f4822bc85f9f5 100644 --- a/data/bamseek/bamseekbioschemas.jsonld +++ b/data/bamseek/bamseekbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "BAMseek", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://code.google.com/archive/p/bamseek/" diff --git a/data/bamsi/bamsibioschemas.jsonld b/data/bamsi/bamsibioschemas.jsonld index a018bdb4a5e4e..3cd1c79426876 100644 --- a/data/bamsi/bamsibioschemas.jsonld +++ b/data/bamsi/bamsibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "BAMSI", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bamsi.research.it.uu.se/" diff --git a/data/bamsignals/bamsignalsbioschemas.jsonld b/data/bamsignals/bamsignalsbioschemas.jsonld index fb864d80ccaeb..87d1354100015 100644 --- a/data/bamsignals/bamsignalsbioschemas.jsonld +++ b/data/bamsignals/bamsignalsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "bamsignals", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/bamsignals.html", "sc:version": "1.6.0" diff --git a/data/bamsignals/bioconda_bamsignals.yaml b/data/bamsignals/bioconda_bamsignals.yaml index af114fdcc2737..5f11655d8144a 100644 --- a/data/bamsignals/bioconda_bamsignals.yaml +++ b/data/bamsignals/bioconda_bamsignals.yaml @@ -5,7 +5,6 @@ description: This package allows to efficiently obtain count vectors from indexe home: https://bioconductor.org/packages/3.10/bioc/html/bamsignals.html identifiers: - biotools:bamsignals -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-bamsignals diff --git a/data/bamstats/bamstatsbioschemas.jsonld b/data/bamstats/bamstatsbioschemas.jsonld index fa91e0112202e..ba64882e9af9f 100644 --- a/data/bamstats/bamstatsbioschemas.jsonld +++ b/data/bamstats/bamstatsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "bamstats", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.htslib.org/", "sc:version": "1.0.0" diff --git a/data/bamtools/bamtoolsbioschemas.jsonld b/data/bamtools/bamtoolsbioschemas.jsonld index b0c13f1e52b4d..412db15e73f5a 100644 --- a/data/bamtools/bamtoolsbioschemas.jsonld +++ b/data/bamtools/bamtoolsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "MIT", "sc:name": "BamTools", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/pezmaster31/bamtools" diff --git a/data/bamview/bamviewbioschemas.jsonld b/data/bamview/bamviewbioschemas.jsonld index 0b32072a35517..e1239ac77ab23 100644 --- a/data/bamview/bamviewbioschemas.jsonld +++ b/data/bamview/bamviewbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "BamView", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bamview.sourceforge.net/" } \ No newline at end of file diff --git a/data/banana/bananabioschemas.jsonld b/data/banana/bananabioschemas.jsonld index 4b3232b243c2a..aeee58b6b4afa 100644 --- a/data/banana/bananabioschemas.jsonld +++ b/data/banana/bananabioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "EMBOSS Contributors", "UK MRC", - "Wellcome Trust" + "EMBOSS Contributors", + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Plot bending and curvature data for B-DNA.", "sc:funder": [ "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "banana", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/banana.html", "sc:version": "r6" diff --git a/data/band_dyn_prog/band_dyn_progbioschemas.jsonld b/data/band_dyn_prog/band_dyn_progbioschemas.jsonld index e402787e7f569..479d0ea6c3bb2 100644 --- a/data/band_dyn_prog/band_dyn_progbioschemas.jsonld +++ b/data/band_dyn_prog/band_dyn_progbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Dynamic programming in a band is well suited to the problem of aligning long reads between themselves and can be used as a core component of methods for obtaining a consensus sequence from the long reads alone.", "sc:name": "BAND_DYN_PROG", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://forgemia.inra.fr/jean-francois.gibrat/BAND_DYN_PROG" } \ No newline at end of file diff --git a/data/bandage/bandagebioschemas.jsonld b/data/bandage/bandagebioschemas.jsonld index fd3c7913e8c7a..022f7c29ac74b 100644 --- a/data/bandage/bandagebioschemas.jsonld +++ b/data/bandage/bandagebioschemas.jsonld @@ -11,29 +11,29 @@ "@id": "https://bio.tools/bandage", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ryan Wick", - "Australia" + "Australia", + "Ryan Wick" ], "sc:additionalType": "Desktop application", "sc:author": "Ryan Wick", "sc:contributor": [ + "Justin Zobel", + "Rayan Chikhi", "Kathryn Holt", "Elmar Pruesse", - "Rayan Chikhi", - "Justin Zobel", "Mark Schultz" ], "sc:description": "GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.", "sc:license": "GPL-3.0", "sc:name": "Bandage", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ - "unimelb.edu.au", - "University of Melbourne, Australia" + "University of Melbourne, Australia", + "unimelb.edu.au" ], "sc:url": "https://rrwick.github.io/Bandage/", "sc:version": "1" diff --git a/data/bankit/bankitbioschemas.jsonld b/data/bankit/bankitbioschemas.jsonld index 033f9faaea2f4..98ba6165696eb 100644 --- a/data/bankit/bankitbioschemas.jsonld +++ b/data/bankit/bankitbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-based submission of one or a few sequences to GenBank.", "sc:name": "BankIt", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/BankIt/" } \ No newline at end of file diff --git a/data/banocc/banoccbioschemas.jsonld b/data/banocc/banoccbioschemas.jsonld index 84779a8642d1e..b0b4074c73135 100644 --- a/data/banocc/banoccbioschemas.jsonld +++ b/data/banocc/banoccbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "MIT", "sc:name": "banocc", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/banocc.html", diff --git a/data/bar-plus/bar-plusbioschemas.jsonld b/data/bar-plus/bar-plusbioschemas.jsonld index ea6dd94bee2ce..4bd1da91120c6 100644 --- a/data/bar-plus/bar-plusbioschemas.jsonld +++ b/data/bar-plus/bar-plusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "BAR-PLUS is a web tool for functional and structural annotation of protein sequences based on a large scale genome cross comparison and a non-hierarchical clustering procedure. Sequence annotation is derived from UniProtKB, GO, Pfam and PDB.\n\nThis is a legacy version, please refer to https://bio.tools/bar for the latest release.", "sc:name": "BAR-PLUS", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "https://bar.biocomp.unibo.it/bar2.0/", diff --git a/data/bar/barbioschemas.jsonld b/data/bar/barbioschemas.jsonld index 229e8d64317e1..79bf3b834e725 100644 --- a/data/bar/barbioschemas.jsonld +++ b/data/bar/barbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "It is for the annotation of protein sequences relying on a comparative large-scale analysis on the entire UniProt. With BAR 3.0 and a sequence you can annotate when possible: function, structure, protein domains. Also if your sequence falls into a cluster with a structural/some structural template/s we provide an alignment towards the template/templates based on the Cluster-HMM that allows you to directly compute your 3D model. Cluster HMMs are available for downloading.", "sc:name": "BAR", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "https://bar.biocomp.unibo.it/bar3/", diff --git a/data/barcod/barcodbioschemas.jsonld b/data/barcod/barcodbioschemas.jsonld index ee87708231d46..e0d640667a111 100644 --- a/data/barcod/barcodbioschemas.jsonld +++ b/data/barcod/barcodbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "BARCOD", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://wwwabi.snv.jussieu.fr/public/Barcod/", "sc:version": "1.0" diff --git a/data/barcode_generator/barcode_generatorbioschemas.jsonld b/data/barcode_generator/barcode_generatorbioschemas.jsonld index 9ec15c0a494df..3935b66514ebc 100644 --- a/data/barcode_generator/barcode_generatorbioschemas.jsonld +++ b/data/barcode_generator/barcode_generatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The program generates barcodes for sequences suitable for Illumina sequencing.", "sc:name": "Barcode generator", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://comailab.genomecenter.ucdavis.edu/index.php/Barcode_generator" } \ No newline at end of file diff --git a/data/barcosel/barcoselbioschemas.jsonld b/data/barcosel/barcoselbioschemas.jsonld index ecea3da0a21de..3800b49177aae 100644 --- a/data/barcosel/barcoselbioschemas.jsonld +++ b/data/barcosel/barcoselbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "It is a web tool for selecting an optimal set of barcode sequences. User must provide a set of candidate barcodes from which the defined number of barcodes is selected.", "sc:name": "BARCOSEL", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://ekhidna2.biocenter.helsinki.fi/barcosel/" diff --git a/data/barcrawl_bartab/barcrawl_bartabbioschemas.jsonld b/data/barcrawl_bartab/barcrawl_bartabbioschemas.jsonld index 463c5cdb9b11d..a00794c6699e6 100644 --- a/data/barcrawl_bartab/barcrawl_bartabbioschemas.jsonld +++ b/data/barcrawl_bartab/barcrawl_bartabbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Barcrawl Bartab", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.phyloware.com/Phyloware/XSTK.html" } \ No newline at end of file diff --git a/data/barnaba/barnababioschemas.jsonld b/data/barnaba/barnababioschemas.jsonld index cd55d524b628a..9ba303972188c 100644 --- a/data/barnaba/barnababioschemas.jsonld +++ b/data/barnaba/barnababioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Barnaba", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/srnas/barnaba" } \ No newline at end of file diff --git a/data/barnacle/barnaclebioschemas.jsonld b/data/barnacle/barnaclebioschemas.jsonld index a856a071f3931..bf1365a7b8f8f 100644 --- a/data/barnacle/barnaclebioschemas.jsonld +++ b/data/barnacle/barnaclebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.", "sc:name": "BARNACLE", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "binf.ku.dk", "sc:url": "http://sourceforge.net/projects/barnacle-rna/", diff --git a/data/barrnap/barrnapbioschemas.jsonld b/data/barrnap/barrnapbioschemas.jsonld index d31140bfd91ef..d17b7b6161e57 100644 --- a/data/barrnap/barrnapbioschemas.jsonld +++ b/data/barrnap/barrnapbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/barrnap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Torsten Seemann", - "Australia" + "Australia", + "Torsten Seemann" ], "sc:additionalType": "Command-line tool", "sc:author": "Torsten Seemann", @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "Barrnap", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "unimelb.edu.au", diff --git a/data/bartender/bartenderbioschemas.jsonld b/data/bartender/bartenderbioschemas.jsonld index 99a06cabd93f5..f635a35fc6360 100644 --- a/data/bartender/bartenderbioschemas.jsonld +++ b/data/bartender/bartenderbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/bartender", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sasha Levy", - "Song Wu" + "Song Wu", + "Sasha Levy" ], "sc:additionalType": "Library", "sc:description": "Fast and accurate clustering algorithm to count barcode reads.", "sc:name": "Bartender", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/LaoZZZZZ/bartender-1.1", diff --git a/data/basecallqc/basecallqcbioschemas.jsonld b/data/basecallqc/basecallqcbioschemas.jsonld index 6c3732deb7c1b..f5b75ca1362bf 100644 --- a/data/basecallqc/basecallqcbioschemas.jsonld +++ b/data/basecallqc/basecallqcbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "basecallQC", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/basecallQC.html", "sc:version": "1.4.0" diff --git a/data/basespacer/basespacerbioschemas.jsonld b/data/basespacer/basespacerbioschemas.jsonld index 3ac46063c81ff..c7b546c998053 100644 --- a/data/basespacer/basespacerbioschemas.jsonld +++ b/data/basespacer/basespacerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Apache-2.0", "sc:name": "BaseSpaceR", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BaseSpaceR.html", "sc:version": "1.18.0" diff --git a/data/basespacer/bioconda_basespacer.yaml b/data/basespacer/bioconda_basespacer.yaml index 3565dc04f86e3..2ab7b0dd9b53d 100644 --- a/data/basespacer/bioconda_basespacer.yaml +++ b/data/basespacer/bioconda_basespacer.yaml @@ -4,7 +4,6 @@ description: A rich R interface to Illumina's BaseSpace cloud computing environm home: https://bioconductor.org/packages/3.10/bioc/html/BaseSpaceR.html identifiers: - biotools:basespacer -- doi:10.1038/nmeth.3252 license: Apache License 2.0 name: bioconductor-basespacer summary: R SDK for BaseSpace RESTful API diff --git a/data/basic/basicbioschemas.jsonld b/data/basic/basicbioschemas.jsonld index 4c644196af32e..cb5c7dfa0598e 100644 --- a/data/basic/basicbioschemas.jsonld +++ b/data/basic/basicbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Background and shading correction of optical microscopy images.", "sc:name": "BaSiC", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://sites.imagej.net/BaSiC/" } \ No newline at end of file diff --git a/data/basic4cseq/basic4cseqbioschemas.jsonld b/data/basic4cseq/basic4cseqbioschemas.jsonld index 50672ab680963..66c654dda69c3 100644 --- a/data/basic4cseq/basic4cseqbioschemas.jsonld +++ b/data/basic4cseq/basic4cseqbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "Basic4Cseq", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Basic4Cseq.html", "sc:version": "1.10.0" diff --git a/data/basics/basicsbioschemas.jsonld b/data/basics/basicsbioschemas.jsonld index 0ba32d5a62362..90a857ee3d3a3 100644 --- a/data/basics/basicsbioschemas.jsonld +++ b/data/basics/basicsbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/basics", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Catalina A. Vallejos", - "Nils Eling" + "Nils Eling", + "Catalina A. Vallejos" ], "sc:additionalType": "Library", "sc:description": "Bayesian Analysis of Single-Cell Sequencing data is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments. It could perform built-in data normalisation and technical noise quantification. BASiCS provides an intuitive detection criterion for highly variable genes within a single group of cells. Also, it can compare gene expression patterns between two or more pre-specified groups of cells.", "sc:license": "GPL-2.0", "sc:name": "BASiCS", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BASiCS.html", "sc:version": "1.2.1" diff --git a/data/basiliscan/basiliscanbioschemas.jsonld b/data/basiliscan/basiliscanbioschemas.jsonld index 90e588684db95..d697b3e820189 100644 --- a/data/basiliscan/basiliscanbioschemas.jsonld +++ b/data/basiliscan/basiliscanbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12864-018-5322-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/BASILIScan", "@type": "sc:SoftwareApplication", @@ -37,11 +33,15 @@ "sc:license": "Unlicense", "sc:name": "BASILIScan", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://basilisc.com/" + }, + { + "@id": "https://doi.org/10.1186/s12864-018-5322-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/basilisk/basiliskbioschemas.jsonld b/data/basilisk/basiliskbioschemas.jsonld index 743f30c8207c6..5f5ebc432a80c 100644 --- a/data/basilisk/basiliskbioschemas.jsonld +++ b/data/basilisk/basiliskbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Probabilistic model of the conformational space of amino acid side chains in proteins. It models the chi angles in continuous space, including the influence of the protein's backbone.", "sc:name": "BASILISK", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "binf.ku.dk", "sc:url": "http://sourceforge.net/projects/basilisk-dbn/", diff --git a/data/bastion6/bastion6bioschemas.jsonld b/data/bastion6/bastion6bioschemas.jsonld index 90bb2160e7d4f..0046f3c343f87 100644 --- a/data/bastion6/bastion6bioschemas.jsonld +++ b/data/bastion6/bastion6bioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "Bastion6", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bastion6.erc.monash.edu/" } \ No newline at end of file diff --git a/data/basys/basysbioschemas.jsonld b/data/basys/basysbioschemas.jsonld index 8840b8ebff660..307327f771eba 100644 --- a/data/basys/basysbioschemas.jsonld +++ b/data/basys/basysbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways.", "sc:name": "BASys", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://basys.ca" } \ No newline at end of file diff --git a/data/bat_detective/bat_detectivebioschemas.jsonld b/data/bat_detective/bat_detectivebioschemas.jsonld index 3b1cfb2912b1e..bb5d215b40653 100644 --- a/data/bat_detective/bat_detectivebioschemas.jsonld +++ b/data/bat_detective/bat_detectivebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "Bat Detective", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.batdetective.org/" } \ No newline at end of file diff --git a/data/batchmap/batchmapbioschemas.jsonld b/data/batchmap/batchmapbioschemas.jsonld index 5952034c2509f..feaf69ac000a4 100644 --- a/data/batchmap/batchmapbioschemas.jsonld +++ b/data/batchmap/batchmapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Parallel implementation of the OneMap R package for fast computation of F1 linkage maps in outcrossing species.", "sc:name": "BatchMap", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/bschiffthaler/BatchMap" diff --git a/data/batchqc/batchqcbioschemas.jsonld b/data/batchqc/batchqcbioschemas.jsonld index 12b9d9c2ee70f..ec124aea041ad 100644 --- a/data/batchqc/batchqcbioschemas.jsonld +++ b/data/batchqc/batchqcbioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btw538", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/batchqc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Solaiappan Manimaran", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC5167063", "pubmed:27540268", { "@id": "https://doi.org/10.1093/bioinformatics/btw538" - } + }, + "pmcid:PMC5167063" ], "sc:description": "Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This can produce technical biases that can lead to incorrect results. This is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. Its diagnostics help determine if batch adjustment is needed, and how correction should be applied.", "sc:featureList": [ @@ -46,6 +42,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BatchQC.html", "sc:version": "1.2.1" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btw538", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/batman/batmanbioschemas.jsonld b/data/batman/batmanbioschemas.jsonld index 33b967a77264b..2ae556a16eff4 100644 --- a/data/batman/batmanbioschemas.jsonld +++ b/data/batman/batmanbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/batman", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jie Hao", - "William Astle" + "William Astle", + "Jie Hao" ], "sc:additionalType": "Library", "sc:citation": "pubmed:18612301", diff --git a/data/batmat/batmatbioschemas.jsonld b/data/batmat/batmatbioschemas.jsonld index 0f3525ab5173e..44da44f0748c1 100644 --- a/data/batmat/batmatbioschemas.jsonld +++ b/data/batmat/batmatbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Google-based, open source, automatic search tool for training materials.", "sc:name": "BATMat", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://imbatmat.com/" } \ No newline at end of file diff --git a/data/batmeth2/batmeth2bioschemas.jsonld b/data/batmeth2/batmeth2bioschemas.jsonld index b99585ff7c3c2..f15efaf996992 100644 --- a/data/batmeth2/batmeth2bioschemas.jsonld +++ b/data/batmeth2/batmeth2bioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2593-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/BatMeth2", "@type": "sc:SoftwareApplication", @@ -22,30 +18,34 @@ "Library" ], "sc:citation": [ - "pmcid:PMC6343306", { "@id": "https://doi.org/10.1186/s12859-018-2593-4" }, - "pubmed:30669962" + "pubmed:30669962", + "pmcid:PMC6343306" ], "sc:description": "Integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping.", "sc:featureList": [ { - "@id": "edam:operation_3186" + "@id": "edam:operation_3206" }, { "@id": "edam:operation_3207" }, { - "@id": "edam:operation_3206" + "@id": "edam:operation_3186" } ], "sc:name": "BatMeth2", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/GuoliangLi-HZAU/BatMeth2" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2593-4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/bats/batsbioschemas.jsonld b/data/bats/batsbioschemas.jsonld index 884ee82cb237a..1c98b366be443 100644 --- a/data/bats/batsbioschemas.jsonld +++ b/data/bats/batsbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/bats", "@type": "sc:SoftwareApplication", "sc:additionalType": [ + "Library", "Desktop application", - "Command-line tool", - "Library" + "Command-line tool" ], "sc:citation": "pubmed:17877802", "sc:description": "It consists of a collection of libraries that can be used to run basic sequence analysis tasks. Routines for global alignment (LCS from Fragments, Edit Distance with Gaps), local alignment (approximata string matching with K mismateches or differences), and statistical analysis (Filter, Z-Score and Model Generation ) are included.", "sc:name": "BATS", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.math.unipa.it/~raffaele/BATS/index.html" } \ No newline at end of file diff --git a/data/bayescall/bayescallbioschemas.jsonld b/data/bayescall/bayescallbioschemas.jsonld index c73a6e74a12ec..dfb2f2786aade 100644 --- a/data/bayescall/bayescallbioschemas.jsonld +++ b/data/bayescall/bayescallbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/bayescall", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wei-Chun Kao", - "Yun S. Song" + "Yun S. Song", + "Wei-Chun Kao" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:19661376", @@ -20,9 +20,9 @@ "sc:license": "GPL-3.0", "sc:name": "BayesCall", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bayescall.sourceforge.net/" } \ No newline at end of file diff --git a/data/bayescan/bayescanbioschemas.jsonld b/data/bayescan/bayescanbioschemas.jsonld index b58ce6894bddb..4c38ce2d9ace3 100644 --- a/data/bayescan/bayescanbioschemas.jsonld +++ b/data/bayescan/bayescanbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.", "sc:name": "BayeScan", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://cmpg.unibe.ch/software/bayescan/" diff --git a/data/bayesembler/bayesemblerbioschemas.jsonld b/data/bayesembler/bayesemblerbioschemas.jsonld index baf96d63d63b2..407d285f182a8 100644 --- a/data/bayesembler/bayesemblerbioschemas.jsonld +++ b/data/bayesembler/bayesemblerbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "MIT", "sc:name": "Bayesembler", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "binf.ku.dk", "sc:url": "http://bioinformatics-centre.github.io/bayesembler/", diff --git a/data/bayesforest/bayesforestbioschemas.jsonld b/data/bayesforest/bayesforestbioschemas.jsonld index a0465cb3c40f4..59cb35031768d 100644 --- a/data/bayesforest/bayesforestbioschemas.jsonld +++ b/data/bayesforest/bayesforestbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "BayesForest", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/inuritdino/BayesForest/wiki" } \ No newline at end of file diff --git a/data/bayesfst/bayesfstbioschemas.jsonld b/data/bayesfst/bayesfstbioschemas.jsonld index 53ec64a4ae516..c562ed2e712df 100644 --- a/data/bayesfst/bayesfstbioschemas.jsonld +++ b/data/bayesfst/bayesfstbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Bayesian estimation of the coancestry coefficient FST", "sc:name": "BAYESFST", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.reading.ac.uk/Statistics/genetics/software.html" } \ No newline at end of file diff --git a/data/bayesknockdown/bayesknockdownbioschemas.jsonld b/data/bayesknockdown/bayesknockdownbioschemas.jsonld index f18b769dbfbe3..72dbfa2325c2c 100644 --- a/data/bayesknockdown/bayesknockdownbioschemas.jsonld +++ b/data/bayesknockdown/bayesknockdownbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "BayesKnockdown", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BayesKnockdown.html", "sc:version": "1.0.0" diff --git a/data/bayesmd/bayesmdbioschemas.jsonld b/data/bayesmd/bayesmdbioschemas.jsonld index b1a6cc79a3c1f..46e015d0f87bd 100644 --- a/data/bayesmd/bayesmdbioschemas.jsonld +++ b/data/bayesmd/bayesmdbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/bayesmd", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Ole Winther", "Anders Krogh", - "Man-Hung Eric Tang", - "Ole Winther" + "Man-Hung Eric Tang" ], "sc:additionalType": [ "Command-line tool", @@ -22,9 +22,9 @@ "sc:description": "Flexible, fully Bayesian model for motif discovery consisting of motif, background and alignment modules. It can be customized to different kind of biological applications, e.g. microarray, ChIP-chip, ditag, CAGE data analysis by integrating appropriately chosen features and functionalities.", "sc:name": "BayesMD", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "binf.ku.dk", "sc:url": "http://bayesmd.binf.ku.dk/", diff --git a/data/bayesmendel/bayesmendelbioschemas.jsonld b/data/bayesmendel/bayesmendelbioschemas.jsonld index 6cbec17421d23..515d9c0d172fe 100644 --- a/data/bayesmendel/bayesmendelbioschemas.jsonld +++ b/data/bayesmendel/bayesmendelbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "R package for Mendelian risk prediction. It includes R implementation of the BRCAPRO and CRCAPRO models, as well as functionality to adapt BRCAPRO and CRCAPRO to specific population and to develop new Mendelian risk prediction models for other syndromes.", "sc:name": "BayesMendel", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bcb.dfci.harvard.edu/bayesmendel/software.php" diff --git a/data/bayesmix/bayesmixbioschemas.jsonld b/data/bayesmix/bayesmixbioschemas.jsonld index a3c5755455085..495bc107805c2 100644 --- a/data/bayesmix/bayesmixbioschemas.jsonld +++ b/data/bayesmix/bayesmixbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "BayesMix is a piece of computer software, a suite of R functions and C routines with a graphical user interface, which can be used as a tool for performing model-based inference for differential gene expression, using a non-parametric Bayesian mixture probability model for the distribution of gene intensities under different conditions.", "sc:name": "BayesMix", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinformatics.mdanderson.org/main/BayesMix:Overview", "sc:version": "0.8.8" diff --git a/data/bayesmotif/bayesmotifbioschemas.jsonld b/data/bayesmotif/bayesmotifbioschemas.jsonld index 180966b6aae0d..8e859f6b29bf4 100644 --- a/data/bayesmotif/bayesmotifbioschemas.jsonld +++ b/data/bayesmotif/bayesmotifbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "BayesMotif is a de novo identification algorithm for finding a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions.", "sc:name": "BayesMotif", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://mleg.cse.sc.edu/BayesMotif/", diff --git a/data/bayespeak/bayespeakbioschemas.jsonld b/data/bayespeak/bayespeakbioschemas.jsonld index 0d3441584ab24..70bf1d5212927 100644 --- a/data/bayespeak/bayespeakbioschemas.jsonld +++ b/data/bayespeak/bayespeakbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jonathan Cairns", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:21914728", "sc:description": "This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.", diff --git a/data/bayespi-bar2/bayespi-bar2bioschemas.jsonld b/data/bayespi-bar2/bayespi-bar2bioschemas.jsonld index 0cb0dd3ed2559..261bb262f7a30 100644 --- a/data/bayespi-bar2/bayespi-bar2bioschemas.jsonld +++ b/data/bayespi-bar2/bayespi-bar2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3389/fgene.2019.00282", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/BayesPI-BAR2", "@type": "sc:SoftwareApplication", @@ -18,31 +22,27 @@ ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:31001324", "pmcid:PMC6454009", { "@id": "https://doi.org/10.3389/fgene.2019.00282" - } + }, + "pubmed:31001324" ], "sc:description": "Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts.", "sc:featureList": [ { - "@id": "edam:operation_3202" + "@id": "edam:operation_0477" }, { - "@id": "edam:operation_0477" + "@id": "edam:operation_3202" } ], "sc:name": "BayesPI-BAR2", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://folk.uio.no/junbaiw/BayesPI-BAR2/" - }, - { - "@id": "https://doi.org/10.3389/fgene.2019.00282", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/bayessc/bayesscbioschemas.jsonld b/data/bayessc/bayesscbioschemas.jsonld index 7cd8e3e0568de..26bc8b044ac9f 100644 --- a/data/bayessc/bayesscbioschemas.jsonld +++ b/data/bayessc/bayesscbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "BayeSSC", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.stanford.edu/group/hadlylab/ssc/index.html" } \ No newline at end of file diff --git a/data/bayestyper/bayestyperbioschemas.jsonld b/data/bayestyper/bayestyperbioschemas.jsonld index 376f5622b7f7d..085492db650a9 100644 --- a/data/bayestyper/bayestyperbioschemas.jsonld +++ b/data/bayestyper/bayestyperbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Perform genotyping of all types of variation (including SNPs, indels and complex structural variants) based on an input set of variants and read k-mer counts.", "sc:name": "BayesTyper", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/bioinformatics-centre/BayesTyper" } \ No newline at end of file diff --git a/data/baynorm/baynormbioschemas.jsonld b/data/baynorm/baynormbioschemas.jsonld index 5ffc45898ee87..7043697e93503 100644 --- a/data/baynorm/baynormbioschemas.jsonld +++ b/data/baynorm/baynormbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "bayNorm", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://bioconductor.org/packages/release/bioc/html/bayNorm.html" } \ No newline at end of file diff --git a/data/bayseq/bayseqbioschemas.jsonld b/data/bayseq/bayseqbioschemas.jsonld index 1f62da7384c99..a5353e73267ad 100644 --- a/data/bayseq/bayseqbioschemas.jsonld +++ b/data/bayseq/bayseqbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas J. Hardcastle", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.", "sc:license": "GPL-3.0", diff --git a/data/bayz/bayzbioschemas.jsonld b/data/bayz/bayzbioschemas.jsonld index 28a4d6aeae686..4f057a4fcdb51 100644 --- a/data/bayz/bayzbioschemas.jsonld +++ b/data/bayz/bayzbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Proprietary", "sc:name": "Bayz", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.bayz.biz", diff --git a/data/bazam/bazambioschemas.jsonld b/data/bazam/bazambioschemas.jsonld index bbe24afb08738..a932b5ebbf424 100644 --- a/data/bazam/bazambioschemas.jsonld +++ b/data/bazam/bazambioschemas.jsonld @@ -9,28 +9,32 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13059-019-1688-1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Bazam", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Simon Sadedin", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6472072", + "pubmed:30999943", { "@id": "https://doi.org/10.1186/s13059-019-1688-1" }, - "pubmed:30999943" + "pmcid:PMC6472072" ], "sc:description": "Method for read extraction and realignment of high-throughput sequencing data.", "sc:featureList": [ - { - "@id": "edam:operation_3198" - }, { "@id": "edam:operation_3192" }, { "@id": "edam:operation_3227" + }, + { + "@id": "edam:operation_3198" } ], "sc:license": "LGPL-2.1", @@ -40,10 +44,6 @@ "Mac" ], "sc:url": "https://github.com/ssadedin/bazam" - }, - { - "@id": "https://doi.org/10.1186/s13059-019-1688-1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/bbcanalyzer/bbcanalyzerbioschemas.jsonld b/data/bbcanalyzer/bbcanalyzerbioschemas.jsonld index 5a13c2ec9d6b9..cb66d60dac8cf 100644 --- a/data/bbcanalyzer/bbcanalyzerbioschemas.jsonld +++ b/data/bbcanalyzer/bbcanalyzerbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sarah Sandmann", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package visualizes the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.", "sc:license": "GPL-3.0", "sc:name": "BBCAnalyzer", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BBCAnalyzer.html", "sc:version": "1.4.0" diff --git a/data/bbknn/bbknnbioschemas.jsonld b/data/bbknn/bbknnbioschemas.jsonld index d4c12308b71a3..bf303d8836ea1 100644 --- a/data/bbknn/bbknnbioschemas.jsonld +++ b/data/bbknn/bbknnbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "BBKNN", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/Teichlab/bbknn" } \ No newline at end of file diff --git a/data/bbmri-eu_catalog/bbmri-eu_catalogbioschemas.jsonld b/data/bbmri-eu_catalog/bbmri-eu_catalogbioschemas.jsonld index 65a75eb83cd10..c9e6e688cb4a4 100644 --- a/data/bbmri-eu_catalog/bbmri-eu_catalogbioschemas.jsonld +++ b/data/bbmri-eu_catalog/bbmri-eu_catalogbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "BBMRI-EU catalog", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "TUM", "sc:url": "http://bbmri.eu" diff --git a/data/bbmri-nl_catalog/bbmri-nl_catalogbioschemas.jsonld b/data/bbmri-nl_catalog/bbmri-nl_catalogbioschemas.jsonld index 4b29552dbf69b..9a9e8bba86294 100644 --- a/data/bbmri-nl_catalog/bbmri-nl_catalogbioschemas.jsonld +++ b/data/bbmri-nl_catalog/bbmri-nl_catalogbioschemas.jsonld @@ -15,13 +15,13 @@ "sc:description": "Database of collections of biomaterial and associated data subsumed under the umbrella of BBMRI-NL.", "sc:name": "BBMRI-NL catalog", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ - "VUMC", - "UGroningen" + "UGroningen", + "VUMC" ], "sc:url": "https://www.bbmri.nl/biobanks/bbmri-nl-catalogue/" } \ No newline at end of file diff --git a/data/bbmri-portal/bbmri-portalbioschemas.jsonld b/data/bbmri-portal/bbmri-portalbioschemas.jsonld index 0c2fb9a1203f6..7eec84c04e294 100644 --- a/data/bbmri-portal/bbmri-portalbioschemas.jsonld +++ b/data/bbmri-portal/bbmri-portalbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A reference for scientists seeking information about biological samples and data suitable for their research.", "sc:name": "BBMRI-Portal", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "TUM", "sc:url": "https://www.bbmriportal.eu/bbmri2.0/jsp/core/login.jsf" diff --git a/data/bbseq/bbseqbioschemas.jsonld b/data/bbseq/bbseqbioschemas.jsonld index 89d3ec709a1df..5052d7eeea5e6 100644 --- a/data/bbseq/bbseqbioschemas.jsonld +++ b/data/bbseq/bbseqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "An R package for analyzing RNA-Seq transcriptional count data.", "sc:name": "BBSeq", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.bios.unc.edu/research/genomic_software/BBSeq/" diff --git a/data/bc_snpmax/bc_snpmaxbioschemas.jsonld b/data/bc_snpmax/bc_snpmaxbioschemas.jsonld index 308114f978ca9..7ea5691eda1c2 100644 --- a/data/bc_snpmax/bc_snpmaxbioschemas.jsonld +++ b/data/bc_snpmax/bc_snpmaxbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Proprietary", "sc:name": "BC SNPmax", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bcplatforms.com/" } \ No newline at end of file diff --git a/data/bcbio-nextgen/bcbio-nextgenbioschemas.jsonld b/data/bcbio-nextgen/bcbio-nextgenbioschemas.jsonld index 9cd452b221a29..bf3c5ce1a9174 100644 --- a/data/bcbio-nextgen/bcbio-nextgenbioschemas.jsonld +++ b/data/bcbio-nextgen/bcbio-nextgenbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Bcbio-nextgen", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/chapmanb/bcbb/blob/master/nextgen/README.md" } \ No newline at end of file diff --git a/data/bcbiornaseq/bcbiornaseqbioschemas.jsonld b/data/bcbiornaseq/bcbiornaseqbioschemas.jsonld index af1021a96ffd1..7da1a88ad1f05 100644 --- a/data/bcbiornaseq/bcbiornaseqbioschemas.jsonld +++ b/data/bcbiornaseq/bcbiornaseqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "bcbioRNASeq", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioinformatics.sph.harvard.edu/bcbioRNASeq/", "sc:version": "0.2.5" diff --git a/data/bcbtoolkit/bcbtoolkitbioschemas.jsonld b/data/bcbtoolkit/bcbtoolkitbioschemas.jsonld index e59e08e431bb6..52b8be53b3eca 100644 --- a/data/bcbtoolkit/bcbtoolkitbioschemas.jsonld +++ b/data/bcbtoolkit/bcbtoolkitbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "BCBtoolkit", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://toolkit.bcblab.com/" } \ No newline at end of file diff --git a/data/bcepred/bcepredbioschemas.jsonld b/data/bcepred/bcepredbioschemas.jsonld index 2c98e94e1747f..7cd6606fb241f 100644 --- a/data/bcepred/bcepredbioschemas.jsonld +++ b/data/bcepred/bcepredbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The BcePred server predicts B cell epitope based on physio-chemical properties of amino acids.", "sc:name": "BcePred", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/bcepred/" } \ No newline at end of file diff --git a/data/bcf-tools-cat/bcf-tools-catbioschemas.jsonld b/data/bcf-tools-cat/bcf-tools-catbioschemas.jsonld index 7ded171fba2f0..b7090cfb3f5a8 100644 --- a/data/bcf-tools-cat/bcf-tools-catbioschemas.jsonld +++ b/data/bcf-tools-cat/bcf-tools-catbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Concatenate BCF files.", "sc:name": "bcf-tools-cat", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.htslib.org/", "sc:version": "1.0.0" diff --git a/data/bcf-tools-index/bcf-tools-indexbioschemas.jsonld b/data/bcf-tools-index/bcf-tools-indexbioschemas.jsonld index da93afd498967..7b560cd667d62 100644 --- a/data/bcf-tools-index/bcf-tools-indexbioschemas.jsonld +++ b/data/bcf-tools-index/bcf-tools-indexbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool allows the user to index sorted BCF for random access.", "sc:name": "bcf-tools-index", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.htslib.org/", "sc:version": "1.0.0" diff --git a/data/bcf_view_mpileup/bcf_view_mpileupbioschemas.jsonld b/data/bcf_view_mpileup/bcf_view_mpileupbioschemas.jsonld index d41730159124d..f5803e150cdd7 100644 --- a/data/bcf_view_mpileup/bcf_view_mpileupbioschemas.jsonld +++ b/data/bcf_view_mpileup/bcf_view_mpileupbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "bcf_view_mpileup", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.htslib.org/", "sc:version": "1.0.2" diff --git a/data/bcftools/bcftoolsbioschemas.jsonld b/data/bcftools/bcftoolsbioschemas.jsonld index fdcaf62c4a39b..8205daf228e84 100644 --- a/data/bcftools/bcftoolsbioschemas.jsonld +++ b/data/bcftools/bcftoolsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "bcftools", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "sanger.ac.uk", "sc:url": "http://www.htslib.org/", diff --git a/data/bcheck_rnpb/bcheck_rnpbbioschemas.jsonld b/data/bcheck_rnpb/bcheck_rnpbbioschemas.jsonld index 80e105a051294..fa69aa27244cb 100644 --- a/data/bcheck_rnpb/bcheck_rnpbbioschemas.jsonld +++ b/data/bcheck_rnpb/bcheck_rnpbbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-8683-7845", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/1471-2164-11-432", "@type": "sc:CreativeWork" @@ -30,9 +26,9 @@ "@id": "edam:data_3496" }, "sc:additionalType": [ + "Database portal", "Command-line tool", - "Web application", - "Database portal" + "Web application" ], "sc:applicationSubCategory": { "@id": "edam:topic_0114" @@ -41,29 +37,29 @@ "@id": "http://orcid.org/0000-0001-8683-7845" }, "sc:citation": [ - "pubmed:20626900", - "pmcid:PMC2996960", { "@id": "https://doi.org/10.1186/1471-2164-11-432" - } + }, + "pmcid:PMC2996960", + "pubmed:20626900" ], "sc:contributor": [ - "Ivo Hofacker", - "Austrian GEN-AU projects \"bioinformatics integration network III\"" + "Austrian GEN-AU projects \"bioinformatics integration network III\"", + "Ivo Hofacker" ], "sc:description": "Wrapper tool for rnpB gene prediction by combining speed of rnabob descriptor model and sensitivity of infernal covariance model.", "sc:featureList": [ { - "@id": "edam:operation_0346" + "@id": "edam:operation_0489" }, { - "@id": "edam:operation_0362" + "@id": "edam:operation_0349" }, { - "@id": "edam:operation_0349" + "@id": "edam:operation_0346" }, { - "@id": "edam:operation_0489" + "@id": "edam:operation_0362" } ], "sc:funder": "Austrian GEN-AU projects \"bioinformatics integration network III\"", @@ -78,6 +74,10 @@ "@id": "http://rna.tbi.univie.ac.at/bcheck/help.html" }, "sc:url": "http://rna.tbi.univie.ac.at/bcheck/index.html" + }, + { + "@id": "http://orcid.org/0000-0001-8683-7845", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/bcigepred/bcigepredbioschemas.jsonld b/data/bcigepred/bcigepredbioschemas.jsonld index f57c63e063c4c..723d0b331a0a2 100644 --- a/data/bcigepred/bcigepredbioschemas.jsonld +++ b/data/bcigepred/bcigepredbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-5145-0384", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/BCIgEPred", "@type": "sc:SoftwareApplication", @@ -22,10 +26,6 @@ "sc:name": "BCIgEPred", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/brsaran/BCIgePred" - }, - { - "@id": "https://orcid.org/0000-0001-5145-0384", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/bcl/bclbioschemas.jsonld b/data/bcl/bclbioschemas.jsonld index bacc234fa8050..b7949b96c926c 100644 --- a/data/bcl/bclbioschemas.jsonld +++ b/data/bcl/bclbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Bio Chemical Library is a software package that provides unique tools for biological research, such as protein structure determination from sparse experimental data.", "sc:name": "BCL", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.meilerlab.org/research/show/w_text_id/92" } \ No newline at end of file diff --git a/data/bcm/bcmbioschemas.jsonld b/data/bcm/bcmbioschemas.jsonld index 7ea9524292ca7..e69214cf16b21 100644 --- a/data/bcm/bcmbioschemas.jsonld +++ b/data/bcm/bcmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MPL-2.0", "sc:name": "BCM", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://ccb.nki.nl/software/bcm/" } \ No newline at end of file diff --git a/data/bcm_srchlausequtl/bcm_srchlausequtlbioschemas.jsonld b/data/bcm_srchlausequtl/bcm_srchlausequtlbioschemas.jsonld index 800e6f2b7d2e4..d41dccb829ece 100644 --- a/data/bcm_srchlausequtl/bcm_srchlausequtlbioschemas.jsonld +++ b/data/bcm_srchlausequtl/bcm_srchlausequtlbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "BCM Search Launcher Sequence Utilities", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://searchlauncher.bcm.tmc.edu/seq-util/seq-util.html" } \ No newline at end of file diff --git a/data/bcode/bcodebioschemas.jsonld b/data/bcode/bcodebioschemas.jsonld index 8c0949b0efa9b..5943709fe3862 100644 --- a/data/bcode/bcodebioschemas.jsonld +++ b/data/bcode/bcodebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/bcode", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alessandro Cassini", - "Edoardo Colzani" + "Edoardo Colzani", + "Alessandro Cassini" ], "sc:additionalType": "Desktop application", "sc:description": "Stand-alone software application which allows calculation of disability-adjusted life years (DALYs) for a selection of 32 communicable diseases and six healthcare-associated infections.", diff --git a/data/bcov/bcovbioschemas.jsonld b/data/bcov/bcovbioschemas.jsonld index ec1a808405989..f55554030b403 100644 --- a/data/bcov/bcovbioschemas.jsonld +++ b/data/bcov/bcovbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Prediction of β-sheet topology.", "sc:name": "BCov", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "http://biocomp.unibo.it/savojard/bcov/index.html", diff --git a/data/bcrank/bcrankbioschemas.jsonld b/data/bcrank/bcrankbioschemas.jsonld index 65a09a7261c7d..d1a64f33f4b76 100644 --- a/data/bcrank/bcrankbioschemas.jsonld +++ b/data/bcrank/bcrankbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "BCRANK", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BCRANK.html", "sc:version": "1.36.0" diff --git a/data/bcrgt/bcrgtbioschemas.jsonld b/data/bcrgt/bcrgtbioschemas.jsonld index b5887fb3bac68..c72af30cba81a 100644 --- a/data/bcrgt/bcrgtbioschemas.jsonld +++ b/data/bcrgt/bcrgtbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "BCRgt is a Bayesian Cluster Regression based genotyping approach to genotype samples with Copy Number Alterations (CNAs). This is motivated by the facts that cancer tissues often have large regions of genetic structural alterations such as CNAs, and that researchers have been interested in genotyping SNPs from such samples.", "sc:name": "BCRgt", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://publichealth.lsuhsc.edu/BCRgt.html", "sc:version": "1.0" diff --git a/data/bcrocsurface/bcrocsurfacebioschemas.jsonld b/data/bcrocsurface/bcrocsurfacebioschemas.jsonld index b97345afad5cb..dda2d842940a6 100644 --- a/data/bcrocsurface/bcrocsurfacebioschemas.jsonld +++ b/data/bcrocsurface/bcrocsurfacebioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-017-1914-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/bcrocsurface", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Khanh To Duc", "sc:additionalType": [ - "Web application", - "Library" + "Library", + "Web application" ], "sc:citation": [ - "pubmed:29151019", { "@id": "https://doi.org/10.1186/s12859-017-1914-3" }, - "pmcid:PMC5694622" + "pmcid:PMC5694622", + "pubmed:29151019" ], "sc:description": "Correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests.", "sc:featureList": { @@ -31,15 +35,11 @@ "sc:license": "GPL-2.0", "sc:name": "bcROCsurface", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://khanhtoduc.shinyapps.io/bcROCsurface_shiny/" - }, - { - "@id": "https://doi.org/10.1186/s12859-017-1914-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/bcseq_bias/bcseq_biasbioschemas.jsonld b/data/bcseq_bias/bcseq_biasbioschemas.jsonld index f25f569ca3335..2432335984bfc 100644 --- a/data/bcseq_bias/bcseq_biasbioschemas.jsonld +++ b/data/bcseq_bias/bcseq_biasbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Tool for quantifying gene expression from single cell RNA-seq.", "sc:name": "BCseq (bias-corrected sequencing analysis)", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www-rcf.usc.edu/~liangche/software.html" } \ No newline at end of file diff --git a/data/bdbm/bdbmbioschemas.jsonld b/data/bdbm/bdbmbioschemas.jsonld index 4b7208eded618..f50f3989e8657 100644 --- a/data/bdbm/bdbmbioschemas.jsonld +++ b/data/bdbm/bdbmbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "GPL-3.0", "sc:name": "BLAST DataBase Manager", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.sing-group.org/BDBM", "sc:version": "1.0.2" diff --git a/data/bdvis/bdvisbioschemas.jsonld b/data/bdvis/bdvisbioschemas.jsonld index 580415ae89be8..089322349c539 100644 --- a/data/bdvis/bdvisbioschemas.jsonld +++ b/data/bdvis/bdvisbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "bdvis", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/bdvis/index.html" } \ No newline at end of file diff --git a/data/beachmat/beachmatbioschemas.jsonld b/data/beachmat/beachmatbioschemas.jsonld index 27ae83ab887c1..965763635009f 100644 --- a/data/beachmat/beachmatbioschemas.jsonld +++ b/data/beachmat/beachmatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "beachmat", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/beachmat.html" } \ No newline at end of file diff --git a/data/beacon/beaconbioschemas.jsonld b/data/beacon/beaconbioschemas.jsonld index a4671716a2cd0..da284eba3d995 100644 --- a/data/beacon/beaconbioschemas.jsonld +++ b/data/beacon/beaconbioschemas.jsonld @@ -22,23 +22,23 @@ { "@id": "https://doi.org/10.1186/S12864-015-1826-4" }, - "pubmed:26283419", - "pmcid:PMC4539851" + "pmcid:PMC4539851", + "pubmed:26283419" ], "sc:description": "Automated tool for Bacterial GEnome Annotation ComparisON.", "sc:featureList": [ { - "@id": "edam:operation_0362" + "@id": "edam:operation_3209" }, { - "@id": "edam:operation_3209" + "@id": "edam:operation_0362" } ], "sc:name": "BEACON", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.cbrc.kaust.edu.sa/BEACON/" } diff --git a/data/beacon_designer/beacon_designerbioschemas.jsonld b/data/beacon_designer/beacon_designerbioschemas.jsonld index 61d259455041e..bdaf5f451ad06 100644 --- a/data/beacon_designer/beacon_designerbioschemas.jsonld +++ b/data/beacon_designer/beacon_designerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.", "sc:name": "Beacon Designer", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.premierbiosoft.com/molecular_beacons/index.html", "sc:version": "8.14" diff --git a/data/beaconlab_pscan/beaconlab_pscanbioschemas.jsonld b/data/beaconlab_pscan/beaconlab_pscanbioschemas.jsonld index bb688cb50b632..9e68d3b236c61 100644 --- a/data/beaconlab_pscan/beaconlab_pscanbioschemas.jsonld +++ b/data/beaconlab_pscan/beaconlab_pscanbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/beaconlab_pscan", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Giulio Pavesi", - "Federico Zambelli" + "Federico Zambelli", + "Giulio Pavesi" ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences", "sc:license": "GPL-3.0", "sc:name": "Pscan", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-MILANO", "sc:url": "http://www.beaconlab.it/pscan", diff --git a/data/beadarray/beadarraybioschemas.jsonld b/data/beadarray/beadarraybioschemas.jsonld index 0afbdc92dc2d4..008b4d0b4f8a8 100644 --- a/data/beadarray/beadarraybioschemas.jsonld +++ b/data/beadarray/beadarraybioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-8853-9435", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/beadarray", "@type": "sc:SoftwareApplication", @@ -20,8 +16,8 @@ "@id": "http://orcid.org/0000-0002-8853-9435" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:17586828", "sc:description": "The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.", @@ -29,11 +25,15 @@ "sc:name": "beadarray", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/beadarray.html", "sc:version": "2.24.0" + }, + { + "@id": "http://orcid.org/0000-0002-8853-9435", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/beadarraysnp/beadarraysnpbioschemas.jsonld b/data/beadarraysnp/beadarraysnpbioschemas.jsonld index c59460b51cb01..8b8e9900b84b3 100644 --- a/data/beadarraysnp/beadarraysnpbioschemas.jsonld +++ b/data/beadarraysnp/beadarraysnpbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jan Oosting", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:17586828", "sc:description": "Importing data from Illumina SNP experiments and performing copy number calculations and reports.", @@ -21,8 +21,8 @@ "sc:name": "beadarraySNP", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/beadarraySNP.html", "sc:version": "1.40.0" diff --git a/data/beaddatapackr/beaddatapackrbioschemas.jsonld b/data/beaddatapackr/beaddatapackrbioschemas.jsonld index 35d12b6a622be..020e79abe77b9 100644 --- a/data/beaddatapackr/beaddatapackrbioschemas.jsonld +++ b/data/beaddatapackr/beaddatapackrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-7800-3848", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/beaddatapackr", "@type": "sc:SoftwareApplication", @@ -16,8 +20,8 @@ "@id": "http://orcid.org/0000-0002-7800-3848" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC2956622", @@ -27,16 +31,12 @@ "sc:license": "GPL-2.0", "sc:name": "BeadDataPackR", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BeadDataPackR.html", "sc:version": "1.26.0" - }, - { - "@id": "http://orcid.org/0000-0002-7800-3848", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/beads/beadsbioschemas.jsonld b/data/beads/beadsbioschemas.jsonld index 57e114f9220ca..c84bf6e61959c 100644 --- a/data/beads/beadsbioschemas.jsonld +++ b/data/beads/beadsbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/beads", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Thomas Down", "Nicole Cheung", - "Julie Ahringer" + "Julie Ahringer", + "Thomas Down" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:21646344", diff --git a/data/beam/beambioschemas.jsonld b/data/beam/beambioschemas.jsonld index 8567a21efe2ad..f8c1a99929a1a 100644 --- a/data/beam/beambioschemas.jsonld +++ b/data/beam/beambioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/beam", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Marco Pietrosanto", - "Contact List" + "Contact List", + "Marco Pietrosanto" ], "sc:additionalType": "Web application", "sc:description": "Analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance.", "sc:name": "BEAM", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://beam.uniroma2.it/home" } \ No newline at end of file diff --git a/data/bean-counter/bean-counterbioschemas.jsonld b/data/bean-counter/bean-counterbioschemas.jsonld index 8652e688a94c5..79467644408fa 100644 --- a/data/bean-counter/bean-counterbioschemas.jsonld +++ b/data/bean-counter/bean-counterbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "BEAN-counter", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/csbio/BEAN-counter" } \ No newline at end of file diff --git a/data/beap/beapbioschemas.jsonld b/data/beap/beapbioschemas.jsonld index e34fd33321314..28f8cee0a9759 100644 --- a/data/beap/beapbioschemas.jsonld +++ b/data/beap/beapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "BEAP uses a short starting DNA fragment, often a EST or partial gene segment, as “primer”, to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the “primer” therefore help to “extend” the length of the original sequence for constructing a “full length” sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis.", "sc:name": "BEAP", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.animalgenome.org/bioinfo/tools/beap/" } \ No newline at end of file diff --git a/data/bear/bearbioschemas.jsonld b/data/bear/bearbioschemas.jsonld index 1d996351dba1c..335f5c0bd901e 100644 --- a/data/bear/bearbioschemas.jsonld +++ b/data/bear/bearbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "RNA secondary structure analysis, comparison and classification, motif finding and phylogeny.", "sc:name": "BEAR Brand nEw Alphabet for RNA", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "ELIXIR-ITA-TORVERGATA", "sc:url": "http://bioinformatica.uniroma2.it/BEAR/BEAR_Encoder.zip", diff --git a/data/bearscc/bearsccbioschemas.jsonld b/data/bearscc/bearsccbioschemas.jsonld index 9534d9494a8b3..7a832f19e4b74 100644 --- a/data/bearscc/bearsccbioschemas.jsonld +++ b/data/bearscc/bearsccbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "BEARscc", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BEARscc.html", "sc:version": "1.0.0" diff --git a/data/beast/beastbioschemas.jsonld b/data/beast/beastbioschemas.jsonld index 02c7c654aa40c..071c38fd7aa74 100644 --- a/data/beast/beastbioschemas.jsonld +++ b/data/beast/beastbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The Bayesian Evolutionary Analysis Sampling Trees is a cross-platform program for Bayesian analysis of molecular sequences using MCMC (Markov chain Monte Carlo). It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.", "sc:name": "BEAST", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://beast.bio.ed.ac.uk/" } \ No newline at end of file diff --git a/data/beast2/beast2bioschemas.jsonld b/data/beast2/beast2bioschemas.jsonld index d820b9342129c..2ed62f6570ea8 100644 --- a/data/beast2/beast2bioschemas.jsonld +++ b/data/beast2/beast2bioschemas.jsonld @@ -18,18 +18,18 @@ ], "sc:citation": [ "pmcid:PMC3985171", - "pubmed:24722319", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003537" - } + }, + "pubmed:24722319" ], "sc:description": "Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. It uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. It includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.", "sc:featureList": [ { - "@id": "edam:operation_3478" + "@id": "edam:operation_0551" }, { - "@id": "edam:operation_0551" + "@id": "edam:operation_3478" } ], "sc:name": "BEAST 2", diff --git a/data/beastling/beastlingbioschemas.jsonld b/data/beastling/beastlingbioschemas.jsonld index 9f7dad6671fe5..09efad9f42cc2 100644 --- a/data/beastling/beastlingbioschemas.jsonld +++ b/data/beastling/beastlingbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Open source software tool designed to simplify the preparation of Bayesian phylogenetic analyses of linguistic data using the BEAST 2 platform.", "sc:name": "BEASTling", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/glottobank/BEASTling_paper" } \ No newline at end of file diff --git a/data/beat/beatbioschemas.jsonld b/data/beat/beatbioschemas.jsonld index b4e869218e1f4..14cfa41d9daa6 100644 --- a/data/beat/beatbioschemas.jsonld +++ b/data/beat/beatbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "BEAT", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BEAT.html", diff --git a/data/beat/bioconda_beat.yaml b/data/beat/bioconda_beat.yaml index 542fb1a092787..a4f9b4f1d2ab8 100644 --- a/data/beat/bioconda_beat.yaml +++ b/data/beat/bioconda_beat.yaml @@ -3,7 +3,6 @@ description: Model-based analysis of single-cell methylation data home: https://bioconductor.org/packages/3.10/bioc/html/BEAT.html identifiers: - biotools:beat -- doi:10.1038/nmeth.3252 license: LGPL (>= 3.0) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-beat diff --git a/data/beatmusic/beatmusicbioschemas.jsonld b/data/beatmusic/beatmusicbioschemas.jsonld index a42b2f2341a26..496e35dc4fcdb 100644 --- a/data/beatmusic/beatmusicbioschemas.jsonld +++ b/data/beatmusic/beatmusicbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/beatmusic", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jean Marc Kwasigroch", "Marianne Rooman", "Yves Dehouck", - "Dimitri Gilis" + "Dimitri Gilis", + "Jean Marc Kwasigroch" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:23723246", "sc:description": "This program evaluates the change in binding affinity between proteins (or protein chains) caused by single-site mutations in their sequence.", "sc:name": "BeAtMuSiC", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://babylone.ulb.ac.be/beatmusic" } \ No newline at end of file diff --git a/data/beatsonlab-microbialgenomics/beatsonlab-microbialgenomicsbioschemas.jsonld b/data/beatsonlab-microbialgenomics/beatsonlab-microbialgenomicsbioschemas.jsonld index 76e235ed0c27c..5803a78ba22be 100644 --- a/data/beatsonlab-microbialgenomics/beatsonlab-microbialgenomicsbioschemas.jsonld +++ b/data/beatsonlab-microbialgenomics/beatsonlab-microbialgenomicsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software to understand the molecular mechanisms of infectious disease and to identify therapeutic and diagnostic targets via NGS data.", "sc:name": "BeatsonLab-MicrobialGenomics", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "University of Queensland", "sc:url": "https://github.com/BeatsonLab-MicrobialGenomics" diff --git a/data/becas/becasbioschemas.jsonld b/data/becas/becasbioschemas.jsonld index 19ffb53d603ad..1f096810108d7 100644 --- a/data/becas/becasbioschemas.jsonld +++ b/data/becas/becasbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "BECAS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinformatics.ua.pt/software/becas/" } \ No newline at end of file diff --git a/data/beclear/beclearbioschemas.jsonld b/data/beclear/beclearbioschemas.jsonld index 0a92c2fd089f2..7a23b5a4f034a 100644 --- a/data/beclear/beclearbioschemas.jsonld +++ b/data/beclear/beclearbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "BEclear", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BEclear.html", "sc:version": "1.6.0" diff --git a/data/becon/beconbioschemas.jsonld b/data/becon/beconbioschemas.jsonld index efde29cb30054..ea2ac48b6987a 100644 --- a/data/becon/beconbioschemas.jsonld +++ b/data/becon/beconbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Interpreting DNA methylation findings from blood in the context of brain.", "sc:name": "BECon", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://redgar598.shinyapps.io/BECon/" } \ No newline at end of file diff --git a/data/bed_bayesian/bed_bayesianbioschemas.jsonld b/data/bed_bayesian/bed_bayesianbioschemas.jsonld index 3088df5ad26ec..89b573e0a6559 100644 --- a/data/bed_bayesian/bed_bayesianbioschemas.jsonld +++ b/data/bed_bayesian/bed_bayesianbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Detection and comparison of epialleles within multiple tumour regions enables phylogenetic analyses, identification of differentially expressed epialleles, and provides a measure of epigenetic heterogeneity.", "sc:name": "Bayesian Epiallele Detection (BED)", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/james-e-barrett/bed" } \ No newline at end of file diff --git a/data/bedgraphtobigwig/bedgraphtobigwigbioschemas.jsonld b/data/bedgraphtobigwig/bedgraphtobigwigbioschemas.jsonld index 266b2977fda05..4a20ccc20392d 100644 --- a/data/bedgraphtobigwig/bedgraphtobigwigbioschemas.jsonld +++ b/data/bedgraphtobigwig/bedgraphtobigwigbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Convert bedGraph to bigWig file.", "sc:name": "bedGraphToBigWig", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.encodeproject.org/software/bedgraphtobigwig/" } \ No newline at end of file diff --git a/data/bedtools/bedtoolsbioschemas.jsonld b/data/bedtools/bedtoolsbioschemas.jsonld index 309e204e2de9a..415784a5cdfc2 100644 --- a/data/bedtools/bedtoolsbioschemas.jsonld +++ b/data/bedtools/bedtoolsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bedtools Discussion Forum", "sc:additionalType": [ - "Command-line tool", - "Suite" + "Suite", + "Command-line tool" ], "sc:citation": "pubmed:20110278", "sc:description": "BEDTools is an extensive suite of utilities for comparing genomic features in BED format.", diff --git a/data/bedtools_bamtobed/bedtools_bamtobedbioschemas.jsonld b/data/bedtools_bamtobed/bedtools_bamtobedbioschemas.jsonld index 23fdb5cb97495..16270c73f1cc7 100644 --- a/data/bedtools_bamtobed/bedtools_bamtobedbioschemas.jsonld +++ b/data/bedtools_bamtobed/bedtools_bamtobedbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Convert a BAM file to a BED file. The end coordinate is computed by inspecting the CIGAR string. The QNAME for the alignment is used as the BED name field and, by default, the MAPQ is used as the BED score.", "sc:name": "bedtools_bamtobed", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/arq5x/bedtools2", diff --git a/data/bedtools_coveragebed_counts/bedtools_coveragebed_countsbioschemas.jsonld b/data/bedtools_coveragebed_counts/bedtools_coveragebed_countsbioschemas.jsonld index a99e1217d5517..b666ec9c17cf9 100644 --- a/data/bedtools_coveragebed_counts/bedtools_coveragebed_countsbioschemas.jsonld +++ b/data/bedtools_coveragebed_counts/bedtools_coveragebed_countsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Count the number of intervals in a BAM or BED file (the source) that overlap another BED file (the target).", "sc:name": "bedtools_coveragebed_counts", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/arq5x/bedtools3", "sc:version": "0.1.0" diff --git a/data/bedtools_genomecoveragebed_histogram/bedtools_genomecoveragebed_histogrambioschemas.jsonld b/data/bedtools_genomecoveragebed_histogram/bedtools_genomecoveragebed_histogrambioschemas.jsonld index 4d46a66173b5d..393208441cfed 100644 --- a/data/bedtools_genomecoveragebed_histogram/bedtools_genomecoveragebed_histogrambioschemas.jsonld +++ b/data/bedtools_genomecoveragebed_histogram/bedtools_genomecoveragebed_histogrambioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "bedtools_genomecoveragebed_histogram", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/arq5x/bedtools4", "sc:version": "0.1.0" diff --git a/data/bedtools_intersectbed/bedtools_intersectbedbioschemas.jsonld b/data/bedtools_intersectbed/bedtools_intersectbedbioschemas.jsonld index 386eed575a077..00d7749e42007 100644 --- a/data/bedtools_intersectbed/bedtools_intersectbedbioschemas.jsonld +++ b/data/bedtools_intersectbed/bedtools_intersectbedbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Report overlaps between two feature files.", "sc:name": "bedtools_intersectbed", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/arq5x/bedtools6", diff --git a/data/bedtools_intersectbed_bam/bedtools_intersectbed_bambioschemas.jsonld b/data/bedtools_intersectbed_bam/bedtools_intersectbed_bambioschemas.jsonld index 02bb935e772bb..36f4c73f7b669 100644 --- a/data/bedtools_intersectbed_bam/bedtools_intersectbed_bambioschemas.jsonld +++ b/data/bedtools_intersectbed_bam/bedtools_intersectbed_bambioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "bedtools_intersectbed_bam", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/arq5x/bedtools5", "sc:version": "0.1.0" diff --git a/data/bedtools_mergebedgraph/bedtools_mergebedgraphbioschemas.jsonld b/data/bedtools_mergebedgraph/bedtools_mergebedgraphbioschemas.jsonld index ae52c511479e4..5d8b6680b6822 100644 --- a/data/bedtools_mergebedgraph/bedtools_mergebedgraphbioschemas.jsonld +++ b/data/bedtools_mergebedgraph/bedtools_mergebedgraphbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Merge multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.", "sc:name": "bedtools_mergebedgraph", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/arq5x/bedtools7", "sc:version": "0.1.0" diff --git a/data/bedtools_multiintersectbed/bedtools_multiintersectbedbioschemas.jsonld b/data/bedtools_multiintersectbed/bedtools_multiintersectbedbioschemas.jsonld index 19402a64bb0c3..b7d18ab15cd27 100644 --- a/data/bedtools_multiintersectbed/bedtools_multiintersectbedbioschemas.jsonld +++ b/data/bedtools_multiintersectbed/bedtools_multiintersectbedbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "bedtools_multiintersectbed", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/arq5x/bedtools8", "sc:version": "0.1.0" diff --git a/data/bedutils/bedutilsbioschemas.jsonld b/data/bedutils/bedutilsbioschemas.jsonld index 33e3780a0d3ea..31c497a48bfde 100644 --- a/data/bedutils/bedutilsbioschemas.jsonld +++ b/data/bedutils/bedutilsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/bedutils", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yunlong Liu", - "Marcus Breese" + "Marcus Breese", + "Yunlong Liu" ], "sc:additionalType": "Command-line tool", "sc:description": "Suite of software tools for working with next-generation sequencing datasets.", diff --git a/data/beere/beerebioschemas.jsonld b/data/beere/beerebioschemas.jsonld index e758b1cc34ac3..dd31b1ae60e8d 100644 --- a/data/beere/beerebioschemas.jsonld +++ b/data/beere/beerebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKZ428", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/BEERE", "@type": "sc:SoftwareApplication", @@ -28,10 +24,10 @@ "sc:description": "Tool for Biomedical Entity Expansion, Ranking, and Exploration.", "sc:featureList": [ { - "@id": "edam:operation_2421" + "@id": "edam:operation_3280" }, { - "@id": "edam:operation_3280" + "@id": "edam:operation_2421" }, { "@id": "edam:operation_2422" @@ -45,6 +41,10 @@ "Windows" ], "sc:url": "http://discovery.informatics.uab.edu/beere/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ428", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/beetlebase/beetlebasebioschemas.jsonld b/data/beetlebase/beetlebasebioschemas.jsonld index 1afb7ac4d3cb9..29396c40638cf 100644 --- a/data/beetlebase/beetlebasebioschemas.jsonld +++ b/data/beetlebase/beetlebasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The database contains genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules, it has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum.", "sc:name": "BeetleBase", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://beetlebase.org/" } \ No newline at end of file diff --git a/data/bel_commons/bel_commonsbioschemas.jsonld b/data/bel_commons/bel_commonsbioschemas.jsonld index 88f08fa106696..6b64105252af9 100644 --- a/data/bel_commons/bel_commonsbioschemas.jsonld +++ b/data/bel_commons/bel_commonsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "BEL Commons", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://bel-commons.scai.fraunhofer.de/" } \ No newline at end of file diff --git a/data/benchmarker/benchmarkerbioschemas.jsonld b/data/benchmarker/benchmarkerbioschemas.jsonld index 10312791e8619..fc073be764cb7 100644 --- a/data/benchmarker/benchmarkerbioschemas.jsonld +++ b/data/benchmarker/benchmarkerbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/J.AJHG.2019.03.027", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Benchmarker", "@type": "sc:SoftwareApplication", @@ -23,10 +19,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC6556976", - "pubmed:31056107", { "@id": "https://doi.org/10.1016/J.AJHG.2019.03.027" - } + }, + "pubmed:31056107" ], "sc:description": "Benchmarking gene and variant prioritization algorithms for GWAS data.", "sc:featureList": { @@ -35,11 +31,15 @@ "sc:license": "GPL-3.0", "sc:name": "Benchmarker", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/RebeccaFine/benchmarker" + }, + { + "@id": "https://doi.org/10.1016/J.AJHG.2019.03.027", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/berex/berexbioschemas.jsonld b/data/berex/berexbioschemas.jsonld index ba3207d0133be..bdca855a4ced1 100644 --- a/data/berex/berexbioschemas.jsonld +++ b/data/berex/berexbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "BEReX is a new biomedical knowledge integration, search and exploration tool. BEReX integrates eight popular databases (STRING, DrugBank, KEGG, PhamGKB, BioGRID, GO, HPRD and MSigDB) and delineates an integrated network by combining the information available from these databases.", "sc:name": "BEReX", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://infos.korea.ac.kr/berex/", diff --git a/data/berkeley_phylogenomics_group/berkeley_phylogenomics_groupbioschemas.jsonld b/data/berkeley_phylogenomics_group/berkeley_phylogenomics_groupbioschemas.jsonld index 87dae13bba69b..16fc304a91b03 100644 --- a/data/berkeley_phylogenomics_group/berkeley_phylogenomics_groupbioschemas.jsonld +++ b/data/berkeley_phylogenomics_group/berkeley_phylogenomics_groupbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.", "sc:name": "Berkeley Phylogenomics Group", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://phylogenomics.berkeley.edu/" } \ No newline at end of file diff --git a/data/besst/besstbioschemas.jsonld b/data/besst/besstbioschemas.jsonld index 9bf9750c0d732..f8e38e9bea3dd 100644 --- a/data/besst/besstbioschemas.jsonld +++ b/data/besst/besstbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "BESST", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "nada.su.se", "sc:url": "https://github.com/ksahlin/BESST", diff --git a/data/best_literature/best_literaturebioschemas.jsonld b/data/best_literature/best_literaturebioschemas.jsonld index bd407c30d16d7..8c081d636d4f9 100644 --- a/data/best_literature/best_literaturebioschemas.jsonld +++ b/data/best_literature/best_literaturebioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0164680" }, - "pmcid:PMC5070740", - "pubmed:27760149" + "pubmed:27760149", + "pmcid:PMC5070740" ], "sc:description": "Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "BEST", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://best.korea.ac.kr/" } diff --git a/data/bestsel/bestselbioschemas.jsonld b/data/bestsel/bestselbioschemas.jsonld index 2a529466e8314..181451437f39e 100644 --- a/data/bestsel/bestselbioschemas.jsonld +++ b/data/bestsel/bestselbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/bestsel", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "András Micsonai", - "József Kardos" + "József Kardos", + "András Micsonai" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:29893907", "sc:description": "Beta Structure Selection. Novel method for the secondary structure determination and fold recognition from protein circular dichroism spectra.", "sc:name": "BeStSel", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bestsel.elte.hu/information.php" } \ No newline at end of file diff --git a/data/betacavityweb/betacavitywebbioschemas.jsonld b/data/betacavityweb/betacavitywebbioschemas.jsonld index ae24095c19797..9313a83a6814a 100644 --- a/data/betacavityweb/betacavitywebbioschemas.jsonld +++ b/data/betacavityweb/betacavitywebbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This software computes molecular voids and channels with guaranteed mathematical correctness and computational efficiency and also computes their geometrical properties.", "sc:name": "BetaCavityWeb", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://voronoi.hanyang.ac.kr/betacavityweb/" diff --git a/data/betaseq/betaseqbioschemas.jsonld b/data/betaseq/betaseqbioschemas.jsonld index bc717862130d8..591fb74d1d24e 100644 --- a/data/betaseq/betaseqbioschemas.jsonld +++ b/data/betaseq/betaseqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "BETASEQ", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://yunliweb.its.unc.edu/betaseq/" } \ No newline at end of file diff --git a/data/betaserpentine/betaserpentinebioschemas.jsonld b/data/betaserpentine/betaserpentinebioschemas.jsonld index 72bd550a9e325..617d0ccabfbcb 100644 --- a/data/betaserpentine/betaserpentinebioschemas.jsonld +++ b/data/betaserpentine/betaserpentinebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/BetaSerpentine", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Stanislav A. Bondarev", - "Andrey V. Kajava" + "Andrey V. Kajava", + "Stanislav A. Bondarev" ], "sc:additionalType": [ "Web application", @@ -22,8 +22,8 @@ "sc:license": "Other", "sc:name": "BetaSerpentine", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioinfo.montp.cnrs.fr/b-serpentine", diff --git a/data/betatpred/betatpredbioschemas.jsonld b/data/betatpred/betatpredbioschemas.jsonld index ef41f33a64667..73d46c102b866 100644 --- a/data/betatpred/betatpredbioschemas.jsonld +++ b/data/betatpred/betatpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The server is developed for predicting ß-turns in a protein from the amino acid sequence. It allows the user * to predict turns in a protein using existing statistical algorithms. * to predict the type of ß-turn such as Type I, I', II, II', VI, VIII and non-specific i.e., advanced prediction. * to predict the consensus ß-turn in a protein.", "sc:name": "BetaTPred", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/betatpred/" } \ No newline at end of file diff --git a/data/betatpred2/betatpred2bioschemas.jsonld b/data/betatpred2/betatpred2bioschemas.jsonld index 67ad8559af7c9..2884367553b44 100644 --- a/data/betatpred2/betatpred2bioschemas.jsonld +++ b/data/betatpred2/betatpred2bioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/betatpred2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Harpreet Kaur", - "Dr. G.P.S. Raghava" + "Dr. G.P.S. Raghava", + "Harpreet Kaur" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:12592033", "sc:description": "The aim of this server is to predict beta turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For beta turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED.", "sc:name": "BetatPred2", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/betatpred2/" } \ No newline at end of file diff --git a/data/betaturns/betaturnsbioschemas.jsonld b/data/betaturns/betaturnsbioschemas.jsonld index 6b9a658061910..efcae49d8be54 100644 --- a/data/betaturns/betaturnsbioschemas.jsonld +++ b/data/betaturns/betaturnsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/betaturns", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Harpreet Kaur", - "Dr. G.P.S. Raghava" + "Dr. G.P.S. Raghava", + "Harpreet Kaur" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:15145798", diff --git a/data/betavoid/betavoidbioschemas.jsonld b/data/betavoid/betavoidbioschemas.jsonld index 113ce6681b508..5914241d579f5 100644 --- a/data/betavoid/betavoidbioschemas.jsonld +++ b/data/betavoid/betavoidbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This software recognizes molecular voids in the van der Waals surface or the Lee-Richards (solvent accessible) surface and computes their mass properties such the volume and the boundary area.", "sc:name": "BetaVoid", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://voronoi.hanyang.ac.kr/software.htm#BetaVoidWin" } \ No newline at end of file diff --git a/data/betaware/betawarebioschemas.jsonld b/data/betaware/betawarebioschemas.jsonld index 6c57cd97e55b0..f8802c6199620 100644 --- a/data/betaware/betawarebioschemas.jsonld +++ b/data/betaware/betawarebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "BetAware", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "http://betaware.biocomp.unibo.it/BetAware/default/index", diff --git a/data/bew/bewbioschemas.jsonld b/data/bew/bewbioschemas.jsonld index 55f0863eb5a6e..440854e03c534 100644 --- a/data/bew/bewbioschemas.jsonld +++ b/data/bew/bewbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Novel software workbench for the operation and analysis of Biofilms experimental data.", "sc:name": "BEW", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://sing.ei.uvigo.es/bew" diff --git a/data/bfptool/bfptoolbioschemas.jsonld b/data/bfptool/bfptoolbioschemas.jsonld index fefd953ed40b3..de937e101412d 100644 --- a/data/bfptool/bfptoolbioschemas.jsonld +++ b/data/bfptool/bfptoolbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13628-016-0033-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/bfptool", "@type": "sc:SoftwareApplication", @@ -32,11 +28,15 @@ "sc:license": "GPL-3.0", "sc:name": "BFPtool", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/smitdaniel/BFPtool" + }, + { + "@id": "https://doi.org/10.1186/s13628-016-0033-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/bfrm/bfrmbioschemas.jsonld b/data/bfrm/bfrmbioschemas.jsonld index 358b35e86db9e..caa5b67d03372 100644 --- a/data/bfrm/bfrmbioschemas.jsonld +++ b/data/bfrm/bfrmbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Software for Bayesian Factor Regression Models – modelling and analysis of sparse latent factor models use in applications in pathway analysis and predictive modelling with large-scale gene expression data sets, with links to studies in gene expression analysis.", "sc:name": "BFRM", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.stat.duke.edu/research/software/west/bfrm/", diff --git a/data/bgafun/bgafunbioschemas.jsonld b/data/bgafun/bgafunbioschemas.jsonld index face4a0115bb5..f6d2902436669 100644 --- a/data/bgafun/bgafunbioschemas.jsonld +++ b/data/bgafun/bgafunbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "bgafun", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/bgafun.html", "sc:version": "1.36.0" diff --git a/data/bgafun/bioconda_bgafun.yaml b/data/bgafun/bioconda_bgafun.yaml index 153cdc37a9835..7ebb68f8f3c0a 100644 --- a/data/bgafun/bioconda_bgafun.yaml +++ b/data/bgafun/bioconda_bgafun.yaml @@ -4,7 +4,6 @@ description: A method to identify specifity determining residues in protein fami home: https://bioconductor.org/packages/3.10/bioc/html/bgafun.html identifiers: - biotools:bgafun -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-bgafun summary: BGAfun A method to identify specifity determining residues in protein families diff --git a/data/bgeedb/bgeedbbioschemas.jsonld b/data/bgeedb/bgeedbbioschemas.jsonld index a980d76278e28..cd20934365f71 100644 --- a/data/bgeedb/bgeedbbioschemas.jsonld +++ b/data/bgeedb/bgeedbbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/bgeedb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Frederic Bastian", - "Andrea Komljenovic" + "Andrea Komljenovic", + "Frederic Bastian" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.", "sc:license": "GPL-2.0", "sc:name": "BgeeDB", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BgeeDB.html", diff --git a/data/bgf/bgfbioschemas.jsonld b/data/bgf/bgfbioschemas.jsonld index 84c24a5f406d3..bdc0c109ddd7c 100644 --- a/data/bgf/bgfbioschemas.jsonld +++ b/data/bgf/bgfbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "BGF", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bgf.genomics.org.cn/", "sc:version": "1.01" diff --git a/data/bgmix/bgmixbioschemas.jsonld b/data/bgmix/bgmixbioschemas.jsonld index ab3394fe9b57b..8e2589cf2a5bd 100644 --- a/data/bgmix/bgmixbioschemas.jsonld +++ b/data/bgmix/bgmixbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "BGmix", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BGmix.html", "sc:version": "1.34.0" diff --git a/data/bgmut/bgmutbioschemas.jsonld b/data/bgmut/bgmutbioschemas.jsonld index 8958b6b23c56d..bfb79b5faff90 100644 --- a/data/bgmut/bgmutbioschemas.jsonld +++ b/data/bgmut/bgmutbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "BGMUT", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/projects/gv/rbc/xslcgi.fcgi?cmd=bgmut/home" } \ No newline at end of file diff --git a/data/bgsmtr/bgsmtrbioschemas.jsonld b/data/bgsmtr/bgsmtrbioschemas.jsonld index 91db30951782f..4969c5fc4adcd 100644 --- a/data/bgsmtr/bgsmtrbioschemas.jsonld +++ b/data/bgsmtr/bgsmtrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "bgsmtr", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/bgsmtr/index.html" diff --git a/data/bgx/bgxbioschemas.jsonld b/data/bgx/bgxbioschemas.jsonld index 5bad584baef8c..5b38ec3568b12 100644 --- a/data/bgx/bgxbioschemas.jsonld +++ b/data/bgx/bgxbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "bgx", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/bgx.html", "sc:version": "1.40.0" diff --git a/data/bhc/bhcbioschemas.jsonld b/data/bhc/bhcbioschemas.jsonld index c785af1890a25..b9c3eda2ccefd 100644 --- a/data/bhc/bhcbioschemas.jsonld +++ b/data/bhc/bhcbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Rich Savage", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This method performs bottom-up hierarchical clustering using a Dirichlet Process to model uncertainty in the data and a Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data.", "sc:license": "GPL-3.0", "sc:name": "BHC", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BHC.html", "sc:version": "1.26.0" diff --git a/data/bhrcr/bhrcrbioschemas.jsonld b/data/bhrcr/bhrcrbioschemas.jsonld index 899aae8bacbc0..22cb95a5a53ee 100644 --- a/data/bhrcr/bhrcrbioschemas.jsonld +++ b/data/bhrcr/bhrcrbioschemas.jsonld @@ -19,19 +19,19 @@ "biotools:primaryContact": "Colin B. Fogarty = 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-bufferedmatrix diff --git a/data/bufferedmatrix/bufferedmatrixbioschemas.jsonld b/data/bufferedmatrix/bufferedmatrixbioschemas.jsonld index 8eb44b7a393a7..7c72f3a4d1721 100644 --- a/data/bufferedmatrix/bufferedmatrixbioschemas.jsonld +++ b/data/bufferedmatrix/bufferedmatrixbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "BufferedMatrix", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BufferedMatrix.html", "sc:version": "1.38.0" diff --git a/data/bufferedmatrixmethods/bioconda_bufferedmatrixmethods.yaml b/data/bufferedmatrixmethods/bioconda_bufferedmatrixmethods.yaml index 69ce4ccd1267b..822220246e37c 100644 --- a/data/bufferedmatrixmethods/bioconda_bufferedmatrixmethods.yaml +++ b/data/bufferedmatrixmethods/bioconda_bufferedmatrixmethods.yaml @@ -3,7 +3,6 @@ description: Microarray analysis methods that use BufferedMatrix objects home: https://bioconductor.org/packages/3.10/bioc/html/BufferedMatrixMethods.html identifiers: - biotools:bufferedmatrixmethods -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-bufferedmatrixmethods diff --git a/data/bugasbase/bugasbasebioschemas.jsonld b/data/bugasbase/bugasbasebioschemas.jsonld index f0420efb3e549..1aa0d5c8e0756 100644 --- a/data/bugasbase/bugasbasebioschemas.jsonld +++ b/data/bugasbase/bugasbasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A relational database containing microbial gene expression and comparative genomic hybridisation experimental data. The data is mostly derived from whole genome microarrays designed by the BµG@S group, however data from other microarrays is included and the database is being modified to support RNA-Seq analysis. Public access is available for datasets that have been published and login credentials can be obtained for data submission.", "sc:name": "BugaSbase", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bugs.sgul.ac.uk/bugsbase/" } \ No newline at end of file diff --git a/data/bujnicki_lab_tools/bujnicki_lab_toolsbioschemas.jsonld b/data/bujnicki_lab_tools/bujnicki_lab_toolsbioschemas.jsonld index 11ef56ee9d692..706496e05cb1c 100644 --- a/data/bujnicki_lab_tools/bujnicki_lab_toolsbioschemas.jsonld +++ b/data/bujnicki_lab_tools/bujnicki_lab_toolsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Range of bioinformatics tools including Blast, PsiBlast, PhyloTable.", "sc:name": "Bujnicki Lab Tools", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.genesilico.pl/", "sc:version": "1" diff --git a/data/bumhmm/bumhmmbioschemas.jsonld b/data/bumhmm/bumhmmbioschemas.jsonld index 17d87c3a29ba1..9aa17ff9d6923 100644 --- a/data/bumhmm/bumhmmbioschemas.jsonld +++ b/data/bumhmm/bumhmmbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "BUMHMM", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BUMHMM.html", "sc:version": "1.4.0" diff --git a/data/bumphunter/bumphunterbioschemas.jsonld b/data/bumphunter/bumphunterbioschemas.jsonld index 3988ba2941e7b..aec8bfd3a2473 100644 --- a/data/bumphunter/bumphunterbioschemas.jsonld +++ b/data/bumphunter/bumphunterbioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btu049", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/bumphunter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Rafael A. Irizarry", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:24478339", + "pmcid:PMC4016708", { "@id": "https://doi.org/10.1093/bioinformatics/btu049" }, - "pmcid:PMC4016708" + "pubmed:24478339" ], "sc:description": "Tools for finding bumps in genomic data.", "sc:featureList": { @@ -35,12 +31,16 @@ "sc:license": "Artistic-2.0", "sc:name": "bumphunter", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/bumphunter.html", "sc:version": "1.14.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btu049", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/burrito/burritobioschemas.jsonld b/data/burrito/burritobioschemas.jsonld index 12032fd7611d5..ad72bdec88874 100644 --- a/data/burrito/burritobioschemas.jsonld +++ b/data/burrito/burritobioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Elhanan Borenstein", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:29545787", { "@id": "https://doi.org/10.3389/fmicb.2018.00365" }, - "pmcid:PMC5837987", - "pubmed:29545787" + "pmcid:PMC5837987" ], "sc:description": "Web-based tool for interactive exploration of metagenomic datasets, linking taxonomic and functional microbiome profiles.", "sc:featureList": [ diff --git a/data/bus/bioconda_bus.yaml b/data/bus/bioconda_bus.yaml index a4394c01d4bc1..369b0bf01c18d 100644 --- a/data/bus/bioconda_bus.yaml +++ b/data/bus/bioconda_bus.yaml @@ -4,7 +4,6 @@ description: This package can be used to compute associations among genes (gene- home: https://bioconductor.org/packages/3.10/bioc/html/BUS.html identifiers: - biotools:bus -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-bus diff --git a/data/bus/busbioschemas.jsonld b/data/bus/busbioschemas.jsonld index e7f1614629224..7c3dcf5ab71c6 100644 --- a/data/bus/busbioschemas.jsonld +++ b/data/bus/busbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "BUS", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/BUS.html", diff --git a/data/busca/buscabioschemas.jsonld b/data/busca/buscabioschemas.jsonld index d25b35ba91efd..99ff63f1b9961 100644 --- a/data/busca/buscabioschemas.jsonld +++ b/data/busca/buscabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Prediction of protein subcellular localization from sequence", "sc:name": "BUSCA", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "http://busca.biocomp.unibo.it", diff --git a/data/bustools/bustoolsbioschemas.jsonld b/data/bustools/bustoolsbioschemas.jsonld index f26c68d5289ad..8d1ec94af52d5 100644 --- a/data/bustools/bustoolsbioschemas.jsonld +++ b/data/bustools/bustoolsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Páll Melsted", - "Vasilis Ntranos", - "Lior Pachter" + "Lior Pachter", + "Vasilis Ntranos" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:31073610", @@ -22,8 +22,8 @@ "sc:name": "BUStools", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://BUStools.github.io/" } \ No newline at end of file diff --git a/data/bwa-sw/bwa-swbioschemas.jsonld b/data/bwa-sw/bwa-swbioschemas.jsonld index 3426fd6bea0cc..fab84db6c995b 100644 --- a/data/bwa-sw/bwa-swbioschemas.jsonld +++ b/data/bwa-sw/bwa-swbioschemas.jsonld @@ -9,35 +9,23 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2164-15-264", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btp698", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-4874-2874", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/bwa-sw", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "bwa team", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:24626854", + "pmcid:PMC4051166", { "@id": "https://doi.org/10.1093/bioinformatics/btp698" }, - "pmcid:PMC4051166", "pubmed:24708189", - "pmcid:PMC2828108", - "pubmed:24626854", { "@id": "https://doi.org/10.1186/1471-2164-15-264" }, - "pubmed:20080505" + "pubmed:20080505", + "pmcid:PMC2828108" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-4874-2874" @@ -47,6 +35,18 @@ "sc:name": "BWA-SW", "sc:operatingSystem": "Linux", "sc:url": "http://bio-bwa.sourceforge.net/" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btp698", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://doi.org/10.1186/1471-2164-15-264", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-4874-2874", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/bwa/bwabioschemas.jsonld b/data/bwa/bwabioschemas.jsonld index b75c400200df7..dbeaad555df77 100644 --- a/data/bwa/bwabioschemas.jsonld +++ b/data/bwa/bwabioschemas.jsonld @@ -9,34 +9,26 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-14-184", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btp324", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/bwa", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "bwa team", "sc:additionalType": [ - "Workbench", - "Command-line tool" + "Command-line tool", + "Workbench" ], "sc:citation": [ - { - "@id": "https://doi.org/10.1186/1471-2105-14-184" - }, "pmcid:PMC2705234", + "pubmed:28286147", { "@id": "https://doi.org/10.1093/bioinformatics/btp324" }, - "pubmed:19451168", - "pmcid:PMC3694458", "pubmed:23758764", - "pubmed:28286147" + "pmcid:PMC3694458", + "pubmed:19451168", + { + "@id": "https://doi.org/10.1186/1471-2105-14-184" + } ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-4874-2874" @@ -45,14 +37,22 @@ "sc:license": "MIT", "sc:name": "BWA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bio-bwa.sourceforge.net" }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-184", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0003-4874-2874", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btp324", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/bx-python/bx-pythonbioschemas.jsonld b/data/bx-python/bx-pythonbioschemas.jsonld index a3f9e4342dd50..0210ec1fea2b7 100644 --- a/data/bx-python/bx-pythonbioschemas.jsonld +++ b/data/bx-python/bx-pythonbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "bx-python", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/bxlab/bx-python" } \ No newline at end of file diff --git a/data/bykdb/bykdbbioschemas.jsonld b/data/bykdb/bykdbbioschemas.jsonld index f557ec4157602..219f71e899d2e 100644 --- a/data/bykdb/bykdbbioschemas.jsonld +++ b/data/bykdb/bykdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Bacterial protein tYrosine Kinase database (BYKdb). Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences.", "sc:name": "BYKdb", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bykdb.ibcp.fr/BYKdb/" } \ No newline at end of file diff --git a/data/bypassr/bypassrbioschemas.jsonld b/data/bypassr/bypassrbioschemas.jsonld index 2d50deb91bea8..dea864a4daae1 100644 --- a/data/bypassr/bypassrbioschemas.jsonld +++ b/data/bypassr/bypassrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Implementation of a new method for inferring branch lengths and site-specific substitution rates from nucleotide sequences. It makes use of the Bayesian Markov Chain Monte Carlo method and of the uniformization (randomization) technique to calculate sequence substitution probabilities in complicated DNA substitution models such as general time reversible model (GTR).", "sc:name": "BYPASSR", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.cmt.ua.ac.be/lcovaci/lucian/ligia/bypassr.html" diff --git a/data/bystro/bystrobioschemas.jsonld b/data/bystro/bystrobioschemas.jsonld index aea40f07ba0ba..ffe8015d91007 100644 --- a/data/bystro/bystrobioschemas.jsonld +++ b/data/bystro/bystrobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Bystro", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://bystro.io/" } \ No newline at end of file diff --git a/data/bz-rates/bz-ratesbioschemas.jsonld b/data/bz-rates/bz-ratesbioschemas.jsonld index 2882b4432daeb..0bbb9cb2db4bb 100644 --- a/data/bz-rates/bz-ratesbioschemas.jsonld +++ b/data/bz-rates/bz-ratesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-tool that allows to compute mutation rates from fluctuation assays.", "sc:name": "bz-rates", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.lcqb.upmc.fr/bzrates" } \ No newline at end of file diff --git a/data/bzscan/bzscanbioschemas.jsonld b/data/bzscan/bzscanbioschemas.jsonld index f975aee849678..6c2008023822a 100644 --- a/data/bzscan/bzscanbioschemas.jsonld +++ b/data/bzscan/bzscanbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures.", "sc:name": "BZScan", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://tagc.univ-mrs.fr/welcome/spip.php?rubrique7", "sc:version": "2" diff --git a/data/c-intersecture/c-intersecturebioschemas.jsonld b/data/c-intersecture/c-intersecturebioschemas.jsonld index 4f7be5cdb4838..d43bed0d8765e 100644 --- a/data/c-intersecture/c-intersecturebioschemas.jsonld +++ b/data/c-intersecture/c-intersecturebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "C-InterSecture", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/NuriddinovMA/C-InterSecture" } \ No newline at end of file diff --git a/data/c-state/c-statebioschemas.jsonld b/data/c-state/c-statebioschemas.jsonld index ad4527a3b47d1..f983e5e28120e 100644 --- a/data/c-state/c-statebioschemas.jsonld +++ b/data/c-state/c-statebioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/c-state", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rakesh K Mishra", + "Surabhi Srivastava", "Divya Tej Sowpati", - "Surabhi Srivastava" + "Rakesh K Mishra" ], "sc:additionalType": "Web application", "sc:description": "Webapp written using Vue and d3.js for epigenetic data visualization by biologists.", "sc:license": "MIT", "sc:name": "C-state", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ccmb.res.in/rakeshmishra/c-state/" } \ No newline at end of file diff --git a/data/cabernet/cabernetbioschemas.jsonld b/data/cabernet/cabernetbioschemas.jsonld index be4028eb9e83b..494bbfc0a327b 100644 --- a/data/cabernet/cabernetbioschemas.jsonld +++ b/data/cabernet/cabernetbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A Cytoscape 3.2.0 app for the generation, the simulation, the analysis and the visualization of Boolean models of gene regulatory networks, particularly focused on the investigation of their robustness.", "sc:name": "CABERNET", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bimib.disco.unimib.it/index.php/CABERNET" } \ No newline at end of file diff --git a/data/cabog/cabogbioschemas.jsonld b/data/cabog/cabogbioschemas.jsonld index bb4d8a2d755d5..ac11975c9da59 100644 --- a/data/cabog/cabogbioschemas.jsonld +++ b/data/cabog/cabogbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Celera Assembler is scientific software for DNA research.", "sc:name": "CABOG", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://wgs-assembler.sourceforge.net/" } \ No newline at end of file diff --git a/data/cabri/cabribioschemas.jsonld b/data/cabri/cabribioschemas.jsonld index 49f1cb58cf6ad..94955a58622b0 100644 --- a/data/cabri/cabribioschemas.jsonld +++ b/data/cabri/cabribioschemas.jsonld @@ -13,19 +13,19 @@ "biotools:primaryContact": "Paolo Romano", "sc:additionalType": "Database portal", "sc:author": [ + "Domenico Marra", "Brendan Vaughan", - "Francesca Piersigilli", - "Domenico Marra" + "Francesca Piersigilli" ], "sc:contributor": [ - "Louis Rechaussat", - "Manfred Kracht", - "Herbert Milch", + "Common Access to Biological Resources and Information (CABRI), EU 5th FP (1996-1999)", + "Beatrice Dutertre", "Francois Guissart", + "Manfred Kracht", "Louis Jones", "Gerrit Stegehuis", - "Beatrice Dutertre", - "Common Access to Biological Resources and Information (CABRI), EU 5th FP (1996-1999)" + "Herbert Milch", + "Louis Rechaussat" ], "sc:description": "Common Access to Biological Resources and Information - A collection of European Biological Resource Centre catalogues.", "sc:funder": "Common Access to Biological Resources and Information (CABRI), EU 5th FP (1996-1999)", diff --git a/data/cabs-flex/cabs-flexbioschemas.jsonld b/data/cabs-flex/cabs-flexbioschemas.jsonld index 68e4963249035..629eb2d882af7 100644 --- a/data/cabs-flex/cabs-flexbioschemas.jsonld +++ b/data/cabs-flex/cabs-flexbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "CABS-flex", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://biocomp.chem.uw.edu.pl/CABSflex" } \ No newline at end of file diff --git a/data/cabs-fold/cabs-foldbioschemas.jsonld b/data/cabs-fold/cabs-foldbioschemas.jsonld index 195c01a56eea6..36b932743d36c 100644 --- a/data/cabs-fold/cabs-foldbioschemas.jsonld +++ b/data/cabs-fold/cabs-foldbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "CABS-fold is a web server for the de novo and consensus-based prediction of protein structure. The web server output is a coarse grained trajectory of generated conformations.", "sc:name": "CABS-fold", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://biocomp.chem.uw.edu.pl/CABSfold" diff --git a/data/cachedas/cachedasbioschemas.jsonld b/data/cachedas/cachedasbioschemas.jsonld index dd0f7a659aca4..27f493b707741 100644 --- a/data/cachedas/cachedasbioschemas.jsonld +++ b/data/cachedas/cachedasbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", + "UK BBSRC", "EMBOSS Contributors", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:description": "Generate server cache file for DAS servers or for the DAS registry.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", + "Wellcome Trust", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "cachedas", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/cachedas.html", "sc:version": "r6" diff --git a/data/cachedbfetch/cachedbfetchbioschemas.jsonld b/data/cachedbfetch/cachedbfetchbioschemas.jsonld index eaa6594fa0fad..7d7626c8bb334 100644 --- a/data/cachedbfetch/cachedbfetchbioschemas.jsonld +++ b/data/cachedbfetch/cachedbfetchbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", "EMBOSS Contributors", - "Wellcome Trust" + "UK MRC", + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Generate server cache file for Dbfetch/WSDbfetch data sources.", "sc:funder": [ @@ -31,8 +31,8 @@ "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/cachedbfetch.html", "sc:version": "r6" diff --git a/data/cacheebeyesearch/cacheebeyesearchbioschemas.jsonld b/data/cacheebeyesearch/cacheebeyesearchbioschemas.jsonld index 44588c030ca7f..3bb2fc612e92e 100644 --- a/data/cacheebeyesearch/cacheebeyesearchbioschemas.jsonld +++ b/data/cacheebeyesearch/cacheebeyesearchbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "EMBOSS Contributors", "Wellcome Trust", - "UK BBSRC", "UK MRC", - "EMBOSS Contributors" + "UK BBSRC" ], "sc:description": "Generate server cache file for EB-eye search domains.", "sc:funder": [ - "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "cacheebeyesearch", @@ -31,8 +31,8 @@ "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/cacheebeyesearch.html", "sc:version": "r6" diff --git a/data/cacheensembl/cacheensemblbioschemas.jsonld b/data/cacheensembl/cacheensemblbioschemas.jsonld index f405f1c05d40d..eabfad4c7a362 100644 --- a/data/cacheensembl/cacheensemblbioschemas.jsonld +++ b/data/cacheensembl/cacheensemblbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK BBSRC", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "EMBOSS Contributors" ], "sc:description": "Generate server cache file for an Ensembl server.", "sc:funder": [ + "UK BBSRC", "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "cacheensembl", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/cad-score/cad-scorebioschemas.jsonld b/data/cad-score/cad-scorebioschemas.jsonld index 308c949e32d49..bc00bfb39fda1 100644 --- a/data/cad-score/cad-scorebioschemas.jsonld +++ b/data/cad-score/cad-scorebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/cad-score", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:22933340", "sc:description": "New evaluation function quantifying differences between physical contacts in a model and the reference structure.", "sc:name": "CAD-score", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ibt.lt/en/laboratories/bioinfo_en/software/cad-score/" } \ No newline at end of file diff --git a/data/cadd_phred/cadd_phredbioschemas.jsonld b/data/cadd_phred/cadd_phredbioschemas.jsonld index d6b8a1e6d99a8..e4dc057900db1 100644 --- a/data/cadd_phred/cadd_phredbioschemas.jsonld +++ b/data/cadd_phred/cadd_phredbioschemas.jsonld @@ -20,21 +20,21 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:24487276", - "pmcid:PMC3992975", { "@id": "https://doi.org/10.1038/ng.2892" - } + }, + "pmcid:PMC3992975" ], "sc:description": "Combined Annotation Dependent Depletion (CADD) - tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.", "sc:featureList": [ { - "@id": "edam:operation_2436" + "@id": "edam:operation_2238" }, { - "@id": "edam:operation_3226" + "@id": "edam:operation_2436" }, { - "@id": "edam:operation_2238" + "@id": "edam:operation_3226" } ], "sc:license": "Unlicense", diff --git a/data/cadgene/cadgenebioschemas.jsonld b/data/cadgene/cadgenebioschemas.jsonld index 172d521613fc9..21de434ba40ab 100644 --- a/data/cadgene/cadgenebioschemas.jsonld +++ b/data/cadgene/cadgenebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CADgene", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinfo.life.hust.edu.cn/CADgene/browseGene.php?GeneID=5728" } \ No newline at end of file diff --git a/data/cadnano/cadnanobioschemas.jsonld b/data/cadnano/cadnanobioschemas.jsonld index 85b159f55c586..570727885211c 100644 --- a/data/cadnano/cadnanobioschemas.jsonld +++ b/data/cadnano/cadnanobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "This software simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs.", "sc:name": "Cadnano", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://cadnano.org/" } \ No newline at end of file diff --git a/data/cafa/cafabioschemas.jsonld b/data/cafa/cafabioschemas.jsonld index 8bfb3a984ff5b..3a9716a077a69 100644 --- a/data/cafa/cafabioschemas.jsonld +++ b/data/cafa/cafabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "CAFA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://simtk.org/home/cafa", "sc:version": "0.41" diff --git a/data/cafe_calculation_of_free_energy/cafe_calculation_of_free_energybioschemas.jsonld b/data/cafe_calculation_of_free_energy/cafe_calculation_of_free_energybioschemas.jsonld index 0f7760ff96aca..76bee3d3f58b6 100644 --- a/data/cafe_calculation_of_free_energy/cafe_calculation_of_free_energybioschemas.jsonld +++ b/data/cafe_calculation_of_free_energy/cafe_calculation_of_free_energybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "CaFE", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/huiliucode/cafe_plugin" } \ No newline at end of file diff --git a/data/cafe_sequence_analysis/cafe_sequence_analysisbioschemas.jsonld b/data/cafe_sequence_analysis/cafe_sequence_analysisbioschemas.jsonld index dead3bb52478d..bcf4a434df428 100644 --- a/data/cafe_sequence_analysis/cafe_sequence_analysisbioschemas.jsonld +++ b/data/cafe_sequence_analysis/cafe_sequence_analysisbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkx351", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cafe_sequence_analysis", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yang Lu", - "Prof. Fengzhu Sun" + "Prof. Fengzhu Sun", + "Yang Lu" ], "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:citation": [ { @@ -42,11 +38,15 @@ ], "sc:name": "CAFE", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/younglululu/CAFE" + }, + { + "@id": "https://doi.org/10.1093/nar/gkx351", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cafe_variome/cafe_variomebioschemas.jsonld b/data/cafe_variome/cafe_variomebioschemas.jsonld index 4268567b1892d..0392620e2a0f9 100644 --- a/data/cafe_variome/cafe_variomebioschemas.jsonld +++ b/data/cafe_variome/cafe_variomebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Cafe Variome", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.cafevariome.org/" } \ No newline at end of file diff --git a/data/cager/cagerbioschemas.jsonld b/data/cager/cagerbioschemas.jsonld index a84271c150675..6498ebfa2ca99 100644 --- a/data/cager/cagerbioschemas.jsonld +++ b/data/cager/cagerbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkv054", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cager", "@type": "sc:SoftwareApplication", @@ -33,8 +37,8 @@ "sc:license": "GPL-3.0", "sc:name": "CAGEr", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CAGEr.html", @@ -43,10 +47,6 @@ { "@id": "http://orcid.org/0000-0003-4191-3714", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/nar/gkv054", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cagexplorer/cagexplorerbioschemas.jsonld b/data/cagexplorer/cagexplorerbioschemas.jsonld index 5756c889f8d5b..f0e202fff7a21 100644 --- a/data/cagexplorer/cagexplorerbioschemas.jsonld +++ b/data/cagexplorer/cagexplorerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R package that facilitates the detection and visualization of changes in the relative transcription from promoter regions in multi-promoter genes, all in the context of overall gene expression. Multiple samples can be compared simultaneously.", "sc:name": "CAGExploreR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://fantom.gsc.riken.jp/software/" } \ No newline at end of file diff --git a/data/cai/caibioschemas.jsonld b/data/cai/caibioschemas.jsonld index 0c73f7622161c..85ad031cc9b3c 100644 --- a/data/cai/caibioschemas.jsonld +++ b/data/cai/caibioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "Wellcome Trust", "UK MRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Calculate codon adaptation index.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "cai", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/cake/cakebioschemas.jsonld b/data/cake/cakebioschemas.jsonld index 1ac87d585a417..9f7d6a1ac493c 100644 --- a/data/cake/cakebioschemas.jsonld +++ b/data/cake/cakebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.", "sc:name": "Cake", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cakesomatic.sourceforge.net/" } \ No newline at end of file diff --git a/data/calchas/calchasbioschemas.jsonld b/data/calchas/calchasbioschemas.jsonld index 234e6eb03ff5d..7cb0d715b1331 100644 --- a/data/calchas/calchasbioschemas.jsonld +++ b/data/calchas/calchasbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12911-015-0200-4", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/calchas", "@type": "sc:SoftwareApplication", @@ -22,10 +26,10 @@ "sc:additionalType": "Web application", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0218" + "@id": "edam:topic_0089" }, { - "@id": "edam:topic_0089" + "@id": "edam:topic_0218" }, { "@id": "edam:topic_3063" @@ -36,11 +40,11 @@ ], "sc:author": "Lefteris Koumakis", "sc:citation": [ - "pmcid:PMC4591066", - "pubmed:26423616", { "@id": "https://doi.org/10.1186/s12911-015-0200-4" - } + }, + "pubmed:26423616", + "pmcid:PMC4591066" ], "sc:description": "A web based framework that takes advantage of domain specific ontologies, and Natural Language Processing, aiming to empower exploration of biomedical resources via semantic-based querying and search. The NLP engine analyzes the input free-text query and translates it into targeted queries with terms from the underlying ontology. Each query is passed to the semantically-annotated tools repository, and based on similarity matches, it ranks the available resources.", "sc:featureList": [ @@ -69,10 +73,6 @@ }, "sc:url": "http://calchas.ics.forth.gr", "sc:version": "1.0" - }, - { - "@id": "https://doi.org/10.1186/s12911-015-0200-4", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/calib/calibbioschemas.jsonld b/data/calib/calibbioschemas.jsonld index 7e532874c998e..d4960b7b43798 100644 --- a/data/calib/calibbioschemas.jsonld +++ b/data/calib/calibbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hui Zhao", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.", "sc:license": "GPL-3.0", diff --git a/data/calis-p/calis-pbioschemas.jsonld b/data/calis-p/calis-pbioschemas.jsonld index b7010f104b787..574c2b448b00b 100644 --- a/data/calis-p/calis-pbioschemas.jsonld +++ b/data/calis-p/calis-pbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1073/pnas.1722325115", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/calis-p", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Manuel Kleiner", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:29844191", + "pmcid:PMC6004456", { "@id": "https://doi.org/10.1073/pnas.1722325115" - }, - "pubmed:29844191", - "pmcid:PMC6004456" + } ], "sc:description": "Directly extract stable carbon isotope fingerprints (SIFs) of individual species in a microbial community from a metaproteomic dataset. It takes the scored peptide-spectrum match (PSM) tables for samples and the calibration material, and the raw MS data in mzML format as input.", "sc:featureList": { @@ -35,6 +31,10 @@ "Linux" ], "sc:url": "https://sourceforge.net/projects/calis-p/" + }, + { + "@id": "https://doi.org/10.1073/pnas.1722325115", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/calmate/calmatebioschemas.jsonld b/data/calmate/calmatebioschemas.jsonld index 763a0a3cf71b2..7b90b0f5c56e6 100644 --- a/data/calmate/calmatebioschemas.jsonld +++ b/data/calmate/calmatebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "CalMaTe is a multi-array post-processing method of allele-specific copy-number estimates (ASCNs).", "sc:name": "CalMaTe", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://cran.r-project.org/web/packages/calmate/index.html", diff --git a/data/calmorph/calmorphbioschemas.jsonld b/data/calmorph/calmorphbioschemas.jsonld index 4f4b3a99d9b4a..7a090e8ced5aa 100644 --- a/data/calmorph/calmorphbioschemas.jsonld +++ b/data/calmorph/calmorphbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Program that outputs a large amount of data on cell cycle phase, cell forms, etc., for individual cells, from a set of pictures of cell walls, cell nuclei, and actins.", "sc:name": "CalMorph", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://scmd.gi.k.u-tokyo.ac.jp/datamine/calmorph/" } \ No newline at end of file diff --git a/data/cam/cambioschemas.jsonld b/data/cam/cambioschemas.jsonld index 4e221313caed5..3081da45c0799 100644 --- a/data/cam/cambioschemas.jsonld +++ b/data/cam/cambioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "CAM", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/ridgelab/cam" } \ No newline at end of file diff --git a/data/camels/camelsbioschemas.jsonld b/data/camels/camelsbioschemas.jsonld index 95b2cbf5387bc..babc92a11cf13 100644 --- a/data/camels/camelsbioschemas.jsonld +++ b/data/camels/camelsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "In silico prediction of calmodulin binding proteins and their binding sites.", "sc:name": "CaMELS", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://camels.pythonanywhere.com/" } \ No newline at end of file diff --git a/data/cameo/cameobioschemas.jsonld b/data/cameo/cameobioschemas.jsonld index a224330a45702..4e05a5c5184e1 100644 --- a/data/cameo/cameobioschemas.jsonld +++ b/data/cameo/cameobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CAMEO", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://cameo3d.org/", diff --git a/data/camera/camerabioschemas.jsonld b/data/camera/camerabioschemas.jsonld index 9ec1bb3c8076f..6c81f9270ae73 100644 --- a/data/camera/camerabioschemas.jsonld +++ b/data/camera/camerabioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1021/ac202450g", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/camera", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Steffen Neumann", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:22111785", { "@id": "https://doi.org/10.1021/ac202450g" }, - "pmcid:PMC3658281" + "pmcid:PMC3658281", + "pubmed:22111785" ], "sc:description": "Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments.", "sc:featureList": { @@ -31,16 +35,12 @@ "sc:license": "GPL-2.0", "sc:name": "CAMERA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CAMERA.html", "sc:version": "1.30.0" - }, - { - "@id": "https://doi.org/10.1021/ac202450g", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/camp/campbioschemas.jsonld b/data/camp/campbioschemas.jsonld index 406ce22d745d6..5fdd5f3c0bc37 100644 --- a/data/camp/campbioschemas.jsonld +++ b/data/camp/campbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CAMP", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bicnirrh.res.in/antimicrobial" } \ No newline at end of file diff --git a/data/campo/campobioschemas.jsonld b/data/campo/campobioschemas.jsonld index 482e2d3aed7a4..95a8f22c6d58c 100644 --- a/data/campo/campobioschemas.jsonld +++ b/data/campo/campobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CAMPO is a tool to analyze conserved regions from a multiple sequence alignment", "sc:name": "CAMPO", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://schubert.bio.uniroma1.it/campo.html" } \ No newline at end of file diff --git a/data/camur/camurbioschemas.jsonld b/data/camur/camurbioschemas.jsonld index 80c2bc2ea6c09..7de12e0f26cb7 100644 --- a/data/camur/camurbioschemas.jsonld +++ b/data/camur/camurbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "New method and software package able to extract multiple, alternative, and equivalent classification models.", "sc:name": "CAMUR", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://dmb.iasi.cnr.it/camur.php" } \ No newline at end of file diff --git a/data/canary/canarybioschemas.jsonld b/data/canary/canarybioschemas.jsonld index 2251496836b93..62df420e70aba 100644 --- a/data/canary/canarybioschemas.jsonld +++ b/data/canary/canarybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Canary", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/PapenfussLab/Canary" } \ No newline at end of file diff --git a/data/cancer/cancerbioschemas.jsonld b/data/cancer/cancerbioschemas.jsonld index b2d485c9ce655..09647e02248c2 100644 --- a/data/cancer/cancerbioschemas.jsonld +++ b/data/cancer/cancerbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Karim Mezhoud", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package is a user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available cancer data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).", "sc:license": "GPL-2.0", "sc:name": "canceR", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/canceR.html", "sc:version": "1.6.0" diff --git a/data/cancera1de/cancera1debioschemas.jsonld b/data/cancera1de/cancera1debioschemas.jsonld index cb44e5b8ea803..91f45b47e72db 100644 --- a/data/cancera1de/cancera1debioschemas.jsonld +++ b/data/cancera1de/cancera1debioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Ka-Chun Wong", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC6548890", { "@id": "https://doi.org/10.1016/J.ISCI.2019.04.035" }, - "pmcid:PMC6548890", "pubmed:31103852" ], "sc:description": "Early Cancer Detection from Multianalyte Blood Test Results using Artificial Intelligence", @@ -32,9 +32,9 @@ "sc:license": "Unlicense", "sc:name": "CancerA1DE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://cancer.cs.cityu.edu.hk/" } diff --git a/data/cancerclass/cancerclassbioschemas.jsonld b/data/cancerclass/cancerclassbioschemas.jsonld index 5e23261357f6a..1734bbd0ef257 100644 --- a/data/cancerclass/cancerclassbioschemas.jsonld +++ b/data/cancerclass/cancerclassbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "cancerclass", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cancerclass.html", "sc:version": "1.18.0" diff --git a/data/cancerinsilico/bioconda_cancerinsilico.yaml b/data/cancerinsilico/bioconda_cancerinsilico.yaml index cc99b45b2ca8d..adc78d53e51a1 100644 --- a/data/cancerinsilico/bioconda_cancerinsilico.yaml +++ b/data/cancerinsilico/bioconda_cancerinsilico.yaml @@ -6,7 +6,6 @@ description: The CancerInSilico package provides an R interface for running math home: https://bioconductor.org/packages/3.10/bioc/html/CancerInSilico.html identifiers: - biotools:cancerinsilico -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-cancerinsilico diff --git a/data/cancerinsilico/cancerinsilicobioschemas.jsonld b/data/cancerinsilico/cancerinsilicobioschemas.jsonld index 54b4f536d081a..90ce4fe3eac68 100644 --- a/data/cancerinsilico/cancerinsilicobioschemas.jsonld +++ b/data/cancerinsilico/cancerinsilicobioschemas.jsonld @@ -15,16 +15,16 @@ "Thomas D. Sherman" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides an R interface for running mathematical models of tumor progression. It has the underlying models implemented in C++ and the output and analysis features implemented in R.", "sc:license": "GPL-2.0", "sc:name": "CancerInSilico", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CancerInSilico.html", "sc:version": "1.0.0" diff --git a/data/cancermine/cancerminebioschemas.jsonld b/data/cancermine/cancerminebioschemas.jsonld index 358384ee580b7..f4e0f89b6ec3b 100644 --- a/data/cancermine/cancerminebioschemas.jsonld +++ b/data/cancermine/cancerminebioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "MIT", "sc:name": "CancerMine", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bionlp.bcgsc.ca/cancermine/" } \ No newline at end of file diff --git a/data/cancermutationanalysis/cancermutationanalysisbioschemas.jsonld b/data/cancermutationanalysis/cancermutationanalysisbioschemas.jsonld index caa0c6460ed6a..6d4f3b7020254 100644 --- a/data/cancermutationanalysis/cancermutationanalysisbioschemas.jsonld +++ b/data/cancermutationanalysis/cancermutationanalysisbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "CancerMutationAnalysis", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CancerMutationAnalysis.html", "sc:version": "1.16.0" diff --git a/data/cancerouspdomains/cancerouspdomainsbioschemas.jsonld b/data/cancerouspdomains/cancerouspdomainsbioschemas.jsonld index 29b0a916a7852..1f11e9827d07c 100644 --- a/data/cancerouspdomains/cancerouspdomainsbioschemas.jsonld +++ b/data/cancerouspdomains/cancerouspdomainsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains.", "sc:name": "Cancerouspdomains", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.cancerouspdomains.ir/" } \ No newline at end of file diff --git a/data/cancerppd/cancerppdbioschemas.jsonld b/data/cancerppd/cancerppdbioschemas.jsonld index 3e38f7b303e74..9a99b6b15b45a 100644 --- a/data/cancerppd/cancerppdbioschemas.jsonld +++ b/data/cancerppd/cancerppdbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKU892", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cancerppd", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Gajendra P. S. Raghava", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC4384006", "pubmed:25270878", { "@id": "https://doi.org/10.1093/NAR/GKU892" - } + }, + "pmcid:PMC4384006" ], "sc:description": "A repository of experimentally verified anticancer peptides (ACPs) and anticancer proteins. Data were manually collected from published research articles, patents and from other databases.", "sc:featureList": { @@ -32,10 +28,14 @@ "sc:name": "CancerPPD", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://crdd.osdd.net/raghava/cancerppd/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKU892", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cancerpred/cancerpredbioschemas.jsonld b/data/cancerpred/cancerpredbioschemas.jsonld index c460f3973d525..d338f7ed130db 100644 --- a/data/cancerpred/cancerpredbioschemas.jsonld +++ b/data/cancerpred/cancerpredbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "CancerPred is a web-server specially trained for predicting the Cancerlectins. Lectins are important biomolecules and play important functions in many processes e.g cell to cell recognition, host-pathogen interactions etc. In the same way Cancerlectins are those lectins which are known to play roles in cancer metastasis and tumor progress, oncogenesis etc. CancerPred is mainly designed for distinguishing Cancerlectins from Non-cancer lectins.", "sc:name": "CancerPred", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/cancer_pred/" } \ No newline at end of file diff --git a/data/cancerresource/cancerresourcebioschemas.jsonld b/data/cancerresource/cancerresourcebioschemas.jsonld index e60c80c210649..4ba41d127d9fd 100644 --- a/data/cancerresource/cancerresourcebioschemas.jsonld +++ b/data/cancerresource/cancerresourcebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/cancerresource", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Bjoern Gohlke", - "Robert Preissner" + "Robert Preissner", + "Bjoern Gohlke" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:20952398", diff --git a/data/cancersubtypes/bioconda_cancersubtypes.yaml b/data/cancersubtypes/bioconda_cancersubtypes.yaml index 6e742e386e9f0..d2aaeec892c28 100644 --- a/data/cancersubtypes/bioconda_cancersubtypes.yaml +++ b/data/cancersubtypes/bioconda_cancersubtypes.yaml @@ -6,7 +6,6 @@ description: CancerSubtypes integrates the current common computational biology home: https://bioconductor.org/packages/3.10/bioc/html/CancerSubtypes.html identifiers: - biotools:cancersubtypes -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-cancersubtypes diff --git a/data/cand/candbioschemas.jsonld b/data/cand/candbioschemas.jsonld index 5acafac883251..4138b8ff44957 100644 --- a/data/cand/candbioschemas.jsonld +++ b/data/cand/candbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Caitlin McHugh", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Functions to perform the CAnD test on a set of ancestry proportions. For a particular ancestral subpopulation, a user will supply the estimated ancestry proportion for each sample, and each chromosome or chromosomal segment of interest. A p-value for each chromosome as well as an overall p-value will be returned for each test. Plotting functions are also available.", "sc:license": "Artistic-2.0", "sc:name": "CAnD", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CAnD.html", "sc:version": "1.6.0" diff --git a/data/candi/candibioschemas.jsonld b/data/candi/candibioschemas.jsonld index 6c9363f404120..a305f0b84535d 100644 --- a/data/candi/candibioschemas.jsonld +++ b/data/candi/candibioschemas.jsonld @@ -19,27 +19,27 @@ "biotools:primaryContact": "M. A. Badgeley", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6499410", "pubmed:30304439", { "@id": "https://doi.org/10.1093/bioinformatics/bty855" - }, - "pmcid:PMC6499410" + } ], "sc:description": "R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis.", "sc:featureList": [ { - "@id": "edam:operation_3553" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_3553" } ], "sc:license": "GPL-3.0", "sc:name": "CANDI", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://candi.nextgenhealthcare.org/" } diff --git a/data/caneapp/caneappbioschemas.jsonld b/data/caneapp/caneappbioschemas.jsonld index 57ea2e9518081..78a798b5daebc 100644 --- a/data/caneapp/caneappbioschemas.jsonld +++ b/data/caneapp/caneappbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12864-015-2346-Y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/caneapp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dmitry Velmeshev", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC4710974", { "@id": "https://doi.org/10.1186/S12864-015-2346-Y" }, + "pmcid:PMC4710974", "pubmed:26758513" ], "sc:description": "Application for Comprehensive automated Analysis of Next-generation sequencing Experiments.", @@ -36,11 +32,15 @@ ], "sc:name": "CANEapp", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app" + }, + { + "@id": "https://doi.org/10.1186/S12864-015-2346-Y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/canevolve/canevolvebioschemas.jsonld b/data/canevolve/canevolvebioschemas.jsonld index 177dede1436dd..7bd35ba811237 100644 --- a/data/canevolve/canevolvebioschemas.jsonld +++ b/data/canevolve/canevolvebioschemas.jsonld @@ -9,14 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0056228", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/canevolve", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:23418540", "pmcid:PMC3572035", + "pubmed:23418540", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0056228" } @@ -27,15 +31,11 @@ }, "sc:name": "canEvolve", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.canevolve.org/AnalysisResults/AnalysisResults.html" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0056228", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cansar/cansarbioschemas.jsonld b/data/cansar/cansarbioschemas.jsonld index 977e0650d33b4..27ccdef1572f2 100644 --- a/data/cansar/cansarbioschemas.jsonld +++ b/data/cansar/cansarbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research.", "sc:name": "canSAR", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cansar.icr.ac.uk/" } \ No newline at end of file diff --git a/data/cansnper/cansnperbioschemas.jsonld b/data/cansnper/cansnperbioschemas.jsonld index 5832559d6fbd2..7b1bd526ec9f6 100644 --- a/data/cansnper/cansnperbioschemas.jsonld +++ b/data/cansnper/cansnperbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Efficient and user-friendly genotype classification pipeline based on an easily expandable database of predefined canonical single nucleotide polymorphisms.", "sc:name": "CanSNPer", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/adrlar/CanSNPer" } \ No newline at end of file diff --git a/data/canvar/canvarbioschemas.jsonld b/data/canvar/canvarbioschemas.jsonld index ba3464e9ae701..584a9330b1c0e 100644 --- a/data/canvar/canvarbioschemas.jsonld +++ b/data/canvar/canvarbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.10058.1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/canvar", "@type": "sc:SoftwareApplication", @@ -20,22 +24,22 @@ { "@id": "https://doi.org/10.12688/F1000RESEARCH.10058.1" }, - "pmcid:PMC5200944", - "pubmed:28105316" + "pubmed:28105316", + "pmcid:PMC5200944" ], "sc:description": "Variant level frequency data from cancer germline sequencing studies.", "sc:featureList": [ { - "@id": "edam:operation_0224" + "@id": "edam:operation_3229" }, { - "@id": "edam:operation_3229" + "@id": "edam:operation_3227" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_3227" + "@id": "edam:operation_3196" } ], "sc:license": "MIT", @@ -45,10 +49,6 @@ "Linux" ], "sc:url": "https://canvar.icr.ac.uk" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.10058.1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/caomicsv/caomicsvbioschemas.jsonld b/data/caomicsv/caomicsvbioschemas.jsonld index 4f72d91fabef7..a68db1c0660b2 100644 --- a/data/caomicsv/caomicsvbioschemas.jsonld +++ b/data/caomicsv/caomicsvbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "caOmicsV", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/caOmicsV.html", "sc:version": "1.4.0" diff --git a/data/cap3/cap3bioschemas.jsonld b/data/cap3/cap3bioschemas.jsonld index 513b53b0cc7e1..28ddd82daaace 100644 --- a/data/cap3/cap3bioschemas.jsonld +++ b/data/cap3/cap3bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-based contig assembly.", "sc:name": "CAP3 Sequence Assembly Program", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://biosrv.cab.unina.it/webcap3/" } \ No newline at end of file diff --git a/data/capdsd/capdsdbioschemas.jsonld b/data/capdsd/capdsdbioschemas.jsonld index aaeffd5a7da63..cfa70f82b3194 100644 --- a/data/capdsd/capdsdbioschemas.jsonld +++ b/data/capdsd/capdsdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An extension of DSD  that takes in to account a measure of interaction confidence while also incorporating directed pathway data.", "sc:name": "capDSD", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://dsd.cs.tufts.edu/capdsd/" } \ No newline at end of file diff --git a/data/cape/capebioschemas.jsonld b/data/cape/capebioschemas.jsonld index 447601d32ed4a..7caa7c1016cbb 100644 --- a/data/cape/capebioschemas.jsonld +++ b/data/cape/capebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003270", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cape", "@type": "sc:SoftwareApplication", @@ -18,8 +22,8 @@ { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003270" }, - "pubmed:24204223", - "pmcid:PMC3808451" + "pmcid:PMC3808451", + "pubmed:24204223" ], "sc:description": "Combine complementary information across multiple related phenotypes to infer directed epistatic interactions between genetic markers. This analysis can be applied to a variety of engineered and natural populations.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "GPL-3.0", "sc:name": "CAPE", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/cape/" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003270", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/capiu/capiubioschemas.jsonld b/data/capiu/capiubioschemas.jsonld index da2bfe8396669..56203fb30771e 100644 --- a/data/capiu/capiubioschemas.jsonld +++ b/data/capiu/capiubioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Novel approach for clustering samples (treatments, patients, condition etc) by using annotational information about the genes. The algorithm searches all pre-defined gene classes for classes that exhibit a strong clustering of the samples. These are then used to split the samples in two groups until no significant splits can be found. The result is visualized as a tree with gene classes as nodes and groups of samples as leaves.", "sc:name": "CAPIU", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinformatics.mpimp-golm.mpg.de/research-projects-publications/tools-services/capiu" } \ No newline at end of file diff --git a/data/car/carbioschemas.jsonld b/data/car/carbioschemas.jsonld index a07f3b011a308..bf083eaa24326 100644 --- a/data/car/carbioschemas.jsonld +++ b/data/car/carbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-014-0381-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/car", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr. Chin Lung Lu", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:25431302", { "@id": "https://doi.org/10.1186/S12859-014-0381-3" }, - "pubmed:25431302", "pmcid:PMC4253983" ], "sc:description": "Contig assembly of prokaryotic draft genomes using rearrangements.", @@ -31,11 +27,15 @@ }, "sc:name": "CAR", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://genome.cs.nthu.edu.tw/CAR/" + }, + { + "@id": "https://doi.org/10.1186/S12859-014-0381-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/carboxylator/carboxylatorbioschemas.jsonld b/data/carboxylator/carboxylatorbioschemas.jsonld index 1175218b4109c..aea15917f10c2 100644 --- a/data/carboxylator/carboxylatorbioschemas.jsonld +++ b/data/carboxylator/carboxylatorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Carboxylator", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://csb.cse.yzu.edu.tw/Carboxylator/" } \ No newline at end of file diff --git a/data/cardiacprofiler/cardiacprofilerbioschemas.jsonld b/data/cardiacprofiler/cardiacprofilerbioschemas.jsonld index d7b01984a6e30..6b14c03b029cc 100644 --- a/data/cardiacprofiler/cardiacprofilerbioschemas.jsonld +++ b/data/cardiacprofiler/cardiacprofilerbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Victor Chang Cardiac Research Institute", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pmcid:PMC6381356", + "pubmed:30666509", { "@id": "https://doi.org/10.1007/s12551-019-00498-2" - }, - "pmcid:PMC6381356", - "pubmed:30666509" + } ], "sc:description": "R package for extraction and visualisation of heart rate profiles from wearable fitness trackers.", "sc:featureList": [ @@ -40,9 +40,9 @@ "sc:license": "MIT", "sc:name": "CardiacProfileR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/VCCRI/CardiacProfileR" } diff --git a/data/cardinal/cardinalbioschemas.jsonld b/data/cardinal/cardinalbioschemas.jsonld index 360e2703b56de..d3d98fe998723 100644 --- a/data/cardinal/cardinalbioschemas.jsonld +++ b/data/cardinal/cardinalbioschemas.jsonld @@ -25,15 +25,15 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0121" + "@id": "edam:topic_0092" }, { - "@id": "edam:topic_0092" + "@id": "edam:topic_0121" } ], "sc:citation": [ - "pubmed:25777525", "pmcid:PMC4495298", + "pubmed:25777525", { "@id": "https://doi.org/10.1093/bioinformatics/btv146" } @@ -46,8 +46,8 @@ "sc:name": "Cardinal", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Cardinal.html", "sc:version": "1.6.0" diff --git a/data/cardiofan/cardiofanbioschemas.jsonld b/data/cardiofan/cardiofanbioschemas.jsonld index ac8563e093c1c..800b1ae7a7b52 100644 --- a/data/cardiofan/cardiofanbioschemas.jsonld +++ b/data/cardiofan/cardiofanbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "MIT", "sc:name": "CardioFAN", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/YasharVahedein/CardioFAN" diff --git a/data/cargo/cargobioschemas.jsonld b/data/cargo/cargobioschemas.jsonld index 25edfb4fb8292..10619381070f6 100644 --- a/data/cargo/cargobioschemas.jsonld +++ b/data/cargo/cargobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.", "sc:name": "CARGO", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html" } \ No newline at end of file diff --git a/data/carmaweb/carmawebbioschemas.jsonld b/data/carmaweb/carmawebbioschemas.jsonld index 3a7d6dd52dc5b..fef288aad633d 100644 --- a/data/carmaweb/carmawebbioschemas.jsonld +++ b/data/carmaweb/carmawebbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor.", "sc:name": "CARMAweb", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://carmaweb.genome.tugraz.at/carma/" } \ No newline at end of file diff --git a/data/carna/carnabioschemas.jsonld b/data/carna/carnabioschemas.jsonld index 4ac2f7514c347..e2a5c3caa41e6 100644 --- a/data/carna/carnabioschemas.jsonld +++ b/data/carna/carnabioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gks491", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-8231-3323", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/carna", "@type": "sc:SoftwareApplication", @@ -33,23 +25,23 @@ { "@id": "edam:data_2044" }, - { - "@id": "edam:data_0872" - }, { "@id": "edam:data_2968" }, { "@id": "edam:data_1916" + }, + { + "@id": "edam:data_0872" } ], "sc:additionalType": "Web application", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0097" + "@id": "edam:topic_0080" }, { - "@id": "edam:topic_0080" + "@id": "edam:topic_0097" } ], "sc:author": [ @@ -59,11 +51,11 @@ "Sebastian Will" ], "sc:citation": [ + "pmcid:PMC3394245", + "pubmed:22689637", { "@id": "https://doi.org/10.1093/nar/gks491" - }, - "pmcid:PMC3394245", - "pubmed:22689637" + } ], "sc:description": "Alignment of RNA structure ensembles.", "sc:featureList": { @@ -72,9 +64,9 @@ "sc:isAccessibleForFree": true, "sc:name": "CARNA web server", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "University Freiburg", @@ -85,6 +77,14 @@ }, "sc:url": "http://rna.informatik.uni-freiburg.de/CARNA/", "sc:version": "1.2.5" + }, + { + "@id": "http://orcid.org/0000-0001-8231-3323", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gks491", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/carnac/carnacbioschemas.jsonld b/data/carnac/carnacbioschemas.jsonld index 535adb3810bc9..7324714d99518 100644 --- a/data/carnac/carnacbioschemas.jsonld +++ b/data/carnac/carnacbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.", "sc:name": "CARNAC", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioinfo.lifl.fr/carnac" diff --git a/data/carrie/carriebioschemas.jsonld b/data/carrie/carriebioschemas.jsonld index 36fd502cf027b..9acfdb9b7c38e 100644 --- a/data/carrie/carriebioschemas.jsonld +++ b/data/carrie/carriebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.", "sc:name": "CARRIE", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://zlab.bu.edu/CARRIE-web" } \ No newline at end of file diff --git a/data/carrot/carrotbioschemas.jsonld b/data/carrot/carrotbioschemas.jsonld index 9feff1645fa6b..b859d905ced9d 100644 --- a/data/carrot/carrotbioschemas.jsonld +++ b/data/carrot/carrotbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "CARROT is a tool for relationship inference that leverages linkage disequilibrium to differentiate between rotated relationships, such as (first-, second-, etc) uncle-niece.", "sc:name": "CARROT", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://carrot.stanford.edu/" } \ No newline at end of file diff --git a/data/cartaj/cartajbioschemas.jsonld b/data/cartaj/cartajbioschemas.jsonld index 11291ec8759c7..f5f99ba8720be 100644 --- a/data/cartaj/cartajbioschemas.jsonld +++ b/data/cartaj/cartajbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/cartaj", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web service" + "Web service", + "Command-line tool" ], "sc:citation": "pubmed:22326420", "sc:description": "This software automatically predicts the topological family of any RNA three-way junction, given only the information from the secondary structure: the sequence and the canonical Watson–Crick pairings.", "sc:name": "Cartaj", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://cartaj.lri.fr/" } \ No newline at end of file diff --git a/data/carthagene/carthagenebioschemas.jsonld b/data/carthagene/carthagenebioschemas.jsonld index f509f3e195313..0a11807d2ed48 100644 --- a/data/carthagene/carthagenebioschemas.jsonld +++ b/data/carthagene/carthagenebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Genetic/radiated hybrid mapping software that looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms. It solves marker ordering problems and can also join maps (genetic or radiated hybrid) on various pedigrees: backcross, RI (ri self, ri sib), F2 intercross, phase known outbreds, haploid and diploid radiation hybrids up to now.", "sc:name": "CarthaGene 1.3 beta", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://forgemia.inra.fr/thomas.schiex/carthagene" } \ No newline at end of file diff --git a/data/cartogratree/cartogratreebioschemas.jsonld b/data/cartogratree/cartogratreebioschemas.jsonld index 7a78bc369e859..2eb6c510f0a18 100644 --- a/data/cartogratree/cartogratreebioschemas.jsonld +++ b/data/cartogratree/cartogratreebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "CartograTree is a web-based application that allows researchers to identify, filter, compare, and visualize geo-referenced biotic and abiotic data. Its goal is to support numerous multi-disciplinary research endeavors including: phylogenetics, population structure, and association studies.", "sc:name": "CartograTree", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://dendrome.ucdavis.edu/cartogratree/" } \ No newline at end of file diff --git a/data/cas-analyzer/cas-analyzerbioschemas.jsonld b/data/cas-analyzer/cas-analyzerbioschemas.jsonld index 2b7a5acaf394c..b8f7398fc9267 100644 --- a/data/cas-analyzer/cas-analyzerbioschemas.jsonld +++ b/data/cas-analyzer/cas-analyzerbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Unlicense", "sc:name": "Cas-analyzer", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.rgenome.net/cas-analyzer/" diff --git a/data/cas-designer/cas-designerbioschemas.jsonld b/data/cas-designer/cas-designerbioschemas.jsonld index 4aa24693e38fe..cedd6d8a37f6d 100644 --- a/data/cas-designer/cas-designerbioschemas.jsonld +++ b/data/cas-designer/cas-designerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Cas-Designer", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://rgenome.net/cas-designer/" } \ No newline at end of file diff --git a/data/cas/casbioschemas.jsonld b/data/cas/casbioschemas.jsonld index f9d022a5bda19..92ec1d352b649 100644 --- a/data/cas/casbioschemas.jsonld +++ b/data/cas/casbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "It is a software for simulating radiogenic aberrations in detail.This software simulates chromosomal rearrangements produced by ionizing radiation during the G0/G1 phase of the cell cycle. It gives a cell-by-cell record of simulated rearrangements, much as in an actual experiment.", "sc:name": "CAS", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://radiobiology.math.berkeley.edu/CAS/index.html" } \ No newline at end of file diff --git a/data/cas_image_analysis/cas_image_analysisbioschemas.jsonld b/data/cas_image_analysis/cas_image_analysisbioschemas.jsonld index 9b635429a4517..2eb66d91d625d 100644 --- a/data/cas_image_analysis/cas_image_analysisbioschemas.jsonld +++ b/data/cas_image_analysis/cas_image_analysisbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1007/s12021-017-9340-2", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cas_image_analysis", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Karolina Nurzynska", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5671565", - "pubmed:28849545", { "@id": "https://doi.org/10.1007/s12021-017-9340-2" - } + }, + "pmcid:PMC5671565", + "pubmed:28849545" ], "sc:description": "Cell Annotation Software was designed for neuroscience research by researchers specializing in an image processing domain.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "CAS", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://home.agh.edu.pl/~pioro/cas/" - }, - { - "@id": "https://doi.org/10.1007/s12021-017-9340-2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cascade/cascadebioschemas.jsonld b/data/cascade/cascadebioschemas.jsonld index 3293fbcbe22e7..8732c0bc448e0 100644 --- a/data/cascade/cascadebioschemas.jsonld +++ b/data/cascade/cascadebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This package is an integrated solution adding several new and original key features such as the ability to predict changes in gene expressions after a biological perturbation in the network and graphical outputs that allow monitoring the spread of a signal through the network.", "sc:name": "Cascade", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www-math.u-strasbg.fr/genpred/spip.php?article3" } \ No newline at end of file diff --git a/data/cascade_visualization/cascade_visualizationbioschemas.jsonld b/data/cascade_visualization/cascade_visualizationbioschemas.jsonld index fef6c8bb64beb..87fe7a4ec4b76 100644 --- a/data/cascade_visualization/cascade_visualizationbioschemas.jsonld +++ b/data/cascade_visualization/cascade_visualizationbioschemas.jsonld @@ -17,11 +17,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4727405", + "pubmed:26810393", { "@id": "https://doi.org/10.1186/s12864-016-2389-8" }, - "pubmed:26810393" + "pmcid:PMC4727405" ], "sc:description": "Cascade is a web based tool for the intuitive 3D visualization of RNA-seq data from cancer genomics experiments.", "sc:featureList": { @@ -36,13 +36,13 @@ ], "sc:url": "http://bioinfo.iric.ca/~shifmana/Cascade/" }, - { - "@id": "http://orcid.org/0000-0003-2140-7590", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12864-016-2389-8", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-2140-7590", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/casian/casianbioschemas.jsonld b/data/casian/casianbioschemas.jsonld index 763cd6c970fc4..116975f8d66ed 100644 --- a/data/casian/casianbioschemas.jsonld +++ b/data/casian/casianbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "CaSiAn", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://r3lab.uni.lu/web/casa" } \ No newline at end of file diff --git a/data/casnp/casnpbioschemas.jsonld b/data/casnp/casnpbioschemas.jsonld index 3d15ea1671af5..315d78ba69f87 100644 --- a/data/casnp/casnpbioschemas.jsonld +++ b/data/casnp/casnpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database for storing and interrogating quantitative copy number alterations (CNA) data from SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, it will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study. It also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization.", "sc:name": "CaSNP", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://cistrome.dfci.harvard.edu/CaSNP/" } \ No newline at end of file diff --git a/data/casper/casperbioschemas.jsonld b/data/casper/casperbioschemas.jsonld index 07603e0071b3c..e592ffe50495e 100644 --- a/data/casper/casperbioschemas.jsonld +++ b/data/casper/casperbioschemas.jsonld @@ -14,15 +14,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David Rossell", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pmcid:PMC4005600", - "pubmed:24795787", { "@id": "https://doi.org/10.1214/13-AOAS687" - } + }, + "pubmed:24795787" ], "sc:description": "Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.", "sc:featureList": { @@ -31,9 +31,9 @@ "sc:license": "GPL-2.0", "sc:name": "casper", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/casper.html", "sc:version": "2.8.0" diff --git a/data/cassis/cassisbioschemas.jsonld b/data/cassis/cassisbioschemas.jsonld index 7e45972d40c1f..6f5c69d3a99d6 100644 --- a/data/cassis/cassisbioschemas.jsonld +++ b/data/cassis/cassisbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "cluster assignment by islands of sites, is a tool to predict secondary metabolite (SM) gene clusters around a given anchor (or backbone) gene.", "sc:name": "CASSIS", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sbi.hki-jena.de/cassis/" } \ No newline at end of file diff --git a/data/cassys/cassysbioschemas.jsonld b/data/cassys/cassysbioschemas.jsonld index 3a3ab3ae52871..0acd9265dc825 100644 --- a/data/cassys/cassysbioschemas.jsonld +++ b/data/cassys/cassysbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "An integrated system that supports all steps of computational ChIP-seq data analysis and supersedes the laborious application of several single command line tools. It provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping) and the detection of enriched regions (peakdetection) to various follow-up analyses.", "sc:name": "CASSys", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.zbh.uni-hamburg.de/en/research/application-oriented-bioinformatics/researchprojects/cassys.html" } \ No newline at end of file diff --git a/data/castp/castpbioschemas.jsonld b/data/castp/castpbioschemas.jsonld index 5dafa18b74c89..62764aead9b46 100644 --- a/data/castp/castpbioschemas.jsonld +++ b/data/castp/castpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.", "sc:name": "CASTp", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://sts.bioe.uic.edu/castp/" } \ No newline at end of file diff --git a/data/catalysis_hub/catalysis_hubbioschemas.jsonld b/data/catalysis_hub/catalysis_hubbioschemas.jsonld index 9510c59fcff11..30febac8a4ad5 100644 --- a/data/catalysis_hub/catalysis_hubbioschemas.jsonld +++ b/data/catalysis_hub/catalysis_hubbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/S41597-019-0081-Y", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Catalysis_Hub", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kirsten Winther", - "Thomas Bligaard" + "Thomas Bligaard", + "Kirsten Winther" ], "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31138816", + "pmcid:PMC6538711", { "@id": "https://doi.org/10.1038/S41597-019-0081-Y" - }, - "pubmed:31138816", - "pmcid:PMC6538711" + } ], "sc:description": "Web-platform for sharing data and software for computational catalysis research.", "sc:featureList": [ @@ -37,14 +41,10 @@ "sc:name": "Catalysis Hub", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.catalysis-hub.org" - }, - { - "@id": "https://doi.org/10.1038/S41597-019-0081-Y", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/catalyst/catalystbioschemas.jsonld b/data/catalyst/catalystbioschemas.jsonld index 3c187158ecced..6ce03e0401338 100644 --- a/data/catalyst/catalystbioschemas.jsonld +++ b/data/catalyst/catalystbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "CATALYST", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CATALYST.html", diff --git a/data/catalytic_site_identification/catalytic_site_identificationbioschemas.jsonld b/data/catalytic_site_identification/catalytic_site_identificationbioschemas.jsonld index 6cdf3266a2f17..e4392b3a65487 100644 --- a/data/catalytic_site_identification/catalytic_site_identificationbioschemas.jsonld +++ b/data/catalytic_site_identification/catalytic_site_identificationbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/catalytic_site_identification", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:23680785", "sc:description": "Provides the ability to find structural matches to a user-specified catalytic site among all Protein Data Bank (PDB) proteins. The web server can also examine a user-specified protein to identify structural matches to a library of catalytic sites.", diff --git a/data/catana/catanabioschemas.jsonld b/data/catana/catanabioschemas.jsonld index 5359820b0b1db..dc954485d15ef 100644 --- a/data/catana/catanabioschemas.jsonld +++ b/data/catana/catanabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "CATANA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/shiauck/CATANA", "sc:version": "1.0" diff --git a/data/catch/catchbioschemas.jsonld b/data/catch/catchbioschemas.jsonld index ee148ad5eebb5..e3d364697ec7b 100644 --- a/data/catch/catchbioschemas.jsonld +++ b/data/catch/catchbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool for exploring patterns in ChIP profiling data.", "sc:name": "CATCH", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://catch.cmbi.ru.nl" } \ No newline at end of file diff --git a/data/catdb/catdbbioschemas.jsonld b/data/catdb/catdbbioschemas.jsonld index 6b19db4ab8a3d..7f924ceccef68 100644 --- a/data/catdb/catdbbioschemas.jsonld +++ b/data/catdb/catdbbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkm757", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/catdb", "@type": "sc:SoftwareApplication", @@ -39,10 +43,10 @@ ], "sc:citation": [ "pubmed:17940091", + "pmcid:PMC2238931", { "@id": "https://doi.org/10.1093/nar/gkm757" - }, - "pmcid:PMC2238931" + } ], "sc:description": "This database contains data on 105 Arabidopsis transcriptome projects (3262 hybridized samples) in public access out of a total of 172 projects (~6440 hybridized samples).", "sc:featureList": { @@ -56,10 +60,6 @@ ], "sc:provider": "Unité de Recherche en Génomique Végétale", "sc:url": "http://urgv.evry.inra.fr/CATdb" - }, - { - "@id": "https://doi.org/10.1093/nar/gkm757", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/category/bioconda_category.yaml b/data/category/bioconda_category.yaml index 3b926110dedf0..e396ed5568051 100644 --- a/data/category/bioconda_category.yaml +++ b/data/category/bioconda_category.yaml @@ -3,7 +3,6 @@ description: A collection of tools for performing category (gene set enrichment) home: https://bioconductor.org/packages/3.10/bioc/html/Category.html identifiers: - biotools:category -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-category summary: Category Analysis diff --git a/data/category/categorybioschemas.jsonld b/data/category/categorybioschemas.jsonld index e988a6bccec39..c554812a65c2b 100644 --- a/data/category/categorybioschemas.jsonld +++ b/data/category/categorybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "Category", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Category.html", "sc:version": "2.40.0" diff --git a/data/categorycompare/categorycomparebioschemas.jsonld b/data/categorycompare/categorycomparebioschemas.jsonld index 0dcfc2e1a1d2a..6520943ef3a03 100644 --- a/data/categorycompare/categorycomparebioschemas.jsonld +++ b/data/categorycompare/categorycomparebioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "http://orcid.org/0000-0001-8141-7788", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.3389/fgene.2014.00098", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/categorycompare", "@type": "sc:SoftwareApplication", @@ -24,15 +28,15 @@ }, "edam:has_output": [ { - "@id": "edam:data_2600" + "@id": "edam:data_1669" }, { - "@id": "edam:data_1669" + "@id": "edam:data_2600" } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { @@ -56,16 +60,12 @@ "sc:license": "GPL-2.0", "sc:name": "categoryCompare", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/categoryCompare.html", "sc:version": "1.18.0" - }, - { - "@id": "https://doi.org/10.3389/fgene.2014.00098", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cath/cathbioschemas.jsonld b/data/cath/cathbioschemas.jsonld index 4f6190df7342f..fa985ec1a1a18 100644 --- a/data/cath/cathbioschemas.jsonld +++ b/data/cath/cathbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "CATH is a manually curated classification of protein domain structures. Each protein has been chopped into structural domains and assigned into homologous superfamilies (groups of domains that are related by evolution). This classification procedure uses a combination of automated and manual techniques which include computational algorithms, empirical and statistical evidence, literature review and expert analysis.", "sc:name": "CATH", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.cathdb.info/" diff --git a/data/cato/catobioschemas.jsonld b/data/cato/catobioschemas.jsonld index e0af4ccf7cce3..bf11cd382ed6c 100644 --- a/data/cato/catobioschemas.jsonld +++ b/data/cato/catobioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0159586", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cato", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Peter LaPan", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC4961376", "pubmed:27459605", + "pmcid:PMC4961376", { "@id": "https://doi.org/10.1371/journal.pone.0159586" } @@ -33,6 +29,10 @@ "sc:name": "CATO", "sc:operatingSystem": "Windows", "sc:url": "https://sourceforge.net/projects/cato-clone-alignment-tool/" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0159586", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/catrapid/catrapidbioschemas.jsonld b/data/catrapid/catrapidbioschemas.jsonld index 2f7503945b4c6..0a9f3198936fa 100644 --- a/data/catrapid/catrapidbioschemas.jsonld +++ b/data/catrapid/catrapidbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Aan algorithm to estimate the binding propensity of protein-RNA pairs. By combining secondary structure, hydrogen bonding and van der Waals contributions, catRAPID predicts protein-RNA associations with great accuracy.", "sc:name": "catRAPID", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://s.tartaglialab.com/page/catrapid_group" } \ No newline at end of file diff --git a/data/cats/catsbioschemas.jsonld b/data/cats/catsbioschemas.jsonld index adc8c20e68c95..1e985d6e119df 100644 --- a/data/cats/catsbioschemas.jsonld +++ b/data/cats/catsbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/cats", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Suite", - "Web application" + "Web application", + "Suite" ], "sc:description": "A unification of several software tools for sequence analysis developed at the IPK Gatersleben. The web BLAST server utilizes a homology search against the current cereal genome sequence resources (barley, rye and bread wheat). Kmasker plants is able to mask sequences originating from ten agronomically important plants based on mathematical defined repeats, furthermore, selection of sequences applicable for guideRNA construction for genome editing (CRISPR) or for fluorescence in situ hybridization is also possible. MISA web searches a nucleotide sequence for microsatellites and is able generate molecular markers or primer. Within BRIDGE the complete barley collection of the IPK genebank can be visually explored in an interactive manner through diversity, certain phenotyped traits, and based on sequence polymorphisms. The barley genome explorer (BARLEX) is a system to visually inspect the reference genome sequence of barley.", "sc:license": "Other", "sc:name": "Crop Analyis Tools Suite (CATS)", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://cats.ipk-gatersleben.de/" } \ No newline at end of file diff --git a/data/causalr/bioconda_causalr.yaml b/data/causalr/bioconda_causalr.yaml index 69eaa11119d0f..ec2a0f08545a4 100644 --- a/data/causalr/bioconda_causalr.yaml +++ b/data/causalr/bioconda_causalr.yaml @@ -4,7 +4,6 @@ description: Causal network analysis methods for regulator prediction and networ home: https://bioconductor.org/packages/3.10/bioc/html/CausalR.html identifiers: - biotools:causalr -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-causalr diff --git a/data/causalr/causalrbioschemas.jsonld b/data/causalr/causalrbioschemas.jsonld index d62b4e3c017d3..ff9ab797e4619 100644 --- a/data/causalr/causalrbioschemas.jsonld +++ b/data/causalr/causalrbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/causalr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Glyn Bradley", "Steven Barrett", - "Bhushan Bonde", - "Glyn Bradley" + "Bhushan Bonde" ], "sc:additionalType": [ "Library", diff --git a/data/causaltrail/causaltrailbioschemas.jsonld b/data/causaltrail/causaltrailbioschemas.jsonld index 317435c1800cf..9aada97d0f8a2 100644 --- a/data/causaltrail/causaltrailbioschemas.jsonld +++ b/data/causaltrail/causaltrailbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.7647.1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/causaltrail", "@type": "sc:SoftwareApplication", @@ -20,31 +24,27 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:26913195", + "pmcid:PMC4743151", { "@id": "https://doi.org/10.12688/F1000RESEARCH.7647.1" - }, - "pmcid:PMC4743151", - "pubmed:26913195" + } ], "sc:description": "Provides causal hypotheses testing using causal bayesian networks (CBN) and the do-calculus. Includes include multiple data import methods, a flexible query language for formulating hypotheses, as well as an intuitive graphical user interface.", "sc:featureList": [ { - "@id": "edam:operation_3658" + "@id": "edam:operation_0337" }, { "@id": "edam:operation_2238" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_3658" } ], "sc:license": "GPL-3.0", "sc:name": "CausalTrail", "sc:url": "https://github.com/unisb-bioinf/causaltrail" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.7647.1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/caver/caverbioschemas.jsonld b/data/caver/caverbioschemas.jsonld index a58ac62d81a0b..81258ec8c0331 100644 --- a/data/caver/caverbioschemas.jsonld +++ b/data/caver/caverbioschemas.jsonld @@ -12,18 +12,18 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Vilem Sustr", - "Jan Brezovsky", - "Ondrej Strnad", + "Barbora Kozlikova", + "Eva Chovancova", "Antonin Pavelka", - "Artur Gora", "Petr Benes", - "Jiri Sochor", - "Petr Medek", - "Eva Chovancova", "Martin Klvana", + "Jan Brezovsky", + "Jiri Sochor", + "Vilem Sustr", + "Artur Gora", "Jiri Damborsky", - "Barbora Kozlikova", + "Petr Medek", + "Ondrej Strnad", "Lada Biedermannova" ], "sc:description": "A tool for identification and analysis of tunnels and channels in static and dynamic protein structures.", @@ -31,12 +31,12 @@ "sc:name": "CAVER", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ - "International Centre for Clinical Research, Brno, Czech Republic", "Masaryk University, Brno, Czech Republic", + "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories" ], "sc:url": "http://www.caver.cz", diff --git a/data/caver_analyst/caver_analystbioschemas.jsonld b/data/caver_analyst/caver_analystbioschemas.jsonld index 3e69ef12975cb..d674ed0a8a594 100644 --- a/data/caver_analyst/caver_analystbioschemas.jsonld +++ b/data/caver_analyst/caver_analystbioschemas.jsonld @@ -12,32 +12,32 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:author": [ + "Lukas Daniel", + "Matus Kotry", "David Bednar", - "Martin Bezdeka", "Barbora Kozlikova", - "Antonin Pavelka", - "Artur Gora", - "Matus Kotry", - "Ondrej Strnad", - "Martin Manak", + "Jiri Damborsky", + "Jan Brezovsky", "Vilem Sustr", - "Jiri Sochor", "Eva Sebestova", - "Jiri Damborsky", - "Lukas Daniel", + "Martin Bezdeka", + "Ondrej Strnad", + "Antonin Pavelka", + "Artur Gora", "Petr Benes", - "Jan Brezovsky" + "Jiri Sochor", + "Martin Manak" ], "sc:description": "A tool for interactive visualization and analysis of tunnels, channels and cavities in protein structures.", "sc:name": "CAVER Analyst", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "University of West Bohemia, Plzen, Czech Republic", "Masaryk University, Brno, Czech Republic", + "University of West Bohemia, Plzen, Czech Republic", "Loschmidt Laboratories" ], "sc:url": "http://www.caver.cz", diff --git a/data/caver_pymol_plugin/caver_pymol_pluginbioschemas.jsonld b/data/caver_pymol_plugin/caver_pymol_pluginbioschemas.jsonld index 2d0cf055d009d..eaf3758761a7a 100644 --- a/data/caver_pymol_plugin/caver_pymol_pluginbioschemas.jsonld +++ b/data/caver_pymol_plugin/caver_pymol_pluginbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Library", "sc:author": [ - "Petr Medek", "Lada Biedermannova", - "Jan Brezovsky", - "Artur Gora", - "Barbora Kozlikova", - "Martin Klvana", "Vilem Sustr", - "Jiri Sochor", + "Martin Klvana", + "Artur Gora", "Jiri Damborsky", - "Antonin Pavelka", - "Eva Chovancova", + "Petr Medek", "Petr Benes", - "Ondrej Strnad" + "Barbora Kozlikova", + "Eva Chovancova", + "Ondrej Strnad", + "Antonin Pavelka", + "Jiri Sochor", + "Jan Brezovsky" ], "sc:description": "A PyMOL plugin for identification and analysis of tunnels and channels in static protein structures.", "sc:license": "GPL-3.0", "sc:name": "CAVER PyMOL plugin", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ "Loschmidt Laboratories", diff --git a/data/caver_web/caver_webbioschemas.jsonld b/data/caver_web/caver_webbioschemas.jsonld index e18fe90368935..99ae295c77fd1 100644 --- a/data/caver_web/caver_webbioschemas.jsonld +++ b/data/caver_web/caver_webbioschemas.jsonld @@ -13,20 +13,20 @@ "sc:additionalType": "Web application", "sc:author": [ "Jan Brezovsky", - "Jan Stourac", - "Jiri Damborsky" + "Jiri Damborsky", + "Jan Stourac" ], "sc:contributor": "Antonin Pavelka", "sc:description": "A web interface for identification and analysis of tunnels and channels in static protein structures with automated starting point detection.", "sc:name": "CAVER Web", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ - "International Centre for Clinical Research, Brno, Czech Republic", "Masaryk University, Brno, Czech Republic", + "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories" ], "sc:url": "http://loschmidt.chemi.muni.cz/caverweb/", diff --git a/data/caverdock/caverdockbioschemas.jsonld b/data/caverdock/caverdockbioschemas.jsonld index 3dd716d45f60b..43ff90ee9d7f4 100644 --- a/data/caverdock/caverdockbioschemas.jsonld +++ b/data/caverdock/caverdockbioschemas.jsonld @@ -12,24 +12,24 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Ondrej Vavra", "Jan Plhak", + "Ondrej Vavra", "Jiri Filipovic" ], "sc:contributor": [ + "Ludek Matyska", "Sergio Manuel Marques", "Jiri Damborsky", - "David Bednar", - "Ludek Matyska", - "Jan Brezovsky" + "Jan Brezovsky", + "David Bednar" ], "sc:description": "Performs rapid analysis of transport processes in proteins. It models the transportation of a ligand from outside environment into the protein active or binding site and vice versa. It implements a novel algorithm to produce contiguous ligand trajectory and estimation of a binding energy along the pathway. The current version uses CAVER for pathway identification and heavily modified Autodock Vina as a docking engine.", "sc:license": "Proprietary", "sc:name": "CaverDock", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://loschmidt.chemi.muni.cz/caverdock/", "sc:version": "1.0" diff --git a/data/caw/cawbioschemas.jsonld b/data/caw/cawbioschemas.jsonld index 9560d147a14cc..3a004e5353558 100644 --- a/data/caw/cawbioschemas.jsonld +++ b/data/caw/cawbioschemas.jsonld @@ -16,8 +16,8 @@ "@id": "https://orcid.org/0000-0003-2827-9261" }, "sc:additionalType": [ - "Command-line tool", - "Workflow" + "Workflow", + "Command-line tool" ], "sc:description": "Project has changed name: sarek", "sc:license": "MIT", @@ -26,12 +26,12 @@ "sc:url": "https://nf-co.re/sarek", "sc:version": [ "1.2.4", - "1.2.0", - "1.0", "1.2.5", - "1.2.2", - "1.2.1", "1.2.3", + "1.2.1", + "1.2.0", + "1.2.2", + "1.0", "1.1" ] }, diff --git a/data/cazy/cazybioschemas.jsonld b/data/cazy/cazybioschemas.jsonld index 199ce2656dbb2..ad71cf6bd749e 100644 --- a/data/cazy/cazybioschemas.jsonld +++ b/data/cazy/cazybioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkt1178", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cazy", "@type": "sc:SoftwareApplication", @@ -24,11 +28,11 @@ "@id": "edam:topic_0821" }, "sc:citation": [ + "pmcid:PMC3965031", + "pubmed:24270786", { "@id": "https://doi.org/10.1093/nar/gkt1178" - }, - "pmcid:PMC3965031", - "pubmed:24270786" + } ], "sc:description": "The database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.", "sc:featureList": { @@ -37,15 +41,11 @@ "sc:name": "Carbohydrate-active enzymes database (CAZy)", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "AFMB", "sc:url": "http://www.cazy.org/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkt1178", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cbaf/cbafbioschemas.jsonld b/data/cbaf/cbafbioschemas.jsonld index 2d959ff429102..f79568343d7b4 100644 --- a/data/cbaf/cbafbioschemas.jsonld +++ b/data/cbaf/cbafbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "cbaf", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cbaf.html", "sc:version": "1.2.0" diff --git a/data/cbarbel/cbarbelbioschemas.jsonld b/data/cbarbel/cbarbelbioschemas.jsonld index 88f0a7dec2bca..d04830d0a7477 100644 --- a/data/cbarbel/cbarbelbioschemas.jsonld +++ b/data/cbarbel/cbarbelbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes.", "sc:name": "The catfish genome database (cBARBEL)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://catfishgenome.org" } \ No newline at end of file diff --git a/data/cbcanalyzer/cbcanalyzerbioschemas.jsonld b/data/cbcanalyzer/cbcanalyzerbioschemas.jsonld index 13d7f875fc17d..f08655cc17aa3 100644 --- a/data/cbcanalyzer/cbcanalyzerbioschemas.jsonld +++ b/data/cbcanalyzer/cbcanalyzerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "CBCAnalyzer ( compensatory base change) is a custom written software toolbox consisting of three parts, CTTransform, CBCDetect, and CBCTree. CTTransform reads several CT-file formats (ct, RNAviz ct or Mac ct), and generates a so called “bracket-dot-bracket” format that typically is used as input for other tools such as RNAforester, RNAmovie or MARNA. The latter one creates a multiple alignment based on primary sequences and secondary structures that now can be used as input for CBCDetect. It consists of three parts, CTTransform, CBCDetect, and CBCTree. CTTransform reads several CT-file formats and generates a so called “bracket-dot-bracket” format that typically is used as input for other tools such as RNAforester, RNAmovie or MARNA. The latter one creates a multiple alignment based on primary sequences and secondary structures that now can be used as input for CBCDetect. The count matrix obtained by CBCDetect is used as input for CBCTree.", "sc:name": "CBCAnalyzer 1.1 beta", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://cbcanalyzer.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.php" } \ No newline at end of file diff --git a/data/cbgt/cbgtbioschemas.jsonld b/data/cbgt/cbgtbioschemas.jsonld index fb96cc303f2f5..913c6f37fbb51 100644 --- a/data/cbgt/cbgtbioschemas.jsonld +++ b/data/cbgt/cbgtbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006998", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0002-1513-1551", "@type": "schema:Person" @@ -30,24 +34,20 @@ ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:31060045", "pmcid:PMC6534331", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006998" - } + }, + "pubmed:31060045" ], "sc:description": "Spiking Neural Network of cortico-basal ganglia-thalamus (CBGT) pathways.", "sc:license": "Other", "sc:name": "CBGT", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/CoAxLab/CBGT" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006998", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cbo/cbobioschemas.jsonld b/data/cbo/cbobioschemas.jsonld index b9c3a7ed32492..246b6bc545dc7 100644 --- a/data/cbo/cbobioschemas.jsonld +++ b/data/cbo/cbobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CBO", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://cbo.biocomplexity.indiana.edu/" } \ No newline at end of file diff --git a/data/cbs_das_protein_viewer/cbs_das_protein_viewerbioschemas.jsonld b/data/cbs_das_protein_viewer/cbs_das_protein_viewerbioschemas.jsonld index eb0881e632636..0544e1706482a 100644 --- a/data/cbs_das_protein_viewer/cbs_das_protein_viewerbioschemas.jsonld +++ b/data/cbs_das_protein_viewer/cbs_das_protein_viewerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Other", "sc:name": "CBS DAS protein viewer", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.cbs.dtu.dk/cgi-bin/proview/view_encode?id=Z69720.1-001" diff --git a/data/cbspredict/cbspredictbioschemas.jsonld b/data/cbspredict/cbspredictbioschemas.jsonld index 6e274f19c1cc8..20be0109bee78 100644 --- a/data/cbspredict/cbspredictbioschemas.jsonld +++ b/data/cbspredict/cbspredictbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Given a protein structure (PDB file), cbsPredict will identify potential carbohydrate-binding sites based on detection of coplanar, aromatic residues located on the protein surface.", "sc:name": "cbsPredict", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://doxey.uwaterloo.ca/cgi-bin/cbsPredict.cgi" diff --git a/data/ccancer/ccancerbioschemas.jsonld b/data/ccancer/ccancerbioschemas.jsonld index 066e82cb3d0a4..5b9ec82ab2f60 100644 --- a/data/ccancer/ccancerbioschemas.jsonld +++ b/data/ccancer/ccancerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene list.", "sc:name": "CCancer", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://mips.helmholtz-muenchen.de/proj/ccancer" } \ No newline at end of file diff --git a/data/ccap/ccapbioschemas.jsonld b/data/ccap/ccapbioschemas.jsonld index aadf699430823..508ff1d763a36 100644 --- a/data/ccap/ccapbioschemas.jsonld +++ b/data/ccap/ccapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Culture collection of algae and protozoa (CCAP)", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ccap.ac.uk/index.htm" } \ No newline at end of file diff --git a/data/ccb/ccbbioschemas.jsonld b/data/ccb/ccbbioschemas.jsonld index 06a8e455f5bd0..cd53f20b1f905 100644 --- a/data/ccb/ccbbioschemas.jsonld +++ b/data/ccb/ccbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Cell Cycle Browser (CCB)", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cellcycle.renci.org/", "sc:version": "1.0" diff --git a/data/cccpp/cccppbioschemas.jsonld b/data/cccpp/cccppbioschemas.jsonld index ce4fe14a272ca..754766ebd9b82 100644 --- a/data/cccpp/cccppbioschemas.jsonld +++ b/data/cccpp/cccppbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "This software computes the void parts of the proteins, i.e. cavities, channels and pockets.", "sc:name": "CCCPP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CCCPP" } \ No newline at end of file diff --git a/data/ccfold/ccfoldbioschemas.jsonld b/data/ccfold/ccfoldbioschemas.jsonld index 66ba0a18840e6..f7173cb26e2de 100644 --- a/data/ccfold/ccfoldbioschemas.jsonld +++ b/data/ccfold/ccfoldbioschemas.jsonld @@ -12,14 +12,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sergei Strelkov", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Rapid and accurate prediction of coiled-coil structures.", "sc:name": "CCFold", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://pharm.kuleuven.be/apps/biocryst/ccfold.php" diff --git a/data/ccharppi/ccharppibioschemas.jsonld b/data/ccharppi/ccharppibioschemas.jsonld index daee0f4765f39..8b5efb74cd2dc 100644 --- a/data/ccharppi/ccharppibioschemas.jsonld +++ b/data/ccharppi/ccharppibioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7786-2109", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/ccharppi", "@type": "sc:SoftwareApplication", @@ -20,8 +24,8 @@ "sc:description": "Many of protein structural characterization tools integrated into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions.", "sc:name": "CCharPPI", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ @@ -30,10 +34,6 @@ ], "sc:url": "https://life.bsc.es/pid/ccharppi/", "sc:version": "1" - }, - { - "@id": "http://orcid.org/0000-0001-7786-2109", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/cchmmprof/cchmmprofbioschemas.jsonld b/data/cchmmprof/cchmmprofbioschemas.jsonld index bea0143315876..c8269326bdc2d 100644 --- a/data/cchmmprof/cchmmprofbioschemas.jsonld +++ b/data/cchmmprof/cchmmprofbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An HMM-based predictor of coiled-coil segments in proteins.", "sc:name": "CCHMMPROF", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", diff --git a/data/cclasso/cclassobioschemas.jsonld b/data/cclasso/cclassobioschemas.jsonld index e190856bfc352..8a350595aea54 100644 --- a/data/cclasso/cclassobioschemas.jsonld +++ b/data/cclasso/cclassobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Novel method based on least squares with ℓ1 penalty to infer the correlation network for latent variables of compositional data from metagenomic data.", "sc:name": "CCLasso", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.math.pku.edu.cn/teachers/dengmh/CCLasso/" } \ No newline at end of file diff --git a/data/ccle_gdsc/ccle_gdscbioschemas.jsonld b/data/ccle_gdsc/ccle_gdscbioschemas.jsonld index cd5dc107ed643..8fa135a63e656 100644 --- a/data/ccle_gdsc/ccle_gdscbioschemas.jsonld +++ b/data/ccle_gdsc/ccle_gdscbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jason Roszik", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:description": "Databases which contain gene expression levels from next generation sequencing and also drug screening data for a large number of cancer cell lines.", "sc:name": "CCLE GDSC", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://public.tableau.com/profile/jason.roszik#!/vizhome/CCLE_GDSC_correlations/CCLE_GDSC" } \ No newline at end of file diff --git a/data/ccmap/ccmapbioschemas.jsonld b/data/ccmap/ccmapbioschemas.jsonld index 1bd2c6c136326..f64540bb665f4 100644 --- a/data/ccmap/ccmapbioschemas.jsonld +++ b/data/ccmap/ccmapbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alex Pickering", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Finds drugs and drug combinations that are predicted to reverse or mimic gene expression signatures. These drugs might reverse diseases or mimic healthy lifestyles.", "sc:license": "MIT", "sc:name": "ccmap", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ccmap.html", "sc:version": "1.0.0" diff --git a/data/ccmetagen/ccmetagenbioschemas.jsonld b/data/ccmetagen/ccmetagenbioschemas.jsonld index 035ad0a3af045..aa79907b7d346 100644 --- a/data/ccmetagen/ccmetagenbioschemas.jsonld +++ b/data/ccmetagen/ccmetagenbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Vanessa R. Marcelino", "sc:additionalType": [ - "Web application", "Web service", + "Web application", "Command-line tool" ], "sc:description": "Pipeline to classify organisms in metagenomes or metatranscriptomes accurately.", "sc:license": "GPL-3.0", "sc:name": "CCMetagen", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://cge.cbs.dtu.dk/services/ccmetagen/" diff --git a/data/ccp4/ccp4bioschemas.jsonld b/data/ccp4/ccp4bioschemas.jsonld index 12812ee9497cd..33f26d843f33c 100644 --- a/data/ccp4/ccp4bioschemas.jsonld +++ b/data/ccp4/ccp4bioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Software suite for Macromolecular X-Ray Crystallography, including data processing, phasing and structure refinement.", "sc:name": "CCP4", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://www.ccp4.ac.uk", diff --git a/data/ccp4_wiki/ccp4_wikibioschemas.jsonld b/data/ccp4_wiki/ccp4_wikibioschemas.jsonld index 5a96e879c9cc0..55b9f9a440380 100644 --- a/data/ccp4_wiki/ccp4_wikibioschemas.jsonld +++ b/data/ccp4_wiki/ccp4_wikibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "CCP4 Community Knowledge base.", "sc:name": "CCP4 Wiki", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://ccp4wiki.org" diff --git a/data/ccp4mg/ccp4mgbioschemas.jsonld b/data/ccp4mg/ccp4mgbioschemas.jsonld index 756059e4c5356..e8af8eda0be01 100644 --- a/data/ccp4mg/ccp4mgbioschemas.jsonld +++ b/data/ccp4mg/ccp4mgbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "CCP4mg", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://www.ccp4.ac.uk/MG/", diff --git a/data/ccpdb/ccpdbbioschemas.jsonld b/data/ccpdb/ccpdbbioschemas.jsonld index 7a0ca2fd13d3f..6eb37c0cb5c2f 100644 --- a/data/ccpdb/ccpdbbioschemas.jsonld +++ b/data/ccpdb/ccpdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is complied from the literature and the Protein Data Bank (PDB), where all datasets were derived from PDB.", "sc:name": "ccPDB", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://crdd.osdd.net/raghava/ccpdb/" diff --git a/data/ccpn/ccpnbioschemas.jsonld b/data/ccpn/ccpnbioschemas.jsonld index a3fc11f3bd5a1..10d8f0ff2fcdc 100644 --- a/data/ccpn/ccpnbioschemas.jsonld +++ b/data/ccpn/ccpnbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A graphical NMR assignment and data analysis program.", "sc:name": "CcpNmr Analysis", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "Instruct", "sc:url": "http://www.ccpn.ac.uk/v3-software", diff --git a/data/ccpromise/ccpromisebioschemas.jsonld b/data/ccpromise/ccpromisebioschemas.jsonld index 7791742a85d7b..3f214bed9882d 100644 --- a/data/ccpromise/ccpromisebioschemas.jsonld +++ b/data/ccpromise/ccpromisebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "CCPROMISE", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CCPROMISE.html", diff --git a/data/ccrel/ccrelbioschemas.jsonld b/data/ccrel/ccrelbioschemas.jsonld index 8bf966af51a7a..db52313258526 100644 --- a/data/ccrel/ccrelbioschemas.jsonld +++ b/data/ccrel/ccrelbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Case-Control association analysis with RELlated individuals, is a program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers.", "sc:name": "CCREL", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.stat.auckland.ac.nz/~browning/ccrel/ccrel.htm" } \ No newline at end of file diff --git a/data/ccrepe/ccrepebioschemas.jsonld b/data/ccrepe/ccrepebioschemas.jsonld index 1a48f388eca51..a6f3701f917a8 100644 --- a/data/ccrepe/ccrepebioschemas.jsonld +++ b/data/ccrepe/ccrepebioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/ccrepe", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Craig Bielski", + "Emma Schwager", "George Weingart", - "Emma Schwager" + "Craig Bielski" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package is designed to assess the significance of general similarity measures in compositional datasets. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.", "sc:license": "MIT", "sc:name": "ccrepe", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ccrepe.html", diff --git a/data/ccrxp/ccrxpbioschemas.jsonld b/data/ccrxp/ccrxpbioschemas.jsonld index ec5b09b39c2f6..b6296d5abf453 100644 --- a/data/ccrxp/ccrxpbioschemas.jsonld +++ b/data/ccrxp/ccrxpbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CCRXP", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://ccrxp.netasa.org" } \ No newline at end of file diff --git a/data/cct/cctbioschemas.jsonld b/data/cct/cctbioschemas.jsonld index 77ad284667da2..13c54a357234d 100644 --- a/data/cct/cctbioschemas.jsonld +++ b/data/cct/cctbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "CCT (Current Comparative Table) is a software package that you can install and set-up on your own system to help you to maintain and search databases.", "sc:name": "CCT", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://sourceforge.net/projects/orb-cct" diff --git a/data/cctop/cctopbioschemas.jsonld b/data/cctop/cctopbioschemas.jsonld index 0c503fc5d8e7e..f2e7f1fca3c89 100644 --- a/data/cctop/cctopbioschemas.jsonld +++ b/data/cctop/cctopbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Tusnády GE", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4489262", { "@id": "https://doi.org/10.1093/NAR/GKV451" }, + "pmcid:PMC4489262", "pubmed:25943549" ], "sc:description": "Web-based application providing transmembrane topology prediction.", @@ -28,8 +28,8 @@ "sc:name": "CCTOP", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://cctop.enzim.ttk.mta.hu/" }, diff --git a/data/cd-hit/cd-hitbioschemas.jsonld b/data/cd-hit/cd-hitbioschemas.jsonld index fe34ee76e3df5..e1d83826b8eed 100644 --- a/data/cd-hit/cd-hitbioschemas.jsonld +++ b/data/cd-hit/cd-hitbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "cd-hit", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/weizhongli/cdhit", "sc:version": "4.6.1" diff --git a/data/cd-search/cd-searchbioschemas.jsonld b/data/cd-search/cd-searchbioschemas.jsonld index b60a01f2d0f50..9ef860e9eb6d9 100644 --- a/data/cd-search/cd-searchbioschemas.jsonld +++ b/data/cd-search/cd-searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.", "sc:name": "CD-Search", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi" } \ No newline at end of file diff --git a/data/cdd/cddbioschemas.jsonld b/data/cdd/cddbioschemas.jsonld index 665192f6eab7a..08ecd519579e2 100644 --- a/data/cdd/cddbioschemas.jsonld +++ b/data/cdd/cddbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkq1189", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-1516-0712", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/cdd", "@type": "sc:SoftwareApplication", @@ -17,30 +25,22 @@ }, "sc:additionalType": "Database portal", "sc:citation": [ + "pmcid:PMC3013737", { "@id": "https://doi.org/10.1093/nar/gkq1189" }, - "pubmed:21109532", - "pmcid:PMC3013737", - "pubmed:25414356" + "pubmed:25414356", + "pubmed:21109532" ], "sc:description": "Resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. It includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships.", "sc:name": "Conserved domain database CDD", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "NCBI", "sc:url": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml" - }, - { - "@id": "https://doi.org/10.1093/nar/gkq1189", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-1516-0712", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/cddapp/cddappbioschemas.jsonld b/data/cddapp/cddappbioschemas.jsonld index 06799bcd5a7d8..ccac6b7e5ce6e 100644 --- a/data/cddapp/cddappbioschemas.jsonld +++ b/data/cddapp/cddappbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Cytoscape3 extension that supports the annotation of protein networks with information about domains and specific functional sites (features) from the National Center for Biotechnology Information (NCBI) Conserved Domain Database (CDD).", "sc:name": "cddApp", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://apps.cytoscape.org/apps/cddapp" } \ No newline at end of file diff --git a/data/cddb/cddbbioschemas.jsonld b/data/cddb/cddbbioschemas.jsonld index 9b0c1928a1d3e..46cc6aef206d1 100644 --- a/data/cddb/cddbbioschemas.jsonld +++ b/data/cddb/cddbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Database for comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a coarse-grained computational approach that is applied to most structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify protein domains flexibility, functional-transitions associated domains, and correlations in molecular motions.", "sc:name": "CDDB", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.cdyn.org" diff --git a/data/cde/cdebioschemas.jsonld b/data/cde/cdebioschemas.jsonld index 13e71e46ab86e..3cc1ed75a986b 100644 --- a/data/cde/cdebioschemas.jsonld +++ b/data/cde/cdebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "CDE", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cde.nlm.nih.gov/home" } \ No newline at end of file diff --git a/data/cdfread/cdfreadbioschemas.jsonld b/data/cdfread/cdfreadbioschemas.jsonld index 2ad4163ce875e..20c6822a16278 100644 --- a/data/cdfread/cdfreadbioschemas.jsonld +++ b/data/cdfread/cdfreadbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A simple reader of mass spectra in netCDF.", "sc:name": "cdfread", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://cdfread.sourceforge.net/" } \ No newline at end of file diff --git a/data/cdh/cdhbioschemas.jsonld b/data/cdh/cdhbioschemas.jsonld index 5309e3847e345..60978164553a0 100644 --- a/data/cdh/cdhbioschemas.jsonld +++ b/data/cdh/cdhbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "CDH", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00024", diff --git a/data/cdk/cdkbioschemas.jsonld b/data/cdk/cdkbioschemas.jsonld index 95d521372cb05..3a2bbeda790b7 100644 --- a/data/cdk/cdkbioschemas.jsonld +++ b/data/cdk/cdkbioschemas.jsonld @@ -14,15 +14,15 @@ "sc:author": [ "John May", "Christoph Steinbeck", - "Rajarshi Guha", - "Egon Willighagen" + "Egon Willighagen", + "Rajarshi Guha" ], "sc:description": "Open source Java library for bio- and cheminformatics.", "sc:license": "LGPL-2.1", "sc:name": "The Chemistry Development Kit", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "maastrichtuniversity.nl", "sc:url": "http://github.com/cdk/cdk/", diff --git a/data/cdna/cdnabioschemas.jsonld b/data/cdna/cdnabioschemas.jsonld index 27d74e9802289..006428c77f03b 100644 --- a/data/cdna/cdnabioschemas.jsonld +++ b/data/cdna/cdnabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "cDNA Analysis Package", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.g-language.org/data/cdna/", "sc:version": "0.1.0" diff --git a/data/cdrom/cdrombioschemas.jsonld b/data/cdrom/cdrombioschemas.jsonld index 714ccfcf6ad35..52935dc6a618c 100644 --- a/data/cdrom/cdrombioschemas.jsonld +++ b/data/cdrom/cdrombioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Raquel Assis", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC4832533", - "pubmed:27080514", { "@id": "https://doi.org/10.1186/S12862-016-0644-X" - } + }, + "pmcid:PMC4832533", + "pubmed:27080514" ], "sc:description": "Classification of Duplicate gene RetentiOn Mechanisms.", "sc:featureList": [ @@ -36,9 +36,9 @@ ], "sc:name": "CDROM", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://cran.rstudio.com/web/packages/CDROM/" } diff --git a/data/cdsbank/cdsbankbioschemas.jsonld b/data/cdsbank/cdsbankbioschemas.jsonld index 28b40dd6f5536..99e972946f078 100644 --- a/data/cdsbank/cdsbankbioschemas.jsonld +++ b/data/cdsbank/cdsbankbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Bart Hazes", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:24580755", { "@id": "https://doi.org/10.1186/1471-2105-15-61" }, - "pmcid:PMC3942066" + "pmcid:PMC3942066", + "pubmed:24580755" ], "sc:description": "Taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences.", "sc:featureList": { @@ -29,8 +29,8 @@ "sc:name": "CDSbank", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://hazeslab.med.ualberta.ca/CDSbank/" }, diff --git a/data/ceas/ceasbioschemas.jsonld b/data/ceas/ceasbioschemas.jsonld index 5adba7c44750b..15c14b976dba2 100644 --- a/data/ceas/ceasbioschemas.jsonld +++ b/data/ceas/ceasbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.", "sc:name": "CEAS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://ceas.cbi.pku.edu.cn" } \ No newline at end of file diff --git a/data/cedar_ondemand/cedar_ondemandbioschemas.jsonld b/data/cedar_ondemand/cedar_ondemandbioschemas.jsonld index eae9a14dac571..8789352c09730 100644 --- a/data/cedar_ondemand/cedar_ondemandbioschemas.jsonld +++ b/data/cedar_ondemand/cedar_ondemandbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-1.0", "sc:name": "CEDAR OnDemand", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://chrome.google.com/webstore/search/CEDAROnDemand" } \ No newline at end of file diff --git a/data/cega/cegabioschemas.jsonld b/data/cega/cegabioschemas.jsonld index c5e6a6407d6d5..9b43058401b9a 100644 --- a/data/cega/cegabioschemas.jsonld +++ b/data/cega/cegabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Provides access to precomputed sets of conserved sequences from different species and at different levels of the vertebrate phylogeny.", "sc:name": "CEGA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://cega.ezlab.org/" diff --git a/data/cell-motility/cell-motilitybioschemas.jsonld b/data/cell-motility/cell-motilitybioschemas.jsonld index a1e110c9c4356..001252ca625cd 100644 --- a/data/cell-motility/cell-motilitybioschemas.jsonld +++ b/data/cell-motility/cell-motilitybioschemas.jsonld @@ -28,11 +28,11 @@ "@id": "edam:topic_2229" }, "sc:citation": [ + "pubmed:16762054", + "pmcid:PMC1523222", { "@id": "https://doi.org/10.1186/1471-2105-7-289" - }, - "pmcid:PMC1523222", - "pubmed:16762054" + } ], "sc:description": "Cell motion path analysis.", "sc:featureList": { diff --git a/data/cellbase/cellbasebioschemas.jsonld b/data/cellbase/cellbasebioschemas.jsonld index 0f4d719dd2150..59937a84722b3 100644 --- a/data/cellbase/cellbasebioschemas.jsonld +++ b/data/cellbase/cellbasebioschemas.jsonld @@ -22,9 +22,9 @@ "Mac" ], "sc:provider": [ - "cipf.es", + "Computational Genomics Department. Prince Felipe Research Center (CIPF)", "http://bioinfo.cipf.es", - "Computational Genomics Department. Prince Felipe Research Center (CIPF)" + "cipf.es" ], "sc:url": "http://docs.bioinfo.cipf.es/projects/cellbase/wiki" } \ No newline at end of file diff --git a/data/cellbaser/cellbaserbioschemas.jsonld b/data/cellbaser/cellbaserbioschemas.jsonld index 31b950e3347e5..d44afa077d125 100644 --- a/data/cellbaser/cellbaserbioschemas.jsonld +++ b/data/cellbaser/cellbaserbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "cellbaseR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cellbaseR.html", "sc:version": "1.4.0" diff --git a/data/cellcycledb/cellcycledbbioschemas.jsonld b/data/cellcycledb/cellcycledbbioschemas.jsonld index aca13d2b09ccf..8e6f1eb6e8310 100644 --- a/data/cellcycledb/cellcycledbbioschemas.jsonld +++ b/data/cellcycledb/cellcycledbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A collection of genes and proteins involved in human and yeast cell cycle.", "sc:name": "Cell cycle database (CellCycleDB)", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "CNR-ITB", "sc:url": "http://www.itb.cnr.it/cellcycle/index.html" diff --git a/data/cellgrowth/bioconda_cellgrowth.yaml b/data/cellgrowth/bioconda_cellgrowth.yaml index 83d2ae0eda6da..6a80bd6809769 100644 --- a/data/cellgrowth/bioconda_cellgrowth.yaml +++ b/data/cellgrowth/bioconda_cellgrowth.yaml @@ -4,7 +4,6 @@ description: This package provides functionalities for the fitting of cell popul home: https://bioconductor.org/packages/3.10/bioc/html/cellGrowth.html identifiers: - biotools:cellgrowth -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-cellgrowth summary: Fitting cell population growth models diff --git a/data/cellgrowth/cellgrowthbioschemas.jsonld b/data/cellgrowth/cellgrowthbioschemas.jsonld index 2ef825a3b095b..1723e8dd806b3 100644 --- a/data/cellgrowth/cellgrowthbioschemas.jsonld +++ b/data/cellgrowth/cellgrowthbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Julien Gagneur", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides functionalities for the fitting of cell population growth models on experimental OD curves.", "sc:license": "Artistic-2.0", "sc:name": "cellGrowth", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cellGrowth.html", "sc:version": "1.18.0" diff --git a/data/cellhts2/cellhts2bioschemas.jsonld b/data/cellhts2/cellhts2bioschemas.jsonld index 3c09f846054cc..2cf6cab81e248 100644 --- a/data/cellhts2/cellhts2bioschemas.jsonld +++ b/data/cellhts2/cellhts2bioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2164-12-50", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cellhts2", "@type": "sc:SoftwareApplication", @@ -31,36 +27,40 @@ "@id": "edam:topic_3523" }, "sc:citation": [ + "pmcid:PMC3036618", { "@id": "https://doi.org/10.1186/1471-2164-12-50" }, - "pmcid:PMC3036618", "pubmed:21251254" ], "sc:description": "This package analyzes high-throughput assays performed in microtitre plate formats. The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview of the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_1812" }, { - "@id": "edam:operation_2428" + "@id": "edam:operation_2495" }, { "@id": "edam:operation_3435" }, { - "@id": "edam:operation_1812" + "@id": "edam:operation_2428" } ], "sc:license": "Artistic-2.0", "sc:name": "cellHTS2", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cellHTS2.html", "sc:version": "2.38.0" + }, + { + "@id": "https://doi.org/10.1186/1471-2164-12-50", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cellimagelibrary/cellimagelibrarybioschemas.jsonld b/data/cellimagelibrary/cellimagelibrarybioschemas.jsonld index 61ade91ede597..a41c9a5ab296c 100644 --- a/data/cellimagelibrary/cellimagelibrarybioschemas.jsonld +++ b/data/cellimagelibrary/cellimagelibrarybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This Image Library is a repository for images and movies of cells from a variety of organisms. It demonstrates cellular architecture and functions with high quality images, videos, and animations. This comprehensive and easily accessible Library is designed as a public resource first and foremost for research, and secondarily as a tool for education. The long-term goal is the construction of a library of images that will serve as primary data for research.", "sc:name": "The Cell: An Image Library", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.cellimagelibrary.org/" } \ No newline at end of file diff --git a/data/cellity/cellitybioschemas.jsonld b/data/cellity/cellitybioschemas.jsonld index bd9dca1598c3f..e8315d35a2fe8 100644 --- a/data/cellity/cellitybioschemas.jsonld +++ b/data/cellity/cellitybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Tomislav Ilicic", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A support vector machine approach to identifying and filtering low quality cells from single-cell RNA-seq datasets.", "sc:license": "GPL-2.0", "sc:name": "cellity", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cellity.html", "sc:version": "1.2.0" diff --git a/data/cellmapper/cellmapperbioschemas.jsonld b/data/cellmapper/cellmapperbioschemas.jsonld index 0630cc2e64a74..15b70f526fa65 100644 --- a/data/cellmapper/cellmapperbioschemas.jsonld +++ b/data/cellmapper/cellmapperbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13059-016-1062-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cellmapper", "@type": "sc:SoftwareApplication", @@ -24,11 +20,11 @@ "Library" ], "sc:citation": [ + "pmcid:PMC5043525", + "pubmed:27687735", { "@id": "https://doi.org/10.1186/s13059-016-1062-5" - }, - "pmcid:PMC5043525", - "pubmed:27687735" + } ], "sc:description": "Infers cell type-specific expression based on co-expression similarity with known cell type marker genes. Can make accurate predictions using publicly available expression data, even when a cell type has not been isolated before.", "sc:featureList": { @@ -37,12 +33,16 @@ "sc:license": "Artistic-2.0", "sc:name": "CellMapper", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CellMapper.html", "sc:version": "1.0.0" }, + { + "@id": "https://doi.org/10.1186/s13059-016-1062-5", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0002-2381-2170", "@type": "schema:Person" diff --git a/data/cellminercdb/cellminercdbbioschemas.jsonld b/data/cellminercdb/cellminercdbbioschemas.jsonld index f4e6474fad238..7fb40717c1c1d 100644 --- a/data/cellminercdb/cellminercdbbioschemas.jsonld +++ b/data/cellminercdb/cellminercdbbioschemas.jsonld @@ -18,22 +18,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6615556", "pubmed:31113817", { "@id": "https://doi.org/10.1158/0008-5472.CAN-18-2047" - } + }, + "pmcid:PMC6615556" ], "sc:description": "Web application for exploration and analysis of cancer cell line pharmacogenomic data across different sources.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_0264" }, { - "@id": "edam:operation_3800" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_0264" + "@id": "edam:operation_3800" } ], "sc:license": "Unlicense", diff --git a/data/cellmissy/cellmissybioschemas.jsonld b/data/cellmissy/cellmissybioschemas.jsonld index 55999a3f7f22b..7d1fa4a51d725 100644 --- a/data/cellmissy/cellmissybioschemas.jsonld +++ b/data/cellmissy/cellmissybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Apache-2.0", "sc:name": "Cellmissy", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/compomics/cellmissy", diff --git a/data/cellmix/cellmixbioschemas.jsonld b/data/cellmix/cellmixbioschemas.jsonld index f5b9858798efa..26ed1552c2de1 100644 --- a/data/cellmix/cellmixbioschemas.jsonld +++ b/data/cellmix/cellmixbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "CellMix , an R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples.", "sc:name": "CellMix", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://web.cbio.uct.ac.za/~renaud/CRAN/web/CellMix/", "sc:version": "1.6.2" diff --git a/data/cellnetanalyzer/cellnetanalyzerbioschemas.jsonld b/data/cellnetanalyzer/cellnetanalyzerbioschemas.jsonld index 1303fd8e62f9d..c7383a238f00e 100644 --- a/data/cellnetanalyzer/cellnetanalyzerbioschemas.jsonld +++ b/data/cellnetanalyzer/cellnetanalyzerbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1752-0509-1-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cellnetanalyzer", "@type": "sc:SoftwareApplication", @@ -20,26 +16,30 @@ "@id": "http://orcid.org/0000-0003-2563-7561" }, "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC1847467", { "@id": "https://doi.org/10.1186/1752-0509-1-2" }, + "pubmed:21315797", "pubmed:17408509", - "pubmed:21315797" + "pmcid:PMC1847467" ], "sc:description": "CellNetAnalyzer (CNA) is a MATLAB toolbox providing various computational methods for analyzing structure and function of metabolic, signaling, and regulatory networks. \n\nMetabolic networks can be analyzed by means of stoichiometric and constraint-based modeling techniques while signal transduction and (gene) regulatory networks can be represented and analyzed as logical networks (Boolean or multivalued logic) or as interaction graphs. Computations can be started within a GUI (interactive network maps) or from command line (via API functions).", "sc:name": "CellNetAnalyzer", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www2.mpi-magdeburg.mpg.de/projects/cna/cna.html" }, + { + "@id": "https://doi.org/10.1186/1752-0509-1-2", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0003-2563-7561", "@type": "schema:Person" diff --git a/data/cellnetvis/cellnetvisbioschemas.jsonld b/data/cellnetvis/cellnetvisbioschemas.jsonld index eb95ef1f4d407..182564bbe5621 100644 --- a/data/cellnetvis/cellnetvisbioschemas.jsonld +++ b/data/cellnetvis/cellnetvisbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "CellNetVis", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo03.ibi.unicamp.br/lnbio/IIS2/cellnetvis/" } \ No newline at end of file diff --git a/data/cellnoptr/cellnoptrbioschemas.jsonld b/data/cellnoptr/cellnoptrbioschemas.jsonld index 2fe6fb1d06320..8b85e6a6811ac 100644 --- a/data/cellnoptr/cellnoptrbioschemas.jsonld +++ b/data/cellnoptr/cellnoptrbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "T.Cokelaer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.", "sc:license": "GPL-3.0", diff --git a/data/cellpack/cellpackbioschemas.jsonld b/data/cellpack/cellpackbioschemas.jsonld index 9f48efd078d83..7096dc6206a3d 100644 --- a/data/cellpack/cellpackbioschemas.jsonld +++ b/data/cellpack/cellpackbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Support forum", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:25437435", + "pmcid:PMC4281296", { "@id": "https://doi.org/10.1038/NMETH.3204" - }, - "pmcid:PMC4281296", - "pubmed:25437435" + } ], "sc:description": "Virtual mesoscope to model and visualize structural systems biology.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:name": "cellPACK", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.cellpack.org/" }, diff --git a/data/cellpd/cellpdbioschemas.jsonld b/data/cellpd/cellpdbioschemas.jsonld index c297640629f10..7acb72733c644 100644 --- a/data/cellpd/cellpdbioschemas.jsonld +++ b/data/cellpd/cellpdbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "CellPD", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://sourceforge.net/projects/cellpd/" diff --git a/data/cellsim/cellsimbioschemas.jsonld b/data/cellsim/cellsimbioschemas.jsonld index e34af29f32064..1f9cb6c16e0ef 100644 --- a/data/cellsim/cellsimbioschemas.jsonld +++ b/data/cellsim/cellsimbioschemas.jsonld @@ -31,9 +31,9 @@ "sc:license": "MIT", "sc:name": "CellSim", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.cellsim.nwsuaflmz.com/", "sc:version": "1.0.1" diff --git a/data/cellsort/cellsortbioschemas.jsonld b/data/cellsort/cellsortbioschemas.jsonld index 3b1ef1f8fd2b8..e57678c94793d 100644 --- a/data/cellsort/cellsortbioschemas.jsonld +++ b/data/cellsort/cellsortbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "CellSort", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://tyolab.northwestern.edu/tools/" } \ No newline at end of file diff --git a/data/celltag/celltagbioschemas.jsonld b/data/celltag/celltagbioschemas.jsonld index bb1596a0bb3c4..92cad9f538331 100644 --- a/data/celltag/celltagbioschemas.jsonld +++ b/data/celltag/celltagbioschemas.jsonld @@ -25,29 +25,29 @@ ], "sc:citation": [ "pubmed:31072405", - "pmcid:PMC6509836", { "@id": "https://doi.org/10.1186/S13059-019-1699-Y" - } + }, + "pmcid:PMC6509836" ], "sc:description": "Genetic barcode-based sample multiplexing for single-cell genomics.", "sc:featureList": [ { - "@id": "edam:operation_3891" + "@id": "edam:operation_1812" }, { "@id": "edam:operation_3200" }, { - "@id": "edam:operation_1812" + "@id": "edam:operation_3891" } ], "sc:license": "MIT", "sc:name": "CellTag", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/morris-lab/CellTag-Classifier" }, diff --git a/data/celltracer/celltracerbioschemas.jsonld b/data/celltracer/celltracerbioschemas.jsonld index 55e8e2c104e5d..c6e11e4050b95 100644 --- a/data/celltracer/celltracerbioschemas.jsonld +++ b/data/celltracer/celltracerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Integrated graphical user interface written in Matlab that implements a few novel methods for automating cell segmentation/lineage reconstruction. It is designed for biologists without training in image processing or programing  to extract single cell information from microscopy images arising in their studies.", "sc:name": "CellTracer", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.stat.duke.edu/research/software/west/celltracer/", "sc:version": "1.0.3" diff --git a/data/celltrans/celltransbioschemas.jsonld b/data/celltrans/celltransbioschemas.jsonld index bdd43c265504e..e26fd8491f8c5 100644 --- a/data/celltrans/celltransbioschemas.jsonld +++ b/data/celltrans/celltransbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Thomas Buder", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5478290", "pubmed:28659714", { "@id": "https://doi.org/10.1177/1177932217712241" - }, - "pmcid:PMC5478290" + } ], "sc:description": "Automated tool to quantify stochastic cell state transitions between distinct cell states from FACS and flow cytometry experiments, to estimate equilibrium cell state proportions and the needed time equilibrium.", "sc:featureList": { diff --git a/data/celltree/celltreebioschemas.jsonld b/data/celltree/celltreebioschemas.jsonld index b1de059ef4d18..924e621b4f729 100644 --- a/data/celltree/celltreebioschemas.jsonld +++ b/data/celltree/celltreebioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-016-1175-6", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/celltree", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David duVerle", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pubmed:27620863", - "pmcid:PMC5020541", { "@id": "https://doi.org/10.1186/s12859-016-1175-6" - } + }, + "pmcid:PMC5020541" ], "sc:description": "This packages computes a Latent Dirichlet Allocation (LDA) model of single-cell RNA-seq data and builds a compact tree modelling the relationship between individual cells over time or space.", "sc:featureList": { @@ -31,16 +35,12 @@ "sc:license": "Artistic-2.0", "sc:name": "cellTree", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cellTree.html", "sc:version": "1.4.0" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1175-6", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cellxpress/cellxpressbioschemas.jsonld b/data/cellxpress/cellxpressbioschemas.jsonld index fd6f4f747f980..f65da624c4e58 100644 --- a/data/cellxpress/cellxpressbioschemas.jsonld +++ b/data/cellxpress/cellxpressbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-14-S16-S4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cellxpress", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lit-Hsin Loo", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC3853218", { "@id": "https://doi.org/10.1186/1471-2105-14-S16-S4" }, - "pubmed:24564609" + "pubmed:24564609", + "pmcid:PMC3853218" ], "sc:description": "A fast and user-friendly platform for profiling cellular phenotypes.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "cellXpress", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.cellxpress.org/" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-S16-S4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/censor/censorbioschemas.jsonld b/data/censor/censorbioschemas.jsonld index 95fda461cb61d..5389f56c6b2c8 100644 --- a/data/censor/censorbioschemas.jsonld +++ b/data/censor/censorbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Protein and nucleotide sequence repeat identification and masking. Screens query sequences against a reference collection of repeats and \"censors\" (masks) homologous portions with masking symbols, as well as generating a report classifying all found repeats.", "sc:name": "CENSOR", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ "GIRI", diff --git a/data/census_travel/census_travelbioschemas.jsonld b/data/census_travel/census_travelbioschemas.jsonld index 76f01e4648afb..fccff0204e8e4 100644 --- a/data/census_travel/census_travelbioschemas.jsonld +++ b/data/census_travel/census_travelbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1098/RSTB.2018.0260", "@type": "sc:CreativeWork" }, + { + "@id": "https://orcid.org/0000-0003-0885-8004", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/Census_Travel", "@type": "sc:SoftwareApplication", @@ -21,10 +25,10 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31104596", { "@id": "https://doi.org/10.1098/RSTB.2018.0260" }, - "pubmed:31104596", "pmcid:PMC6558561" ], "sc:description": "Probabilistic census-travel model to predict introduction sites of exotic plant, animal and human pathogens.", @@ -34,15 +38,11 @@ "sc:license": "Unlicense", "sc:name": "Census Travel", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://epi-models.shinyapps.io/Census_Travel/" - }, - { - "@id": "https://orcid.org/0000-0003-0885-8004", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/centdist/centdistbioschemas.jsonld b/data/centdist/centdistbioschemas.jsonld index ad46e944f6408..3e9532806d062 100644 --- a/data/centdist/centdistbioschemas.jsonld +++ b/data/centdist/centdistbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Co-motif scanning program to identify co-transcription factors. It ranks co-transcription factors based on their distribution around CHIP-seq peaks.", "sc:name": "CENTDIST", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://biogpu.ddns.comp.nus.edu.sg/~chipseq/webseqtools2/TASKS/Motif_Enrichment/submit.php?email=guest" diff --git a/data/centiscape/centiscapebioschemas.jsonld b/data/centiscape/centiscapebioschemas.jsonld index 2a6559e86b038..439be835e10f6 100644 --- a/data/centiscape/centiscapebioschemas.jsonld +++ b/data/centiscape/centiscapebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.4477.2", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/centiscape", "@type": "sc:SoftwareApplication", @@ -18,19 +22,19 @@ "Plug-in" ], "sc:citation": [ + "pubmed:26594322", { "@id": "https://doi.org/10.12688/F1000RESEARCH.4477.2" }, - "pmcid:PMC4647866", - "pubmed:26594322" + "pmcid:PMC4647866" ], "sc:description": "Calculate centrality indexes used for the identification of the most important nodes in a network. Suite of algorithms dedicated to network nodes centrality analysis, computing several centralities for undirected, directed and weighted networks. The results of the topological analysis can be integrated with data set from lab experiments, like expression or phosphorylation levels for each protein represented in the network.", "sc:featureList": [ { - "@id": "edam:operation_2497" + "@id": "edam:operation_3562" }, { - "@id": "edam:operation_3562" + "@id": "edam:operation_2497" } ], "sc:license": "GPL-3.0", @@ -42,10 +46,6 @@ ], "sc:url": "http://www.cbmc.it/~scardonig/centiscape/centiscape.php", "sc:version": "2.2" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.4477.2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/centiserver/centiserverbioschemas.jsonld b/data/centiserver/centiserverbioschemas.jsonld index d8a213d7f2eb2..57238f4a8715b 100644 --- a/data/centiserver/centiserverbioschemas.jsonld +++ b/data/centiserver/centiserverbioschemas.jsonld @@ -14,16 +14,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mahdi Jalili", "sc:additionalType": [ - "Command-line tool", "Library", + "Command-line tool", "Web application" ], "sc:citation": [ + "pubmed:26571275", "pmcid:PMC4646361", { "@id": "https://doi.org/10.1371/journal.pone.0143111" - }, - "pubmed:26571275" + } ], "sc:description": "CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file.", "sc:featureList": { diff --git a/data/centomd/centomdbioschemas.jsonld b/data/centomd/centomdbioschemas.jsonld index 811a55071e727..22dd7d347075a 100644 --- a/data/centomd/centomdbioschemas.jsonld +++ b/data/centomd/centomdbioschemas.jsonld @@ -17,11 +17,11 @@ "Database portal" ], "sc:citation": [ - "pmcid:PMC5241210", - "pubmed:28116331", { "@id": "https://doi.org/10.1002/mgg3.262" - } + }, + "pmcid:PMC5241210", + "pubmed:28116331" ], "sc:description": "Genetic mutation database for rare diseases that enables to search, sort and filter genetic variants from clinically diagnosed individuals worldwide and make symptoms-based queries.", "sc:featureList": [ @@ -39,8 +39,8 @@ "sc:name": "CentoMD", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.centogene.com/mutation-database-centomd.html", "sc:version": "5.3" diff --git a/data/centroidfold/centroidfoldbioschemas.jsonld b/data/centroidfold/centroidfoldbioschemas.jsonld index 1ed3bbb587382..e59a254c1c3fa 100644 --- a/data/centroidfold/centroidfoldbioschemas.jsonld +++ b/data/centroidfold/centroidfoldbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).", "sc:name": "CentroidFold", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://rtools.cbrc.jp/centroidfold/" diff --git a/data/centroidhomfold-last/centroidhomfold-lastbioschemas.jsonld b/data/centroidhomfold-last/centroidhomfold-lastbioschemas.jsonld index dc5f6d2032782..e6396ff042b58 100644 --- a/data/centroidhomfold-last/centroidhomfold-lastbioschemas.jsonld +++ b/data/centroidhomfold-last/centroidhomfold-lastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CentroidHomfold-LAST predicts the secondary structure of an RNA sequence using automatically collected homologous sequences.", "sc:name": "CentroidHomfold-LAST", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://rtools.cbrc.jp/centroidhomfold/" } \ No newline at end of file diff --git a/data/centrosomedb/centrosomedbbioschemas.jsonld b/data/centrosomedb/centrosomedbbioschemas.jsonld index 2900042c259f7..4e57401b717b8 100644 --- a/data/centrosomedb/centrosomedbbioschemas.jsonld +++ b/data/centrosomedb/centrosomedbbioschemas.jsonld @@ -35,8 +35,8 @@ }, "sc:name": "CentrosomeDB", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "cnb.csic.es", diff --git a/data/cepa/cepabioschemas.jsonld b/data/cepa/cepabioschemas.jsonld index 5d45bccac9e9a..31645f0be8a42 100644 --- a/data/cepa/cepabioschemas.jsonld +++ b/data/cepa/cepabioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "GPL-3.0", "sc:name": "CePa", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/CePa/", "sc:version": "0.6" diff --git a/data/cerebro/cerebrobioschemas.jsonld b/data/cerebro/cerebrobioschemas.jsonld index 91b5c52092942..046cc50c0d855 100644 --- a/data/cerebro/cerebrobioschemas.jsonld +++ b/data/cerebro/cerebrobioschemas.jsonld @@ -18,8 +18,8 @@ "sc:license": "MIT", "sc:name": "Cerebro", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/romanhaa/Cerebro" } \ No newline at end of file diff --git a/data/cerebroviz/cerebrovizbioschemas.jsonld b/data/cerebroviz/cerebrovizbioschemas.jsonld index 155c7cc5aa16a..8a33d2bf8f5ff 100644 --- a/data/cerebroviz/cerebrovizbioschemas.jsonld +++ b/data/cerebroviz/cerebrovizbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:28011779", + "pmcid:PMC5870797", { "@id": "https://doi.org/10.1093/bioinformatics/btw726" - }, - "pmcid:PMC5870797" + } ], "sc:description": "cerebroViz is an R package that can map spatiotemporal brain data to vector graphic diagrams of the human brain.", "sc:featureList": { diff --git a/data/cerena/cerenabioschemas.jsonld b/data/cerena/cerenabioschemas.jsonld index ab91b48424996..3e62426f78e3b 100644 --- a/data/cerena/cerenabioschemas.jsonld +++ b/data/cerena/cerenabioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Plug-in", "sc:citation": [ - "pubmed:26807911", + "pmcid:PMC4726759", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0146732" }, - "pmcid:PMC4726759" + "pubmed:26807911" ], "sc:description": "ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "CERENA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://cerenadevelopers.github.io/CERENA/" } diff --git a/data/cerenkov2/cerenkov2bioschemas.jsonld b/data/cerenkov2/cerenkov2bioschemas.jsonld index b0bc4584a0e31..cdaf397b6ac96 100644 --- a/data/cerenkov2/cerenkov2bioschemas.jsonld +++ b/data/cerenkov2/cerenkov2bioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Stephen Ramsey", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6364436", "pubmed:30727967", { "@id": "https://doi.org/10.1186/s12859-019-2637-4" - } + }, + "pmcid:PMC6364436" ], "sc:description": "Software pipeline and associated machine-learning framework for identifying regulatory single nucleotide polymorphisms (rSNPs) in the noncoding genome for post-analysis of genetic regions identified in genome-wide association studies (GWAS).", "sc:featureList": [ @@ -37,8 +37,8 @@ "sc:name": "CERENKOV2", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/ramseylab/cerenkov", "sc:version": "v0.1-alpha" diff --git a/data/cermit/cermitbioschemas.jsonld b/data/cermit/cermitbioschemas.jsonld index 4d4ed24008274..c260ac98d1242 100644 --- a/data/cermit/cermitbioschemas.jsonld +++ b/data/cermit/cermitbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Fast sequence motif identification algorithm that utilizes suffix arrays to efficiently find optimal motifs in large sequence sets (such as tens of thousands of sequences identified by chromatin or RNA immunopreciptation experiments). It uses rank-order statistics and accounts for quantitative information for each sequence.", "sc:name": "cERMIT", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://ohlerlab.mdc-berlin.de/software/cERMIT_82/", "sc:version": "1.0" diff --git a/data/cesam/cesambioschemas.jsonld b/data/cesam/cesambioschemas.jsonld index 54e6550277b42..5bd70e96c92ab 100644 --- a/data/cesam/cesambioschemas.jsonld +++ b/data/cesam/cesambioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/ng.3722", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cesam", "@type": "sc:SoftwareApplication", @@ -20,11 +16,11 @@ "sc:additionalType": "Command-line tool", "sc:author": "Joachim Weischenfeldt", "sc:citation": [ - "pmcid:PMC5791882", - "pubmed:27869826", { "@id": "https://doi.org/10.1038/ng.3722" - } + }, + "pubmed:27869826", + "pmcid:PMC5791882" ], "sc:description": "Cis expression structural alteration mapping", "sc:featureList": { @@ -35,6 +31,10 @@ "sc:operatingSystem": "Linux", "sc:url": "https://bitbucket.org/weischen/cesam", "sc:version": "0.0.1" + }, + { + "@id": "https://doi.org/10.1038/ng.3722", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ceu_mass_mediator/ceu_mass_mediatorbioschemas.jsonld b/data/ceu_mass_mediator/ceu_mass_mediatorbioschemas.jsonld index c4df5d5a7fee7..91700fea0905a 100644 --- a/data/ceu_mass_mediator/ceu_mass_mediatorbioschemas.jsonld +++ b/data/ceu_mass_mediator/ceu_mass_mediatorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "CEU Mass Mediator", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://ceumass.eps.uspceu.es/", "sc:version": "3.0" diff --git a/data/cexor/cexorbioschemas.jsonld b/data/cexor/cexorbioschemas.jsonld index d8e3b0adf0b4c..1e51f22000512 100644 --- a/data/cexor/cexorbioschemas.jsonld +++ b/data/cexor/cexorbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "CexoR", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CexoR.html", diff --git a/data/cfassay/cfassaybioschemas.jsonld b/data/cfassay/cfassaybioschemas.jsonld index b1368edb440f4..3d6ce4d23ae0c 100644 --- a/data/cfassay/cfassaybioschemas.jsonld +++ b/data/cfassay/cfassaybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Herbert Braselmann", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.", "sc:license": "GPL-3.0", "sc:name": "CFAssay", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CFAssay.html", "sc:version": "1.8.0" diff --git a/data/cfinder/cfinderbioschemas.jsonld b/data/cfinder/cfinderbioschemas.jsonld index 8c68f8c65eaf9..788e7dc13dbc3 100644 --- a/data/cfinder/cfinderbioschemas.jsonld +++ b/data/cfinder/cfinderbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pubmed:26346608", + "pmcid:PMC4562109", { "@id": "https://doi.org/10.1186/S13104-015-1382-7" - }, - "pmcid:PMC4562109" + } ], "sc:description": "Definition and quantification of multiple haplotypes in a mixed sample.", "sc:featureList": { diff --git a/data/cfm-id/cfm-idbioschemas.jsonld b/data/cfm-id/cfm-idbioschemas.jsonld index 06bf6dd22c069..0660d4e0eb5c2 100644 --- a/data/cfm-id/cfm-idbioschemas.jsonld +++ b/data/cfm-id/cfm-idbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CFM-ID", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://cfmid.wishartlab.com" } \ No newline at end of file diff --git a/data/cfquant-automatic/cfquant-automaticbioschemas.jsonld b/data/cfquant-automatic/cfquant-automaticbioschemas.jsonld index 319360cea051b..64a1b90af3f52 100644 --- a/data/cfquant-automatic/cfquant-automaticbioschemas.jsonld +++ b/data/cfquant-automatic/cfquant-automaticbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1128/mSphere.00676-18", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/CFQuant-automatic", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pmcid:PMC6315083", - "pubmed:30602526", { "@id": "https://doi.org/10.1128/mSphere.00676-18" - } + }, + "pubmed:30602526" ], "sc:description": "Analyzes images of cell colonies that emit a luminescent/fluorescent signal in the form of a luminescent halo around the colony. Automatically identifies both the colonies and their emitted luminescent halos and returns quantitative data on features", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "Unlicense", "sc:name": "CFQuant-automatic", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://www.energylabtau.com/cfquant" + }, + { + "@id": "https://doi.org/10.1128/mSphere.00676-18", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cg-cat/cg-catbioschemas.jsonld b/data/cg-cat/cg-catbioschemas.jsonld index e85021702fa6a..3c466f71d3e60 100644 --- a/data/cg-cat/cg-catbioschemas.jsonld +++ b/data/cg-cat/cg-catbioschemas.jsonld @@ -16,14 +16,14 @@ "sc:license": "GPL-2.0", "sc:name": "CG-CAT", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": [ - "CeBiTec", "Bielefeld University", - "BiBiServ" + "BiBiServ", + "CeBiTec" ], "sc:url": "http://bibiserv.cebitec.uni-bielefeld.de/cgcat", "sc:version": "1" diff --git a/data/cgap/cgapbioschemas.jsonld b/data/cgap/cgapbioschemas.jsonld index 85ff72bb5dafa..b4bcc2ef3853d 100644 --- a/data/cgap/cgapbioschemas.jsonld +++ b/data/cgap/cgapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.", "sc:name": "Cancer Genome Anatomy Project", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://cgap.nci.nih.gov/" diff --git a/data/cgbayesnets/cgbayesnetsbioschemas.jsonld b/data/cgbayesnets/cgbayesnetsbioschemas.jsonld index 80f337c7b803f..0b4dc2d383a2f 100644 --- a/data/cgbayesnets/cgbayesnetsbioschemas.jsonld +++ b/data/cgbayesnets/cgbayesnetsbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003676", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cgbayesnets", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact form", "sc:additionalType": "Plug-in", "sc:citation": [ - "pmcid:PMC4055564", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003676" }, - "pubmed:24922310" + "pubmed:24922310", + "pmcid:PMC4055564" ], "sc:description": "Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data.", "sc:featureList": { @@ -28,14 +32,10 @@ "sc:name": "CGBayesNets", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cgbayesnets.com/" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003676", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cgd/cgdbioschemas.jsonld b/data/cgd/cgdbioschemas.jsonld index 5b433d4a2f310..2727427daad51 100644 --- a/data/cgd/cgdbioschemas.jsonld +++ b/data/cgd/cgdbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Candida genome database CGD", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.candidagenome.org/" } \ No newline at end of file diff --git a/data/cgen/cgenbioschemas.jsonld b/data/cgen/cgenbioschemas.jsonld index 40566d68287eb..dec56e7556884 100644 --- a/data/cgen/cgenbioschemas.jsonld +++ b/data/cgen/cgenbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "William Wheeler", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An R package for analysis of case-control studies in genetic epidemiology.", "sc:license": "GPL-2.0", diff --git a/data/cghbase/cghbasebioschemas.jsonld b/data/cghbase/cghbasebioschemas.jsonld index e1d1db0480bed..2aa85cc6bf6d4 100644 --- a/data/cghbase/cghbasebioschemas.jsonld +++ b/data/cghbase/cghbasebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "CGHbase", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CGHbase.html", "sc:version": "1.34.0" diff --git a/data/cghcall/cghcallbioschemas.jsonld b/data/cghcall/cghcallbioschemas.jsonld index 8e64f5fafeb79..c68272d775cdf 100644 --- a/data/cghcall/cghcallbioschemas.jsonld +++ b/data/cghcall/cghcallbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mark van de Wiel", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.", "sc:license": "GPL-3.0", "sc:name": "CGHcall", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CGHcall.html", "sc:version": "2.36.0" diff --git a/data/cghmcr/cghmcrbioschemas.jsonld b/data/cghmcr/cghmcrbioschemas.jsonld index d4b90dbd2f79f..3871a52ab5a03 100644 --- a/data/cghmcr/cghmcrbioschemas.jsonld +++ b/data/cghmcr/cghmcrbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "cghMCR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cghMCR.html", "sc:version": "1.32.0" diff --git a/data/cghnormaliter/cghnormaliterbioschemas.jsonld b/data/cghnormaliter/cghnormaliterbioschemas.jsonld index 8e387df3e2a60..2410460124cb6 100644 --- a/data/cghnormaliter/cghnormaliterbioschemas.jsonld +++ b/data/cghnormaliter/cghnormaliterbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bart P.P. van Houte", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).", "sc:license": "GPL-3.0", diff --git a/data/cghra/cghrabioschemas.jsonld b/data/cghra/cghrabioschemas.jsonld index d7b963d5f7f86..0c927ba11437b 100644 --- a/data/cghra/cghrabioschemas.jsonld +++ b/data/cghra/cghrabioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/cghra", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Fabrice Jardin", - "Sylvain Marescha" + "Sylvain Marescha", + "Fabrice Jardin" ], "sc:additionalType": "Desktop application", "sc:description": "Combines a user-friendly graphical interface and a powerful object-oriented command-line interface to handle a full aCGH analysis, as is illustrated in an original series of 107 Diffuse Large B-Cell Lymphomas.", "sc:name": "cghRA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinformatics.ovsa.fr/cghRA", "sc:version": "1.6.0." diff --git a/data/cghregions/cghregionsbioschemas.jsonld b/data/cghregions/cghregionsbioschemas.jsonld index 8f6d8547bf26f..e77ca78162645 100644 --- a/data/cghregions/cghregionsbioschemas.jsonld +++ b/data/cghregions/cghregionsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "CGHregions", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CGHregions.html", "sc:version": "1.32.0" diff --git a/data/cgmanalysis/cgmanalysisbioschemas.jsonld b/data/cgmanalysis/cgmanalysisbioschemas.jsonld index 5c476edd9a1f6..24f7c6e880d55 100644 --- a/data/cgmanalysis/cgmanalysisbioschemas.jsonld +++ b/data/cgmanalysis/cgmanalysisbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "cgmanalysis", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/cgmanalysis/index.html" } \ No newline at end of file diff --git a/data/cgqtl/cgqtlbioschemas.jsonld b/data/cgqtl/cgqtlbioschemas.jsonld index cd493cccae140..48bb49544b568 100644 --- a/data/cgqtl/cgqtlbioschemas.jsonld +++ b/data/cgqtl/cgqtlbioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC1906769", + "pubmed:17584498", { "@id": "https://doi.org/10.1186/1471-2164-8-183" }, - "pubmed:17584498" + "pmcid:PMC1906769" ], "sc:description": "Database for candidate genes for QTL for milk production traits in cattle", "sc:featureList": { @@ -27,8 +27,8 @@ "sc:license": "Not licensed", "sc:name": "cgQTL", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://cowry.agri.huji.ac.il/QTLMAP/qtlmap.htm" diff --git a/data/cgrnb/cgrnbbioschemas.jsonld b/data/cgrnb/cgrnbbioschemas.jsonld index 98e7303b8449b..e50c3e8ece0a3 100644 --- a/data/cgrnb/cgrnbbioschemas.jsonld +++ b/data/cgrnb/cgrnbbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1752-0509-7-S2-S7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cgrnb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Webmaster", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC3851836", + "pubmed:24565134", { "@id": "https://doi.org/10.1186/1752-0509-7-S2-S7" }, - "pubmed:24565134" + "pmcid:PMC3851836" ], "sc:description": "A web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "cGRNB", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://www.scbit.org/cgrnb/" - }, - { - "@id": "https://doi.org/10.1186/1752-0509-7-S2-S7", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cgrtools/cgrtoolsbioschemas.jsonld b/data/cgrtools/cgrtoolsbioschemas.jsonld index 746d2ed3985b4..bea659d75f854 100644 --- a/data/cgrtools/cgrtoolsbioschemas.jsonld +++ b/data/cgrtools/cgrtoolsbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/CGRtools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alexandre Varnek", "Timur Madzhidov", - "Ramil Nugmanov" + "Ramil Nugmanov", + "Alexandre Varnek" ], "sc:additionalType": "Library", "sc:author": "Ramil Nugmanov", @@ -23,8 +23,8 @@ "sc:name": "CGRtools", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/cimm-kzn/CGRtools" } \ No newline at end of file diff --git a/data/cgview/cgviewbioschemas.jsonld b/data/cgview/cgviewbioschemas.jsonld index bb68002407914..d11056fb95043 100644 --- a/data/cgview/cgviewbioschemas.jsonld +++ b/data/cgview/cgviewbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.", "sc:name": "CGView", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://stothard.afns.ualberta.ca/cgview_server/" diff --git a/data/chainy/chainybioschemas.jsonld b/data/chainy/chainybioschemas.jsonld index fb0b4e57ea98f..c96571ec6b94c 100644 --- a/data/chainy/chainybioschemas.jsonld +++ b/data/chainy/chainybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Chainy", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://maplab.imppc.org/chainy/" } \ No newline at end of file diff --git a/data/champ/champbioschemas.jsonld b/data/champ/champbioschemas.jsonld index 77ebd0c0b0862..9f66d4134acff 100644 --- a/data/champ/champbioschemas.jsonld +++ b/data/champ/champbioschemas.jsonld @@ -9,23 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/j.ymeth.2014.10.036", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/champ", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yuan Tian", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4304833", { "@id": "https://doi.org/10.1016/j.ymeth.2014.10.036" }, + "pmcid:PMC4304833", "pubmed:25461817" ], "sc:description": "The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.", @@ -46,6 +42,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChAMP.html", "sc:version": "2.4.1" + }, + { + "@id": "https://doi.org/10.1016/j.ymeth.2014.10.036", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/changegfffeatures/changegfffeaturesbioschemas.jsonld b/data/changegfffeatures/changegfffeaturesbioschemas.jsonld index 9b190bc5de873..31f0a651c598e 100644 --- a/data/changegfffeatures/changegfffeaturesbioschemas.jsonld +++ b/data/changegfffeatures/changegfffeaturesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Changes one feature name by an other name (the feature name can be found on the 3rd column).", "sc:name": "changegfffeatures", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/changename/changenamebioschemas.jsonld b/data/changename/changenamebioschemas.jsonld index 4b42eb510c924..eabd2958316f5 100644 --- a/data/changename/changenamebioschemas.jsonld +++ b/data/changename/changenamebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Change the chromosome name or gene name of a singla fasta, gff or sam file. For this tool, it can not treat mutiple-chromosome, gene files.", "sc:name": "changename", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/changetagname/changetagnamebioschemas.jsonld b/data/changetagname/changetagnamebioschemas.jsonld index cd000fea10330..4e2a538a6b13b 100644 --- a/data/changetagname/changetagnamebioschemas.jsonld +++ b/data/changetagname/changetagnamebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Changes the name of tag of a list of transcripts.", "sc:name": "changetagname", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", diff --git a/data/channelsdb/channelsdbbioschemas.jsonld b/data/channelsdb/channelsdbbioschemas.jsonld index 0bcd5bb968248..4c4ee16b9e842 100644 --- a/data/channelsdb/channelsdbbioschemas.jsonld +++ b/data/channelsdb/channelsdbbioschemas.jsonld @@ -13,22 +13,22 @@ "biotools:primaryContact": "Karel Berka", "sc:additionalType": "Database portal", "sc:author": [ - "Dominik Toušek", "David Sehnal", - "Lukáš Pravda" + "Lukáš Pravda", + "Dominik Toušek" ], "sc:contributor": [ "Michal Otyepka", - "Jaroslav Koča", "Radka Svobodová Vařeková", - "Karel Berka", - "Veronika Navrátilová" + "Veronika Navrátilová", + "Jaroslav Koča", + "Karel Berka" ], "sc:description": "A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.", "sc:name": "ChannelsDB", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://ncbr.muni.cz/ChannelsDB/", diff --git a/data/chaos/chaosbioschemas.jsonld b/data/chaos/chaosbioschemas.jsonld index ef6484597d445..5f3a0f4726056 100644 --- a/data/chaos/chaosbioschemas.jsonld +++ b/data/chaos/chaosbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", "EMBOSS Contributors", - "Wellcome Trust" + "UK BBSRC", + "Wellcome Trust", + "UK MRC" ], "sc:description": "Draw a chaos game representation plot for a nucleotide sequence.", "sc:funder": [ @@ -26,8 +26,8 @@ "sc:license": "GPL-3.0", "sc:name": "chaos", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ diff --git a/data/chaos_dialign/chaos_dialignbioschemas.jsonld b/data/chaos_dialign/chaos_dialignbioschemas.jsonld index 9cdf4a0f80728..8d3f58e6ab058 100644 --- a/data/chaos_dialign/chaos_dialignbioschemas.jsonld +++ b/data/chaos_dialign/chaos_dialignbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.", "sc:name": "CHAOS DIALIGN WWW server", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://dialign.gobics.de/chaos-dialign-submission" } \ No newline at end of file diff --git a/data/characteristic_direction_method/characteristic_direction_methodbioschemas.jsonld b/data/characteristic_direction_method/characteristic_direction_methodbioschemas.jsonld index 1f97a83081195..6a3270b2ae7bc 100644 --- a/data/characteristic_direction_method/characteristic_direction_methodbioschemas.jsonld +++ b/data/characteristic_direction_method/characteristic_direction_methodbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-15-79", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/characteristic_direction_method", "@type": "sc:SoftwareApplication", @@ -31,11 +27,15 @@ }, "sc:name": "Characteristic Direction Method", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.maayanlab.net/CD/" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-15-79", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/charge/chargebioschemas.jsonld b/data/charge/chargebioschemas.jsonld index da3ded1c878c7..5e21b72b2e101 100644 --- a/data/charge/chargebioschemas.jsonld +++ b/data/charge/chargebioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "EMBOSS Contributors", + "UK MRC", + "Wellcome Trust" ], "sc:description": "Draw a protein charge plot.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "charge", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": [ diff --git a/data/charge_bioconductor/charge_bioconductorbioschemas.jsonld b/data/charge_bioconductor/charge_bioconductorbioschemas.jsonld index bdfd422a4d051..6cf2f62e38f7d 100644 --- a/data/charge_bioconductor/charge_bioconductorbioschemas.jsonld +++ b/data/charge_bioconductor/charge_bioconductorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "CHARGE", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CHARGE.html", "sc:version": "1.0.0" diff --git a/data/charm/charmbioschemas.jsonld b/data/charm/charmbioschemas.jsonld index 09f2a062a257a..b5a1282d7fde6 100644 --- a/data/charm/charmbioschemas.jsonld +++ b/data/charm/charmbioschemas.jsonld @@ -18,11 +18,11 @@ "Library" ], "sc:citation": [ - "pmcid:PMC3062148", - "pubmed:20858772", { "@id": "https://doi.org/10.1093/biostatistics/kxq055" - } + }, + "pubmed:20858772", + "pmcid:PMC3062148" ], "sc:description": "This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools.", "sc:featureList": { @@ -31,9 +31,9 @@ "sc:license": "GPL-2.0", "sc:name": "charm", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/charm.html", "sc:version": "2.20.0" diff --git a/data/charprotdb/charprotdbbioschemas.jsonld b/data/charprotdb/charprotdbbioschemas.jsonld index 79765c64c9bba..44ad2bf7de527 100644 --- a/data/charprotdb/charprotdbbioschemas.jsonld +++ b/data/charprotdb/charprotdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Curated database of biochemically characterized proteins. The initial data set was collected through manual literature curation, and has been expanded by importing selected records from publicly available protein collections. Annotations include gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.", "sc:name": "CharProtDB", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.jcvi.org/charprotdb/index.cgi/home" } \ No newline at end of file diff --git a/data/chase_chromatin_analysis_and_exploration/chase_chromatin_analysis_and_explorationbioschemas.jsonld b/data/chase_chromatin_analysis_and_exploration/chase_chromatin_analysis_and_explorationbioschemas.jsonld index 7575af97d4f7a..fad107499791d 100644 --- a/data/chase_chromatin_analysis_and_exploration/chase_chromatin_analysis_and_explorationbioschemas.jsonld +++ b/data/chase_chromatin_analysis_and_exploration/chase_chromatin_analysis_and_explorationbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "LGPL-3.0", "sc:name": "ChAsE", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/hyounesy/ChAsE/", diff --git a/data/chat/chatbioschemas.jsonld b/data/chat/chatbioschemas.jsonld index f3b9c4cf74e95..00aba7158dbb7 100644 --- a/data/chat/chatbioschemas.jsonld +++ b/data/chat/chatbioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC5860084", - "pubmed:29036271", { "@id": "https://doi.org/10.1093/bioinformatics/btx454" - } + }, + "pubmed:29036271" ], "sc:description": "Text mining approach to organize and evaluate scientific literature on cancer.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "CHAT", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://chat.lionproject.net/" }, diff --git a/data/chea3/chea3bioschemas.jsonld b/data/chea3/chea3bioschemas.jsonld index 967051a06b9e1..b71dc71613274 100644 --- a/data/chea3/chea3bioschemas.jsonld +++ b/data/chea3/chea3bioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1093/NAR/GKZ446", "@type": "sc:CreativeWork" }, - { - "@id": "https://orcid.org/0000-0002-6904-1017", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/ChEA3", "@type": "sc:SoftwareApplication", @@ -25,32 +21,36 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31114921", + "pmcid:PMC6602523", { "@id": "https://doi.org/10.1093/NAR/GKZ446" - }, - "pmcid:PMC6602523", - "pubmed:31114921" + } ], "sc:description": "Transcription factor enrichment analysis by orthogonal omics integration.", "sc:featureList": [ { - "@id": "edam:operation_3766" + "@id": "edam:operation_3463" }, { "@id": "edam:operation_2436" }, { - "@id": "edam:operation_3463" + "@id": "edam:operation_3766" } ], "sc:license": "Unlicense", "sc:name": "ChEA3", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://amp.pharm.mssm.edu/ChEA3" + }, + { + "@id": "https://orcid.org/0000-0002-6904-1017", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/chebi/chebibioschemas.jsonld b/data/chebi/chebibioschemas.jsonld index 0f68afe9ccd14..b838de5b08b41 100644 --- a/data/chebi/chebibioschemas.jsonld +++ b/data/chebi/chebibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Dictionary of molecular entities focused on small chemical compounds. \"Molecular entity\" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.", "sc:name": "ChEBI", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI Databases", "sc:url": "http://www.ebi.ac.uk/chebi/" diff --git a/data/chebi_ws/chebi_wsbioschemas.jsonld b/data/chebi_ws/chebi_wsbioschemas.jsonld index c21ac25face22..3ec83dbe0fe8a 100644 --- a/data/chebi_ws/chebi_wsbioschemas.jsonld +++ b/data/chebi_ws/chebi_wsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. \"Molecular entity\" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.", "sc:name": "ChEBI WS", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ebi.ac.uk/chebi/webServices.do", "sc:version": "1" diff --git a/data/checkmyindex/checkmyindexbioschemas.jsonld b/data/checkmyindex/checkmyindexbioschemas.jsonld index 959b29992587b..a02f31f17f51f 100644 --- a/data/checkmyindex/checkmyindexbioschemas.jsonld +++ b/data/checkmyindex/checkmyindexbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:license": "GPL-3.0", "sc:name": "checkMyIndex", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://checkmyindex.pasteur.fr", diff --git a/data/checktrans/checktransbioschemas.jsonld b/data/checktrans/checktransbioschemas.jsonld index d6a7c9efeda60..77b6925d02a45 100644 --- a/data/checktrans/checktransbioschemas.jsonld +++ b/data/checktrans/checktransbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK MRC", "Wellcome Trust", - "UK BBSRC", "EMBOSS Contributors", - "UK MRC" + "UK BBSRC" ], "sc:description": "Report STOP codons and ORF statistics of a protein.", "sc:funder": [ - "UK MRC", "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "checktrans", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ diff --git a/data/chembl/chemblbioschemas.jsonld b/data/chembl/chemblbioschemas.jsonld index ec29eeb7371b7..0137f73d6c6f6 100644 --- a/data/chembl/chemblbioschemas.jsonld +++ b/data/chembl/chemblbioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-5859-1064", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/chembl", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "ChEMBL Help", "sc:additionalType": [ - "Database portal", - "Web API" + "Web API", + "Database portal" ], "sc:citation": "pubmed:19194660", "sc:contributor": { @@ -24,16 +28,12 @@ "sc:description": "Database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.", "sc:name": "ChEMBL", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Identifiers.org", "sc:url": "https://www.ebi.ac.uk/chembldb/" - }, - { - "@id": "http://orcid.org/0000-0002-5859-1064", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/chembl_biologicals_blast_search/chembl_biologicals_blast_searchbioschemas.jsonld b/data/chembl_biologicals_blast_search/chembl_biologicals_blast_searchbioschemas.jsonld index 9d59ccebd4ddc..1a92f6a335a70 100644 --- a/data/chembl_biologicals_blast_search/chembl_biologicals_blast_searchbioschemas.jsonld +++ b/data/chembl_biologicals_blast_search/chembl_biologicals_blast_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "BLAST search against biological molecules (e.g. mAbs) stored in ChEMBL database.", "sc:name": "ChEMBL API", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "https://www.ebi.ac.uk/chembl/compound", diff --git a/data/chembl_ntd_small_molecule_search/chembl_ntd_small_molecule_searchbioschemas.jsonld b/data/chembl_ntd_small_molecule_search/chembl_ntd_small_molecule_searchbioschemas.jsonld index 7ea974f32f705..229612ff49618 100644 --- a/data/chembl_ntd_small_molecule_search/chembl_ntd_small_molecule_searchbioschemas.jsonld +++ b/data/chembl_ntd_small_molecule_search/chembl_ntd_small_molecule_searchbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Search against small molecules stored in ChEMBL NTD database.", "sc:name": "ChEMBL NTD Small Molecule Search", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "EMBL-EBI", diff --git a/data/chembl_small_molecule_search/chembl_small_molecule_searchbioschemas.jsonld b/data/chembl_small_molecule_search/chembl_small_molecule_searchbioschemas.jsonld index 2a8ed3a1d130e..fa73cd6b13629 100644 --- a/data/chembl_small_molecule_search/chembl_small_molecule_searchbioschemas.jsonld +++ b/data/chembl_small_molecule_search/chembl_small_molecule_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Search against small molecules stored in ChEMBL database.", "sc:name": "ChEMBL Small Molecule Search", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "https://www.ebi.ac.uk/chembl/compound", diff --git a/data/chemdis-mixture/chemdis-mixturebioschemas.jsonld b/data/chemdis-mixture/chemdis-mixturebioschemas.jsonld index 5f925e5ba540e..651c3fd6633f0 100644 --- a/data/chemdis-mixture/chemdis-mixturebioschemas.jsonld +++ b/data/chemdis-mixture/chemdis-mixturebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ChemDIS-Mixture", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://cwtung.kmu.edu.tw/chemdis/mixture" } \ No newline at end of file diff --git a/data/chemgps-np/chemgps-npbioschemas.jsonld b/data/chemgps-np/chemgps-npbioschemas.jsonld index 7c7d66d39c1f1..7e3d748ff951e 100644 --- a/data/chemgps-np/chemgps-npbioschemas.jsonld +++ b/data/chemgps-np/chemgps-npbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/chemgps-np", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web service", "Web application", + "Web service", "Web API" ], "sc:description": "A tool tuned for navigation in biologically relevant chemical space.", "sc:name": "ChemGPS-NP", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://chemgps.bmc.uu.se/", diff --git a/data/chemhits/chemhitsbioschemas.jsonld b/data/chemhits/chemhitsbioschemas.jsonld index 73c547f52e02f..dbb0002351ff4 100644 --- a/data/chemhits/chemhitsbioschemas.jsonld +++ b/data/chemhits/chemhitsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ChemHits", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "HITS", "sc:url": "http://sabio.h-its.org/chemHits/", diff --git a/data/chemical_identifier_resolver/chemical_identifier_resolverbioschemas.jsonld b/data/chemical_identifier_resolver/chemical_identifier_resolverbioschemas.jsonld index d4ab8e70364d0..bfdbf301e042a 100644 --- a/data/chemical_identifier_resolver/chemical_identifier_resolverbioschemas.jsonld +++ b/data/chemical_identifier_resolver/chemical_identifier_resolverbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "NCI CADD Chemical Identifier Resolver", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://cactus.nci.nih.gov/chemical/structure/documentation", "sc:version": "1" diff --git a/data/chemmaps/chemmapsbioschemas.jsonld b/data/chemmaps/chemmapsbioschemas.jsonld index 203d934da9994..91eb3826212c6 100644 --- a/data/chemmaps/chemmapsbioschemas.jsonld +++ b/data/chemmaps/chemmapsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Webserver to easily browse, navigate and mine chemical space. The first version features more than 8000 approved, in development, and rejected drugs, as well as over 47 000 environmental chemicals.", "sc:name": "ChemMaps", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.chemmaps.com/" } \ No newline at end of file diff --git a/data/chemmine_tools/chemmine_toolsbioschemas.jsonld b/data/chemmine_tools/chemmine_toolsbioschemas.jsonld index 0b2683f8e3a93..14b915174f095 100644 --- a/data/chemmine_tools/chemmine_toolsbioschemas.jsonld +++ b/data/chemmine_tools/chemmine_toolsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available.", "sc:name": "ChemMine Tools", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://chemmine.ucr.edu" } \ No newline at end of file diff --git a/data/chemmineob/chemmineobbioschemas.jsonld b/data/chemmineob/chemmineobbioschemas.jsonld index e936b11628206..4f507c0bad5d9 100644 --- a/data/chemmineob/chemmineobbioschemas.jsonld +++ b/data/chemmineob/chemmineobbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "This package provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. This package aims to make a subset of these utilities available from within R.", "sc:name": "ChemmineOB", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChemmineOB.html", "sc:version": "1.12.0" diff --git a/data/chemminer/chemminerbioschemas.jsonld b/data/chemminer/chemminerbioschemas.jsonld index 95c04108ff234..8d355aa7f32cc 100644 --- a/data/chemminer/chemminerbioschemas.jsonld +++ b/data/chemminer/chemminerbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btn307", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/chemminer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas Girke", "edam:has_input": [ { - "@id": "edam:data_2050" + "@id": "edam:data_1463" }, { - "@id": "edam:data_1463" + "@id": "edam:data_2050" } ], "edam:has_output": [ @@ -41,55 +37,59 @@ "@id": "edam:topic_2258" }, "sc:citation": [ + "pmcid:PMC2638865", + "pubmed:18596077", { "@id": "https://doi.org/10.1093/bioinformatics/btn307" - }, - "pmcid:PMC2638865", - "pubmed:18596077" + } ], "sc:description": "Cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.", "sc:featureList": [ { - "@id": "edam:operation_2424" + "@id": "edam:operation_2425" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_3438" }, { - "@id": "edam:operation_2945" + "@id": "edam:operation_3432" }, { - "@id": "edam:operation_3429" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_3432" + "@id": "edam:operation_2945" }, { "@id": "edam:operation_2421" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_2424" }, { - "@id": "edam:operation_2425" + "@id": "edam:operation_0335" }, { - "@id": "edam:operation_3438" + "@id": "edam:operation_3429" } ], "sc:isAccessibleForFree": true, "sc:license": "Artistic-2.0", "sc:name": "ChemmineR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:softwareHelp": { "@id": "http://bioconductor.org/packages/release/bioc/html/ChemmineR.html" }, "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChemmineR.html", "sc:version": "2.26.1" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btn307", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/chemotion_eln/chemotion_elnbioschemas.jsonld b/data/chemotion_eln/chemotion_elnbioschemas.jsonld index 353f474f6b961..de80431e368b4 100644 --- a/data/chemotion_eln/chemotion_elnbioschemas.jsonld +++ b/data/chemotion_eln/chemotion_elnbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "AGPL-3.0", "sc:name": "chemotion_ELN", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/ComPlat/chemotion_ELN" } \ No newline at end of file diff --git a/data/chemprot/chemprotbioschemas.jsonld b/data/chemprot/chemprotbioschemas.jsonld index fef9424540ffd..b46b9cd104772 100644 --- a/data/chemprot/chemprotbioschemas.jsonld +++ b/data/chemprot/chemprotbioschemas.jsonld @@ -30,11 +30,11 @@ "@id": "edam:topic_0602" }, "sc:citation": [ - "pmcid:PMC3531079", "pubmed:23185041", { "@id": "https://doi.org/10.1093/nar/gks1166" - } + }, + "pmcid:PMC3531079" ], "sc:description": "Ressource of annotated and predicted chemical-protein interactions.", "sc:featureList": { @@ -45,16 +45,16 @@ "sc:name": "ChemProt", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "CBS", "sc:softwareHelp": [ { - "@id": "http://www.cbs.dtu.dk/services/ChemProt-2.0/instructions.php" + "@id": "http://potentia.cbs.dtu.dk/ChemProt/New/Help.html" }, { - "@id": "http://potentia.cbs.dtu.dk/ChemProt/New/Help.html" + "@id": "http://www.cbs.dtu.dk/services/ChemProt-2.0/instructions.php" } ], "sc:url": "http://cbs.dtu.dk/services/ChemProt-2.0/", diff --git a/data/chemsar/chemsarbioschemas.jsonld b/data/chemsar/chemsarbioschemas.jsonld index 2e6b43720733a..76fbb5ddc4c49 100644 --- a/data/chemsar/chemsarbioschemas.jsonld +++ b/data/chemsar/chemsarbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This web server provides online access to realize a full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model. It provides a browser-based pipelining which requires no programming skills.", "sc:name": "ChemSAR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://chemsar.scbdd.com/" } \ No newline at end of file diff --git a/data/chemspider/chemspiderbioschemas.jsonld b/data/chemspider/chemspiderbioschemas.jsonld index c8e84c88452eb..31a0fef204973 100644 --- a/data/chemspider/chemspiderbioschemas.jsonld +++ b/data/chemspider/chemspiderbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Various search options for searching the ChemSpider database.", "sc:name": "ChemSpider", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.chemspider.com/", "sc:version": "1" diff --git a/data/chemsuite/chemsuitebioschemas.jsonld b/data/chemsuite/chemsuitebioschemas.jsonld index 2e27920f55593..8cd38e33e4302 100644 --- a/data/chemsuite/chemsuitebioschemas.jsonld +++ b/data/chemsuite/chemsuitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "ChemSuite", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://14.139.57.41/chemsuiteweb/" diff --git a/data/cheripic/cheripicbioschemas.jsonld b/data/cheripic/cheripicbioschemas.jsonld index d24c4713c7ad8..50a3d731b08aa 100644 --- a/data/cheripic/cheripicbioschemas.jsonld +++ b/data/cheripic/cheripicbioschemas.jsonld @@ -18,22 +18,22 @@ "Command-line tool" ], "sc:citation": [ + "pmcid:PMC6323790", { "@id": "https://doi.org/10.1186/s12859-018-2515-5" }, - "pmcid:PMC6323790", "pubmed:30616525" ], "sc:description": "Computing Homozygosity Enriched Regions In genomes to Prioritize Identification of Candidate variants (CHERIPIC) - tools to pick causative mutation from bulks segregant sequencing.", "sc:featureList": [ - { - "@id": "edam:operation_3226" - }, { "@id": "edam:operation_3227" }, { "@id": "edam:operation_0524" + }, + { + "@id": "edam:operation_3226" } ], "sc:license": "MIT", diff --git a/data/chia-pet2/chia-pet2bioschemas.jsonld b/data/chia-pet2/chia-pet2bioschemas.jsonld index e9c5cc6bd841b..1543701763044 100644 --- a/data/chia-pet2/chia-pet2bioschemas.jsonld +++ b/data/chia-pet2/chia-pet2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKW809", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/chia-pet2", "@type": "sc:SoftwareApplication", @@ -24,22 +28,18 @@ "sc:description": "Versatile and flexible pipeline for ChIA-PET data analysis.", "sc:featureList": [ { - "@id": "edam:operation_2478" + "@id": "edam:operation_3222" }, { - "@id": "edam:operation_3222" + "@id": "edam:operation_2478" } ], "sc:name": "ChIA-PET2", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/GuipengLi/ChIA-PET2" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKW809", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/chicago/chicagobioschemas.jsonld b/data/chicago/chicagobioschemas.jsonld index b0be26bba2ef8..b2ef675d4c648 100644 --- a/data/chicago/chicagobioschemas.jsonld +++ b/data/chicago/chicagobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-0383-3943", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/chicago", "@type": "sc:SoftwareApplication", @@ -16,15 +20,15 @@ "@id": "http://orcid.org/0000-0002-0383-3943" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pmcid:PMC4908757", + "pubmed:27306882", { "@id": "https://doi.org/10.1186/s13059-016-0992-2" - }, - "pubmed:27306882" + } ], "sc:description": "A pipeline for analysing Capture Hi-C data.", "sc:featureList": { @@ -33,17 +37,13 @@ "sc:license": "Artistic-2.0", "sc:name": "Chicago", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Chicago.html", "sc:version": "1.2.0" }, - { - "@id": "http://orcid.org/0000-0002-0383-3943", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s13059-016-0992-2", "@type": "sc:CreativeWork" diff --git a/data/chickspress/chickspressbioschemas.jsonld b/data/chickspress/chickspressbioschemas.jsonld index 885c3b3206531..f89e75a4bd133 100644 --- a/data/chickspress/chickspressbioschemas.jsonld +++ b/data/chickspress/chickspressbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/Chickspress", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Shane C Burgess", + "Eric H Lyons", "Fiona M McCarthy", - "Eric H Lyons" + "Shane C Burgess" ], "sc:additionalType": "Web application", "sc:description": "Chickspress Genome Browser.", diff --git a/data/chicmaxima/chicmaximabioschemas.jsonld b/data/chicmaxima/chicmaximabioschemas.jsonld index b22385e10fb2a..8556875de06d3 100644 --- a/data/chicmaxima/chicmaximabioschemas.jsonld +++ b/data/chicmaxima/chicmaximabioschemas.jsonld @@ -9,42 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13059-019-1706-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ChiCMaxima", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Y. Ben Zouari", - "T. Sexton" + "T. Sexton", + "Y. Ben Zouari" ], "sc:additionalType": "Suite", "sc:citation": [ - "pmcid:PMC6532271", - "pubmed:31118054", { "@id": "https://doi.org/10.1186/s13059-019-1706-3" - } + }, + "pubmed:31118054", + "pmcid:PMC6532271" ], "sc:description": "Pipeline for analyzing and identificantion of chromation loops in CHi-C promoters data.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_3501" } ], "sc:license": "GPL-2.0", "sc:name": "ChiCMaxima", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/yousra291987/ChiCMaxima" - }, - { - "@id": "https://doi.org/10.1186/s13059-019-1706-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/chicp/chicpbioschemas.jsonld b/data/chicp/chicpbioschemas.jsonld index 2b00860142b9d..d7881152b55ff 100644 --- a/data/chicp/chicpbioschemas.jsonld +++ b/data/chicp/chicpbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CHiCP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.chicp.org/" } \ No newline at end of file diff --git a/data/chilibot/chilibotbioschemas.jsonld b/data/chilibot/chilibotbioschemas.jsonld index 3d92e06c1e849..8dab05b5e6553 100644 --- a/data/chilibot/chilibotbioschemas.jsonld +++ b/data/chilibot/chilibotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. The results are returned as a graph.", "sc:name": "Chilibot", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.chilibot.net/" } \ No newline at end of file diff --git a/data/chilin/chilinbioschemas.jsonld b/data/chilin/chilinbioschemas.jsonld index db3896240d299..abd5ace03df5c 100644 --- a/data/chilin/chilinbioschemas.jsonld +++ b/data/chilin/chilinbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-016-1274-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/chilin", "@type": "sc:SoftwareApplication", @@ -41,6 +37,10 @@ "Mac" ], "sc:url": "https://github.com/cfce/chilin" + }, + { + "@id": "https://doi.org/10.1186/S12859-016-1274-4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/chimera/chimerabioschemas.jsonld b/data/chimera/chimerabioschemas.jsonld index 57a8089117ffe..eaf9b03e6aab2 100644 --- a/data/chimera/chimerabioschemas.jsonld +++ b/data/chimera/chimerabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Chimera", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://www.cgl.ucsf.edu/chimera/", diff --git a/data/chimera_fusion/chimera_fusionbioschemas.jsonld b/data/chimera_fusion/chimera_fusionbioschemas.jsonld index c0698a4dc572a..b8de39a0202c9 100644 --- a/data/chimera_fusion/chimera_fusionbioschemas.jsonld +++ b/data/chimera_fusion/chimera_fusionbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "chimera", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/chimera.html", "sc:version": "1.22.0" diff --git a/data/chimeraviz/chimeravizbioschemas.jsonld b/data/chimeraviz/chimeravizbioschemas.jsonld index 35bb1d47ea36e..20d7c27d43601 100644 --- a/data/chimeraviz/chimeravizbioschemas.jsonld +++ b/data/chimeraviz/chimeravizbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "chimeraviz", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://bioconductor.org/packages/release/bioc/html/chimeraviz.html", "sc:version": "1.6.0" diff --git a/data/chimerdb/chimerdbbioschemas.jsonld b/data/chimerdb/chimerdbbioschemas.jsonld index c3734e6b0fd78..4b1f93621f6a2 100644 --- a/data/chimerdb/chimerdbbioschemas.jsonld +++ b/data/chimerdb/chimerdbbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/chimerdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "J. Kang", - "S. Lee" + "S. Lee", + "J. Kang" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:19906715", diff --git a/data/chinook/chinookbioschemas.jsonld b/data/chinook/chinookbioschemas.jsonld index 5b71bf8fb09ad..b78cc79ae4cb2 100644 --- a/data/chinook/chinookbioschemas.jsonld +++ b/data/chinook/chinookbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application.", "sc:name": "Chinook", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bcgsc.bc.ca/chinook/" } \ No newline at end of file diff --git a/data/chip-array/chip-arraybioschemas.jsonld b/data/chip-array/chip-arraybioschemas.jsonld index 81fd63541625a..abef9303101e9 100644 --- a/data/chip-array/chip-arraybioschemas.jsonld +++ b/data/chip-array/chip-arraybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.", "sc:name": "ChIP-Array", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://jjwanglab.org/chip-array/" } \ No newline at end of file diff --git a/data/chipanalyser/chipanalyserbioschemas.jsonld b/data/chipanalyser/chipanalyserbioschemas.jsonld index 2505efcd11fd8..ca755988c76ee 100644 --- a/data/chipanalyser/chipanalyserbioschemas.jsonld +++ b/data/chipanalyser/chipanalyserbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ChIPanalyser", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPanalyser.html", "sc:version": "1.2.0" diff --git a/data/chipchipnorm/chipchipnormbioschemas.jsonld b/data/chipchipnorm/chipchipnormbioschemas.jsonld index 10c645fd82054..a9a331131527d 100644 --- a/data/chipchipnorm/chipchipnormbioschemas.jsonld +++ b/data/chipchipnorm/chipchipnormbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "R package that can be incorporated into the normalization workflow for chip-chip data, chromatin immunoprecipitation (ChIP) with microarray technology (chip).", "sc:name": "chipchipnorm", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://compbio.med.harvard.edu/software.html", "sc:version": "1.0.1" diff --git a/data/chipcomp/chipcompbioschemas.jsonld b/data/chipcomp/chipcompbioschemas.jsonld index 43835dca2b2b5..7420b45df1c0a 100644 --- a/data/chipcomp/chipcompbioschemas.jsonld +++ b/data/chipcomp/chipcompbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btv094", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/chipcomp", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:25682068", + "pmcid:PMC4542775", { "@id": "https://doi.org/10.1093/bioinformatics/btv094" - }, - "pmcid:PMC4542775", - "pubmed:25682068" + } ], "sc:description": "Detects differentially bound sharp binding sites across multiple conditions considering matching control.", "sc:featureList": { @@ -37,10 +41,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPComp.html", "sc:version": "1.4.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btv094", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/chipenrich/chipenrichbioschemas.jsonld b/data/chipenrich/chipenrichbioschemas.jsonld index 7ebd7afe36767..64278e9fc0832 100644 --- a/data/chipenrich/chipenrichbioschemas.jsonld +++ b/data/chipenrich/chipenrichbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gku463", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/chipenrich", "@type": "sc:SoftwareApplication", @@ -22,27 +18,27 @@ }, "edam:has_output": [ { - "@id": "edam:data_1276" + "@id": "edam:data_2884" }, { - "@id": "edam:data_2884" + "@id": "edam:data_1276" } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3572" + "@id": "edam:topic_3169" }, { - "@id": "edam:topic_3169" + "@id": "edam:topic_3572" } ], "sc:citation": [ - "pubmed:24878920", "pmcid:PMC4117744", + "pubmed:24878920", { "@id": "https://doi.org/10.1093/nar/gku463" } @@ -67,6 +63,10 @@ { "@id": "http://orcid.org/0000-0001-6155-5702", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gku463", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/chipexoqual/chipexoqualbioschemas.jsonld b/data/chipexoqual/chipexoqualbioschemas.jsonld index eec53e85715c2..a3ced59f60282 100644 --- a/data/chipexoqual/chipexoqualbioschemas.jsonld +++ b/data/chipexoqual/chipexoqualbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "ChIPexoQual", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPexoQual.html", "sc:version": "1.4.0" diff --git a/data/chipmeta/chipmetabioschemas.jsonld b/data/chipmeta/chipmetabioschemas.jsonld index 4f3155bef3a07..65e0c4e17bf51 100644 --- a/data/chipmeta/chipmetabioschemas.jsonld +++ b/data/chipmeta/chipmetabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/chipmeta", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Debashis Ghosh", - "Zhaohui S. Qin" + "Zhaohui S. Qin", + "Debashis Ghosh" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:19447789", diff --git a/data/chipmunk/chipmunkbioschemas.jsonld b/data/chipmunk/chipmunkbioschemas.jsonld index 443a4fbc95874..b815a741da40c 100644 --- a/data/chipmunk/chipmunkbioschemas.jsonld +++ b/data/chipmunk/chipmunkbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ChIPMunk", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://autosome.ru/ChIPMunk/" } \ No newline at end of file diff --git a/data/chippeakanno/chippeakannobioschemas.jsonld b/data/chippeakanno/chippeakannobioschemas.jsonld index 505ff6639c9f8..94ea493db06b6 100644 --- a/data/chippeakanno/chippeakannobioschemas.jsonld +++ b/data/chippeakanno/chippeakannobioschemas.jsonld @@ -15,17 +15,17 @@ "Lihua Julie Zhu" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:23975789", "sc:description": "The package includes functions to retrieve the sequences around the peak, obtain enriched GO terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other TF binding sites supplied by users. New functions have been added for finding the peaks with bi-directional promoters with summary statistics, for summarizing the occurrence of motifs in peaks and for adding other IDs to annotated peaks or enrichedGO.", "sc:license": "GPL-2.0", "sc:name": "ChIPpeakAnno", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html", "sc:version": "3.8.7" diff --git a/data/chipqc/chipqcbioschemas.jsonld b/data/chipqc/chipqcbioschemas.jsonld index 92012d6af7f28..1d60ace78b2b6 100644 --- a/data/chipqc/chipqcbioschemas.jsonld +++ b/data/chipqc/chipqcbioschemas.jsonld @@ -9,25 +9,33 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-1790-5469", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.3389/fgene.2014.00075", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/chipqc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Tom Carroll", { "@id": "http://orcid.org/0000-0002-1790-5469" - } + }, + "Tom Carroll" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC3989762", + "pubmed:24782889", { "@id": "https://doi.org/10.3389/fgene.2014.00075" - }, - "pubmed:24782889" + } ], "sc:description": "Quality metrics for ChIPseq data.", "sc:featureList": { @@ -42,14 +50,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPQC.html", "sc:version": "1.10.2" - }, - { - "@id": "https://doi.org/10.3389/fgene.2014.00075", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-1790-5469", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/chips/chipsbioschemas.jsonld b/data/chips/chipsbioschemas.jsonld index b36b2a7077994..03caa1c8e258f 100644 --- a/data/chips/chipsbioschemas.jsonld +++ b/data/chips/chipsbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "EMBOSS Contributors", - "UK BBSRC", - "Wellcome Trust" + "UK MRC", + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Calculate Nc codon usage statistic.", "sc:funder": [ - "UK MRC", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "chips", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/chips.html", "sc:version": "r6" diff --git a/data/chipseeker/chipseekerbioschemas.jsonld b/data/chipseeker/chipseekerbioschemas.jsonld index 1994c560fbd10..213b8749aca87 100644 --- a/data/chipseeker/chipseekerbioschemas.jsonld +++ b/data/chipseeker/chipseekerbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6485-8781", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/chipseeker", "@type": "sc:SoftwareApplication", @@ -25,15 +29,11 @@ "sc:name": "ChIPseeker", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPseeker.html", "sc:version": "1.10.3" - }, - { - "@id": "http://orcid.org/0000-0002-6485-8781", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/chipseq/bioconda_chipseq.yaml b/data/chipseq/bioconda_chipseq.yaml index c568c10937e08..a98eb7585e16e 100644 --- a/data/chipseq/bioconda_chipseq.yaml +++ b/data/chipseq/bioconda_chipseq.yaml @@ -3,7 +3,6 @@ description: Tools for helping process short read data for chipseq experiments home: https://bioconductor.org/packages/3.10/bioc/html/chipseq.html identifiers: - biotools:chipseq -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-chipseq summary: 'chipseq: A package for analyzing chipseq data' diff --git a/data/chipseq/chipseqbioschemas.jsonld b/data/chipseq/chipseqbioschemas.jsonld index d957ec707c56a..cceec4ad27196 100644 --- a/data/chipseq/chipseqbioschemas.jsonld +++ b/data/chipseq/chipseqbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Tools for helping process short read data for chipseq experiments.", "sc:license": "Artistic-2.0", diff --git a/data/chipseqr/chipseqrbioschemas.jsonld b/data/chipseqr/chipseqrbioschemas.jsonld index 20dbec80a9a49..16f7d4ff99ea6 100644 --- a/data/chipseqr/chipseqrbioschemas.jsonld +++ b/data/chipseqr/chipseqrbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1186/1471-2105-12-39", "@type": "sc:CreativeWork" }, + { + "@id": "http://orcid.org/0000-0002-3331-6496", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/chipseqr", "@type": "sc:SoftwareApplication", @@ -20,15 +24,15 @@ "@id": "http://orcid.org/0000-0002-3331-6496" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ { "@id": "https://doi.org/10.1186/1471-2105-12-39" }, - "pubmed:21281468", - "pmcid:PMC3045301" + "pmcid:PMC3045301", + "pubmed:21281468" ], "sc:description": "Identify protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but it is flexible enough to handle other types of experiments as well.", "sc:featureList": { @@ -37,16 +41,12 @@ "sc:license": "GPL-2.0", "sc:name": "ChIPseqR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPseqR.html", "sc:version": "1.28.0" - }, - { - "@id": "http://orcid.org/0000-0002-3331-6496", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/chipseqspike/chipseqspikebioschemas.jsonld b/data/chipseqspike/chipseqspikebioschemas.jsonld index 0cf31f8da7aa7..6e109e033ca3e 100644 --- a/data/chipseqspike/chipseqspikebioschemas.jsonld +++ b/data/chipseqspike/chipseqspikebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "ChIPSeqSpike", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPSeqSpike.html", diff --git a/data/chipsim/bioconda_chipsim.yaml b/data/chipsim/bioconda_chipsim.yaml index e8e2ca0795511..7c3a01c807e01 100644 --- a/data/chipsim/bioconda_chipsim.yaml +++ b/data/chipsim/bioconda_chipsim.yaml @@ -5,7 +5,6 @@ description: A general framework for the simulation of ChIP-seq data. Although c home: https://bioconductor.org/packages/3.10/bioc/html/ChIPsim.html identifiers: - biotools:chipsim -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-chipsim diff --git a/data/chipsim/chipsimbioschemas.jsonld b/data/chipsim/chipsimbioschemas.jsonld index 9c652dd844ee5..5e257e4b08279 100644 --- a/data/chipsim/chipsimbioschemas.jsonld +++ b/data/chipsim/chipsimbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "ChIPsim", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPsim.html", "sc:version": "1.28.0" diff --git a/data/chipster/chipsterbioschemas.jsonld b/data/chipster/chipsterbioschemas.jsonld index 62f8c8254ded4..e28d9ac91bf3f 100644 --- a/data/chipster/chipsterbioschemas.jsonld +++ b/data/chipster/chipsterbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/chipster", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", "Desktop application", - "Workbench" + "Workbench", + "Command-line tool" ], "sc:description": "Free, open source software for analyzing high-throughput data such as NGS. It is available as a ready-to-run virtual machine (VM) containing a large collection of up-to-date analysis tools and reference data, such as Ensembl genomes indexed for aligners. The tools can be used on command line, or via an intuitive client GUI.", "sc:license": "GPL-3.0", "sc:name": "Chipster", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "csc.fi", "sc:url": "http://chipster.csc.fi/", diff --git a/data/chipsummitdb/chipsummitdbbioschemas.jsonld b/data/chipsummitdb/chipsummitdbbioschemas.jsonld index 56221e235d010..aead37e423056 100644 --- a/data/chipsummitdb/chipsummitdbbioschemas.jsonld +++ b/data/chipsummitdb/chipsummitdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "ChIPSummitDB", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://summit.med.unideb.hu/summitdb/" } \ No newline at end of file diff --git a/data/chipulate/chipulatebioschemas.jsonld b/data/chipulate/chipulatebioschemas.jsonld index d4fcfd3f3054d..f22bfde510cf9 100644 --- a/data/chipulate/chipulatebioschemas.jsonld +++ b/data/chipulate/chipulatebioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Vishaka Datta S", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6445533", + "pubmed:30897079", { "@id": "https://doi.org/10.1371/journal.pcbi.1006921" - }, - "pubmed:30897079", - "pmcid:PMC6445533" + } ], "sc:description": "A Python3 framework to simulate read counts in a ChIP-seq experiment.", "sc:featureList": [ @@ -37,8 +37,8 @@ "sc:name": "ChIPulate", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/vishakad/chipulate" }, diff --git a/data/chipwig/chipwigbioschemas.jsonld b/data/chipwig/chipwigbioschemas.jsonld index 85f4c9e62a166..ddfc59d37f04d 100644 --- a/data/chipwig/chipwigbioschemas.jsonld +++ b/data/chipwig/chipwigbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Random access-enabling lossless and lossy compression method for ChIP-seq data.", "sc:name": "ChIPWig", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/vidarmehr/ChIPWig-v2", "sc:version": "2" diff --git a/data/chipxpress/chipxpressbioschemas.jsonld b/data/chipxpress/chipxpressbioschemas.jsonld index bc0ad7ff23ef5..bc4c547057123 100644 --- a/data/chipxpress/chipxpressbioschemas.jsonld +++ b/data/chipxpress/chipxpressbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "ChIPXpress", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChIPXpress.html", "sc:version": "1.16.0" diff --git a/data/chiron/chironbioschemas.jsonld b/data/chiron/chironbioschemas.jsonld index a7bbb49eee57d..b2598a40f2588 100644 --- a/data/chiron/chironbioschemas.jsonld +++ b/data/chiron/chironbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/chiron", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Haotian Teng", - "Lachlan J M Coin" + "Lachlan J M Coin", + "Haotian Teng" ], "sc:additionalType": "Command-line tool", "sc:description": "A basecaller for Oxford Nanopore Technologies' sequencers.", diff --git a/data/chlorop/chloropbioschemas.jsonld b/data/chlorop/chloropbioschemas.jsonld index 6ddc0003e504c..bb5e1e6d1edc5 100644 --- a/data/chlorop/chloropbioschemas.jsonld +++ b/data/chlorop/chloropbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "ChloroP", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/ChloroP/", diff --git a/data/chngpt/chngptbioschemas.jsonld b/data/chngpt/chngptbioschemas.jsonld index f393334fc1207..fc2bddb842fec 100644 --- a/data/chngpt/chngptbioschemas.jsonld +++ b/data/chngpt/chngptbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1863-x", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/chngpt", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Youyi Fong", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5644082", + "pubmed:29037149", { "@id": "https://doi.org/10.1186/s12859-017-1863-x" }, - "pubmed:29037149" + "pmcid:PMC5644082" ], "sc:description": "Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater.", "sc:featureList": { @@ -33,11 +29,15 @@ "sc:name": "chngpt", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/chngpt/", "sc:version": "2018.6-2" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1863-x", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/chopchop/chopchopbioschemas.jsonld b/data/chopchop/chopchopbioschemas.jsonld index ade09727442ad..2dcb9a83287ac 100644 --- a/data/chopchop/chopchopbioschemas.jsonld +++ b/data/chopchop/chopchopbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Web tool for selecting the optimum target sites for CRISPR/Cas9- or TALEN-directed mutagenesis.", "sc:name": "CHOPCHOP", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "uib.no", diff --git a/data/chopsticks/bioconda_chopsticks.yaml b/data/chopsticks/bioconda_chopsticks.yaml index 339c219303ecb..c4dc8beaa1ace 100644 --- a/data/chopsticks/bioconda_chopsticks.yaml +++ b/data/chopsticks/bioconda_chopsticks.yaml @@ -3,7 +3,6 @@ description: Implements classes and methods for large-scale SNP association stud home: https://bioconductor.org/packages/3.10/bioc/html/chopsticks.html identifiers: - biotools:chopsticks -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-chopsticks diff --git a/data/chopstitch/chopstitchbioschemas.jsonld b/data/chopstitch/chopstitchbioschemas.jsonld index 6b3261fe544a4..2482aa2b99d07 100644 --- a/data/chopstitch/chopstitchbioschemas.jsonld +++ b/data/chopstitch/chopstitchbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/chopstitch", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hamza Khan", - "Inanc Birol" + "Inanc Birol", + "Hamza Khan" ], "sc:additionalType": "Command-line tool", "sc:description": "Finding putative exons and constructing splicegraphs using Trans-ABySS contigs.", diff --git a/data/chpredict/chpredictbioschemas.jsonld b/data/chpredict/chpredictbioschemas.jsonld index 65d46a535aa98..bbc6afa5c8487 100644 --- a/data/chpredict/chpredictbioschemas.jsonld +++ b/data/chpredict/chpredictbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Predicts two types of interactions: C-H...O and C-H...π interactions. For C-H...O interaction, the server predicts the residues whose backbone Cα atoms are involved in interaction with backbone oxygen atoms and for C-H...π interactions, it predicts the residues whose backbone Cα atoms are involved in interaction with π ring system of side chain aromatic moieties.", "sc:name": "CHpredict", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.imtech.res.in/raghava/chpredict" diff --git a/data/chrogps/chrogpsbioschemas.jsonld b/data/chrogps/chrogpsbioschemas.jsonld index 82bedd032fb50..f72d74f2e468d 100644 --- a/data/chrogps/chrogpsbioschemas.jsonld +++ b/data/chrogps/chrogpsbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Oscar Reina", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "We provide intuitive maps to visualize the association between genetic elements, with emphasis on epigenetics. The approach is based on Multi-Dimensional Scaling. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds.", "sc:license": "GPL-2.0", "sc:name": "chroGPS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/chroGPS.html", diff --git a/data/chromagnon/chromagnonbioschemas.jsonld b/data/chromagnon/chromagnonbioschemas.jsonld index 6780081c22a6f..4c846a01fb59a 100644 --- a/data/chromagnon/chromagnonbioschemas.jsonld +++ b/data/chromagnon/chromagnonbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/s41598-018-25922-7", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/chromagnon", "@type": "sc:SoftwareApplication", @@ -22,8 +18,8 @@ { "@id": "https://doi.org/10.1038/s41598-018-25922-7" }, - "pubmed:29765093", - "pmcid:PMC5954143" + "pmcid:PMC5954143", + "pubmed:29765093" ], "sc:description": "Image correction software for chromatic shifts in fluorescence microscopic images.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "GPL-2.0", "sc:name": "Chromagnon", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/macronucleus/chromagnon" + }, + { + "@id": "https://doi.org/10.1038/s41598-018-25922-7", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/chromcontact/chromcontactbioschemas.jsonld b/data/chromcontact/chromcontactbioschemas.jsonld index 1fe19b89c08dc..33c9d312a1137 100644 --- a/data/chromcontact/chromcontactbioschemas.jsonld +++ b/data/chromcontact/chromcontactbioschemas.jsonld @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "ChromContact", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioinfo.sls.kyushu-u.ac.jp/chromcontact/" }, diff --git a/data/chromdraw/chromdrawbioschemas.jsonld b/data/chromdraw/chromdrawbioschemas.jsonld index 515808268f2e4..36bede4e0a3e3 100644 --- a/data/chromdraw/chromdrawbioschemas.jsonld +++ b/data/chromdraw/chromdrawbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-0318-4194", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/chromdraw", "@type": "sc:SoftwareApplication", @@ -29,12 +25,16 @@ "sc:license": "GPL-3.0", "sc:name": "chromDraw", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/chromDraw.html", "sc:version": "2.4.0" + }, + { + "@id": "http://orcid.org/0000-0003-0318-4194", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/chromheatmap/bioconda_chromheatmap.yaml b/data/chromheatmap/bioconda_chromheatmap.yaml index 614321d356a7f..bcc151bb219c2 100644 --- a/data/chromheatmap/bioconda_chromheatmap.yaml +++ b/data/chromheatmap/bioconda_chromheatmap.yaml @@ -5,7 +5,6 @@ description: The ChromHeatMap package can be used to plot genome-wide data (e.g. home: https://bioconductor.org/packages/3.10/bioc/html/ChromHeatMap.html identifiers: - biotools:chromheatmap -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-chromheatmap summary: Heat map plotting by genome coordinate diff --git a/data/chromheatmap/chromheatmapbioschemas.jsonld b/data/chromheatmap/chromheatmapbioschemas.jsonld index f5507c5d3080f..d208af2acccb7 100644 --- a/data/chromheatmap/chromheatmapbioschemas.jsonld +++ b/data/chromheatmap/chromheatmapbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "ChromHeatMap", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ChromHeatMap.html", "sc:version": "1.28.0" diff --git a/data/chromhmm/chromhmmbioschemas.jsonld b/data/chromhmm/chromhmmbioschemas.jsonld index d5168266730c6..168f01f97ac62 100644 --- a/data/chromhmm/chromhmmbioschemas.jsonld +++ b/data/chromhmm/chromhmmbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "ChromHMM", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://compbio.mit.edu/ChromHMM" } \ No newline at end of file diff --git a/data/chromopainter/chromopainterbioschemas.jsonld b/data/chromopainter/chromopainterbioschemas.jsonld index 9caab6d66b856..4881dd7e9cff6 100644 --- a/data/chromopainter/chromopainterbioschemas.jsonld +++ b/data/chromopainter/chromopainterbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pgen.1002453", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-5311-6213", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/chromopainter", "@type": "sc:SoftwareApplication", @@ -25,11 +17,11 @@ "Desktop application" ], "sc:citation": [ - "pubmed:22291602", { "@id": "https://doi.org/10.1371/journal.pgen.1002453" }, - "pmcid:PMC3266881" + "pmcid:PMC3266881", + "pubmed:22291602" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-5311-6213" @@ -41,11 +33,19 @@ "sc:license": "CC-BY-NC-ND-3.0", "sc:name": "ChromoPainter", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://people.maths.bris.ac.uk/~madjl/finestructure-old/chromopainter_info.html" + }, + { + "@id": "https://doi.org/10.1371/journal.pgen.1002453", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-5311-6213", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/chromoviz/chromovizbioschemas.jsonld b/data/chromoviz/chromovizbioschemas.jsonld index e1b518d4b6e8b..f3f889026edcd 100644 --- a/data/chromoviz/chromovizbioschemas.jsonld +++ b/data/chromoviz/chromovizbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ChromoViz", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.snubi.org/software/ChromoViz/", "sc:version": "1.1" diff --git a/data/chromplot/chromplotbioschemas.jsonld b/data/chromplot/chromplotbioschemas.jsonld index 709761276cdaa..75645e9391e0d 100644 --- a/data/chromplot/chromplotbioschemas.jsonld +++ b/data/chromplot/chromplotbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Karen Y. Orostica", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at the end.", "sc:license": "GPL-2.0", "sc:name": "chromPlot", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/chromPlot.html", diff --git a/data/chromstar/chromstarbioschemas.jsonld b/data/chromstar/chromstarbioschemas.jsonld index 9b2a9508d49e1..9ef3bbf3452e7 100644 --- a/data/chromstar/chromstarbioschemas.jsonld +++ b/data/chromstar/chromstarbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Aaron Taudt", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.", "sc:license": "Artistic-2.0", "sc:name": "chromstaR", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/chromstaR.html", "sc:version": "1.0.0" diff --git a/data/chromswitch/chromswitchbioschemas.jsonld b/data/chromswitch/chromswitchbioschemas.jsonld index 9bc93c3985070..a527fb9e92f38 100644 --- a/data/chromswitch/chromswitchbioschemas.jsonld +++ b/data/chromswitch/chromswitchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "chromswitch", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/chromswitch.html", "sc:version": "1.2.1" diff --git a/data/chromvar/chromvarbioschemas.jsonld b/data/chromvar/chromvarbioschemas.jsonld index 9ae6842604415..177c9066b2b11 100644 --- a/data/chromvar/chromvarbioschemas.jsonld +++ b/data/chromvar/chromvarbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/NMETH.4401", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/chromvar", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC5623146", + "pubmed:28825706", { "@id": "https://doi.org/10.1038/NMETH.4401" - }, - "pubmed:28825706" + } ], "sc:description": "Inferring transcription-factor-associated accessibility from single-cell epigenomic data.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "chromVAR", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/GreenleafLab/chromVAR" + }, + { + "@id": "https://doi.org/10.1038/NMETH.4401", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/chronic_vs_clinic/chronic_vs_clinicbioschemas.jsonld b/data/chronic_vs_clinic/chronic_vs_clinicbioschemas.jsonld index b80b2b4f439dd..fed720698b141 100644 --- a/data/chronic_vs_clinic/chronic_vs_clinicbioschemas.jsonld +++ b/data/chronic_vs_clinic/chronic_vs_clinicbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "chronic vs clinic", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bitbucket.org/adv_bio_coll/chronic_vs_clinic" } \ No newline at end of file diff --git a/data/chronos/chronosbioschemas.jsonld b/data/chronos/chronosbioschemas.jsonld index 59979d3e88a86..5fcb277672cfe 100644 --- a/data/chronos/chronosbioschemas.jsonld +++ b/data/chronos/chronosbioschemas.jsonld @@ -15,17 +15,17 @@ "Anastasios Bezerianos" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:26568631", "sc:description": "A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs", "sc:license": "GPL-2.0", "sc:name": "CHRONOS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/CHRONOS/", "sc:version": "1.4.0" diff --git a/data/chsalign/chsalignbioschemas.jsonld b/data/chsalign/chsalignbioschemas.jsonld index ab2c3a1caf716..4b93f6fbeb46d 100644 --- a/data/chsalign/chsalignbioschemas.jsonld +++ b/data/chsalign/chsalignbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0147097", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/chsalign", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jason T.L. Wang", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC4720362", "pubmed:26789998", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0147097" - }, - "pmcid:PMC4720362" + } ], "sc:description": "Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.", "sc:featureList": [ @@ -33,14 +37,10 @@ "sc:name": "CHSalign", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://nature.njit.edu/biosoft/CHSalign/" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0147097", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cibex/cibexbioschemas.jsonld b/data/cibex/cibexbioschemas.jsonld index a1551b6280921..1ec85d0a4206a 100644 --- a/data/cibex/cibexbioschemas.jsonld +++ b/data/cibex/cibexbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Public repository for gene expression experimental data. The database system is compliant with the MIAME standard.", "sc:name": "CIBEX", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://cibex.nig.ac.jp/" } \ No newline at end of file diff --git a/data/cidane/cidanebioschemas.jsonld b/data/cidane/cidanebioschemas.jsonld index 277aae00184f4..df00d3a2c0a85 100644 --- a/data/cidane/cidanebioschemas.jsonld +++ b/data/cidane/cidanebioschemas.jsonld @@ -9,21 +9,25 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13059-015-0865-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cidane", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Knut Reinert", "David Weese", - "Gunnar W. Klau", - "Knut Reinert" + "Gunnar W. Klau" ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4734886", + "pubmed:26831908", { "@id": "https://doi.org/10.1186/s13059-015-0865-0" - }, - "pmcid:PMC4734886", - "pubmed:26831908" + } ], "sc:description": "Genome-based transcript reconstruction and quantification from RNA-seq reads. Its algorithmic core not only reconstructs transcripts ab initio, but also allows the use of the growing annotation of known splice sites, transcription start and end sites, or full-length transcripts, which are available for most model organisms", "sc:featureList": { @@ -33,10 +37,6 @@ "sc:name": "Cidane", "sc:operatingSystem": "Linux", "sc:url": "http://ccb.jhu.edu/software/cidane/" - }, - { - "@id": "https://doi.org/10.1186/s13059-015-0865-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cidd/ciddbioschemas.jsonld b/data/cidd/ciddbioschemas.jsonld index d156d0b8ee0f8..68d361f95dd6a 100644 --- a/data/cidd/ciddbioschemas.jsonld +++ b/data/cidd/ciddbioschemas.jsonld @@ -15,19 +15,19 @@ "biotools:primaryContact": "Paul Scheet", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4341901", + "pubmed:25349306", { "@id": "https://doi.org/10.1158/1535-7163.MCT-14-0260" - }, - "pubmed:25349306", - "pmcid:PMC4341901" + } ], "sc:description": "Cancer in silico Drug Discovery (CIDD) is a platform to integrate data from the TCGA, Connectivity Map (CMap) and Cancer Cell Line Encyclopedia to facilitate and automate discovery of candidate drug compounds with the ultimate goal for treatment or chemo-prevention of cancer.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_2495" }, { "@id": "edam:operation_3223" diff --git a/data/cif/cifbioschemas.jsonld b/data/cif/cifbioschemas.jsonld index 4f009f6451bce..51ffb033cba20 100644 --- a/data/cif/cifbioschemas.jsonld +++ b/data/cif/cifbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them.", "sc:name": "CiF", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.fusariumdb.org/" } \ No newline at end of file diff --git a/data/ciliacarta/ciliacartabioschemas.jsonld b/data/ciliacarta/ciliacartabioschemas.jsonld index ad2f9feb63a2d..60ea1625043bc 100644 --- a/data/ciliacarta/ciliacartabioschemas.jsonld +++ b/data/ciliacarta/ciliacartabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-8122-190X", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216705", "@type": "sc:CreativeWork" @@ -21,18 +17,18 @@ "@id": "https://bio.tools/CiliaCarta", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Martijn A. Huynen", { "@id": "https://orcid.org/0000-0002-8122-190X" - } + }, + "Martijn A. Huynen" ], "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6522010", - "pubmed:31095607", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216705" - } + }, + "pubmed:31095607", + "pmcid:PMC6522010" ], "sc:description": "An integrated and validated compendium of ciliary genes.", "sc:featureList": [ @@ -49,11 +45,15 @@ "sc:license": "Unlicense", "sc:name": "CiliaCarta", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/" + }, + { + "@id": "https://orcid.org/0000-0002-8122-190X", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/cimbinator/cimbinatorbioschemas.jsonld b/data/cimbinator/cimbinatorbioschemas.jsonld index 05cf98d0e55f6..6a0c218b426b8 100644 --- a/data/cimbinator/cimbinatorbioschemas.jsonld +++ b/data/cimbinator/cimbinatorbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "CImbinator", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://cimbinator.bioinfo.cnio.es/CombinationIndex" } \ No newline at end of file diff --git a/data/cindex/bioconda_cindex.yaml b/data/cindex/bioconda_cindex.yaml index e26d74b2db98b..27fafe20bfc2c 100644 --- a/data/cindex/bioconda_cindex.yaml +++ b/data/cindex/bioconda_cindex.yaml @@ -10,7 +10,6 @@ description: The CINdex package addresses important area of high-throughput geno home: https://bioconductor.org/packages/3.10/bioc/html/CINdex.html identifiers: - biotools:cindex -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-cindex diff --git a/data/cindex/cindexbioschemas.jsonld b/data/cindex/cindexbioschemas.jsonld index eba98574f4345..0517d0ba4d1b9 100644 --- a/data/cindex/cindexbioschemas.jsonld +++ b/data/cindex/cindexbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yuriy Gusev", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar. It calculates the chromosome instability index to quantitatively characterize genome-wide DNA copy number alterations. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses at the chromosome and cytoband level.", "sc:license": "GPL-2.0", "sc:name": "CINdex", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CINdex.html", "sc:version": "1.2.0" diff --git a/data/cinna/cinnabioschemas.jsonld b/data/cinna/cinnabioschemas.jsonld index 380048213beb8..6f5a877d9a484 100644 --- a/data/cinna/cinnabioschemas.jsonld +++ b/data/cinna/cinnabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "CINNA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://cran.r-project.org/package=CINNA", diff --git a/data/cipher/cipherbioschemas.jsonld b/data/cipher/cipherbioschemas.jsonld index 805ff2065d2d9..1c42e8df09021 100644 --- a/data/cipher/cipherbioschemas.jsonld +++ b/data/cipher/cipherbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/cipher", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Carlos Guzman", - "Iván D’Orso" + "Iván D’Orso", + "Carlos Guzman" ], "sc:additionalType": "Command-line tool", "sc:description": "Flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction.", diff --git a/data/cipres/cipresbioschemas.jsonld b/data/cipres/cipresbioschemas.jsonld index f1a3403c58eb0..6fa35fc244835 100644 --- a/data/cipres/cipresbioschemas.jsonld +++ b/data/cipres/cipresbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/cipres", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wayne Pfeiffer", + "Mark A. Miller", "Terri Schwartz", - "Mark A. Miller" + "Wayne Pfeiffer" ], "sc:additionalType": "Web application", "sc:description": "Project aims to develop a computational infrastructure for systematics. Other goals of the project include providing a central resource enabling computational systematics and education and training initiatives. The website also contains a substantial list of links to related software.", "sc:name": "CIPRes", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.phylo.org/" } \ No newline at end of file diff --git a/data/circbase/circbasebioschemas.jsonld b/data/circbase/circbasebioschemas.jsonld index 85261fda4d590..e22fdac3f1c3c 100644 --- a/data/circbase/circbasebioschemas.jsonld +++ b/data/circbase/circbasebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Explore public circRNA datasets and download tools to discover circRNAs in RNA-seq data.", "sc:name": "circBase", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.circbase.org/" diff --git a/data/circexplorer2/circexplorer2bioschemas.jsonld b/data/circexplorer2/circexplorer2bioschemas.jsonld index 3f3a4529ec8fd..1996bf16a4ee9 100644 --- a/data/circexplorer2/circexplorer2bioschemas.jsonld +++ b/data/circexplorer2/circexplorer2bioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Li Yang", - "Xiao-Ou Zhang" + "Xiao-Ou Zhang", + "Li Yang" ], "sc:citation": "pubmed:30539552", "sc:description": "Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.", diff --git a/data/circfunbase/circfunbasebioschemas.jsonld b/data/circfunbase/circfunbasebioschemas.jsonld index b40225a6096cb..47185a92a2cb8 100644 --- a/data/circfunbase/circfunbasebioschemas.jsonld +++ b/data/circfunbase/circfunbasebioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/database/baz003", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/CircFunBase", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ming Chen", "sc:additionalType": [ - "Database portal", "Web API", - "Web application" + "Web application", + "Database portal" ], "sc:author": [ "Ming Chen", @@ -28,31 +24,35 @@ "Xianwen Meng" ], "sc:citation": [ + "pmcid:PMC6360206", + "pubmed:30715276", { "@id": "https://doi.org/10.1093/database/baz003" - }, - "pmcid:PMC6360206", - "pubmed:30715276" + } ], "sc:description": "Database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions.", "sc:featureList": [ - { - "@id": "edam:operation_3431" - }, { "@id": "edam:operation_3501" }, { "@id": "edam:operation_2422" + }, + { + "@id": "edam:operation_3431" } ], "sc:name": "CircFunBase", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bis.zju.edu.cn/CircFunBase/" + }, + { + "@id": "https://doi.org/10.1093/database/baz003", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/circos/circosbioschemas.jsonld b/data/circos/circosbioschemas.jsonld index b6c3473b95d21..96305ac0a71a8 100644 --- a/data/circos/circosbioschemas.jsonld +++ b/data/circos/circosbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well.", "sc:name": "Circos", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://circos.ca/" } \ No newline at end of file diff --git a/data/circpro/circprobioschemas.jsonld b/data/circpro/circprobioschemas.jsonld index 78fc783237958..ed8db05b991b8 100644 --- a/data/circpro/circprobioschemas.jsonld +++ b/data/circpro/circprobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/CircPro", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ming Chen", - "Xianwen Meng" + "Xianwen Meng", + "Ming Chen" ], "sc:additionalType": "Command-line tool", "sc:description": "Integrated tool for the identification of circRNAs with protein-coding potential.", diff --git a/data/circrnawrap/circrnawrapbioschemas.jsonld b/data/circrnawrap/circrnawrapbioschemas.jsonld index 746750b5d078a..f0e773d970ca9 100644 --- a/data/circrnawrap/circrnawrapbioschemas.jsonld +++ b/data/circrnawrap/circrnawrapbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "circRNAwrap", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/liaoscience/circRNAwrap" } \ No newline at end of file diff --git a/data/circtools/circtoolsbioschemas.jsonld b/data/circtools/circtoolsbioschemas.jsonld index 0137532e7131c..b262868b24258 100644 --- a/data/circtools/circtoolsbioschemas.jsonld +++ b/data/circtools/circtoolsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "circtools", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/dieterich-lab/circtools" } \ No newline at end of file diff --git a/data/circularlogo/circularlogobioschemas.jsonld b/data/circularlogo/circularlogobioschemas.jsonld index b223448f1d2b5..03ff1e8d29a49 100644 --- a/data/circularlogo/circularlogobioschemas.jsonld +++ b/data/circularlogo/circularlogobioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1680-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/circularlogo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Liguo Wang", - "Zhenqing Ye" + "Zhenqing Ye", + "Liguo Wang" ], "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC5440937", + "pubmed:28532394", { "@id": "https://doi.org/10.1186/s12859-017-1680-2" - }, - "pmcid:PMC5440937", - "pubmed:28532394" + } ], "sc:description": "Web application for creating circular sequence logos for DNA (or RNA) motifs. By virtue of the circular layout, it not only displays nucleotide stacks like the traditional sequence logo, but also depicts intra-motif dependencies using linked arches.", "sc:featureList": { @@ -34,10 +30,14 @@ }, "sc:name": "CircularLogo", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://circularlogo.sourceforge.net/" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1680-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cirdna/cirdnabioschemas.jsonld b/data/cirdna/cirdnabioschemas.jsonld index fcd485ed71b61..5a5ef2d38a233 100644 --- a/data/cirdna/cirdnabioschemas.jsonld +++ b/data/cirdna/cirdnabioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", "EMBOSS Contributors", - "UK MRC" + "Wellcome Trust" ], "sc:description": "Draw circular map of DNA constructs.", "sc:funder": [ - "UK MRC", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "cirdna", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/cirdna.html", "sc:version": "r6" diff --git a/data/cirgo/cirgobioschemas.jsonld b/data/cirgo/cirgobioschemas.jsonld index 7ccf3c8a0ded5..1745292d7a4d5 100644 --- a/data/cirgo/cirgobioschemas.jsonld +++ b/data/cirgo/cirgobioschemas.jsonld @@ -9,27 +9,23 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2671-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/CirGO", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Irina Kuznetsova", - "Artur Lugmayr" + "Artur Lugmayr", + "Irina Kuznetsova" ], "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:citation": [ + "pmcid:PMC6380029", + "pubmed:30777018", { "@id": "https://doi.org/10.1186/s12859-019-2671-2" - }, - "pmcid:PMC6380029", - "pubmed:30777018" + } ], "sc:description": "Visualises non-redundant two-level hierarchically structured ontology terms from gene expression data in a 2D space.", "sc:featureList": [ @@ -51,6 +47,10 @@ "Windows" ], "sc:url": "https://github.com/IrinaVKuznetsova/CirGO.git" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2671-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ciri-full/ciri-fullbioschemas.jsonld b/data/ciri-full/ciri-fullbioschemas.jsonld index 22f145b334cc9..54e6c03b41e09 100644 --- a/data/ciri-full/ciri-fullbioschemas.jsonld +++ b/data/ciri-full/ciri-fullbioschemas.jsonld @@ -22,29 +22,29 @@ ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6339429", + "pubmed:30660194", { "@id": "https://doi.org/10.1186/s13073-019-0614-1" - }, - "pmcid:PMC6339429", - "pubmed:30660194" + } ], "sc:description": "CircRNA Identifier. A de novo circular RNA identification tool.", "sc:featureList": [ - { - "@id": "edam:operation_3799" - }, { "@id": "edam:operation_3644" }, { "@id": "edam:operation_0443" + }, + { + "@id": "edam:operation_3799" } ], "sc:license": "MIT", "sc:name": "CIRI", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/ciri" } diff --git a/data/cisgenome/cisgenomebioschemas.jsonld b/data/cisgenome/cisgenomebioschemas.jsonld index ffc75db7948ec..7e52487a2927f 100644 --- a/data/cisgenome/cisgenomebioschemas.jsonld +++ b/data/cisgenome/cisgenomebioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/cisgenome", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hongkai Ji", + "Admin", "Wing Hung Wong", - "Admin" + "Hongkai Ji" ], "sc:additionalType": "Suite", "sc:citation": "pubmed:18978777", "sc:description": "An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis", "sc:name": "CisGenome", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm" } \ No newline at end of file diff --git a/data/cisminer/cisminerbioschemas.jsonld b/data/cisminer/cisminerbioschemas.jsonld index 0c05b32db772d..be998ad57fea0 100644 --- a/data/cisminer/cisminerbioschemas.jsonld +++ b/data/cisminer/cisminerbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0108065", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cisminer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:25268582", + "pmcid:PMC4182448", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0108065" - }, - "pubmed:25268582", - "pmcid:PMC4182448" + } ], "sc:description": "Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "CisMiner", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://genome.ugr.es:9000/cisminer" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0108065", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cismols/cismolsbioschemas.jsonld b/data/cismols/cismolsbioschemas.jsonld index 16afe244c8ecc..bb28d6ca3e01e 100644 --- a/data/cismols/cismolsbioschemas.jsonld +++ b/data/cismols/cismolsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.", "sc:name": "CisMols", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://cismols.cchmc.org/" } \ No newline at end of file diff --git a/data/cispath/cispathbioschemas.jsonld b/data/cispath/cispathbioschemas.jsonld index c91f2310b26a6..5481ec365e226 100644 --- a/data/cispath/cispathbioschemas.jsonld +++ b/data/cispath/cispathbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Likun Wang", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "R package that uses web browsers to visualize and manage protein-protein interaction networks.", "sc:license": "GPL-3.0", "sc:name": "cisPath", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cisPath.html", "sc:version": "1.14.0" diff --git a/data/cisred/cisredbioschemas.jsonld b/data/cisred/cisredbioschemas.jsonld index 863be115d90f8..46e6993498c09 100644 --- a/data/cisred/cisredbioschemas.jsonld +++ b/data/cisred/cisredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "cisRED is a database system for genome-scale computational discovery of regulatory elements.", "sc:name": "cisRED", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.cisred.org/" diff --git a/data/cisregtest/cisregtestbioschemas.jsonld b/data/cisregtest/cisregtestbioschemas.jsonld index 4ec4155f6ac72..7a61539934292 100644 --- a/data/cisregtest/cisregtestbioschemas.jsonld +++ b/data/cisregtest/cisregtestbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.", "sc:name": "CisRegTest", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.moseslab.csb.utoronto.ca/alan/cis_reg_test.html" } \ No newline at end of file diff --git a/data/cistrome-go/cistrome-gobioschemas.jsonld b/data/cistrome-go/cistrome-gobioschemas.jsonld index af28f49c5af73..092ad5dd4019d 100644 --- a/data/cistrome-go/cistrome-gobioschemas.jsonld +++ b/data/cistrome-go/cistrome-gobioschemas.jsonld @@ -9,49 +9,49 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKZ332", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Cistrome-GO", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "X Shirley Liu", - "Clifford A Meyer" + "Clifford A Meyer", + "X Shirley Liu" ], "sc:additionalType": [ - "Command-line tool", + "Web service", "Web application", - "Web service" + "Command-line tool" ], "sc:citation": [ "pmcid:PMC6602521", + "pubmed:31053864", { "@id": "https://doi.org/10.1093/NAR/GKZ332" - }, - "pubmed:31053864" + } ], "sc:description": "Web server for functional enrichment analysis of transcription factor ChIP-seq peaks.", "sc:featureList": [ { - "@id": "edam:operation_3222" + "@id": "edam:operation_3223" }, { "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3223" + "@id": "edam:operation_3222" } ], "sc:license": "Other", "sc:name": "Cistrome-GO", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://go.cistrome.org/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ332", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cistrome/cistromebioschemas.jsonld b/data/cistrome/cistromebioschemas.jsonld index 340d5c365cc2e..a0fee7dec10de 100644 --- a/data/cistrome/cistromebioschemas.jsonld +++ b/data/cistrome/cistromebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A web-based application with an analysis platform for CHIP-chip/seq and gene expression microarray data.", "sc:name": "Cistrome", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.cistrome.org/Cistrome/Cistrome_Project.html#" } \ No newline at end of file diff --git a/data/cit/citbioschemas.jsonld b/data/cit/citbioschemas.jsonld index 9f4183502e546..7c9edaffeb803 100644 --- a/data/cit/citbioschemas.jsonld +++ b/data/cit/citbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btw135", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cit", "@type": "sc:SoftwareApplication", @@ -18,8 +22,8 @@ { "@id": "https://doi.org/10.1093/bioinformatics/btw135" }, - "pubmed:27153715", - "pmcid:PMC4965632" + "pmcid:PMC4965632", + "pubmed:27153715" ], "sc:description": "cit is a software package that provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "Artistic-2.0", "sc:name": "cit", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/cit/index.html", "sc:version": "2.2" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btw135", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cite-seq-count/cite-seq-countbioschemas.jsonld b/data/cite-seq-count/cite-seq-countbioschemas.jsonld index 7461b5b8a958d..9637b6dbd45c4 100644 --- a/data/cite-seq-count/cite-seq-countbioschemas.jsonld +++ b/data/cite-seq-count/cite-seq-countbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "CITE-seq-Count", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://hoohm.github.io/CITE-seq-Count/" } \ No newline at end of file diff --git a/data/citexplore/citexplorebioschemas.jsonld b/data/citexplore/citexplorebioschemas.jsonld index 39766fadad5eb..fecc01325bb04 100644 --- a/data/citexplore/citexplorebioschemas.jsonld +++ b/data/citexplore/citexplorebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Combine literature search with text mining tools for biology.", "sc:name": "CiteXplore literature database", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/web_guidelines/html/mitigation/frontier_test_02.html" } \ No newline at end of file diff --git a/data/cladepp/cladeppbioschemas.jsonld b/data/cladepp/cladeppbioschemas.jsonld index 42a4d673405b3..1373cdbefbee1 100644 --- a/data/cladepp/cladeppbioschemas.jsonld +++ b/data/cladepp/cladeppbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Clade Phylogenetic Profiling (CladePP) detects local coevolution across hundreds of genomes and points to the evolutionary scale (e.g. mammals, vertebrates, animals, plants) at which coevolution occurred.", "sc:name": "CladePP", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/dolevrahat/CladePP" } \ No newline at end of file diff --git a/data/clantox/clantoxbioschemas.jsonld b/data/clantox/clantoxbioschemas.jsonld index d8481a8161590..669f096ce17f1 100644 --- a/data/clantox/clantoxbioschemas.jsonld +++ b/data/clantox/clantoxbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Classifier of short animal toxins, predicts whether input sequences are toxin-like based on classification system training to known animal toxins. This dscovery prediction tool also outputs presence of signal peptide, the number of cysteine residues and the associated functional annotations.", "sc:name": "ClanTox", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.clantox.cs.huji.ac.il" } \ No newline at end of file diff --git a/data/clap/clapbioschemas.jsonld b/data/clap/clapbioschemas.jsonld index 1948c85b1b863..d4363b2dc733f 100644 --- a/data/clap/clapbioschemas.jsonld +++ b/data/clap/clapbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-15-343", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/clap", "@type": "sc:SoftwareApplication", @@ -32,10 +28,14 @@ "sc:name": "CLAP", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://nslab.mbu.iisc.ernet.in/clap/" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-15-343", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/clark/clarkbioschemas.jsonld b/data/clark/clarkbioschemas.jsonld index 5dfbac418bd15..60a637ce48321 100644 --- a/data/clark/clarkbioschemas.jsonld +++ b/data/clark/clarkbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Classification method based on a supervised sequence classification using discriminative k-mers.", "sc:name": "CLARK", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ebi.ac.uk", "sc:url": "http://clark.cs.ucr.edu/", diff --git a/data/classification_noise/classification_noisebioschemas.jsonld b/data/classification_noise/classification_noisebioschemas.jsonld index 9d6c1e255a6b6..96f9e6074b453 100644 --- a/data/classification_noise/classification_noisebioschemas.jsonld +++ b/data/classification_noise/classification_noisebioschemas.jsonld @@ -20,17 +20,17 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:31116772", + "pmcid:PMC6530857", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0217146" - }, - "pmcid:PMC6530857" + } ], "sc:description": "The effect of uncertainty in patient classification on diagnostic performance estimations.", "sc:license": "MIT", "sc:name": "classification noise", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://imperfect-gold-standard.shinyapps.io/classification-noise/" diff --git a/data/classifyme/classifymebioschemas.jsonld b/data/classifyme/classifymebioschemas.jsonld index 5a15a89209350..13320124de612 100644 --- a/data/classifyme/classifymebioschemas.jsonld +++ b/data/classifyme/classifymebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:license": "Other", "sc:name": "ClassifyMe", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://classifymeapp.com/" } \ No newline at end of file diff --git a/data/classifyr/classifyrbioschemas.jsonld b/data/classifyr/classifyrbioschemas.jsonld index 1dca4c4bf9f91..9fba2ad5e85bc 100644 --- a/data/classifyr/classifyrbioschemas.jsonld +++ b/data/classifyr/classifyrbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dario Strbenac", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:25644269", "sc:description": "The software formalises a framework for classification in R with four stages: data transformation, feature selection, classifier training, and prediction. The requirements of variable types and names are fixed, although specialised variables for functions can be provided. The classification framework is wrapped in a driver loop, that reproducibly carries out a number of cross-validation schemes.", "sc:license": "GPL-3.0", "sc:name": "ClassifyR", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ClassifyR.html", "sc:version": "1.8.1" diff --git a/data/clastr/clastrbioschemas.jsonld b/data/clastr/clastrbioschemas.jsonld index c294b4edc42cf..8289731702b64 100644 --- a/data/clastr/clastrbioschemas.jsonld +++ b/data/clastr/clastrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-6548-709X", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/CLASTR", "@type": "sc:SoftwareApplication", @@ -27,10 +31,6 @@ "sc:name": "CLASTR", "sc:url": "https://web.expasy.org/cellosaurus-str-search/", "sc:version": "1.2" - }, - { - "@id": "https://orcid.org/0000-0001-6548-709X", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/clc_cas_to_sam/clc_cas_to_sambioschemas.jsonld b/data/clc_cas_to_sam/clc_cas_to_sambioschemas.jsonld index b664abfa3e658..b97dab380c72e 100644 --- a/data/clc_cas_to_sam/clc_cas_to_sambioschemas.jsonld +++ b/data/clc_cas_to_sam/clc_cas_to_sambioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Convert a cas file to sam or bam format.", "sc:name": "clc_cas_to_sam", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://bio.tools/clcbio_genomics_workbench", diff --git a/data/clc_extract_consensus/clc_extract_consensusbioschemas.jsonld b/data/clc_extract_consensus/clc_extract_consensusbioschemas.jsonld index 6a126257ce77e..00e1978fc0ff3 100644 --- a/data/clc_extract_consensus/clc_extract_consensusbioschemas.jsonld +++ b/data/clc_extract_consensus/clc_extract_consensusbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Extract a consensus sequence from a read mapping. It operates on a cas file produced by the reference assembly programs.", "sc:name": "clc_extract_consensus", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://bio.tools/clcbio_genomics_workbench", "sc:version": "4.4.2" diff --git a/data/clc_find_variations/clc_find_variationsbioschemas.jsonld b/data/clc_find_variations/clc_find_variationsbioschemas.jsonld index b6787996bc094..499d554df22d5 100644 --- a/data/clc_find_variations/clc_find_variationsbioschemas.jsonld +++ b/data/clc_find_variations/clc_find_variationsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Find positions where the reads indicate a consistent difference from the reference sequences. Optionally, consensus sequences can be written to a fasta file.", "sc:name": "clc_find_variations", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://bio.tools/clcbio_genomics_workbench", "sc:version": "4.4.2" diff --git a/data/clc_find_variations_tab_convertor/clc_find_variations_tab_convertorbioschemas.jsonld b/data/clc_find_variations_tab_convertor/clc_find_variations_tab_convertorbioschemas.jsonld index e1994b8da737b..eba4825bc7b5b 100644 --- a/data/clc_find_variations_tab_convertor/clc_find_variations_tab_convertorbioschemas.jsonld +++ b/data/clc_find_variations_tab_convertor/clc_find_variations_tab_convertorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "clc_find_variations_tab_convertor", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bio.tools/clcbio_genomics_workbench", "sc:version": "0.2" diff --git a/data/clc_mapper/clc_mapperbioschemas.jsonld b/data/clc_mapper/clc_mapperbioschemas.jsonld index 08116e85f8453..118b3e7d42c2b 100644 --- a/data/clc_mapper/clc_mapperbioschemas.jsonld +++ b/data/clc_mapper/clc_mapperbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Map reads on reference sequences.", "sc:name": "clc_mapper", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://bio.tools/clcbio_genomics_workbench", diff --git a/data/clc_mapper_legacy/clc_mapper_legacybioschemas.jsonld b/data/clc_mapper_legacy/clc_mapper_legacybioschemas.jsonld index 13168e785dbd4..cfa08ec0442ad 100644 --- a/data/clc_mapper_legacy/clc_mapper_legacybioschemas.jsonld +++ b/data/clc_mapper_legacy/clc_mapper_legacybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Map some reads to some reference sequences.", "sc:name": "clc_mapper_legacy", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bio.tools/clcbio_genomics_workbench", "sc:version": "4.010.83648" diff --git a/data/clc_mapping_info/clc_mapping_infobioschemas.jsonld b/data/clc_mapping_info/clc_mapping_infobioschemas.jsonld index 7930c128b2454..4735e24f44d74 100644 --- a/data/clc_mapping_info/clc_mapping_infobioschemas.jsonld +++ b/data/clc_mapping_info/clc_mapping_infobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Print information about a read mapping.", "sc:name": "clc_mapping_info", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://bio.tools/clcbio_genomics_workbench", "sc:version": "4.4.2" diff --git a/data/clc_sequence_info/clc_sequence_infobioschemas.jsonld b/data/clc_sequence_info/clc_sequence_infobioschemas.jsonld index 68feb4bfc999a..1f6bc46471f85 100644 --- a/data/clc_sequence_info/clc_sequence_infobioschemas.jsonld +++ b/data/clc_sequence_info/clc_sequence_infobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "clc_sequence_info", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://bio.tools/clcbio_genomics_workbench", "sc:version": "4.010.83648" diff --git a/data/clc_unmapped_reads/clc_unmapped_readsbioschemas.jsonld b/data/clc_unmapped_reads/clc_unmapped_readsbioschemas.jsonld index 5ab22c77366b5..49afab61359a7 100644 --- a/data/clc_unmapped_reads/clc_unmapped_readsbioschemas.jsonld +++ b/data/clc_unmapped_reads/clc_unmapped_readsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Output the unmapped reads.", "sc:name": "clc_unmapped_reads", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://bio.tools/clcbio_genomics_workbench", diff --git a/data/cld/cldbioschemas.jsonld b/data/cld/cldbioschemas.jsonld index a8c5eae459c0e..4b5a0ef5546f1 100644 --- a/data/cld/cldbioschemas.jsonld +++ b/data/cld/cldbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "CLD", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/boutroslab/cld" } \ No newline at end of file diff --git a/data/clean/cleanbioschemas.jsonld b/data/clean/cleanbioschemas.jsonld index 4e2de1eeb5a21..1feb0dda96614 100644 --- a/data/clean/cleanbioschemas.jsonld +++ b/data/clean/cleanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "CLEAN", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://eh3.uc.edu/clean/", "sc:version": "1.3.1" diff --git a/data/clean_ngs/clean_ngsbioschemas.jsonld b/data/clean_ngs/clean_ngsbioschemas.jsonld index 0ff937cf12943..300edd7489129 100644 --- a/data/clean_ngs/clean_ngsbioschemas.jsonld +++ b/data/clean_ngs/clean_ngsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Use adapters definition file ADAPTER.txt and remove the adapters from the input read files. The program writes out the cleansed reads and the rejected reads. Nucleotides are also removed based on quality thresholds from the 5' and 3'.", "sc:name": "clean_ngs", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/adapterremoval/clean_ngs/0.7", "sc:version": "0.7" diff --git a/data/cleaner/cleanerbioschemas.jsonld b/data/cleaner/cleanerbioschemas.jsonld index cb888958948c4..43e37e590659b 100644 --- a/data/cleaner/cleanerbioschemas.jsonld +++ b/data/cleaner/cleanerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Cleaner: R-system software package for the assembly of informative, transcript-specific probe-clusters for Affymetrix expression microarrays.", "sc:name": "Cleaner", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://wiki.c2b2.columbia.edu/califanolab/index.php/Cleaner", "sc:version": "1.03" diff --git a/data/cleanex/cleanexbioschemas.jsonld b/data/cleanex/cleanexbioschemas.jsonld index a0a571f9b4fa5..18481c75fa78d 100644 --- a/data/cleanex/cleanexbioschemas.jsonld +++ b/data/cleanex/cleanexbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.", "sc:name": "CleanEx database of gene expression profiles", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://www.cleanex.isb-sib.ch/" diff --git a/data/cleantranscriptfile/cleantranscriptfilebioschemas.jsonld b/data/cleantranscriptfile/cleantranscriptfilebioschemas.jsonld index 2ce07be217efd..9496723b132a4 100644 --- a/data/cleantranscriptfile/cleantranscriptfilebioschemas.jsonld +++ b/data/cleantranscriptfile/cleantranscriptfilebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Clean a transcript file so that it is useable for S-MART.", "sc:name": "cleantranscriptfile", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/cleanupdtseq/cleanupdtseqbioschemas.jsonld b/data/cleanupdtseq/cleanupdtseqbioschemas.jsonld index 5bbd94b2a27af..eb7d1369c34ad 100644 --- a/data/cleanupdtseq/cleanupdtseqbioschemas.jsonld +++ b/data/cleanupdtseq/cleanupdtseqbioschemas.jsonld @@ -27,10 +27,10 @@ ], "sc:citation": [ "pmcid:PMC4397975", + "pubmed:25827089", { "@id": "https://doi.org/10.1002/0471142727.mb0423s110" - }, - "pubmed:25827089" + } ], "sc:description": "This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.", "sc:featureList": { @@ -39,9 +39,9 @@ "sc:license": "GPL-2.0", "sc:name": "cleanUpdTSeq", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cleanUpdTSeq.html", "sc:version": "1.12.0" diff --git a/data/cleaver/bioconda_cleaver.yaml b/data/cleaver/bioconda_cleaver.yaml index 6dead78bf7674..b0a9b1eb93e0b 100644 --- a/data/cleaver/bioconda_cleaver.yaml +++ b/data/cleaver/bioconda_cleaver.yaml @@ -4,7 +4,6 @@ description: 'In-silico cleavage of polypeptide sequences. The cleavage rules ar home: https://bioconductor.org/packages/3.10/bioc/html/cleaver.html identifiers: - biotools:cleaver -- doi:10.1038/nmeth.3252 license: GPL (>= 3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-cleaver diff --git a/data/cleaver/cleaverbioschemas.jsonld b/data/cleaver/cleaverbioschemas.jsonld index e5c9b851bd460..130577b695000 100644 --- a/data/cleaver/cleaverbioschemas.jsonld +++ b/data/cleaver/cleaverbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sebastian Gibb", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "In-silico cleavage of polypeptide sequences.", "sc:license": "GPL-3.0", "sc:name": "cleaver", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cleaver.html", "sc:version": "1.12.0" diff --git a/data/cleavpredict/cleavpredictbioschemas.jsonld b/data/cleavpredict/cleavpredictbioschemas.jsonld index c5ca895699e7f..6059c72d26839 100644 --- a/data/cleavpredict/cleavpredictbioschemas.jsonld +++ b/data/cleavpredict/cleavpredictbioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:25996941", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0127877" }, - "pubmed:25996941", "pmcid:PMC4440711" ], "sc:description": "A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events.", @@ -31,8 +31,8 @@ }, "sc:name": "CleavPredict", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://cleavpredict.sanfordburnham.org/" diff --git a/data/clic/clicbioschemas.jsonld b/data/clic/clicbioschemas.jsonld index 638d934335ed2..61228f4e56b3d 100644 --- a/data/clic/clicbioschemas.jsonld +++ b/data/clic/clicbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Clustering analysis of large microarray datasets. Genes are first clustered in individual dimensions and then using the ordinal labels of clusters for each dimension, full dimension wide clustering is performed.", "sc:name": "CLIC", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://gexp2.kaist.ac.kr/clic" } \ No newline at end of file diff --git a/data/clic_pathway/clic_pathwaybioschemas.jsonld b/data/clic_pathway/clic_pathwaybioschemas.jsonld index 3a21164fa58d4..b4ad1e0fd3a9c 100644 --- a/data/clic_pathway/clic_pathwaybioschemas.jsonld +++ b/data/clic_pathway/clic_pathwaybioschemas.jsonld @@ -13,12 +13,12 @@ "@id": "https://bio.tools/clic_pathway", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sarah E. Calvo", - "Jun S. Liu" + "Jun S. Liu", + "Sarah E. Calvo" ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": [ "pmcid:PMC5546725", @@ -34,8 +34,8 @@ "sc:name": "CLIC", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.gene-clic.org/" }, diff --git a/data/click2drug/click2drugbioschemas.jsonld b/data/click2drug/click2drugbioschemas.jsonld index fe7ad0b1abb0c..00dd9335f32e6 100644 --- a/data/click2drug/click2drugbioschemas.jsonld +++ b/data/click2drug/click2drugbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Directory of computational drug design tools, containing many links to databases, chemical structure representation, molecular modeling, homology modeling, binding site prediction, docking, screening, target prediction, ligand design, binding free energy estimation etc.", "sc:name": "Click2Drug", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.click2drug.org/" } \ No newline at end of file diff --git a/data/clima/climabioschemas.jsonld b/data/clima/climabioschemas.jsonld index 4ba3610624cee..e9f51bbae4ae1 100644 --- a/data/clima/climabioschemas.jsonld +++ b/data/clima/climabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Cell line integrated molecular authentication.", "sc:name": "CLIMA", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "IRCSS AOU San Martino IST", diff --git a/data/clima_2/clima_2bioschemas.jsonld b/data/clima_2/clima_2bioschemas.jsonld index 70e1251c166b1..a3cf5cebd5d02 100644 --- a/data/clima_2/clima_2bioschemas.jsonld +++ b/data/clima_2/clima_2bioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-4694-3883", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/clima_2", "@type": "sc:SoftwareApplication", @@ -24,18 +20,18 @@ ], "edam:has_input": [ { - "@id": "edam:data_0006" + "@id": "edam:data_1691" }, { - "@id": "edam:data_2892" + "@id": "edam:data_0006" }, { - "@id": "edam:data_1691" + "@id": "edam:data_2892" } ], "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:author": "Paolo Romano", "sc:citation": [ @@ -46,8 +42,8 @@ "pmcid:PMC2686526" ], "sc:contributor": [ - "Paola Visconti", - "Ottavia Aresu" + "Ottavia Aresu", + "Paola Visconti" ], "sc:description": "Cell Line Integrated Molecular Authentication database and Identification tool. It represents a reference for validated molecular authentication of human cell lines independently from the platforms used.", "sc:featureList": [ @@ -63,6 +59,10 @@ "sc:provider": "USMI", "sc:url": "http://bioinformatics.hsanmartino.it/clima2/" }, + { + "@id": "http://orcid.org/0000-0003-4694-3883", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/nar/gkn730", "@type": "sc:CreativeWork" diff --git a/data/clingen_pathogenicity_calculator/clingen_pathogenicity_calculatorbioschemas.jsonld b/data/clingen_pathogenicity_calculator/clingen_pathogenicity_calculatorbioschemas.jsonld index 4a1012432c4c3..bcd42e5e58230 100644 --- a/data/clingen_pathogenicity_calculator/clingen_pathogenicity_calculatorbioschemas.jsonld +++ b/data/clingen_pathogenicity_calculator/clingen_pathogenicity_calculatorbioschemas.jsonld @@ -24,8 +24,8 @@ { "@id": "https://doi.org/10.1186/s13073-016-0391-z" }, - "pmcid:PMC5228115", - "pubmed:28081714" + "pubmed:28081714", + "pmcid:PMC5228115" ], "sc:description": "The tool enables to assess the pathogenity of Mendelian germline sequence variants.", "sc:featureList": [ @@ -33,17 +33,17 @@ "@id": "edam:operation_3226" }, { - "@id": "edam:operation_3225" + "@id": "edam:operation_3438" }, { - "@id": "edam:operation_3438" + "@id": "edam:operation_3225" } ], "sc:license": "OSL-3.0", "sc:name": "ClinGen Pathogenicity Calculator", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://calculator.clinicalgenome.org/site/cg-calculator" diff --git a/data/clinical_ngs_db/clinical_ngs_dbbioschemas.jsonld b/data/clinical_ngs_db/clinical_ngs_dbbioschemas.jsonld index c5660dea8b2c0..f228c5c1b989b 100644 --- a/data/clinical_ngs_db/clinical_ngs_dbbioschemas.jsonld +++ b/data/clinical_ngs_db/clinical_ngs_dbbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Contact form", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC5324660", { "@id": "https://doi.org/10.1002/humu.23160" }, - "pubmed:28008688" + "pubmed:28008688", + "pmcid:PMC5324660" ], "sc:description": "Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "Clinical NGS DB", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://nishio470.wixsite.com/clinical-ngs-db" }, diff --git a/data/clinicallaboratory/clinicallaboratorybioschemas.jsonld b/data/clinicallaboratory/clinicallaboratorybioschemas.jsonld index 3327b3a952ae6..70f3a1272f9b6 100644 --- a/data/clinicallaboratory/clinicallaboratorybioschemas.jsonld +++ b/data/clinicallaboratory/clinicallaboratorybioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Christopher Naugler", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5359993", { "@id": "https://doi.org/10.4103/jpi.jpi_65_16" }, - "pubmed:28400996" + "pubmed:28400996", + "pmcid:PMC5359993" ], "sc:description": "Demand Forecasting of Clinical Laboratory Test Volumes Using Time-series Analysis.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "ClinicalLaboratory", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ClinicalLaboratory/Clinical-Laboratory" } diff --git a/data/clinomicstrailbc/clinomicstrailbcbioschemas.jsonld b/data/clinomicstrailbc/clinomicstrailbcbioschemas.jsonld index 8a1ba41f14c5d..5dd50bb4712bd 100644 --- a/data/clinomicstrailbc/clinomicstrailbcbioschemas.jsonld +++ b/data/clinomicstrailbc/clinomicstrailbcbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/ClinOmicsTrailbc", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": "pubmed:31038669", "sc:description": "Visual analytics tool for breast cancer treatment stratification.", "sc:license": "Unlicense", "sc:name": "ClinOmicsTrailbc", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://clinomicstrail.bioinf.uni-sb.de" } \ No newline at end of file diff --git a/data/clinpred/clinpredbioschemas.jsonld b/data/clinpred/clinpredbioschemas.jsonld index ecb08ea304dc4..66b8e674b8fda 100644 --- a/data/clinpred/clinpredbioschemas.jsonld +++ b/data/clinpred/clinpredbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/j.ajhg.2018.08.005", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ClinPred", "@type": "sc:SoftwareApplication", @@ -21,11 +17,11 @@ "Jacek Majewski" ], "sc:citation": [ + "pubmed:30220433", + "pmcid:PMC6174354", { "@id": "https://doi.org/10.1016/j.ajhg.2018.08.005" - }, - "pubmed:30220433", - "pmcid:PMC6174354" + } ], "sc:description": "Efficient tool for identifying disease-relevant nonsynonymous single nucleotide variants.", "sc:featureList": [ @@ -41,6 +37,10 @@ ], "sc:name": "ClinPred", "sc:url": "https://sites.google.com/site/clinpred/" + }, + { + "@id": "https://doi.org/10.1016/j.ajhg.2018.08.005", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/clinqc/clinqcbioschemas.jsonld b/data/clinqc/clinqcbioschemas.jsonld index 07599b1a25a7d..7e7b4f2fb3c20 100644 --- a/data/clinqc/clinqcbioschemas.jsonld +++ b/data/clinqc/clinqcbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-016-0915-Y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/clinqc", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC4735967", - "pubmed:26830926", { "@id": "https://doi.org/10.1186/S12859-016-0915-Y" - } + }, + "pubmed:26830926" ], "sc:description": "An integrated and user-friendly pipeline for quality control, filtering and trimming of Sanger and NGS sequencing data for hundred to thousands of samples/patients in a single run in clinical research.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "ClinQC", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://sourceforge.net/projects/clinqc/" + }, + { + "@id": "https://doi.org/10.1186/S12859-016-0915-Y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/clintad/clintadbioschemas.jsonld b/data/clintad/clintadbioschemas.jsonld index 6d727eb7cc3e1..10ecf9e078aa5 100644 --- a/data/clintad/clintadbioschemas.jsonld +++ b/data/clintad/clintadbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Quick evaluation of the clinical relevance of copy number variants (CNVs) in the context of topologically associated domains (TADs).", "sc:name": "ClinTAD", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.clintad.com/" } \ No newline at end of file diff --git a/data/clinvar/clinvarbioschemas.jsonld b/data/clinvar/clinvarbioschemas.jsonld index 3e312fd4729aa..e08f1c30ced4a 100644 --- a/data/clinvar/clinvarbioschemas.jsonld +++ b/data/clinvar/clinvarbioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkt1113", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/clinvar", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Donna R. Maglott", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ "pubmed:24234437", @@ -31,25 +27,29 @@ "sc:description": "A freely accessible, public archive of reports of relationships among medically important variants and phenotypes hosted by the NCBI. It integrates and cross-references data from multiple databases at NCBI. In addition to dbSNP and dbVar, it depends on MedGen to represent phenotype, Gene to represent genes, and on human RefSeqs to represent the location of sequence variation. Each record represents the submitter, the variation and the phenotype.", "sc:featureList": [ { - "@id": "edam:operation_3197" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_3436" } ], "sc:name": "ClinVar", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/clinvar/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkt1113", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/clip/clipbioschemas.jsonld b/data/clip/clipbioschemas.jsonld index 70a188305ef7b..14aa2986b8daa 100644 --- a/data/clip/clipbioschemas.jsonld +++ b/data/clip/clipbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "CLIP web server detects selection in immunoglobulin sequences. Web server features include V(D)J germline segment identification with IMGT-alignment, batch submission of sequences and integration of test statistics.", "sc:name": "CLIP", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://clip.med.yale.edu/selection" } \ No newline at end of file diff --git a/data/clip_chlamydomonas/clip_chlamydomonasbioschemas.jsonld b/data/clip_chlamydomonas/clip_chlamydomonasbioschemas.jsonld index 61f5a976f8eaf..2e290f4120d3e 100644 --- a/data/clip_chlamydomonas/clip_chlamydomonasbioschemas.jsonld +++ b/data/clip_chlamydomonas/clip_chlamydomonasbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/CLiP_Chlamydomonas", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Matt Laudon", - "Jonikas lab" + "Jonikas lab", + "Matt Laudon" ], "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:description": "Chlamydomonas Library Project (CLiP) provides access to a collection of mutant strains in the green alga Chlamydomonas reinhardtii, a powerful model system for studying a broad range of fundamental processes including the biology of chloroplasts, photosynthesis, cilia/flagella, eyespots, and algal lipid accumulation.", "sc:license": "Unlicense", "sc:name": "CLiP Chlamydomonas", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.chlamylibrary.org/" } \ No newline at end of file diff --git a/data/clippda/clippdabioschemas.jsonld b/data/clippda/clippdabioschemas.jsonld index 9d8492b54f18c..2581a54defe18 100644 --- a/data/clippda/clippdabioschemas.jsonld +++ b/data/clippda/clippdabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Stephen Nyangoma", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.", "sc:license": "GPL-2.0", "sc:name": "clippda", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/clippda.html", "sc:version": "1.24.0" diff --git a/data/clipper/clipperbioschemas.jsonld b/data/clipper/clipperbioschemas.jsonld index bf0d07bf3b9eb..d049c78c4fc60 100644 --- a/data/clipper/clipperbioschemas.jsonld +++ b/data/clipper/clipperbioschemas.jsonld @@ -28,8 +28,8 @@ "sc:license": "AGPL-3.0", "sc:name": "clipper", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", diff --git a/data/clipz/clipzbioschemas.jsonld b/data/clipz/clipzbioschemas.jsonld index 96229d42d5699..38720351b1b95 100644 --- a/data/clipz/clipzbioschemas.jsonld +++ b/data/clipz/clipzbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CLIPZ", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.clipz.unibas.ch" } \ No newline at end of file diff --git a/data/clomial/clomialbioschemas.jsonld b/data/clomial/clomialbioschemas.jsonld index f66d84cface23..34b312e518c12 100644 --- a/data/clomial/clomialbioschemas.jsonld +++ b/data/clomial/clomialbioschemas.jsonld @@ -35,24 +35,24 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_2640" + "@id": "edam:topic_2269" }, { - "@id": "edam:topic_3360" + "@id": "edam:topic_3168" }, { - "@id": "edam:topic_3168" + "@id": "edam:topic_3360" }, { - "@id": "edam:topic_2269" + "@id": "edam:topic_2640" } ], "sc:citation": [ { "@id": "https://doi.org/10.1371/journal.pcbi.1003703" }, - "pubmed:25010360", - "pmcid:PMC4091710" + "pmcid:PMC4091710", + "pubmed:25010360" ], "sc:description": "This tool fits binomial distributions to counts obtained from NGS data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.", "sc:featureList": { diff --git a/data/clonality/clonalitybioschemas.jsonld b/data/clonality/clonalitybioschemas.jsonld index 9ca40c6b5362a..1f37ec1d8e64e 100644 --- a/data/clonality/clonalitybioschemas.jsonld +++ b/data/clonality/clonalitybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "Clonality", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Clonality.html", "sc:version": "1.22.0" diff --git a/data/clonalorigin/clonaloriginbioschemas.jsonld b/data/clonalorigin/clonaloriginbioschemas.jsonld index 824e7dd295ca4..3695e21f65055 100644 --- a/data/clonalorigin/clonaloriginbioschemas.jsonld +++ b/data/clonalorigin/clonaloriginbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "ClonalOrigin is a tool for recombination detection in bacteria. ClonalOrigin performs a comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.", "sc:name": "ClonalOrigin", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://code.google.com/p/clonalorigin/", "sc:version": "1.0" diff --git a/data/clone_mapper/clone_mapperbioschemas.jsonld b/data/clone_mapper/clone_mapperbioschemas.jsonld index 4c1895e84184d..b8846195ecf0d 100644 --- a/data/clone_mapper/clone_mapperbioschemas.jsonld +++ b/data/clone_mapper/clone_mapperbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Clone Mapper", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinformatics.lif.univ-mrs.fr/RNAiMap/" } \ No newline at end of file diff --git a/data/clonocalc/clonocalcbioschemas.jsonld b/data/clonocalc/clonocalcbioschemas.jsonld index 9020b406bb159..aef784f5aa3d1 100644 --- a/data/clonocalc/clonocalcbioschemas.jsonld +++ b/data/clonocalc/clonocalcbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-017-1575-2", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/clonocalc", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pubmed:28284194", - "pmcid:PMC5346239", { "@id": "https://doi.org/10.1186/s12859-017-1575-2" - } + }, + "pmcid:PMC5346239" ], "sc:description": "GUI for the sub-tasks of processing raw NGS data by wrapping available implementations of various algorithms.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "GPL-3.0", "sc:name": "ClonoCalc", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://bitbucket.org/ClonoSuite/clonocalc-plot" - }, - { - "@id": "https://doi.org/10.1186/s12859-017-1575-2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cloudburst/cloudburstbioschemas.jsonld b/data/cloudburst/cloudburstbioschemas.jsonld index 39d87c910def8..15898f0ad570a 100644 --- a/data/cloudburst/cloudburstbioschemas.jsonld +++ b/data/cloudburst/cloudburstbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes.", "sc:name": "CloudBurst", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://sourceforge.net/projects/cloudburst-bio/" } \ No newline at end of file diff --git a/data/clst/bioconda_clst.yaml b/data/clst/bioconda_clst.yaml index 77a8169846517..51605eb834423 100644 --- a/data/clst/bioconda_clst.yaml +++ b/data/clst/bioconda_clst.yaml @@ -4,7 +4,6 @@ description: Package for modified nearest-neighbor classification based on calcu home: https://bioconductor.org/packages/3.10/bioc/html/clst.html identifiers: - biotools:clst -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-clst diff --git a/data/clst/clstbioschemas.jsonld b/data/clst/clstbioschemas.jsonld index 7b4f061083f81..fb55c0d1dead7 100644 --- a/data/clst/clstbioschemas.jsonld +++ b/data/clst/clstbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "clst", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/clst.html", diff --git a/data/clstutils/bioconda_clstutils.yaml b/data/clstutils/bioconda_clstutils.yaml index 07871e44e99b0..7db48c4d5aa6f 100644 --- a/data/clstutils/bioconda_clstutils.yaml +++ b/data/clstutils/bioconda_clstutils.yaml @@ -4,7 +4,6 @@ description: Tools for performing taxonomic assignment based on phylogeny using home: https://bioconductor.org/packages/3.10/bioc/html/clstutils.html identifiers: - biotools:clstutils -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-clstutils diff --git a/data/clstutils/clstutilsbioschemas.jsonld b/data/clstutils/clstutilsbioschemas.jsonld index adbe3514c329f..d919b4120fbfb 100644 --- a/data/clstutils/clstutilsbioschemas.jsonld +++ b/data/clstutils/clstutilsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "clstutils", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/clstutils.html", "sc:version": "1.22.0" diff --git a/data/clumpak/clumpakbioschemas.jsonld b/data/clumpak/clumpakbioschemas.jsonld index 107e1bafb4d75..1c31a47ca8f1f 100644 --- a/data/clumpak/clumpakbioschemas.jsonld +++ b/data/clumpak/clumpakbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Not licensed", "sc:name": "CLUMPAK", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://clumpak.tau.ac.il/" } \ No newline at end of file diff --git a/data/clumsid/clumsidbioschemas.jsonld b/data/clumsid/clumsidbioschemas.jsonld index b3d58d18f536e..1316162739832 100644 --- a/data/clumsid/clumsidbioschemas.jsonld +++ b/data/clumsid/clumsidbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "CluMSID", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/tdepke/CluMSID/" } \ No newline at end of file diff --git a/data/cluspro/clusprobioschemas.jsonld b/data/cluspro/clusprobioschemas.jsonld index ac4d088270576..f0a106b81092e 100644 --- a/data/cluspro/clusprobioschemas.jsonld +++ b/data/cluspro/clusprobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.", "sc:name": "ClusPro", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://cluspro.bu.edu/login.php" } \ No newline at end of file diff --git a/data/clustage/clustagebioschemas.jsonld b/data/clustage/clustagebioschemas.jsonld index e0004d4c0988e..aff515af3027c 100644 --- a/data/clustage/clustagebioschemas.jsonld +++ b/data/clustage/clustagebioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2154-x", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/clustage", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Egon A. Ozer", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:29678129", { "@id": "https://doi.org/10.1186/s12859-018-2154-x" }, - "pubmed:29678129", "pmcid:PMC5910555" ], "sc:description": "For analyzing and comparing accessory genomic elements (AGEs) between genomes.", @@ -33,6 +29,10 @@ "sc:name": "ClustAGE", "sc:operatingSystem": "Linux", "sc:url": "https://sourceforge.net/projects/clustage/" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2154-x", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/clustal2/clustal2bioschemas.jsonld b/data/clustal2/clustal2bioschemas.jsonld index 0c57f01f09c1a..0141e21e4ff38 100644 --- a/data/clustal2/clustal2bioschemas.jsonld +++ b/data/clustal2/clustal2bioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Clustal helpdesk", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.\nNames occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.", "sc:funder": "Science Foundation Ireland", diff --git a/data/clustal_ws_jabaws/clustal_ws_jabawsbioschemas.jsonld b/data/clustal_ws_jabaws/clustal_ws_jabawsbioschemas.jsonld index d371b32a7da40..d4f5064f6c26e 100644 --- a/data/clustal_ws_jabaws/clustal_ws_jabawsbioschemas.jsonld +++ b/data/clustal_ws_jabaws/clustal_ws_jabawsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Finds the best global alignment for a set of input sequences (nucleic acid or protein).", "sc:name": "Clustal WS (jabaws)", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.compbio.dundee.ac.uk/jabaws/", "sc:version": "1" diff --git a/data/clustalo/clustalobioschemas.jsonld b/data/clustalo/clustalobioschemas.jsonld index f0b0499467ff2..fe72c38a10dc0 100644 --- a/data/clustalo/clustalobioschemas.jsonld +++ b/data/clustalo/clustalobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Clustal helpdesk", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Multiple sequence alignment software. The name is occassionally spelled as ClustalOmega, Clustal Ω, ClustalΩ, Clustal O, ClustalO.", "sc:funder": "Science Foundation Ireland", @@ -21,8 +21,8 @@ "sc:name": "Clustal Omega", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.clustal.org/omega/", "sc:version": "1.0 - 1.2" diff --git a/data/clustalo_ebi/clustalo_ebibioschemas.jsonld b/data/clustalo_ebi/clustalo_ebibioschemas.jsonld index b4a2de12497d6..a5fed8067ab78 100644 --- a/data/clustalo_ebi/clustalo_ebibioschemas.jsonld +++ b/data/clustalo_ebi/clustalo_ebibioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "Des Higgins", - "Web Production" + "Web Production", + "Des Higgins" ], "sc:description": "Multiple sequence alignment using guide trees and HMM profile-profile techniques.", "sc:name": "Clustal Omega (EBI)", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "University College Dublin", diff --git a/data/clustalo_uniprot/clustalo_uniprotbioschemas.jsonld b/data/clustalo_uniprot/clustalo_uniprotbioschemas.jsonld index bc6631d39a65c..e281700589ca1 100644 --- a/data/clustalo_uniprot/clustalo_uniprotbioschemas.jsonld +++ b/data/clustalo_uniprot/clustalo_uniprotbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Align two or more protein sequences on the UniProt web site using ClustalOmega.", "sc:name": "ClustalO UniProt", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.uniprot.org/align" } \ No newline at end of file diff --git a/data/clustalo_ws_jabaws/clustalo_ws_jabawsbioschemas.jsonld b/data/clustalo_ws_jabaws/clustalo_ws_jabawsbioschemas.jsonld index b206f04b4ceaa..6ed8ec902dfef 100644 --- a/data/clustalo_ws_jabaws/clustalo_ws_jabawsbioschemas.jsonld +++ b/data/clustalo_ws_jabaws/clustalo_ws_jabawsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "JABAWS stands for JAva Bioinformatics Analysis Web Services. It is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview.", "sc:name": "ClustalO WS (jabaws)", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.compbio.dundee.ac.uk/jabaws", "sc:version": "1" diff --git a/data/clustalw/clustalwbioschemas.jsonld b/data/clustalw/clustalwbioschemas.jsonld index 7fba410fe4b15..62922363b31bc 100644 --- a/data/clustalw/clustalwbioschemas.jsonld +++ b/data/clustalw/clustalwbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Clustal helpdesk", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Multiple sequence alignment software. Old deprecated versions. Even older versions were CLUSTAL and CLUSTAL V (ClustalV).", "sc:name": "Clustal 1.8 (Clustal W, Clustal X)", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/", "sc:version": "1.8 - 1.83" diff --git a/data/clustalw2_ebi/clustalw2_ebibioschemas.jsonld b/data/clustalw2_ebi/clustalw2_ebibioschemas.jsonld index d3267c18ff2aa..95d48a08982b4 100644 --- a/data/clustalw2_ebi/clustalw2_ebibioschemas.jsonld +++ b/data/clustalw2_ebi/clustalw2_ebibioschemas.jsonld @@ -19,13 +19,13 @@ "sc:description": "General purpose global multiple sequence alignment program for DNA or proteins.", "sc:name": "ClustalW2 (EBI)", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ - "University College Dublin", - "EMBL-EBI" + "EMBL-EBI", + "University College Dublin" ], "sc:url": "http://www.ebi.ac.uk/Tools/msa/clustalw2/", "sc:version": "1" diff --git a/data/clustalw2_phylogeny_api_ebi/clustalw2_phylogeny_api_ebibioschemas.jsonld b/data/clustalw2_phylogeny_api_ebi/clustalw2_phylogeny_api_ebibioschemas.jsonld index b38e8a83aa8f5..83f21baccda3c 100644 --- a/data/clustalw2_phylogeny_api_ebi/clustalw2_phylogeny_api_ebibioschemas.jsonld +++ b/data/clustalw2_phylogeny_api_ebi/clustalw2_phylogeny_api_ebibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Create Neighbor-joining or UPGMA phylogentic trees from a multiple sequence alignment using ClustalW.", "sc:name": "ClustalW2 Phylogeny API EBI", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.ebi.ac.uk/seqdb/confluence/pages/viewpage.action?pageId=54651945", diff --git a/data/clustalw2_phylogeny_ebi/clustalw2_phylogeny_ebibioschemas.jsonld b/data/clustalw2_phylogeny_ebi/clustalw2_phylogeny_ebibioschemas.jsonld index d47f96ed98c52..028762c2332bb 100644 --- a/data/clustalw2_phylogeny_ebi/clustalw2_phylogeny_ebibioschemas.jsonld +++ b/data/clustalw2_phylogeny_ebi/clustalw2_phylogeny_ebibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Phylogenetic tree generation from an alignment using neighbor-joining or UPGMA.", "sc:name": "ClustalW2 Phylogeny (EBI)", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBL-EBI", diff --git a/data/clustalw_pbil/clustalw_pbilbioschemas.jsonld b/data/clustalw_pbil/clustalw_pbilbioschemas.jsonld index faf1478f75090..9b3b569dbc5a1 100644 --- a/data/clustalw_pbil/clustalw_pbilbioschemas.jsonld +++ b/data/clustalw_pbil/clustalw_pbilbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "ClustalW is a general purpose multiple sequence alignment program for DNA or proteins", "sc:name": "ClustalW (PBIL)", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_clustalw.html" } \ No newline at end of file diff --git a/data/clustalw_sib/clustalw_sibbioschemas.jsonld b/data/clustalw_sib/clustalw_sibbioschemas.jsonld index b9db787e086cb..0cf6a9c70b6db 100644 --- a/data/clustalw_sib/clustalw_sibbioschemas.jsonld +++ b/data/clustalw_sib/clustalw_sibbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Multiple alignment of nucleic acid and protein sequences.", "sc:name": "ClustalW (SIB)", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://embnet.vital-it.ch/software/ClustalW.html" diff --git a/data/clustcomp/bioconda_clustcomp.yaml b/data/clustcomp/bioconda_clustcomp.yaml index e56fe03a16ce8..2b891e7a69796 100644 --- a/data/clustcomp/bioconda_clustcomp.yaml +++ b/data/clustcomp/bioconda_clustcomp.yaml @@ -16,7 +16,6 @@ description: clustComp is a package that implements several techniques for the c home: https://bioconductor.org/packages/3.10/bioc/html/clustComp.html identifiers: - biotools:clustcomp -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-clustcomp diff --git a/data/clustcomp/clustcompbioschemas.jsonld b/data/clustcomp/clustcompbioschemas.jsonld index 03da763ec3966..8a1c4cf8fbb54 100644 --- a/data/clustcomp/clustcompbioschemas.jsonld +++ b/data/clustcomp/clustcompbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "clustComp", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/clustComp.html", "sc:version": "1.2.2" diff --git a/data/cluster_buster/cluster_busterbioschemas.jsonld b/data/cluster_buster/cluster_busterbioschemas.jsonld index c6b0866579064..27ae65a5a1268 100644 --- a/data/cluster_buster/cluster_busterbioschemas.jsonld +++ b/data/cluster_buster/cluster_busterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.", "sc:name": "Cluster Buster", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://zlab.bu.edu/cluster-buster/" } \ No newline at end of file diff --git a/data/clusterbootstrap/clusterbootstrapbioschemas.jsonld b/data/clusterbootstrap/clusterbootstrapbioschemas.jsonld index f68a501547a7b..518a51527e724 100644 --- a/data/clusterbootstrap/clusterbootstrapbioschemas.jsonld +++ b/data/clusterbootstrap/clusterbootstrapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "ClusterBootstrap", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cran.r-project.org/package=ClusterBootstrap", "sc:version": "1.0.0" diff --git a/data/clusterexperiment/clusterexperimentbioschemas.jsonld b/data/clusterexperiment/clusterexperimentbioschemas.jsonld index 869ffe654ac86..1c88179afac81 100644 --- a/data/clusterexperiment/clusterexperimentbioschemas.jsonld +++ b/data/clusterexperiment/clusterexperimentbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "clusterExperiment", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/clusterExperiment.html", "sc:version": "1.0.0" diff --git a/data/clusterflow/clusterflowbioschemas.jsonld b/data/clusterflow/clusterflowbioschemas.jsonld index 1be1f4c8b8e38..07e1d9c44f157 100644 --- a/data/clusterflow/clusterflowbioschemas.jsonld +++ b/data/clusterflow/clusterflowbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Phil Ewels", "sc:additionalType": [ - "Command-line tool", - "Workflow" + "Workflow", + "Command-line tool" ], "sc:description": "Simple and flexible bioinformatics pipeline that automates and standardizes bioinformatics analyses on high-performance cluster environments.", "sc:license": "GPL-3.0", diff --git a/data/clustergrammer/clustergrammerbioschemas.jsonld b/data/clustergrammer/clustergrammerbioschemas.jsonld index 675a3d99c1fae..edf84dac5b86b 100644 --- a/data/clustergrammer/clustergrammerbioschemas.jsonld +++ b/data/clustergrammer/clustergrammerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "Clustergrammer", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://maayanlab.github.io/CCLE_Clustergrammer/" } \ No newline at end of file diff --git a/data/clusterjudge/clusterjudgebioschemas.jsonld b/data/clusterjudge/clusterjudgebioschemas.jsonld index ad268b2c84cd9..e694d3649e35b 100644 --- a/data/clusterjudge/clusterjudgebioschemas.jsonld +++ b/data/clusterjudge/clusterjudgebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "ClusterJudge", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ClusterJudge.html", "sc:version": "1.2.0" diff --git a/data/clustermq/clustermqbioschemas.jsonld b/data/clustermq/clustermqbioschemas.jsonld index ed2a1f370fdda..bdcc76a774072 100644 --- a/data/clustermq/clustermqbioschemas.jsonld +++ b/data/clustermq/clustermqbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Apache-2.0", "sc:name": "clustermq", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/mschubert/clustermq" } \ No newline at end of file diff --git a/data/clusterprofiler/clusterprofilerbioschemas.jsonld b/data/clusterprofiler/clusterprofilerbioschemas.jsonld index c7a6e1066aa81..d99f44011859d 100644 --- a/data/clusterprofiler/clusterprofilerbioschemas.jsonld +++ b/data/clusterprofiler/clusterprofilerbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1089/omi.2011.0118", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-6485-8781", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/clusterprofiler", "@type": "sc:SoftwareApplication", @@ -20,13 +28,13 @@ }, "edam:has_output": [ { - "@id": "edam:data_2884" + "@id": "edam:data_1669" }, { "@id": "edam:data_0862" }, { - "@id": "edam:data_1669" + "@id": "edam:data_2884" } ], "sc:additionalType": [ @@ -35,49 +43,41 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0092" + "@id": "edam:topic_3053" }, { - "@id": "edam:topic_3053" + "@id": "edam:topic_0092" } ], "sc:citation": [ - "pubmed:22455463", + "pmcid:PMC3339379", { "@id": "https://doi.org/10.1089/omi.2011.0118" }, - "pmcid:PMC3339379" + "pubmed:22455463" ], "sc:description": "This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.", "sc:featureList": [ { - "@id": "edam:operation_2238" + "@id": "edam:operation_2436" }, { - "@id": "edam:operation_2436" + "@id": "edam:operation_2238" } ], "sc:isAccessibleForFree": true, "sc:license": "Artistic-2.0", "sc:name": "clusterProfiler", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:softwareHelp": { "@id": "http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html" }, "sc:url": "http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html", "sc:version": "3.2.9" - }, - { - "@id": "https://doi.org/10.1089/omi.2011.0118", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-6485-8781", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/clusterscan/clusterscanbioschemas.jsonld b/data/clusterscan/clusterscanbioschemas.jsonld index 924234037c4e5..b9d4ea5295ada 100644 --- a/data/clusterscan/clusterscanbioschemas.jsonld +++ b/data/clusterscan/clusterscanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "ClusterScan", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/pyrevo/ClusterScan" } \ No newline at end of file diff --git a/data/clusterseq/clusterseqbioschemas.jsonld b/data/clusterseq/clusterseqbioschemas.jsonld index bd79dc080479a..d06229e64350c 100644 --- a/data/clusterseq/clusterseqbioschemas.jsonld +++ b/data/clusterseq/clusterseqbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "clusterSeq", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/clusterSeq.html", "sc:version": "1.4.0" diff --git a/data/clustersignificance/bioconda_clustersignificance.yaml b/data/clustersignificance/bioconda_clustersignificance.yaml index 01886a21a1c4d..4d3e24383efc5 100644 --- a/data/clustersignificance/bioconda_clustersignificance.yaml +++ b/data/clustersignificance/bioconda_clustersignificance.yaml @@ -11,7 +11,6 @@ description: The ClusterSignificance package provides tools to assess if class c home: https://bioconductor.org/packages/3.10/bioc/html/ClusterSignificance.html identifiers: - biotools:clustersignificance -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-clustersignificance diff --git a/data/clustersignificance/clustersignificancebioschemas.jsonld b/data/clustersignificance/clustersignificancebioschemas.jsonld index 05f8aa8759b8b..ca268ef9ea5dc 100644 --- a/data/clustersignificance/clustersignificancebioschemas.jsonld +++ b/data/clustersignificance/clustersignificancebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "ClusterSignificance", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ClusterSignificance.html", "sc:version": "1.2.2" diff --git a/data/clusterstab/bioconda_clusterstab.yaml b/data/clusterstab/bioconda_clusterstab.yaml index b2dbe95ebae61..4ff0ae81d483a 100644 --- a/data/clusterstab/bioconda_clusterstab.yaml +++ b/data/clusterstab/bioconda_clusterstab.yaml @@ -4,7 +4,6 @@ description: This package can be used to estimate the number of clusters in a se home: https://bioconductor.org/packages/3.10/bioc/html/clusterStab.html identifiers: - biotools:clusterstab -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-clusterstab summary: Compute cluster stability scores for microarray data diff --git a/data/clusterstab/clusterstabbioschemas.jsonld b/data/clusterstab/clusterstabbioschemas.jsonld index 256bc78d1a044..7748a56c1eea1 100644 --- a/data/clusterstab/clusterstabbioschemas.jsonld +++ b/data/clusterstab/clusterstabbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "clusterStab", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/clusterStab.html", "sc:version": "1.46.0" diff --git a/data/clusterv/clustervbioschemas.jsonld b/data/clusterv/clustervbioschemas.jsonld index 7e1bd54e61aa5..e1031f4a2115b 100644 --- a/data/clusterv/clustervbioschemas.jsonld +++ b/data/clusterv/clustervbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Clusterv", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://homes.di.unimi.it/~valenti/SW/clusterv/", "sc:version": "1.1" diff --git a/data/clusteval/clustevalbioschemas.jsonld b/data/clusteval/clustevalbioschemas.jsonld index 8c55d247e0d01..139de9d9f36f3 100644 --- a/data/clusteval/clustevalbioschemas.jsonld +++ b/data/clusteval/clustevalbioschemas.jsonld @@ -22,10 +22,10 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "http://orcid.org/0000-0002-0282-0462" + "@id": "http://orcid.org/0000-0001-9181-7160" }, { - "@id": "http://orcid.org/0000-0001-9181-7160" + "@id": "http://orcid.org/0000-0002-0282-0462" } ], "sc:additionalType": [ @@ -37,9 +37,9 @@ "sc:description": "Free and extendable opensource platform for objective performance comparison of arbitrary Clustering Methods on different datasets.", "sc:name": "Clusteval", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "bmb.sdu.dk", "sc:url": "http://clusteval.sdu.dk/" diff --git a/data/clustom-cloud/clustom-cloudbioschemas.jsonld b/data/clustom-cloud/clustom-cloudbioschemas.jsonld index 73afd7f0841ff..85e321d544340 100644 --- a/data/clustom-cloud/clustom-cloudbioschemas.jsonld +++ b/data/clustom-cloud/clustom-cloudbioschemas.jsonld @@ -13,9 +13,9 @@ "@id": "https://bio.tools/clustom-cloud", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kyuin Hwang", + "Jeongsu Oh", "Kyung Mo Kim", - "Jeongsu Oh" + "Kyuin Hwang" ], "sc:additionalType": "Desktop application", "sc:citation": [ @@ -32,8 +32,8 @@ "sc:name": "CLUSTOM-CLOUD", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://clustomcloud.kopri.re.kr/" }, diff --git a/data/cma/cmabioschemas.jsonld b/data/cma/cmabioschemas.jsonld index 9a20ac83806d2..b53389cfcb35b 100644 --- a/data/cma/cmabioschemas.jsonld +++ b/data/cma/cmabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "CMA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CMA.html", "sc:version": "1.32.0" diff --git a/data/cmc/cmcbioschemas.jsonld b/data/cmc/cmcbioschemas.jsonld index 6b12dc2dc214c..3cdb80fad7d25 100644 --- a/data/cmc/cmcbioschemas.jsonld +++ b/data/cmc/cmcbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Cross-mapping Correction is a set of modern high-throughput technologies which enable deep sequencing of non-coding RNA species on an unprecedented scale. When mapping such small RNAs to the genome, cross-mapping may occur, in which RNA sequences originating from one genomic locus are inadvertently mapped to a different locus. This may give rise to spurious novel RNAs, as well as spurious editing sites in known miRNAs.", "sc:name": "CMC", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://fantom.gsc.riken.jp/software/", "sc:version": "20100422" diff --git a/data/cmcompare/cmcomparebioschemas.jsonld b/data/cmcompare/cmcomparebioschemas.jsonld index cae1c0a7f64dd..79f071f715726 100644 --- a/data/cmcompare/cmcomparebioschemas.jsonld +++ b/data/cmcompare/cmcomparebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "CMCompare wbe server uses covariance models to compare infernal RNA family models to identify models with poor specificity and explore the relationship between models.", "sc:name": "CMCompare", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://rna.tbi.univie.ac.at/cmcws" diff --git a/data/cmfsm/cmfsmbioschemas.jsonld b/data/cmfsm/cmfsmbioschemas.jsonld index d3c5c7bdaafa9..2c8dae13cbc55 100644 --- a/data/cmfsm/cmfsmbioschemas.jsonld +++ b/data/cmfsm/cmfsmbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Shaoliang PengEmail author", - "Benyun Shi", - "Quan Zou" + "Quan Zou", + "Benyun Shi" ], "sc:additionalType": "Command-line tool", "sc:description": "A parallel acceleration tool for classical frequent subgraph mining algorithm. The core idea is to employ parallel techniques to parallelize extension tasks, so as to reduce computation time. On the other hand, multi-node strategy is employed to solve the problem of memory constraints.", diff --git a/data/cmpi/cmpibioschemas.jsonld b/data/cmpi/cmpibioschemas.jsonld index 77b4dab3a4966..5878663c7f2f8 100644 --- a/data/cmpi/cmpibioschemas.jsonld +++ b/data/cmpi/cmpibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "CELLmicrocosmos 4 PathwayIntegration (CmPI)", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://Cm4.CELLmicrocosmos.org", "sc:version": "4.2" diff --git a/data/cmscaller/cmscallerbioschemas.jsonld b/data/cmscaller/cmscallerbioschemas.jsonld index 7bd855bdcd1cd..e4cf58970d3a6 100644 --- a/data/cmscaller/cmscallerbioschemas.jsonld +++ b/data/cmscaller/cmscallerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CMScaller", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/Lothelab/CMScaller" } \ No newline at end of file diff --git a/data/cmweb/cmwebbioschemas.jsonld b/data/cmweb/cmwebbioschemas.jsonld index 26ba98ef42a14..67c74748de15e 100644 --- a/data/cmweb/cmwebbioschemas.jsonld +++ b/data/cmweb/cmwebbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Contact Map Web Viewer (CMWeb) is an online tool for studying basic properties of residue-residue contact formation and contact clusters. CMWeb can used to visualize contact maps, link contacts and display them in 3D or multiple sequence alignments, predict residue contacts, or calculate various contact statistics.", "sc:name": "CMWeb", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://cmweb.enzim.hu" } \ No newline at end of file diff --git a/data/cn3d/cn3dbioschemas.jsonld b/data/cn3d/cn3dbioschemas.jsonld index 812ec5ed61048..9d2f995314412 100644 --- a/data/cn3d/cn3dbioschemas.jsonld +++ b/data/cn3d/cn3dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web browser helper application that simultaneously displays 3-D structure, sequence, and alignment.", "sc:name": "Cn3D", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml" } \ No newline at end of file diff --git a/data/cnanalysis/cnanalysisbioschemas.jsonld b/data/cnanalysis/cnanalysisbioschemas.jsonld index 4a3b517851b11..ec3ceae8076ee 100644 --- a/data/cnanalysis/cnanalysisbioschemas.jsonld +++ b/data/cnanalysis/cnanalysisbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for rigidity theory-based thermal unfolding simulations of proteins so to link structure with function.", "sc:name": "CNAnalysis", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.cnanalysis.de" } \ No newline at end of file diff --git a/data/cnanorm/cnanormbioschemas.jsonld b/data/cnanorm/cnanormbioschemas.jsonld index afd0ce59b6130..ee3ac7ccc2997 100644 --- a/data/cnanorm/cnanormbioschemas.jsonld +++ b/data/cnanorm/cnanormbioschemas.jsonld @@ -20,17 +20,17 @@ "@id": "http://orcid.org/0000-0001-7530-7611" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:22039209", "sc:description": "Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a \"discrete\" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.", "sc:license": "GPL-2.0", "sc:name": "CNAnorm", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CNAnorm.html", "sc:version": "1.20.0" diff --git a/data/cnanova/cnanovabioschemas.jsonld b/data/cnanova/cnanovabioschemas.jsonld index 2298090c1d999..e623ce8617072 100644 --- a/data/cnanova/cnanovabioschemas.jsonld +++ b/data/cnanova/cnanovabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "CNAnova is a stand-alone software package for identifying recurrent regions of copy number aberrations (CNAs) using SNP microarray data. It runs from the command line on the Linux platforms and is composed of several modules written in the R programming language.", "sc:name": "CNAnova", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.compbio.group.cam.ac.uk/software/cnanova", "sc:version": "1.0" diff --git a/data/cnaseg/cnasegbioschemas.jsonld b/data/cnaseg/cnasegbioschemas.jsonld index 5ea847c6dbde8..c56a16b87ba8d 100644 --- a/data/cnaseg/cnasegbioschemas.jsonld +++ b/data/cnaseg/cnasegbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "CNAseg is a novel framework for the identification of CNA events that uses flowcell-to-flowcell variability to estimate the false positive rate and the depth of coverage to finalize copy number calls. HMMseg uses the Skellam distribution to compare read depth in tumour and control samples, which allows the use of smaller window sizes for copy number estimation and leads to greater sensitivity in pinpointing breakpoints for small CNAs.", "sc:name": "CNAseg", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.compbio.group.cam.ac.uk/software/cnaseg", diff --git a/data/cnatra/cnatrabioschemas.jsonld b/data/cnatra/cnatrabioschemas.jsonld index 7faf874be8f4d..24dcb193569e4 100644 --- a/data/cnatra/cnatrabioschemas.jsonld +++ b/data/cnatra/cnatrabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "CNAtra", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/AISKhalil/CNAtra" } \ No newline at end of file diff --git a/data/cner/bioconda_cner.yaml b/data/cner/bioconda_cner.yaml index d6e2400377ee3..1d3b766d4e2fc 100644 --- a/data/cner/bioconda_cner.yaml +++ b/data/cner/bioconda_cner.yaml @@ -4,7 +4,6 @@ description: Large-scale identification and advanced visualization of sets of co home: https://bioconductor.org/packages/3.10/bioc/html/CNEr.html identifiers: - biotools:cner -- doi:10.1038/nmeth.3252 license: GPL-2 | file LICENSE license_file: LICENSE name: bioconductor-cner diff --git a/data/cner/cnerbioschemas.jsonld b/data/cner/cnerbioschemas.jsonld index 4defd494b5fa2..14900456c8658 100644 --- a/data/cner/cnerbioschemas.jsonld +++ b/data/cner/cnerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "CNEr", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CNEr.html", "sc:version": "1.10.1" diff --git a/data/cnet/cnetbioschemas.jsonld b/data/cnet/cnetbioschemas.jsonld index 975c24a9d30a5..75d2f12c4f789 100644 --- a/data/cnet/cnetbioschemas.jsonld +++ b/data/cnet/cnetbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "CNet", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/bsml320/CNet" } \ No newline at end of file diff --git a/data/cnmtf/cnmtfbioschemas.jsonld b/data/cnmtf/cnmtfbioschemas.jsonld index a0c800c868653..ad22431c8c724 100644 --- a/data/cnmtf/cnmtfbioschemas.jsonld +++ b/data/cnmtf/cnmtfbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "cNMTF", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://lgl15.github.io/cnmtf_web/index.html" } \ No newline at end of file diff --git a/data/cnnh_pss/cnnh_pssbioschemas.jsonld b/data/cnnh_pss/cnnh_pssbioschemas.jsonld index d48dc29698fa8..8e60a8412537c 100644 --- a/data/cnnh_pss/cnnh_pssbioschemas.jsonld +++ b/data/cnnh_pss/cnnh_pssbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ruifeng Xu", "sc:additionalType": [ - "Library", - "Web service" + "Web service", + "Library" ], "sc:description": "have ability to extracts both local contexts and long-range interdependencies by combing multi-scale CNN and highway network. The evaluations on common datasets and comparisons with state-of-the-art methods indicate that CNNH_PSS is an useful and efficient tool for protein secondary structure prediction.", "sc:name": "CNNH_PSS", diff --git a/data/cnogpro/cnogprobioschemas.jsonld b/data/cnogpro/cnogprobioschemas.jsonld index e967df5c5047a..05dc6a8eb6771 100644 --- a/data/cnogpro/cnogprobioschemas.jsonld +++ b/data/cnogpro/cnogprobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Lars-Gustav Snipen", - "Ola Brynildsrud" + "Ola Brynildsrud", + "Lars-Gustav Snipen" ], "sc:description": "Detect and quantify CNVs in prokaryotic whole-genome sequencing data. After aligning WGS reads to a reference genome, we count the individual reads in a sliding window and normalize these counts for bias introduced by differences in GC content.", "sc:license": "GPL-2.0", diff --git a/data/cnordt/cnordtbioschemas.jsonld b/data/cnordt/cnordtbioschemas.jsonld index 321877e8915bd..9db0522a8eff7 100644 --- a/data/cnordt/cnordtbioschemas.jsonld +++ b/data/cnordt/cnordtbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "CNORdt", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CNORdt.html", diff --git a/data/cnorode/cnorodebioschemas.jsonld b/data/cnorode/cnorodebioschemas.jsonld index bc6bfda9dac6c..c7980d51c644b 100644 --- a/data/cnorode/cnorodebioschemas.jsonld +++ b/data/cnorode/cnorodebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "CNORode", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CNORode.html", "sc:version": "1.16.0" diff --git a/data/cnpbayes/cnpbayesbioschemas.jsonld b/data/cnpbayes/cnpbayesbioschemas.jsonld index dea31b2eaad85..dff28a75dc7c6 100644 --- a/data/cnpbayes/cnpbayesbioschemas.jsonld +++ b/data/cnpbayes/cnpbayesbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "CNPBayes", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CNPBayes.html", "sc:version": "1.4.0" diff --git a/data/cnssolve/cnssolvebioschemas.jsonld b/data/cnssolve/cnssolvebioschemas.jsonld index 00e357886f1a1..3becc29c96b4c 100644 --- a/data/cnssolve/cnssolvebioschemas.jsonld +++ b/data/cnssolve/cnssolvebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "CNSsolve (Crystallography & NMR System or CNS) is an X-ray crystallography suite used for refinement, phasing, and molecular replacement", "sc:name": "CNSsolve", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cns-online.org", "sc:version": "1.3" diff --git a/data/cntools/bioconda_cntools.yaml b/data/cntools/bioconda_cntools.yaml index f38864fdc03e6..18fada4140a1f 100644 --- a/data/cntools/bioconda_cntools.yaml +++ b/data/cntools/bioconda_cntools.yaml @@ -5,7 +5,6 @@ description: This package provides tools to convert the output of segmentation a home: https://bioconductor.org/packages/3.10/bioc/html/CNTools.html identifiers: - biotools:cntools -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-cntools diff --git a/data/cntools/cntoolsbioschemas.jsonld b/data/cntools/cntoolsbioschemas.jsonld index 838a5dd58c967..2b613eface337 100644 --- a/data/cntools/cntoolsbioschemas.jsonld +++ b/data/cntools/cntoolsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "J. Zhang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.", "sc:license": "GPL-3.0", diff --git a/data/cnvgsa/bioconda_cnvgsa.yaml b/data/cnvgsa/bioconda_cnvgsa.yaml index 774dcac3edd76..aa936181314ef 100644 --- a/data/cnvgsa/bioconda_cnvgsa.yaml +++ b/data/cnvgsa/bioconda_cnvgsa.yaml @@ -4,7 +4,6 @@ description: This package is intended to facilitate gene-set association with ra home: https://bioconductor.org/packages/3.10/bioc/html/cnvGSA.html identifiers: - biotools:cnvgsa -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-cnvgsa diff --git a/data/cnvhap/cnvhapbioschemas.jsonld b/data/cnvhap/cnvhapbioschemas.jsonld index 48465de4f43a3..d2ceea077dc53 100644 --- a/data/cnvhap/cnvhapbioschemas.jsonld +++ b/data/cnvhap/cnvhapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "cnvHap", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.imperial.ac.uk/people/l.coin", "sc:version": "1.033" diff --git a/data/cnvoffseq/cnvoffseqbioschemas.jsonld b/data/cnvoffseq/cnvoffseqbioschemas.jsonld index 269bda6eee4dc..afc62f1c05489 100644 --- a/data/cnvoffseq/cnvoffseqbioschemas.jsonld +++ b/data/cnvoffseq/cnvoffseqbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU475", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cnvoffseq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4147927", + "pubmed:25161258", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU475" }, - "pubmed:25161258" + "pmcid:PMC4147927" ], "sc:description": "Detecting intergenic copy number variation using off-target exome sequencing data.", "sc:featureList": { @@ -31,10 +27,14 @@ }, "sc:name": "cnvOffSeq", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/cnvoffseq/" + }, + { + "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU475", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cnvpanelizer/bioconda_cnvpanelizer.yaml b/data/cnvpanelizer/bioconda_cnvpanelizer.yaml index 6957386b24497..658d65d35676c 100644 --- a/data/cnvpanelizer/bioconda_cnvpanelizer.yaml +++ b/data/cnvpanelizer/bioconda_cnvpanelizer.yaml @@ -9,7 +9,6 @@ description: A method that allows for the use of a collection of non-matched nor home: https://bioconductor.org/packages/3.10/bioc/html/CNVPanelizer.html identifiers: - biotools:cnvpanelizer -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-cnvpanelizer diff --git a/data/cnvpanelizer/cnvpanelizerbioschemas.jsonld b/data/cnvpanelizer/cnvpanelizerbioschemas.jsonld index d7cd30b96495f..48e658f3239bc 100644 --- a/data/cnvpanelizer/cnvpanelizerbioschemas.jsonld +++ b/data/cnvpanelizer/cnvpanelizerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "CNVPanelizer", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CNVPanelizer.html", "sc:version": "1.4.0" diff --git a/data/cnvrd2/cnvrd2bioschemas.jsonld b/data/cnvrd2/cnvrd2bioschemas.jsonld index b77b5aaff266f..877b557cef3dc 100644 --- a/data/cnvrd2/cnvrd2bioschemas.jsonld +++ b/data/cnvrd2/cnvrd2bioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "CNVrd2", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CNVrd2.html", "sc:version": "1.12.0" diff --git a/data/cnvtools/cnvtoolsbioschemas.jsonld b/data/cnvtools/cnvtoolsbioschemas.jsonld index 11342cc327e9c..9fb4232bb7452 100644 --- a/data/cnvtools/cnvtoolsbioschemas.jsonld +++ b/data/cnvtools/cnvtoolsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chris Barnes", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.", "sc:license": "GPL-3.0", diff --git a/data/coac/coacbioschemas.jsonld b/data/coac/coacbioschemas.jsonld index 9e35eb8702768..1f80f2ccca260 100644 --- a/data/coac/coacbioschemas.jsonld +++ b/data/coac/coacbioschemas.jsonld @@ -9,42 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pcbi.1006772", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/COAC", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "ChengF-Lab", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:30779739", { "@id": "https://doi.org/10.1371/journal.pcbi.1006772" }, + "pubmed:30779739", "pmcid:PMC6396937" ], "sc:description": "Component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications.", "sc:featureList": [ { - "@id": "edam:operation_3766" + "@id": "edam:operation_3463" }, { "@id": "edam:operation_1781" }, { - "@id": "edam:operation_3463" + "@id": "edam:operation_3766" } ], "sc:license": "MPL-2.0", "sc:name": "COAC", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/ChengF-Lab/COAC" + }, + { + "@id": "https://doi.org/10.1371/journal.pcbi.1006772", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/coannealing/coannealingbioschemas.jsonld b/data/coannealing/coannealingbioschemas.jsonld index 2a010ba4e6bab..0369ffba2778b 100644 --- a/data/coannealing/coannealingbioschemas.jsonld +++ b/data/coannealing/coannealingbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CoAnnealing", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "birc.au.dk", "sc:url": "http://www.daimi.au.dk/~mailund/CoAnnealing/", diff --git a/data/cobra_toolbox/cobra_toolboxbioschemas.jsonld b/data/cobra_toolbox/cobra_toolboxbioschemas.jsonld index e0474463df631..44ed2c58dcefb 100644 --- a/data/cobra_toolbox/cobra_toolboxbioschemas.jsonld +++ b/data/cobra_toolbox/cobra_toolboxbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "COBRA Toolbox", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://opencobra.github.io/cobratoolbox/", "sc:version": "3.0" diff --git a/data/cobrapy/cobrapybioschemas.jsonld b/data/cobrapy/cobrapybioschemas.jsonld index 86f17074cb32d..8b3b28d10e91c 100644 --- a/data/cobrapy/cobrapybioschemas.jsonld +++ b/data/cobrapy/cobrapybioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "openCOBRA", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:23927696", { "@id": "https://doi.org/10.1186/1752-0509-7-74" }, - "pmcid:PMC3751080" + "pmcid:PMC3751080", + "pubmed:23927696" ], "sc:description": "COnstraints-Based Reconstruction and Analysis for Python.", "sc:featureList": { diff --git a/data/cocas/cocasbioschemas.jsonld b/data/cocas/cocasbioschemas.jsonld index 6b5e5dcb33469..810d719437446 100644 --- a/data/cocas/cocasbioschemas.jsonld +++ b/data/cocas/cocasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "COCAS", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ciml.univ-mrs.fr/software/cocas/index.html", "sc:version": "2.4" diff --git a/data/cocitestats/cocitestatsbioschemas.jsonld b/data/cocitestats/cocitestatsbioschemas.jsonld index 6a9be54c6dabf..99c73e9c76721 100644 --- a/data/cocitestats/cocitestatsbioschemas.jsonld +++ b/data/cocitestats/cocitestatsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A collection of software tools for dealing with co-citation data.", "sc:license": "CPL-1.0", "sc:name": "CoCiteStats", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CoCiteStats.html", "sc:version": "1.46.0" diff --git a/data/coco/cocobioschemas.jsonld b/data/coco/cocobioschemas.jsonld index 7f134d00de6f7..893dc98948c1b 100644 --- a/data/coco/cocobioschemas.jsonld +++ b/data/coco/cocobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "CoCo", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://gitlabscottgroup.med.usherbrooke.ca/scott-group/coco" } \ No newline at end of file diff --git a/data/cocomaps/cocomapsbioschemas.jsonld b/data/cocomaps/cocomapsbioschemas.jsonld index 3ea3d12b40fa2..d1c7869f62b25 100644 --- a/data/cocomaps/cocomapsbioschemas.jsonld +++ b/data/cocomaps/cocomapsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-2485-7378", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/cocomaps", "@type": "sc:SoftwareApplication", @@ -25,13 +21,17 @@ "sc:description": "Web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of intermolecular contact maps.", "sc:name": "CoCoMaps", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "ELIXIR-ITA-SALERNO", "sc:url": "https://www.molnac.unisa.it/BioTools/cocomaps/", "sc:version": "1" + }, + { + "@id": "http://orcid.org/0000-0003-2485-7378", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/codabc/codabcbioschemas.jsonld b/data/codabc/codabcbioschemas.jsonld index 420a7fcd82f26..085bbdb0addd4 100644 --- a/data/codabc/codabcbioschemas.jsonld +++ b/data/codabc/codabcbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Miguel Arenas", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:25577191", + "pmcid:PMC4379410", { "@id": "https://doi.org/10.1093/MOLBEV/MSU411" - }, - "pmcid:PMC4379410", - "pubmed:25577191" + } ], "sc:description": "A Computational Framework to Coestimate Recombination, Substitution, and Molecular Adaptation Rates by Approximate Bayesian Computation.", "sc:featureList": { diff --git a/data/codatags/codatagsbioschemas.jsonld b/data/codatags/codatagsbioschemas.jsonld index 7ed474477e7ae..b365644dbfcd7 100644 --- a/data/codatags/codatagsbioschemas.jsonld +++ b/data/codatags/codatagsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "CodataGS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/CodataGS/index.html" } \ No newline at end of file diff --git a/data/codcmp/codcmpbioschemas.jsonld b/data/codcmp/codcmpbioschemas.jsonld index edbe751d1b986..5721b2b7d5272 100644 --- a/data/codcmp/codcmpbioschemas.jsonld +++ b/data/codcmp/codcmpbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "UK BBSRC", "EMBOSS Contributors", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:description": "Codon usage table comparison.", "sc:funder": [ - "UK MRC", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "codcmp", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/codcopy/codcopybioschemas.jsonld b/data/codcopy/codcopybioschemas.jsonld index 47ae0a4a57b77..e0a6304e29610 100644 --- a/data/codcopy/codcopybioschemas.jsonld +++ b/data/codcopy/codcopybioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Copy and reformat a codon usage table", "sc:funder": [ + "UK MRC", "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "codcopy", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/codcopy.html", "sc:version": "r6" diff --git a/data/codehop/codehopbioschemas.jsonld b/data/codehop/codehopbioschemas.jsonld index cc563d2f514e1..45723b4652c7a 100644 --- a/data/codehop/codehopbioschemas.jsonld +++ b/data/codehop/codehopbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.", "sc:name": "CODEHOP", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://blocks.fhcrc.org/codehop.html" } \ No newline at end of file diff --git a/data/codelink/codelinkbioschemas.jsonld b/data/codelink/codelinkbioschemas.jsonld index ab23b2227d91b..c76f9a233f61b 100644 --- a/data/codelink/codelinkbioschemas.jsonld +++ b/data/codelink/codelinkbioschemas.jsonld @@ -28,9 +28,9 @@ "sc:license": "GPL-2.0", "sc:name": "codelink", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/codelink.html", "sc:version": "1.42.0" diff --git a/data/coderet/coderetbioschemas.jsonld b/data/coderet/coderetbioschemas.jsonld index b07a5de288305..f5fb24ed36281 100644 --- a/data/coderet/coderetbioschemas.jsonld +++ b/data/coderet/coderetbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "Wellcome Trust", "EMBOSS Contributors", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:description": "Extract CDS, mRNA and translations from feature tables.", "sc:funder": [ - "Wellcome Trust", + "UK BBSRC", "UK MRC", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "coderet", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/coderet.html", "sc:version": "r6" diff --git a/data/codex/codexbioschemas.jsonld b/data/codex/codexbioschemas.jsonld index 19159935efa4b..c234cdfaac1ce 100644 --- a/data/codex/codexbioschemas.jsonld +++ b/data/codex/codexbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yuchao Jiang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A normalization and copy number variation calling procedure for whole exome DNA sequencing data. The tool relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model includes terms that specifically remove biases due to GC content, among others. It also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.", "sc:license": "GPL-2.0", diff --git a/data/codex_ngs/codex_ngsbioschemas.jsonld b/data/codex_ngs/codex_ngsbioschemas.jsonld index 1204101367c3e..5d1e5b803cdb3 100644 --- a/data/codex_ngs/codex_ngsbioschemas.jsonld +++ b/data/codex_ngs/codex_ngsbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKU895", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/codex_ngs", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bertie Gottgens", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:25270877", - "pmcid:PMC4384009", { "@id": "https://doi.org/10.1093/NAR/GKU895" - } + }, + "pubmed:25270877", + "pmcid:PMC4384009" ], "sc:description": "A next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.", "sc:featureList": { @@ -32,10 +28,14 @@ "sc:name": "CODEX", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://codex.stemcells.cam.ac.uk/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKU895", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/codon_congruence/codon_congruencebioschemas.jsonld b/data/codon_congruence/codon_congruencebioschemas.jsonld index e6184c41c6d60..682a2574a7530 100644 --- a/data/codon_congruence/codon_congruencebioschemas.jsonld +++ b/data/codon_congruence/codon_congruencebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Unlicense", "sc:name": "codon congruence", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/ridgelab/codon_congruence" } \ No newline at end of file diff --git a/data/codon_usage_database/codon_usage_databasebioschemas.jsonld b/data/codon_usage_database/codon_usage_databasebioschemas.jsonld index 4153b7bef1ae5..ff465164c1a1a 100644 --- a/data/codon_usage_database/codon_usage_databasebioschemas.jsonld +++ b/data/codon_usage_database/codon_usage_databasebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Codon Usage Database", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.kazusa.or.jp/codon/" } \ No newline at end of file diff --git a/data/codono/codonobioschemas.jsonld b/data/codono/codonobioschemas.jsonld index b44a9353b1450..d55ea85f858ab 100644 --- a/data/codono/codonobioschemas.jsonld +++ b/data/codono/codonobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CodonO is a method for measuring synonymous codon usage bias within and across genomes.", "sc:name": "CodonO", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://digbio.missouri.edu/software/index.html" } \ No newline at end of file diff --git a/data/codonome/codonomebioschemas.jsonld b/data/codonome/codonomebioschemas.jsonld index 536e103b03f5a..cc8f25edd00c3 100644 --- a/data/codonome/codonomebioschemas.jsonld +++ b/data/codonome/codonomebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "CODONOME collects the expression value of each codon (just called \"codonome\") and of each aminoacyl-tRNA synthetase (aaRS). To do this, the software is able to count the total mRNA codon number of any organism and to import and integrate any mRNA expression data source in tabulated text format.", "sc:name": "Codonome", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://apollo11.isto.unibo.it/software/Codonome/" } \ No newline at end of file diff --git a/data/codp/codpbioschemas.jsonld b/data/codp/codpbioschemas.jsonld index 39d7b7e5afb86..1e44495a1e5e6 100644 --- a/data/codp/codpbioschemas.jsonld +++ b/data/codp/codpbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC3651391", { "@id": "https://doi.org/10.1186/1423-0127-20-25" }, - "pubmed:23621914", - "pmcid:PMC3651391" + "pubmed:23621914" ], "sc:description": "Predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein.", "sc:featureList": { diff --git a/data/coeus/coeusbioschemas.jsonld b/data/coeus/coeusbioschemas.jsonld index a1a0b1256c90d..9273075061ba9 100644 --- a/data/coeus/coeusbioschemas.jsonld +++ b/data/coeus/coeusbioschemas.jsonld @@ -34,21 +34,21 @@ "sc:description": "Semantic web application network that combines a set of algorithms to streamline the creation of new semantic web-based knowledge management systems. In a single package, it provides the tools to create new applications, including advanced integration connectors for different data sources along with ontology mapping techniques.", "sc:featureList": [ { - "@id": "edam:operation_3436" + "@id": "edam:operation_0335" }, { "@id": "edam:operation_2422" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_3436" } ], "sc:license": "CC-BY-3.0", "sc:name": "COEUS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioinformatics.ua.pt/coeus/" } diff --git a/data/coev-web/coev-webbioschemas.jsonld b/data/coev-web/coev-webbioschemas.jsonld index 985c0ca07091e..7c703a3d0887d 100644 --- a/data/coev-web/coev-webbioschemas.jsonld +++ b/data/coev-web/coev-webbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The Coev-Web platform is a user-friendly interface of the command-line program Coev. The platform allows the evaluation of coevolving positions and their evolutionary profile based on the aligned sequences and a phylogenetic tree. It can also simulate coevolving pairs of positions along a given phylogenetic tree.", "sc:name": "Coev-Web", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://coev.vital-it.ch/#/" } \ No newline at end of file diff --git a/data/coexnet/coexnetbioschemas.jsonld b/data/coexnet/coexnetbioschemas.jsonld index fd76c9e1de40c..9ab1b61db6f98 100644 --- a/data/coexnet/coexnetbioschemas.jsonld +++ b/data/coexnet/coexnetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "coexnet", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/coexnet.html", "sc:version": "1.2.0" diff --git a/data/coexpnetviz/coexpnetvizbioschemas.jsonld b/data/coexpnetviz/coexpnetvizbioschemas.jsonld index 7b529c3d8cd0f..ffcddb2837a6d 100644 --- a/data/coexpnetviz/coexpnetvizbioschemas.jsonld +++ b/data/coexpnetviz/coexpnetvizbioschemas.jsonld @@ -11,14 +11,14 @@ "@id": "https://bio.tools/coexpnetviz", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Desktop application" + "Desktop application", + "Web application" ], "sc:description": "Comparative co-expression networks construction and visualization.", "sc:name": "CoExpNetViz", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/webtools/coexpr/", diff --git a/data/coexpresso/coexpressobioschemas.jsonld b/data/coexpresso/coexpressobioschemas.jsonld index 64dbaff16f1ed..b8671d5149ad8 100644 --- a/data/coexpresso/coexpressobioschemas.jsonld +++ b/data/coexpresso/coexpressobioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Apache-2.0", "sc:name": "CoExpresso", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://computproteomics.bmb.sdu.dk/Apps/CoExpresso/" } \ No newline at end of file diff --git a/data/cofactor/cofactorbioschemas.jsonld b/data/cofactor/cofactorbioschemas.jsonld index 7a370e3fce274..b8bb75f474cfd 100644 --- a/data/cofactor/cofactorbioschemas.jsonld +++ b/data/cofactor/cofactorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "COFACTOR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://zhanglab.ccmb.med.umich.edu/COFACTOR" } \ No newline at end of file diff --git a/data/cogaps/cogapsbioschemas.jsonld b/data/cogaps/cogapsbioschemas.jsonld index 3b4a52c2af91c..06c266880af2c 100644 --- a/data/cogaps/cogapsbioschemas.jsonld +++ b/data/cogaps/cogapsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "CoGAPS", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CoGAPS.html", diff --git a/data/cogeme/cogemebioschemas.jsonld b/data/cogeme/cogemebioschemas.jsonld index aaf5731d1505e..9c9752fbbe776 100644 --- a/data/cogeme/cogemebioschemas.jsonld +++ b/data/cogeme/cogemebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Phytopathogenic fungi and oomycete EST database.", "sc:name": "COGEME", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "University of Exeter", "sc:url": "http://cogeme.ex.ac.uk/" diff --git a/data/cogena/cogenabioschemas.jsonld b/data/cogena/cogenabioschemas.jsonld index 228c52df3c7bb..c84170af34c56 100644 --- a/data/cogena/cogenabioschemas.jsonld +++ b/data/cogena/cogenabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "cogena", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cogena.html", "sc:version": "1.8.0" diff --git a/data/cognac/cognacbioschemas.jsonld b/data/cognac/cognacbioschemas.jsonld index 9e746000fd723..a027166007167 100644 --- a/data/cognac/cognacbioschemas.jsonld +++ b/data/cognac/cognacbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "COGNAC: a webserver for searching and annotating hydrogen bonded base interactions in RNA 3-dimensional structures.", "sc:name": "COGNAC", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mfrlab.org/grafss/cognac" } \ No newline at end of file diff --git a/data/cogps/bioconda_cogps.yaml b/data/cogps/bioconda_cogps.yaml index a99f5390cb544..6b7488bf3ce19 100644 --- a/data/cogps/bioconda_cogps.yaml +++ b/data/cogps/bioconda_cogps.yaml @@ -4,7 +4,6 @@ description: Gene Set Enrichment Analysis of P-value based statistics for outlie home: https://bioconductor.org/packages/3.10/bioc/html/coGPS.html identifiers: - biotools:cogps -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-cogps diff --git a/data/cogps/cogpsbioschemas.jsonld b/data/cogps/cogpsbioschemas.jsonld index 1612dd9c030ff..22b0a7516caa1 100644 --- a/data/cogps/cogpsbioschemas.jsonld +++ b/data/cogps/cogpsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "coGPS", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/coGPS.html", "sc:version": "1.18.0" diff --git a/data/cogrim/cogrimbioschemas.jsonld b/data/cogrim/cogrimbioschemas.jsonld index 5993d4bae0a6f..9268af8fc68d6 100644 --- a/data/cogrim/cogrimbioschemas.jsonld +++ b/data/cogrim/cogrimbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/gb-2007-8-1-r4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cogrim", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC1839128", "pubmed:17204163", { "@id": "https://doi.org/10.1186/gb-2007-8-1-r4" - }, - "pmcid:PMC1839128" + } ], "sc:description": "COGRIM is an R program of Bayesian hierarchical model and Gibbs Sampling implementation that integrates gene expression, ChIP binding, and transcription factor motif data in a principled and robust fashion.", "sc:featureList": { @@ -35,6 +31,10 @@ "Linux" ], "sc:url": "http://www.cbil.upenn.edu/COGRIM/" + }, + { + "@id": "https://doi.org/10.1186/gb-2007-8-1-r4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cohcap/cohcapbioschemas.jsonld b/data/cohcap/cohcapbioschemas.jsonld index 6970a89de2b09..fdf65aecbfa20 100644 --- a/data/cohcap/cohcapbioschemas.jsonld +++ b/data/cohcap/cohcapbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkt242", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cohcap", "@type": "sc:SoftwareApplication", @@ -40,12 +36,16 @@ "sc:license": "GPL-3.0", "sc:name": "COHCAP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/COHCAP.html", "sc:version": "1.16.0" + }, + { + "@id": "https://doi.org/10.1093/nar/gkt242", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cohorts/cohortsbioschemas.jsonld b/data/cohorts/cohortsbioschemas.jsonld index 54d705bfb2dda..98592f9f041dd 100644 --- a/data/cohorts/cohortsbioschemas.jsonld +++ b/data/cohorts/cohortsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "cohorts", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.github.com/ngiangre/cohorts" diff --git a/data/colib_read/colib_readbioschemas.jsonld b/data/colib_read/colib_readbioschemas.jsonld index da92c87d446e0..06673b2fcd306 100644 --- a/data/colib_read/colib_readbioschemas.jsonld +++ b/data/colib_read/colib_readbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A project and collection of tools for analyzing and comparing next generation sequencing data without the need to first assemble the genome.", "sc:name": "Colib read", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://colibread.inria.fr/" } \ No newline at end of file diff --git a/data/collabonet/collabonetbioschemas.jsonld b/data/collabonet/collabonetbioschemas.jsonld index e98fade9d6c0f..0dabccdd37fb0 100644 --- a/data/collabonet/collabonetbioschemas.jsonld +++ b/data/collabonet/collabonetbioschemas.jsonld @@ -15,26 +15,26 @@ "biotools:primaryContact": "Jaewoo Kang", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6538547", + "pubmed:31138109", { "@id": "https://doi.org/10.1186/S12859-019-2813-6" - }, - "pubmed:31138109", - "pmcid:PMC6538547" + } ], "sc:description": "Collaboration of deep neural networks for biomedical named entity recognition.", "sc:featureList": [ { - "@id": "edam:operation_3625" + "@id": "edam:operation_3280" }, { - "@id": "edam:operation_3280" + "@id": "edam:operation_3625" } ], "sc:license": "MIT", "sc:name": "CollaboNet", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/wonjininfo/CollaboNet" }, diff --git a/data/collapsabel/collapsabelbioschemas.jsonld b/data/collapsabel/collapsabelbioschemas.jsonld index af59ff38684a4..24d1e6e54dad1 100644 --- a/data/collapsabel/collapsabelbioschemas.jsonld +++ b/data/collapsabel/collapsabelbioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC4826552", - "pubmed:27059780", { "@id": "https://doi.org/10.1186/s12859-016-1006-9" - } + }, + "pubmed:27059780" ], "sc:description": "Implements a generalized version of the CDH test for detecting compound heterozygosity on a genome-wide level, due to usage of generalized linear models it allows flexible analysis of binary and continuous traits with covariates.", "sc:featureList": { diff --git a/data/collapsereads/collapsereadsbioschemas.jsonld b/data/collapsereads/collapsereadsbioschemas.jsonld index bad438719e74b..48ca1b732944f 100644 --- a/data/collapsereads/collapsereadsbioschemas.jsonld +++ b/data/collapsereads/collapsereadsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Merges two reads if they have exactly the same genomic coordinates.", "sc:name": "collapsereads", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", diff --git a/data/collect_mgf/collect_mgfbioschemas.jsonld b/data/collect_mgf/collect_mgfbioschemas.jsonld index 41d8bab492341..37b220ed003e7 100644 --- a/data/collect_mgf/collect_mgfbioschemas.jsonld +++ b/data/collect_mgf/collect_mgfbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "collect_mgf", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ms-utils.org/collect_mgf.c" } \ No newline at end of file diff --git a/data/collector/collectorbioschemas.jsonld b/data/collector/collectorbioschemas.jsonld index c50c6d0ba9fb9..1c3f57d480f5f 100644 --- a/data/collector/collectorbioschemas.jsonld +++ b/data/collector/collectorbioschemas.jsonld @@ -15,9 +15,9 @@ "Oriol L. Massaguer" ], "sc:additionalType": [ - "Web service", + "Web application", "Desktop application", - "Web application" + "Web service" ], "sc:description": "Tool that allows extracting from the Open PHACTS Discovery platform series of compounds annotated with experimental data that can be used directly for building QSAR predictive models.", "sc:license": "GPL-3.0", diff --git a/data/colocr/colocrbioschemas.jsonld b/data/colocr/colocrbioschemas.jsonld index a8a6c201320c6..1c53fd945efde 100644 --- a/data/colocr/colocrbioschemas.jsonld +++ b/data/colocr/colocrbioschemas.jsonld @@ -18,26 +18,26 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6612416", "pubmed:31309005", { "@id": "https://doi.org/10.7717/peerj.7255" - } + }, + "pmcid:PMC6612416" ], "sc:description": "R package for conducting co-localization analysis on fluorescence microscopy images.", "sc:featureList": [ { - "@id": "edam:operation_1812" + "@id": "edam:operation_3443" }, { - "@id": "edam:operation_3443" + "@id": "edam:operation_1812" } ], "sc:license": "GPL-3.0", "sc:name": "colocr", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/ropensci/colocr" diff --git a/data/colombo/colombobioschemas.jsonld b/data/colombo/colombobioschemas.jsonld index 0a28572f485b9..5daa9a4b59d76 100644 --- a/data/colombo/colombobioschemas.jsonld +++ b/data/colombo/colombobioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Software framework equipped with a GUI for the statistical analysis of sequences of a genome. It can be equipped with different plugins that actually perform the analysis. The current version is supplied with SIGI-HMM, a tool for the prediction of Genomic Islands.", "sc:name": "COLOMBO", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://www.uni-goettingen.de/en/research/185810.html", diff --git a/data/colombos/colombosbioschemas.jsonld b/data/colombos/colombosbioschemas.jsonld index ada429a4ab040..b34647f7b82a5 100644 --- a/data/colombos/colombosbioschemas.jsonld +++ b/data/colombos/colombosbioschemas.jsonld @@ -19,8 +19,8 @@ "Windows" ], "sc:provider": [ - "Fondazione E. Mach", - "ELIXIR-ITA-MACH" + "ELIXIR-ITA-MACH", + "Fondazione E. Mach" ], "sc:url": "http://colombos.net/", "sc:version": "3.0" diff --git a/data/colonysizedistributions/colonysizedistributionsbioschemas.jsonld b/data/colonysizedistributions/colonysizedistributionsbioschemas.jsonld index c43c6fe5ac1a9..717631cf03dfd 100644 --- a/data/colonysizedistributions/colonysizedistributionsbioschemas.jsonld +++ b/data/colonysizedistributions/colonysizedistributionsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ColonySizeDistributions", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/sbhoyar1/ColonySizeDistributions" } \ No newline at end of file diff --git a/data/colorado-3d/colorado-3dbioschemas.jsonld b/data/colorado-3d/colorado-3dbioschemas.jsonld index 6886cc50b2180..70b3471f02aaf 100644 --- a/data/colorado-3d/colorado-3dbioschemas.jsonld +++ b/data/colorado-3d/colorado-3dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.", "sc:name": "COLORADO-3D", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://asia.genesilico.pl/colorado3d/" } \ No newline at end of file diff --git a/data/colordistance/colordistancebioschemas.jsonld b/data/colordistance/colordistancebioschemas.jsonld index 33684abbae69d..595af8316059b 100644 --- a/data/colordistance/colordistancebioschemas.jsonld +++ b/data/colordistance/colordistancebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.7717/peerj.6398", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/colordistance", "@type": "sc:SoftwareApplication", @@ -27,25 +31,21 @@ "@id": "edam:operation_3799" }, { - "@id": "edam:operation_3798" + "@id": "edam:operation_3443" }, { - "@id": "edam:operation_3443" + "@id": "edam:operation_3798" } ], "sc:license": "GPL-3.0", "sc:name": "colordistance", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://cran.r-project.org/package=colordistance", "sc:version": "1.1.0" - }, - { - "@id": "https://doi.org/10.7717/peerj.6398", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/colorgff/colorgffbioschemas.jsonld b/data/colorgff/colorgffbioschemas.jsonld index dadc7e3c41919..ed90cdc02002d 100644 --- a/data/colorgff/colorgffbioschemas.jsonld +++ b/data/colorgff/colorgffbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Parses a DOOR report file and writes the information in a gff3 out file.", "sc:name": "colorgff", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/coloweb/colowebbioschemas.jsonld b/data/coloweb/colowebbioschemas.jsonld index 206fca884ee43..4f7c07f9d364f 100644 --- a/data/coloweb/colowebbioschemas.jsonld +++ b/data/coloweb/colowebbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:25887597", - "pmcid:PMC4364483", { "@id": "https://doi.org/10.1186/S12864-015-1345-3" - } + }, + "pubmed:25887597", + "pmcid:PMC4364483" ], "sc:description": "A resource for analysis of colocalization of genomic features.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "ColoWeb", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://projects.insilico.us.com/ColoWeb/" } diff --git a/data/coma/comabioschemas.jsonld b/data/coma/comabioschemas.jsonld index 0802d7452e205..46663d0123575 100644 --- a/data/coma/comabioschemas.jsonld +++ b/data/coma/comabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Distant homology detection method based on sequence profile-profile comparison. It takes a protein sequence or multiple sequence alignment as input and searches for remote homologs in SCOP, PDB and PFAM databases.", "sc:name": "COMA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.ibt.lt/bioinformatics/coma/" diff --git a/data/coman/comanbioschemas.jsonld b/data/coman/comanbioschemas.jsonld index 4fd5642cfcbf0..3bcffc42ce470 100644 --- a/data/coman/comanbioschemas.jsonld +++ b/data/coman/comanbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12864-016-2964-Z", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/coman", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yueqiong Ni", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC4982211", { "@id": "https://doi.org/10.1186/S12864-016-2964-Z" }, - "pubmed:27515514", - "pmcid:PMC4982211" + "pubmed:27515514" ], "sc:description": "Comprehensive metatranscriptomics analysis.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "COMAN", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://147.8.185.62/COMAN/" - }, - { - "@id": "https://doi.org/10.1186/S12864-016-2964-Z", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/combenefit/combenefitbioschemas.jsonld b/data/combenefit/combenefitbioschemas.jsonld index 3171c440b411d..793763b5f8be4 100644 --- a/data/combenefit/combenefitbioschemas.jsonld +++ b/data/combenefit/combenefitbioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.1093/bioinformatics/btw230" }, - "pmcid:PMC5018366", - "pubmed:27153664" + "pubmed:27153664", + "pmcid:PMC5018366" ], "sc:description": "Combenefit is a software tool that enables the visualization, analysis and quantification of drug combination effects in terms of synergy and/or antagonism.", "sc:featureList": { diff --git a/data/combfunc/combfuncbioschemas.jsonld b/data/combfunc/combfuncbioschemas.jsonld index fdd15b0b799d5..06fc2b3e5d2ae 100644 --- a/data/combfunc/combfuncbioschemas.jsonld +++ b/data/combfunc/combfuncbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CombFunc", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.sbg.bio.ic.ac.uk/~mwass/combfunc/" } \ No newline at end of file diff --git a/data/combigor/combigorbioschemas.jsonld b/data/combigor/combigorbioschemas.jsonld index 4abb2072cdb3f..388347f7d5461 100644 --- a/data/combigor/combigorbioschemas.jsonld +++ b/data/combigor/combigorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "COMBIgor", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.COMBIgor.com" } \ No newline at end of file diff --git a/data/combiroc/combirocbioschemas.jsonld b/data/combiroc/combirocbioschemas.jsonld index f05ace050a50a..38b77fd207fdb 100644 --- a/data/combiroc/combirocbioschemas.jsonld +++ b/data/combiroc/combirocbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CombiROC", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://combiroc.eu/" } \ No newline at end of file diff --git a/data/come/comebioschemas.jsonld b/data/come/comebioschemas.jsonld index 399a1f9366c0e..86d39884fb2b5 100644 --- a/data/come/comebioschemas.jsonld +++ b/data/come/comebioschemas.jsonld @@ -28,10 +28,10 @@ "sc:description": "A COding potential calculation tool based on Multiple fEatures integrates multiple sequence-derived and experiment-based features to identify and characterize novel lncRNAs in RNA sequencing data.", "sc:featureList": [ { - "@id": "edam:operation_2995" + "@id": "edam:operation_2478" }, { - "@id": "edam:operation_2478" + "@id": "edam:operation_2995" } ], "sc:license": "Not licensed", diff --git a/data/comet-universe/comet-universebioschemas.jsonld b/data/comet-universe/comet-universebioschemas.jsonld index d6ef482175aca..9f8f6e9915cf1 100644 --- a/data/comet-universe/comet-universebioschemas.jsonld +++ b/data/comet-universe/comet-universebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "CoMet is a web server for comparative metagenomics, and is particularly suited for analysis of large collections of metagenomic short read data.", "sc:name": "CoMet", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://comet.gobics.de" diff --git a/data/comet/cometbioschemas.jsonld b/data/comet/cometbioschemas.jsonld index d3923e7034075..fd3f634e79709 100644 --- a/data/comet/cometbioschemas.jsonld +++ b/data/comet/cometbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Comet's Google group", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool.", "sc:license": "Apache-2.0", "sc:name": "Comet", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "lumc.nl", "sc:url": "http://comet-ms.sourceforge.net/", diff --git a/data/comet_visualisation/comet_visualisationbioschemas.jsonld b/data/comet_visualisation/comet_visualisationbioschemas.jsonld index 2ffc1c3e96bf5..cfcf074fa88e0 100644 --- a/data/comet_visualisation/comet_visualisationbioschemas.jsonld +++ b/data/comet_visualisation/comet_visualisationbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-015-0568-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/comet_visualisation", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4422463", "pubmed:25928765", { "@id": "https://doi.org/10.1186/S12859-015-0568-2" - } + }, + "pmcid:PMC4422463" ], "sc:description": "Visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "coMET", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://epigen.kcl.ac.uk/comet/" + }, + { + "@id": "https://doi.org/10.1186/S12859-015-0568-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cometa/cometabioschemas.jsonld b/data/cometa/cometabioschemas.jsonld index 893bd322f6e2c..6c83108716608 100644 --- a/data/cometa/cometabioschemas.jsonld +++ b/data/cometa/cometabioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0121453", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cometa", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jolanta Kawulok", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:25884504", + "pmcid:PMC4401624", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0121453" - }, - "pubmed:25884504", - "pmcid:PMC4401624" + } ], "sc:description": "Assigns a query read (DNA fragment) from metagenomic sample into one of the groups (the most common the taxon).", "sc:featureList": { @@ -29,10 +33,6 @@ "sc:name": "CoMeta", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/jkawulok/cometa" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0121453", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cometgene/cometgenebioschemas.jsonld b/data/cometgene/cometgenebioschemas.jsonld index 303429b95e641..7121a03094566 100644 --- a/data/cometgene/cometgenebioschemas.jsonld +++ b/data/cometgene/cometgenebioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "CoMetGeNe", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://cometgene.lri.fr" } \ No newline at end of file diff --git a/data/comir/comirbioschemas.jsonld b/data/comir/comirbioschemas.jsonld index 3be503e94cbef..45de3b39ccdc4 100644 --- a/data/comir/comirbioschemas.jsonld +++ b/data/comir/comirbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ComiR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.benoslab.pitt.edu/comir/" } \ No newline at end of file diff --git a/data/comm-s/comm-sbioschemas.jsonld b/data/comm-s/comm-sbioschemas.jsonld index 062e2da6d1cf0..2f4956f307596 100644 --- a/data/comm-s/comm-sbioschemas.jsonld +++ b/data/comm-s/comm-sbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "CoMM-S", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/gordonliu810822/CoMM" } \ No newline at end of file diff --git a/data/comma/commabioschemas.jsonld b/data/comma/commabioschemas.jsonld index 2c469fa872cc2..3ec4773a9b50e 100644 --- a/data/comma/commabioschemas.jsonld +++ b/data/comma/commabioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-015-0855-y", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-2098-5743", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/comma", "@type": "sc:SoftwareApplication", @@ -17,8 +25,8 @@ { "@id": "https://doi.org/10.1186/s12859-015-0855-y" }, - "pubmed:26823083", - "pmcid:PMC4959365" + "pmcid:PMC4959365", + "pubmed:26823083" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-2098-5743" @@ -29,19 +37,11 @@ }, "sc:name": "COMMA", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.lcqb.upmc.fr/COMMA/COMMA.html" - }, - { - "@id": "http://orcid.org/0000-0003-2098-5743", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/s12859-015-0855-y", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/command/commandbioschemas.jsonld b/data/command/commandbioschemas.jsonld index 56367b7470be2..891be3f2478f3 100644 --- a/data/command/commandbioschemas.jsonld +++ b/data/command/commandbioschemas.jsonld @@ -9,42 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2643-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/COMMAND", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Marco Moretto", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6348648", { "@id": "https://doi.org/10.1186/s12859-019-2643-6" }, + "pmcid:PMC6348648", "pubmed:30691411" ], "sc:description": "Web-based application used to download, collect and manage gene expression data from public databases.", "sc:featureList": [ - { - "@id": "edam:operation_2495" - }, { "@id": "edam:operation_3800" }, { "@id": "edam:operation_3431" + }, + { + "@id": "edam:operation_2495" } ], "sc:license": "GPL-3.0", "sc:name": "COMMAND", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/marcomoretto/command" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2643-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/comorbidity/comorbiditybioschemas.jsonld b/data/comorbidity/comorbiditybioschemas.jsonld index eaa423890f421..71aa2a88aad37 100644 --- a/data/comorbidity/comorbiditybioschemas.jsonld +++ b/data/comorbidity/comorbiditybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Systematic analysis of disease comorbidities.", "sc:name": "comoRbidity", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://bitbucket.org/ibi_group/comorbidity" } \ No newline at end of file diff --git a/data/comorbidity4j/comorbidity4jbioschemas.jsonld b/data/comorbidity4j/comorbidity4jbioschemas.jsonld index a551456c33b0e..1ff03c65eeec8 100644 --- a/data/comorbidity4j/comorbidity4jbioschemas.jsonld +++ b/data/comorbidity4j/comorbidity4jbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "AGPL-3.0", "sc:name": "Comorbidity4j", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://comorbidity.eu/comorbidity4web/" diff --git a/data/comparalogs_-_a_comparative_platform_of_paralog_and_ortholog_genes_from_tomato_and_grapevine/comparalogs_-_a_comparative_platform_of_paralog_and_ortholog_genes_from_tomato_and_grapevinebioschemas.jsonld b/data/comparalogs_-_a_comparative_platform_of_paralog_and_ortholog_genes_from_tomato_and_grapevine/comparalogs_-_a_comparative_platform_of_paralog_and_ortholog_genes_from_tomato_and_grapevinebioschemas.jsonld index aa144a8815c4b..9dbeee6c80f76 100644 --- a/data/comparalogs_-_a_comparative_platform_of_paralog_and_ortholog_genes_from_tomato_and_grapevine/comparalogs_-_a_comparative_platform_of_paralog_and_ortholog_genes_from_tomato_and_grapevinebioschemas.jsonld +++ b/data/comparalogs_-_a_comparative_platform_of_paralog_and_ortholog_genes_from_tomato_and_grapevine/comparalogs_-_a_comparative_platform_of_paralog_and_ortholog_genes_from_tomato_and_grapevinebioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "Unlicense", "sc:name": "ComParaLogS", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://biosrv.cab.unina.it/comparalogs/gene/search", "sc:version": "1" diff --git a/data/compare_taxofile/compare_taxofilebioschemas.jsonld b/data/compare_taxofile/compare_taxofilebioschemas.jsonld index f2222d9069f7b..f0a6ec6d590d4 100644 --- a/data/compare_taxofile/compare_taxofilebioschemas.jsonld +++ b/data/compare_taxofile/compare_taxofilebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "compare_taxofile", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/compare_TaxoFile/0.1%20beta", "sc:version": "0.1 beta" diff --git a/data/compare_two_lists/compare_two_listsbioschemas.jsonld b/data/compare_two_lists/compare_two_listsbioschemas.jsonld index 52a87961d4bff..9b611238879f6 100644 --- a/data/compare_two_lists/compare_two_listsbioschemas.jsonld +++ b/data/compare_two_lists/compare_two_listsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-6358-8380", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/Compare_Two_Lists", "@type": "sc:SoftwareApplication", @@ -19,10 +23,6 @@ "sc:description": "Simple and fast web tool for everyday list comparison, e.g. of genes. Shows the intersection, union, and Jaccard index. Allows easy copying & pasting of comparison results.", "sc:name": "Compare Two Lists", "sc:url": "https://rnact.crg.eu/compare" - }, - { - "@id": "https://orcid.org/0000-0001-6358-8380", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/comparems2/comparems2bioschemas.jsonld b/data/comparems2/comparems2bioschemas.jsonld index 518029cdd2993..1a733bf140415 100644 --- a/data/comparems2/comparems2bioschemas.jsonld +++ b/data/comparems2/comparems2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-5865-8994", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/comparems2", "@type": "sc:SoftwareApplication", @@ -25,10 +29,6 @@ "sc:provider": "lumc.nl", "sc:url": "http://www.ms-utils.org/compareMS2.html", "sc:version": "1" - }, - { - "@id": "http://orcid.org/0000-0002-5865-8994", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/compareoverlapping/compareoverlappingbioschemas.jsonld b/data/compareoverlapping/compareoverlappingbioschemas.jsonld index 022e36d631bff..ac711b271654d 100644 --- a/data/compareoverlapping/compareoverlappingbioschemas.jsonld +++ b/data/compareoverlapping/compareoverlappingbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "compareoverlapping", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/compareoverlappingsmallquery/compareoverlappingsmallquerybioschemas.jsonld b/data/compareoverlappingsmallquery/compareoverlappingsmallquerybioschemas.jsonld index d43b2f78d769f..d3c364729b6ee 100644 --- a/data/compareoverlappingsmallquery/compareoverlappingsmallquerybioschemas.jsonld +++ b/data/compareoverlappingsmallquery/compareoverlappingsmallquerybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Provide the queries that overlap with a reference, when the query is small.", "sc:name": "compareoverlappingsmallquery", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/compartments/compartmentsbioschemas.jsonld b/data/compartments/compartmentsbioschemas.jsonld index 397a246b759fe..0c918aae67045 100644 --- a/data/compartments/compartmentsbioschemas.jsonld +++ b/data/compartments/compartmentsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/database/bau012", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/compartments", "@type": "sc:SoftwareApplication", @@ -26,21 +22,21 @@ "sc:additionalType": "Database portal", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0140" + "@id": "edam:topic_0218" }, { - "@id": "edam:topic_0092" + "@id": "edam:topic_0140" }, { - "@id": "edam:topic_0218" + "@id": "edam:topic_0092" } ], "sc:citation": [ { "@id": "https://doi.org/10.1093/database/bau012" }, - "pubmed:24573882", - "pmcid:PMC3935310" + "pmcid:PMC3935310", + "pubmed:24573882" ], "sc:description": "COMPARTMENTS is a weekly updated web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. We map all evidence to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.", "sc:featureList": { @@ -51,10 +47,14 @@ "sc:name": "COMPARTMENTS", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://compartments.jensenlab.org/" + }, + { + "@id": "https://doi.org/10.1093/database/bau012", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/compass/compassbioschemas.jsonld b/data/compass/compassbioschemas.jsonld index 2fc7da6c644ee..5611b239c66ed 100644 --- a/data/compass/compassbioschemas.jsonld +++ b/data/compass/compassbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "COMPASS", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/COMPASS.html", "sc:version": "1.12.0" diff --git a/data/compass_sim/compass_simbioschemas.jsonld b/data/compass_sim/compass_simbioschemas.jsonld index 7e99fed3a778a..9ea4e88ce36d6 100644 --- a/data/compass_sim/compass_simbioschemas.jsonld +++ b/data/compass_sim/compass_simbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "COMPletely Arbitrary Sequence Simulator.", "sc:name": "COMPASS", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/WongLabPrograms/COMPASS" } \ No newline at end of file diff --git a/data/compcoder/compcoderbioschemas.jsonld b/data/compcoder/compcoderbioschemas.jsonld index 1a051fdba35aa..2f8ad6148194d 100644 --- a/data/compcoder/compcoderbioschemas.jsonld +++ b/data/compcoder/compcoderbioschemas.jsonld @@ -28,9 +28,9 @@ "sc:license": "GPL-2.0", "sc:name": "compcodeR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/compcodeR.html", "sc:version": "1.10.0" diff --git a/data/compendiumdb/compendiumdbbioschemas.jsonld b/data/compendiumdb/compendiumdbbioschemas.jsonld index fde7cdcace92d..dc95edf87b4f4 100644 --- a/data/compendiumdb/compendiumdbbioschemas.jsonld +++ b/data/compendiumdb/compendiumdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Systematic retrieval and storage of functional genomics data via a MySQL database.", "sc:name": "compendiumdb", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/compendiumdb/" diff --git a/data/compepitools/compepitoolsbioschemas.jsonld b/data/compepitools/compepitoolsbioschemas.jsonld index 606619c27010b..b59d254b6cf97 100644 --- a/data/compepitools/compepitoolsbioschemas.jsonld +++ b/data/compepitools/compepitoolsbioschemas.jsonld @@ -38,9 +38,9 @@ "sc:license": "GPL-3.0", "sc:name": "compEpiTools", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/compEpiTools.html", "sc:version": "1.8.0" diff --git a/data/compgo/compgobioschemas.jsonld b/data/compgo/compgobioschemas.jsonld index cd5d3ffe42769..625a3541de02e 100644 --- a/data/compgo/compgobioschemas.jsonld +++ b/data/compgo/compgobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ashley J. Waardenberg", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package contains functions to accomplish several tasks. It can download full genome databases from UCSC, import .bed files, annotate these .bed file regions with genes from aforementioned database dumps, interface with DAVID to create functional annotation and GO enrichment charts based on gene lists and visualise and compare these enrichments using either directed acyclic graphs or scatterplots.", "sc:license": "GPL-2.0", "sc:name": "CompGO", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CompGO.html", "sc:version": "1.10.0" diff --git a/data/complex_portal/complex_portalbioschemas.jsonld b/data/complex_portal/complex_portalbioschemas.jsonld index 18109fbcd69a3..81c93420dd9a1 100644 --- a/data/complex_portal/complex_portalbioschemas.jsonld +++ b/data/complex_portal/complex_portalbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": [ "Database portal", - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:description": "The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is freely available for search and download.", "sc:license": "CC-BY-4.0", "sc:name": "Complex Portal", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://www.ebi.ac.uk/complexportal/" diff --git a/data/complexbrowser/complexbrowserbioschemas.jsonld b/data/complexbrowser/complexbrowserbioschemas.jsonld index 9f76b0ca858b5..988b8adc576b8 100644 --- a/data/complexbrowser/complexbrowserbioschemas.jsonld +++ b/data/complexbrowser/complexbrowserbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "ComplexBrowser is a R based software for supervised analysis of changes in protein complex abundance and subunit co-expression in proteomic datasets. It uses information contained in CORUM and EBI Complex Portal databases to provide the user with visualizations helping with biological interpretation of obtained results. ComplexBrowser also incorporates a normalization and quality control steps.", "sc:name": "ComplexBrowser", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://computproteomics.bmb.sdu.dk/Apps/ComplexBrowser/", "sc:version": "1.0" diff --git a/data/complexchange/complexchangebioschemas.jsonld b/data/complexchange/complexchangebioschemas.jsonld index 73e8be706a36b..008887fca0022 100644 --- a/data/complexchange/complexchangebioschemas.jsonld +++ b/data/complexchange/complexchangebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "CompleXChange", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://sourceforge.net/projects/complexchange/" } \ No newline at end of file diff --git a/data/complexheatmap/complexheatmapbioschemas.jsonld b/data/complexheatmap/complexheatmapbioschemas.jsonld index 9dbd71387403f..6412b1879d109 100644 --- a/data/complexheatmap/complexheatmapbioschemas.jsonld +++ b/data/complexheatmap/complexheatmapbioschemas.jsonld @@ -27,9 +27,9 @@ "sc:license": "GPL-2.0", "sc:name": "ComplexHeatmap", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html", "sc:version": "1.12.0" diff --git a/data/compmerge/compmergebioschemas.jsonld b/data/compmerge/compmergebioschemas.jsonld index 1e33dd971ac75..61bb94774d676 100644 --- a/data/compmerge/compmergebioschemas.jsonld +++ b/data/compmerge/compmergebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "compmerge", "sc:operatingSystem": "Linux", "sc:provider": [ - "Lab Roderic Guigo Group", - "crg.eu" + "crg.eu", + "Lab Roderic Guigo Group" ], "sc:url": "http://big.crg.cat/services/compmerge", "sc:version": "1.3" diff --git a/data/compo/compobioschemas.jsonld b/data/compo/compobioschemas.jsonld index 38a3257c95611..c2c4fa650102c 100644 --- a/data/compo/compobioschemas.jsonld +++ b/data/compo/compobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Compo is a software for composite motif discovery using discrete models.", "sc:name": "Compo", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://tare.medisin.ntnu.no/compo/index.php" } \ No newline at end of file diff --git a/data/compomics-rover/compomics-roverbioschemas.jsonld b/data/compomics-rover/compomics-roverbioschemas.jsonld index a4d7105db071a..295b3426309cb 100644 --- a/data/compomics-rover/compomics-roverbioschemas.jsonld +++ b/data/compomics-rover/compomics-roverbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A tool to visualize and validate quantitative proteomics data from different sources.", "sc:name": "compomics-rover", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "https://code.google.com/p/compomics-rover/", diff --git a/data/compomics-sigpep/compomics-sigpepbioschemas.jsonld b/data/compomics-sigpep/compomics-sigpepbioschemas.jsonld index 60ae77159be8c..74d34729fe4de 100644 --- a/data/compomics-sigpep/compomics-sigpepbioschemas.jsonld +++ b/data/compomics-sigpep/compomics-sigpepbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Apache-2.0", "sc:name": "Compomics-sigpep", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/compomics/compomics-sigpep", diff --git a/data/compomics-utilities/compomics-utilitiesbioschemas.jsonld b/data/compomics-utilities/compomics-utilitiesbioschemas.jsonld index ef1a4f45c5ca4..4f950e4b7cbcc 100644 --- a/data/compomics-utilities/compomics-utilitiesbioschemas.jsonld +++ b/data/compomics-utilities/compomics-utilitiesbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-12-70", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/compomics-utilities", "@type": "sc:SoftwareApplication", @@ -34,8 +38,8 @@ } ], "sc:citation": [ - "pubmed:21385435", "pmcid:PMC3060842", + "pubmed:21385435", { "@id": "https://doi.org/10.1186/1471-2105-12-70" } @@ -46,17 +50,13 @@ }, "sc:name": "Compomics-utilities", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://compomics.github.io/projects/compomics-utilities.html", "sc:version": "4.3.18" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-12-70", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/compositedriver/compositedriverbioschemas.jsonld b/data/compositedriver/compositedriverbioschemas.jsonld index ccd38b955cd0f..7545b842b98b0 100644 --- a/data/compositedriver/compositedriverbioschemas.jsonld +++ b/data/compositedriver/compositedriverbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "CompositeDriver", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/khuranalab/CompositeDriver", "sc:version": "0.2" diff --git a/data/composition_profiler/composition_profilerbioschemas.jsonld b/data/composition_profiler/composition_profilerbioschemas.jsonld index e7a23eeef67b0..228fdc04701a8 100644 --- a/data/composition_profiler/composition_profilerbioschemas.jsonld +++ b/data/composition_profiler/composition_profilerbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-8-211", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/composition_profiler", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:17578581", "pmcid:PMC1914087", { "@id": "https://doi.org/10.1186/1471-2105-8-211" - }, - "pubmed:17578581" + } ], "sc:description": "Composition Profiler is a web-based tool that automates detection of enrichment or depletion patterns of individual amino acids or groups of amino acids classified by several physico-chemical and structural properties.", "sc:featureList": { @@ -30,12 +26,16 @@ }, "sc:name": "Composition Profiler", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.cprofiler.org/", "sc:version": "1.1" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-8-211", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/compphy/compphybioschemas.jsonld b/data/compphy/compphybioschemas.jsonld index 9e63eea71cf03..49720a276481a 100644 --- a/data/compphy/compphybioschemas.jsonld +++ b/data/compphy/compphybioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12862-014-0253-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/compphy", "@type": "sc:SoftwareApplication", @@ -22,8 +18,8 @@ { "@id": "https://doi.org/10.1186/S12862-014-0253-5" }, - "pmcid:PMC4271409", - "pubmed:25496383" + "pubmed:25496383", + "pmcid:PMC4271409" ], "sc:description": "Web-based collaborative platform for comparing phylogenies.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "CompPhy", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.atgc-montpellier.fr/compphy/" + }, + { + "@id": "https://doi.org/10.1186/S12862-014-0253-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/comprehengsive/comprehengsivebioschemas.jsonld b/data/comprehengsive/comprehengsivebioschemas.jsonld index 2a25cdb88b9a3..1c35eaf035dbc 100644 --- a/data/comprehengsive/comprehengsivebioschemas.jsonld +++ b/data/comprehengsive/comprehengsivebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "LGPL-2.1", "sc:name": "CompreheNGSive", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/alex-r-bigelow/compreheNGSive" } \ No newline at end of file diff --git a/data/compseq/compseqbioschemas.jsonld b/data/compseq/compseqbioschemas.jsonld index 9c92d13c0efcc..05f7aca10771d 100644 --- a/data/compseq/compseqbioschemas.jsonld +++ b/data/compseq/compseqbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "UK MRC", "Wellcome Trust", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK BBSRC", + "UK MRC" ], "sc:description": "Calculate the composition of unique words in sequences.", "sc:funder": [ "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "compseq", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/comptox_chemistry_dashboard/comptox_chemistry_dashboardbioschemas.jsonld b/data/comptox_chemistry_dashboard/comptox_chemistry_dashboardbioschemas.jsonld index f55a2f8360c25..f7ea64d4f4489 100644 --- a/data/comptox_chemistry_dashboard/comptox_chemistry_dashboardbioschemas.jsonld +++ b/data/comptox_chemistry_dashboard/comptox_chemistry_dashboardbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Community data resource for environmental chemistry.", "sc:name": "CompTox Chemistry Dashboard", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://comptox.epa.gov/dashboard" } \ No newline at end of file diff --git a/data/compute_pi_mw/compute_pi_mwbioschemas.jsonld b/data/compute_pi_mw/compute_pi_mwbioschemas.jsonld index 07a68a395ff33..11018ac009b49 100644 --- a/data/compute_pi_mw/compute_pi_mwbioschemas.jsonld +++ b/data/compute_pi_mw/compute_pi_mwbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Compute the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or for user entered sequences", "sc:name": "Compute pI MW", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://web.expasy.org/compute_pi/" } \ No newline at end of file diff --git a/data/computecoverage/computecoveragebioschemas.jsonld b/data/computecoverage/computecoveragebioschemas.jsonld index 353f8274d060f..2825375356258 100644 --- a/data/computecoverage/computecoveragebioschemas.jsonld +++ b/data/computecoverage/computecoveragebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Compute the coverage of a set with respect to another set.", "sc:name": "computecoverage", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/computel/computelbioschemas.jsonld b/data/computel/computelbioschemas.jsonld index 6de8ed1a63ca4..9abbdf9ec0438 100644 --- a/data/computel/computelbioschemas.jsonld +++ b/data/computel/computelbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0125201", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/computel", "@type": "sc:SoftwareApplication", @@ -22,8 +18,8 @@ { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0125201" }, - "pubmed:25923330", - "pmcid:PMC4414351" + "pmcid:PMC4414351", + "pubmed:25923330" ], "sc:description": "Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data.", "sc:featureList": { @@ -35,6 +31,10 @@ "Linux" ], "sc:url": "https://github.com/lilit-nersisyan/computel" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0125201", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/comsin/comsinbioschemas.jsonld b/data/comsin/comsinbioschemas.jsonld index ff5c06eab72db..c114cd80d85ee 100644 --- a/data/comsin/comsinbioschemas.jsonld +++ b/data/comsin/comsinbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes.", "sc:name": "ComSin", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://antares.protres.ru/comsin/." } \ No newline at end of file diff --git a/data/comspari/comsparibioschemas.jsonld b/data/comspari/comsparibioschemas.jsonld index 4acb06ea0a555..5e5e5fc67b1d8 100644 --- a/data/comspari/comsparibioschemas.jsonld +++ b/data/comspari/comsparibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Compares two datasets in netCDF or ASCII format.", "sc:name": "COMSPARI", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.biomechanic.org/comspari" diff --git a/data/comw/comwbioschemas.jsonld b/data/comw/comwbioschemas.jsonld index a53278c342f2c..7aed28837bdd6 100644 --- a/data/comw/comwbioschemas.jsonld +++ b/data/comw/comwbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "CoMW", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/anwarMZ/CoMW" } \ No newline at end of file diff --git a/data/conan-snv/conan-snvbioschemas.jsonld b/data/conan-snv/conan-snvbioschemas.jsonld index fec67071f84ab..f3dadef67091c 100644 --- a/data/conan-snv/conan-snvbioschemas.jsonld +++ b/data/conan-snv/conan-snvbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "MIT", "sc:name": "CoNAn-SNV", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://bitbucket.org/shahlabbcca/conan-snv/src/master/" } \ No newline at end of file diff --git a/data/conan/conanbioschemas.jsonld b/data/conan/conanbioschemas.jsonld index ed9c1f35ea77b..8317d0dc46b66 100644 --- a/data/conan/conanbioschemas.jsonld +++ b/data/conan/conanbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CONAN", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/HITS-MBM/conan" } \ No newline at end of file diff --git a/data/conbase/conbasebioschemas.jsonld b/data/conbase/conbasebioschemas.jsonld index fb0c48f20c343..007d6918403e9 100644 --- a/data/conbase/conbasebioschemas.jsonld +++ b/data/conbase/conbasebioschemas.jsonld @@ -22,22 +22,22 @@ ], "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6444814", + "pubmed:30935387", { "@id": "https://doi.org/10.1186/s13059-019-1673-8" - }, - "pmcid:PMC6444814", - "pubmed:30935387" + } ], "sc:description": "Software for unsupervised discovery of clonal somatic mutations in single cells through read phasing.", "sc:featureList": [ { - "@id": "edam:operation_3227" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3454" + "@id": "edam:operation_3227" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3454" } ], "sc:license": "MIT", diff --git a/data/condel/condelbioschemas.jsonld b/data/condel/condelbioschemas.jsonld index 9a5252a33e1e9..24c97c55bed7e 100644 --- a/data/condel/condelbioschemas.jsonld +++ b/data/condel/condelbioschemas.jsonld @@ -31,20 +31,20 @@ "sc:description": "Method to assess the outcome of non-synonymous SNVs using a CONsensus DELeteriousness score that combines various tools.", "sc:featureList": [ { - "@id": "edam:operation_3436" + "@id": "edam:operation_3226" }, { - "@id": "edam:operation_3225" + "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3226" + "@id": "edam:operation_3225" } ], "sc:name": "Condel", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bbglab.irbbarcelona.org/fannsdb/" } diff --git a/data/condetri/condetribioschemas.jsonld b/data/condetri/condetribioschemas.jsonld index 3fe5fd0834567..04604a98f262c 100644 --- a/data/condetri/condetribioschemas.jsonld +++ b/data/condetri/condetribioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ConDeTri is a content dependent read trimming software for Illumina/Solexa sequencing data", "sc:name": "ConDeTri", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://code.google.com/p/condetri/" } \ No newline at end of file diff --git a/data/condop/condopbioschemas.jsonld b/data/condop/condopbioschemas.jsonld index 81516482fa23d..9cb4d3253bac7 100644 --- a/data/condop/condopbioschemas.jsonld +++ b/data/condop/condopbioschemas.jsonld @@ -14,8 +14,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Angela Serra", - "Roberto Tagliaferri", - "Paola Galdi" + "Paola Galdi", + "Roberto Tagliaferri" ], "edam:has_input": { "@id": "edam:data_2603" @@ -25,8 +25,8 @@ { "@id": "https://doi.org/10.1186/1471-2105-15-145" }, - "pubmed:24884724", - "pmcid:PMC4235196" + "pmcid:PMC4235196", + "pubmed:24884724" ], "sc:description": "R package for CONdition-Dependent Operon Predictions. It is a tool in R to identify from RNA-seq transcriptome profiles operons expressed in a condition/transcriptome-specific manner, based on a Random Forest classifier.", "sc:featureList": { @@ -35,8 +35,8 @@ "sc:name": "CONDOP", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-SALERNO", "sc:url": "https://cran.r-project.org/web/packages/CONDOP/index.html", diff --git a/data/condor/condorbioschemas.jsonld b/data/condor/condorbioschemas.jsonld index cb04afcc91202..cbb4991aa38a5 100644 --- a/data/condor/condorbioschemas.jsonld +++ b/data/condor/condorbioschemas.jsonld @@ -22,11 +22,11 @@ "Web application" ], "sc:citation": [ - "pmcid:PMC4970500", "pubmed:27504081", { "@id": "https://doi.org/10.1107/S1600576716009213" - } + }, + "pmcid:PMC4970500" ], "sc:description": "Simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model.", "sc:featureList": { @@ -35,8 +35,8 @@ "sc:license": "BSD-2-Clause", "sc:name": "Condor", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/FXIhub/condor", diff --git a/data/conekt/conektbioschemas.jsonld b/data/conekt/conektbioschemas.jsonld index ba17fe20595b6..631e3d573b0f9 100644 --- a/data/conekt/conektbioschemas.jsonld +++ b/data/conekt/conektbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/conekt", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Marek Mutwil", - "Sebastian Proost" + "Sebastian Proost", + "Marek Mutwil" ], "sc:additionalType": "Web application", "sc:description": "Analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families.", @@ -20,8 +20,8 @@ "sc:name": "CoNekT", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://conekt.plant.tools/" } \ No newline at end of file diff --git a/data/conet/conetbioschemas.jsonld b/data/conet/conetbioschemas.jsonld index 31dfebc2dd858..9e46b2780f424 100644 --- a/data/conet/conetbioschemas.jsonld +++ b/data/conet/conetbioschemas.jsonld @@ -16,12 +16,12 @@ "sc:additionalType": "Command-line tool", "sc:author": "Karoline Faust", "sc:citation": [ - "pubmed:22796884", "pmcid:PMC3395616", + "pubmed:22807668", + "pubmed:22796884", { "@id": "https://doi.org/10.1371/journal.pcbi.1002606" - }, - "pubmed:22807668" + } ], "sc:contributor": [ "Jean-Sebastien Lerat", @@ -30,15 +30,15 @@ "sc:description": "Tool that detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data.", "sc:name": "CoNet", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ - "VUB", - "vib-kuleuven.be", "VIB", - "KU Leuven" + "KU Leuven", + "vib-kuleuven.be", + "VUB" ], "sc:url": "http://www.raeslab.org/software/conet.html", "sc:version": "1" diff --git a/data/confac/confacbioschemas.jsonld b/data/confac/confacbioschemas.jsonld index d8bdb6603938c..ebe877e673e44 100644 --- a/data/confac/confacbioschemas.jsonld +++ b/data/confac/confacbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CONFAC", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl" } \ No newline at end of file diff --git a/data/confess/confessbioschemas.jsonld b/data/confess/confessbioschemas.jsonld index 084b199ae49c8..f5ce1ada26c0d 100644 --- a/data/confess/confessbioschemas.jsonld +++ b/data/confess/confessbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Diana LOW", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Single Cell Fluidigm Spot Detector.", "sc:license": "GPL-2.0", "sc:name": "CONFESS", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CONFESS.html", diff --git a/data/confined/confinedbioschemas.jsonld b/data/confined/confinedbioschemas.jsonld index 33cde8ebcf379..5d478ce6ae8ab 100644 --- a/data/confined/confinedbioschemas.jsonld +++ b/data/confined/confinedbioschemas.jsonld @@ -15,8 +15,8 @@ "biotools:primaryContact": "Mike Thompson", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6624895", "pubmed:31300005", + "pmcid:PMC6624895", { "@id": "https://doi.org/10.1186/s13059-019-1743-y" } @@ -27,17 +27,17 @@ "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3798" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_3798" } ], "sc:name": "CONFINED", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/cozygene/CONFINED" }, diff --git a/data/confocalgn/confocalgnbioschemas.jsonld b/data/confocalgn/confocalgnbioschemas.jsonld index f5a75bddee848..8bd38c36d6384 100644 --- a/data/confocalgn/confocalgnbioschemas.jsonld +++ b/data/confocalgn/confocalgnbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "ConfocalGN", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00018", "sc:version": "v1.1" diff --git a/data/conics/conicsbioschemas.jsonld b/data/conics/conicsbioschemas.jsonld index 24c7ae9ae8de3..c25843dc85f58 100644 --- a/data/conics/conicsbioschemas.jsonld +++ b/data/conics/conicsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones.", "sc:name": "CONICS", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/diazlab/CONICS" } \ No newline at end of file diff --git a/data/conkit/conkitbioschemas.jsonld b/data/conkit/conkitbioschemas.jsonld index cdb72bab0c714..94585ec8f40b7 100644 --- a/data/conkit/conkitbioschemas.jsonld +++ b/data/conkit/conkitbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions.", "sc:name": "ConKit", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.conkit.org/en/0.9/" } \ No newline at end of file diff --git a/data/conodictor/conodictorbioschemas.jsonld b/data/conodictor/conodictorbioschemas.jsonld index a8aa047e158df..559c14f375442 100644 --- a/data/conodictor/conodictorbioschemas.jsonld +++ b/data/conodictor/conodictorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool that enables fast and accurate classification of conopeptides (the main bioactive component of cone snail venom) into superfamilies based on their amino acid sequence. Predictions are made using Hidden Markov Models and generalized profiles.", "sc:name": "ConoDictor", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://conco.ebc.ee" } \ No newline at end of file diff --git a/data/conoserver/conoserverbioschemas.jsonld b/data/conoserver/conoserverbioschemas.jsonld index cf2b0ab5e91e2..888cd981f07b7 100644 --- a/data/conoserver/conoserverbioschemas.jsonld +++ b/data/conoserver/conoserverbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btm596", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0003-0007-6796", "@type": "schema:Person" @@ -31,16 +35,12 @@ "sc:description": "Database specializing in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.", "sc:name": "Cone snail toxin database ConoServer", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "University of Queensland", "sc:url": "http://www.conoserver.org/" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btm596", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/conplex/conplexbioschemas.jsonld b/data/conplex/conplexbioschemas.jsonld index 88b59e6ec266d..52672ab285eea 100644 --- a/data/conplex/conplexbioschemas.jsonld +++ b/data/conplex/conplexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ConPlex", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://sbi.postech.ac.kr/ConPlex/" } \ No newline at end of file diff --git a/data/conquass/conquassbioschemas.jsonld b/data/conquass/conquassbioschemas.jsonld index 51f5e2b3c4666..524cf2a4d1aa1 100644 --- a/data/conquass/conquassbioschemas.jsonld +++ b/data/conquass/conquassbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A server for Quality Assessment of Protein Model-Structures using Evolutionary Conservation.", "sc:name": "ConQuass", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://bental.tau.ac.il/ConQuass/", diff --git a/data/conr/conrbioschemas.jsonld b/data/conr/conrbioschemas.jsonld index da20cb00567e6..60b0c347aa6d2 100644 --- a/data/conr/conrbioschemas.jsonld +++ b/data/conr/conrbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Gilles Dauby", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5743656", - "pubmed:29299301", { "@id": "https://doi.org/10.1002/ece3.3704" - } + }, + "pubmed:29299301", + "pmcid:PMC5743656" ], "sc:description": "Multi-species estimation of geographical range parameters for preliminary assessment of conservation status following Criterion B of the International Union for Conservation of Nature.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "GPL-2.0", "sc:name": "ConR", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/ConR/", "sc:version": "1.2.2" diff --git a/data/conreal/conrealbioschemas.jsonld b/data/conreal/conrealbioschemas.jsonld index 1adfd2efad37f..a9ae03f37f214 100644 --- a/data/conreal/conrealbioschemas.jsonld +++ b/data/conreal/conrealbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.", "sc:name": "CONREAL", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://conreal.niob.knaw.nl/" } \ No newline at end of file diff --git a/data/cons/consbioschemas.jsonld b/data/cons/consbioschemas.jsonld index 3d103f6af614c..2c10c12da6d0d 100644 --- a/data/cons/consbioschemas.jsonld +++ b/data/cons/consbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", + "Wellcome Trust", "EMBOSS Contributors", - "UK MRC", - "Wellcome Trust" + "UK BBSRC", + "UK MRC" ], "sc:description": "Create a consensus sequence from a multiple alignment.", "sc:funder": [ + "Wellcome Trust", "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "cons", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/consambig/consambigbioschemas.jsonld b/data/consambig/consambigbioschemas.jsonld index 96495a404b0c2..0cfbb7cf8b026 100644 --- a/data/consambig/consambigbioschemas.jsonld +++ b/data/consambig/consambigbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK MRC", + "Wellcome Trust", "UK BBSRC", "EMBOSS Contributors" ], "sc:description": "Create an ambiguous consensus sequence from a multiple alignment.", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "consambig", @@ -31,8 +31,8 @@ "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/consambig.html", "sc:version": "r6" diff --git a/data/consensus/consensusbioschemas.jsonld b/data/consensus/consensusbioschemas.jsonld index 635fd048bd8e8..2257f58d1de3f 100644 --- a/data/consensus/consensusbioschemas.jsonld +++ b/data/consensus/consensusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Consensus server aligns a sequence to a structural template using a consensus of 5 different alignment methods. A measure of reliability is produced for each alignment position in order to predict the suitability of regions for comparative modelling.", "sc:name": "Consensus", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://stormo.wustl.edu/consensus/" } \ No newline at end of file diff --git a/data/consensusclusterplus/consensusclusterplusbioschemas.jsonld b/data/consensusclusterplus/consensusclusterplusbioschemas.jsonld index e5e47dbc295a9..0fbc254e0182f 100644 --- a/data/consensusclusterplus/consensusclusterplusbioschemas.jsonld +++ b/data/consensusclusterplus/consensusclusterplusbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btq170", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/consensusclusterplus", "@type": "sc:SoftwareApplication", @@ -22,13 +18,13 @@ }, "edam:has_output": [ { - "@id": "edam:data_2048" + "@id": "edam:data_1636" }, { - "@id": "edam:data_2884" + "@id": "edam:data_2048" }, { - "@id": "edam:data_1636" + "@id": "edam:data_2884" } ], "sc:additionalType": [ @@ -37,18 +33,18 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3473" + "@id": "edam:topic_0092" }, { - "@id": "edam:topic_0092" + "@id": "edam:topic_3473" } ], "sc:citation": [ + "pmcid:PMC2881355", + "pubmed:20427518", { "@id": "https://doi.org/10.1093/bioinformatics/btq170" - }, - "pubmed:20427518", - "pmcid:PMC2881355" + } ], "sc:description": "Algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.", "sc:featureList": { @@ -58,11 +54,15 @@ "sc:name": "ConsensusClusterPlus", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html", "sc:version": "1.38.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btq170", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/consensuspathdb/consensuspathdbbioschemas.jsonld b/data/consensuspathdb/consensuspathdbbioschemas.jsonld index 84133d5059451..9b5fda8e8ae2a 100644 --- a/data/consensuspathdb/consensuspathdbbioschemas.jsonld +++ b/data/consensuspathdb/consensuspathdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Information on physical molecular interactions, biochemical pathways, and gene regulatory networks in human.", "sc:name": "ConsensusPathDB", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "Max-Planck-Institute for Molecular Genetics in Berlin", "sc:url": "http://cPDB.molgen.mpg.de/" diff --git a/data/consensusseeker/consensusseekerbioschemas.jsonld b/data/consensusseeker/consensusseekerbioschemas.jsonld index e353cf6fb1ff7..7b26b059739a4 100644 --- a/data/consensusseeker/consensusseekerbioschemas.jsonld +++ b/data/consensusseeker/consensusseekerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "consensusSeekeR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/consensusSeekeR.html", "sc:version": "1.2.0" diff --git a/data/conseq/conseqbioschemas.jsonld b/data/conseq/conseqbioschemas.jsonld index 5038028ddc25a..71e9a33f3d0a8 100644 --- a/data/conseq/conseqbioschemas.jsonld +++ b/data/conseq/conseqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Predicts functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue.", "sc:name": "ConSeq", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://conseq.bioinfo.tau.ac.il/" diff --git a/data/consite/consitebioschemas.jsonld b/data/consite/consitebioschemas.jsonld index 15beff8bef3df..3fca10687e2fe 100644 --- a/data/consite/consitebioschemas.jsonld +++ b/data/consite/consitebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Consite", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://consite.genereg.net/" } \ No newline at end of file diff --git a/data/console/consolebioschemas.jsonld b/data/console/consolebioschemas.jsonld index 53ee9166cc7e8..2acbef69fe227 100644 --- a/data/console/consolebioschemas.jsonld +++ b/data/console/consolebioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-15-119", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/console", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Godzik Lab", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4021314", { "@id": "https://doi.org/10.1186/1471-2105-15-119" }, - "pubmed:24766872", - "pmcid:PMC4021314" + "pubmed:24766872" ], "sc:description": "Fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure.", "sc:featureList": { @@ -32,6 +28,10 @@ "sc:license": "GPL-3.0", "sc:name": "ConSole", "sc:url": "http://console.sanfordburnham.org" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-15-119", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/conspred/conspredbioschemas.jsonld b/data/conspred/conspredbioschemas.jsonld index e42cb7d1237de..1fd7c0046f312 100644 --- a/data/conspred/conspredbioschemas.jsonld +++ b/data/conspred/conspredbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Prokaryotic genome annotation framework that performs various intrinsic gene predictions, homology searches, predictions of non-coding genes, and complex features and integrates all evidence into a consensus annotation. It achieves high-quality and comprehensive annotations based on rules and priorities, similar to decision-making in manual curation. Parameters controlling the annotation process are configurable by the user.", "sc:name": "Conspred", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/conspred/", "sc:version": "1.33" diff --git a/data/constax/constaxbioschemas.jsonld b/data/constax/constaxbioschemas.jsonld index 8bf396416adaf..1fc76535605c4 100644 --- a/data/constax/constaxbioschemas.jsonld +++ b/data/constax/constaxbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool for improved taxonomic resolution of environmental fungal ITS sequences.", "sc:name": "CONSTAX", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/natalie-vandepol/compare_taxonomy" } \ No newline at end of file diff --git a/data/consurf-db/consurf-dbbioschemas.jsonld b/data/consurf-db/consurf-dbbioschemas.jsonld index 1e2ea484a9630..f24f00ca51237 100644 --- a/data/consurf-db/consurf-dbbioschemas.jsonld +++ b/data/consurf-db/consurf-dbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A tool provides evolutionary conservation profiles for proteins of known structure in the PDB.", "sc:name": "ConSurf-DB", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://bental.tau.ac.il/new_ConSurfDB/" diff --git a/data/contedb/contedbbioschemas.jsonld b/data/contedb/contedbbioschemas.jsonld index 9d57dc61c15c9..c65ea87428bce 100644 --- a/data/contedb/contedbbioschemas.jsonld +++ b/data/contedb/contedbbioschemas.jsonld @@ -9,49 +9,49 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/database/bay131", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ConTEdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Fei Yi", "Fangqun Ouyang", - "Junhui Wang" + "Junhui Wang", + "Fei Yi" ], "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ + "pmcid:PMC6301336", { "@id": "https://doi.org/10.1093/database/bay131" }, - "pmcid:PMC6301336", "pubmed:30576494" ], "sc:description": "Comprehensive database of transposable elements in conifers.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_0524" }, { "@id": "edam:operation_3216" }, { - "@id": "edam:operation_0524" + "@id": "edam:operation_3431" } ], "sc:license": "Unlicense", "sc:name": "ConTEdb", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genedenovoweb.ticp.net:81/conTEdb/index.php" - }, - { - "@id": "https://doi.org/10.1093/database/bay131", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/context-explorer/context-explorerbioschemas.jsonld b/data/context-explorer/context-explorerbioschemas.jsonld index 208e54ce0c02a..d95f12c7f50ef 100644 --- a/data/context-explorer/context-explorerbioschemas.jsonld +++ b/data/context-explorer/context-explorerbioschemas.jsonld @@ -19,26 +19,26 @@ "biotools:primaryContact": "Joel Ostblom", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC6331134", { "@id": "https://doi.org/10.1371/journal.pcbi.1006384" }, - "pmcid:PMC6331134", "pubmed:30601802" ], "sc:description": "Analysis of spatially organized protein expression in high-throughput screens.", "sc:featureList": [ { - "@id": "edam:operation_3798" + "@id": "edam:operation_3443" }, { - "@id": "edam:operation_3443" + "@id": "edam:operation_3798" } ], "sc:license": "BSD-3-Clause", "sc:name": "Context-explorer", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://contextexplorer.readthedocs.io/en/latest/" diff --git a/data/contibait/contibaitbioschemas.jsonld b/data/contibait/contibaitbioschemas.jsonld index c0d96870f0de7..bc87ad54d7fb3 100644 --- a/data/contibait/contibaitbioschemas.jsonld +++ b/data/contibait/contibaitbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1093/bioinformatics/btx281", "@type": "sc:CreativeWork" }, + { + "@id": "https://orcid.org/0000-0001-7609-5905", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/contibait", "@type": "sc:SoftwareApplication", @@ -24,11 +28,11 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC5860061", - "pubmed:28475666", { "@id": "https://doi.org/10.1093/bioinformatics/btx281" - } + }, + "pmcid:PMC5860061", + "pubmed:28475666" ], "sc:description": "Using strand inheritance data from multiple single cells from the organism whose genome is to be assembled, this tool can cluster unbridged contigs together into putative chromosomes, and order the contigs within those chromosomes.", "sc:featureList": { @@ -43,10 +47,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/contiBAIT.html", "sc:version": "1.2.0" - }, - { - "@id": "https://orcid.org/0000-0001-7609-5905", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/contra_v2/contra_v2bioschemas.jsonld b/data/contra_v2/contra_v2bioschemas.jsonld index 56a324488837c..c516dcc07e8e2 100644 --- a/data/contra_v2/contra_v2bioschemas.jsonld +++ b/data/contra_v2/contra_v2bioschemas.jsonld @@ -24,10 +24,10 @@ }, "sc:citation": [ "pmcid:PMC3125763", - "pubmed:21576231", { "@id": "https://doi.org/10.1093/nar/gkr355" - } + }, + "pubmed:21576231" ], "sc:description": "A tool to identify transcription factor binding sites across species.", "sc:featureList": { @@ -35,9 +35,9 @@ }, "sc:name": "ConTrav2", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://bioit.irc.ugent.be/contrav2/index.php?v2", diff --git a/data/contra_v3/contra_v3bioschemas.jsonld b/data/contra_v3/contra_v3bioschemas.jsonld index 2e794bc8ae126..47d79ef5b49a1 100644 --- a/data/contra_v3/contra_v3bioschemas.jsonld +++ b/data/contra_v3/contra_v3bioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1093/nar/gkx376", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0001-7620-4657", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/contra_v3", "@type": "sc:SoftwareApplication", @@ -25,8 +21,8 @@ { "@id": "https://doi.org/10.1093/nar/gkx376" }, - "pubmed:28472390", - "pmcid:PMC5570180" + "pmcid:PMC5570180", + "pubmed:28472390" ], "sc:contributor": { "@id": "http://orcid.org/0000-0001-7620-4657" @@ -38,6 +34,10 @@ "sc:name": "ConTra v3", "sc:url": "http://bioit2.irc.ugent.be/contra/v3", "sc:version": "v3" + }, + { + "@id": "http://orcid.org/0000-0001-7620-4657", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/conumee/conumeebioschemas.jsonld b/data/conumee/conumeebioschemas.jsonld index 24696ea162a64..7f9a10a57a19d 100644 --- a/data/conumee/conumeebioschemas.jsonld +++ b/data/conumee/conumeebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "conumee", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/conumee.html", "sc:version": "1.8.0" diff --git a/data/convaq/convaqbioschemas.jsonld b/data/convaq/convaqbioschemas.jsonld index 0433866eba264..7865e75927e45 100644 --- a/data/convaq/convaqbioschemas.jsonld +++ b/data/convaq/convaqbioschemas.jsonld @@ -13,19 +13,19 @@ "@id": "https://bio.tools/convaq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jan Baumbach", - "Simon Larsen" + "Simon Larsen", + "Jan Baumbach" ], "sc:additionalType": [ - "Web application", - "Library" + "Library", + "Web application" ], "sc:citation": [ { "@id": "https://doi.org/10.1186/s12864-018-4732-8" }, - "pubmed:29776329", - "pmcid:PMC5960125" + "pmcid:PMC5960125", + "pubmed:29776329" ], "sc:description": "Search for variations that are overrepresented in a population. CNV-based association study between two groups of samples.", "sc:featureList": { @@ -33,9 +33,9 @@ }, "sc:name": "CoNVaQ", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://convaq.compbio.sdu.dk/" }, diff --git a/data/convert-matrix/convert-matrixbioschemas.jsonld b/data/convert-matrix/convert-matrixbioschemas.jsonld index 28edc1597a0ea..a9f44f7b408a7 100644 --- a/data/convert-matrix/convert-matrixbioschemas.jsonld +++ b/data/convert-matrix/convert-matrixbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-8799-8584", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/nar/gkn304", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/convert-matrix", "@type": "sc:SoftwareApplication", @@ -31,18 +23,18 @@ }, "sc:additionalType": [ "Command-line tool", - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:applicationSubCategory": { "@id": "edam:topic_3511" }, "sc:author": "Jacques van Helden", "sc:citation": [ + "pubmed:18495751", { "@id": "https://doi.org/10.1093/nar/gkn304" }, - "pubmed:18495751", "pmcid:PMC2447775" ], "sc:description": "Inter-conversions between various formats of position-specific scoring matrices (PSSM). The program also performs a statistical analysis of the original matrix to provide different position-specific scores (weight, frequencies, information contents), general statistics (marginal frequencies, total information content), and synthetic descriptions (strict and degenerate consensus).", @@ -62,6 +54,14 @@ }, "sc:url": "http://rsat.eu/", "sc:version": "1" + }, + { + "@id": "http://orcid.org/0000-0002-8799-8584", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gkn304", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/convert/bioconda_convert.yaml b/data/convert/bioconda_convert.yaml index 6ef424901d98e..44fa2e6447a59 100644 --- a/data/convert/bioconda_convert.yaml +++ b/data/convert/bioconda_convert.yaml @@ -3,7 +3,6 @@ description: Define coerce methods for microarray data objects. home: https://bioconductor.org/packages/3.10/bioc/html/convert.html identifiers: - biotools:convert -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-convert diff --git a/data/convert/convertbioschemas.jsonld b/data/convert/convertbioschemas.jsonld index 497fd37e2b881..7aa3fb8aef66c 100644 --- a/data/convert/convertbioschemas.jsonld +++ b/data/convert/convertbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yee Hwa (Jean) Yang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Define coerce methods for microarray data objects.", "sc:license": "GPL-3.0", diff --git a/data/convert2annovar/convert2annovarbioschemas.jsonld b/data/convert2annovar/convert2annovarbioschemas.jsonld index c19f4b3eca29e..147ee16d1b372 100644 --- a/data/convert2annovar/convert2annovarbioschemas.jsonld +++ b/data/convert2annovar/convert2annovarbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Convert other genotype calling format into ANNOVAR format.", "sc:name": "convert2annovar", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://annovar.openbioinformatics.org/en/latest/", "sc:version": "1.0.0" diff --git a/data/converttranscriptfile_fastqtofasta/converttranscriptfile_fastqtofastabioschemas.jsonld b/data/converttranscriptfile_fastqtofasta/converttranscriptfile_fastqtofastabioschemas.jsonld index db2ac5c7d1464..a3216781b0b49 100644 --- a/data/converttranscriptfile_fastqtofasta/converttranscriptfile_fastqtofastabioschemas.jsonld +++ b/data/converttranscriptfile_fastqtofasta/converttranscriptfile_fastqtofastabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Convert Fastq File to Fasta File.", "sc:name": "converttranscriptfile_fastqtofasta", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/convmhc/convmhcbioschemas.jsonld b/data/convmhc/convmhcbioschemas.jsonld index 44d75c88fd054..17c0d87f35ce3 100644 --- a/data/convmhc/convmhcbioschemas.jsonld +++ b/data/convmhc/convmhcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ConvMHC", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://jumong.kaist.ac.kr:8080/convmhc" } \ No newline at end of file diff --git a/data/coordinateserver/coordinateserverbioschemas.jsonld b/data/coordinateserver/coordinateserverbioschemas.jsonld index ce6b201d3397c..9faf3b6efb7b0 100644 --- a/data/coordinateserver/coordinateserverbioschemas.jsonld +++ b/data/coordinateserver/coordinateserverbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CoordinateServer", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://coords.litemol.org", "sc:version": "1.4.6" diff --git a/data/coordinatestosequence/coordinatestosequencebioschemas.jsonld b/data/coordinatestosequence/coordinatestosequencebioschemas.jsonld index 52c9eb9e13a05..697965296c625 100644 --- a/data/coordinatestosequence/coordinatestosequencebioschemas.jsonld +++ b/data/coordinatestosequence/coordinatestosequencebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Extract the sequences from a list of coordinates.", "sc:name": "coordinatestosequence", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/copa/copabioschemas.jsonld b/data/copa/copabioschemas.jsonld index e8d50695f3321..7d686c5dd640f 100644 --- a/data/copa/copabioschemas.jsonld +++ b/data/copa/copabioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "Artistic-2.0", "sc:name": "copa", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/copa.html", "sc:version": "1.42.0" diff --git a/data/copap/copapbioschemas.jsonld b/data/copap/copapbioschemas.jsonld index 1682ea833dc9e..03d87d259f3e1 100644 --- a/data/copap/copapbioschemas.jsonld +++ b/data/copap/copapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CoPAP (Co-evolution of Presence-Absence Patterns) webserver allows inference of co-evolving characters (genes, restriction sites, introns, indels, methylation sites) as manifested by co-occurring gains and losses.", "sc:name": "CoPAP", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://copap.tau.ac.il/" } \ No newline at end of file diff --git a/data/copasi/copasibioschemas.jsonld b/data/copasi/copasibioschemas.jsonld index ebb89561a79ac..1bba45e49c88e 100644 --- a/data/copasi/copasibioschemas.jsonld +++ b/data/copasi/copasibioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": [ "Library", - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others. It includes features to define models of biological processes, simulate and analyze these models, generate analysis reports, and import/export models in SBML format.", "sc:license": "Artistic-2.0", diff --git a/data/copheism/copheismbioschemas.jsonld b/data/copheism/copheismbioschemas.jsonld index 698a0af7c401b..d8fb5fe0c0aa2 100644 --- a/data/copheism/copheismbioschemas.jsonld +++ b/data/copheism/copheismbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "MIT", "sc:name": "copheism", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://bitbucket.org/izhbannikov/cophesim", "sc:version": "1.4.1" diff --git a/data/cophosk/cophoskbioschemas.jsonld b/data/cophosk/cophoskbioschemas.jsonld index 000fd6f2ba1ac..c663ba507d3fc 100644 --- a/data/cophosk/cophoskbioschemas.jsonld +++ b/data/cophosk/cophoskbioschemas.jsonld @@ -17,8 +17,8 @@ "@id": "https://bio.tools/CoPhosK", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mark R. Chance", - "Marzieh Ayati" + "Marzieh Ayati", + "Mark R. Chance" ], "sc:additionalType": "Command-line tool", "sc:author": [ @@ -26,11 +26,11 @@ "Mehmet Koyuturk" ], "sc:citation": [ + "pubmed:30811403", { "@id": "https://doi.org/10.1371/journal.pcbi.1006678" }, - "pmcid:PMC6411229", - "pubmed:30811403" + "pmcid:PMC6411229" ], "sc:description": "Method for Co-phosphorylation-based Kinase-substrate interaction prediction (CophosK).", "sc:featureList": [ @@ -38,16 +38,16 @@ "@id": "edam:operation_3639" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_0417" }, { - "@id": "edam:operation_0417" + "@id": "edam:operation_3501" } ], "sc:name": "CoPhosK", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://compbio.case.edu/omics/software/cophosk/index.html" } diff --git a/data/coprarna/coprarnabioschemas.jsonld b/data/coprarna/coprarnabioschemas.jsonld index 09248b2b22717..54e7e509d6896 100644 --- a/data/coprarna/coprarnabioschemas.jsonld +++ b/data/coprarna/coprarnabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gku359", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0001-8231-3323", "@type": "schema:Person" @@ -17,20 +21,20 @@ "@id": "https://bio.tools/coprarna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Patrick Wright", { "@id": "http://orcid.org/0000-0001-8231-3323" - }, - "Patrick Wright" + } ], "edam:has_input": { "@id": "edam:data_3495" }, "edam:has_output": [ { - "@id": "edam:data_2968" + "@id": "edam:data_0872" }, { - "@id": "edam:data_0872" + "@id": "edam:data_2968" }, { "@id": "edam:data_1270" @@ -48,10 +52,10 @@ ], "sc:citation": [ "pubmed:24838564", + "pmcid:PMC4086077", { "@id": "https://doi.org/10.1093/nar/gku359" - }, - "pmcid:PMC4086077" + } ], "sc:description": "sRNA target prediction boosted by comparative information.", "sc:featureList": { @@ -61,22 +65,18 @@ "sc:name": "CopraRNA web server", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ - "University Freiburg", - "rnateam" + "rnateam", + "University Freiburg" ], "sc:softwareHelp": { "@id": "http://rna.informatik.uni-freiburg.de/Help.jsp" }, "sc:url": "http://rna.informatik.uni-freiburg.de/CopraRNA/", "sc:version": "2.0.3.2" - }, - { - "@id": "https://doi.org/10.1093/nar/gku359", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cops/copsbioschemas.jsonld b/data/cops/copsbioschemas.jsonld index 16651b0dd8034..28bd6466df8ce 100644 --- a/data/cops/copsbioschemas.jsonld +++ b/data/cops/copsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.", "sc:name": "COPS", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://cops.services.came.sbg.ac.at/" } \ No newline at end of file diff --git a/data/copycatlayout/copycatlayoutbioschemas.jsonld b/data/copycatlayout/copycatlayoutbioschemas.jsonld index e34ed6f0ca744..c431c8b05a64c 100644 --- a/data/copycatlayout/copycatlayoutbioschemas.jsonld +++ b/data/copycatlayout/copycatlayoutbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-2.0", "sc:name": "copycatLayout", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://apps.cytoscape.org/apps/copycatLayout" } \ No newline at end of file diff --git a/data/copynumber/copynumberbioschemas.jsonld b/data/copynumber/copynumberbioschemas.jsonld index 979cd677cd916..1aa0704b55ffa 100644 --- a/data/copynumber/copynumberbioschemas.jsonld +++ b/data/copynumber/copynumberbioschemas.jsonld @@ -26,19 +26,19 @@ } ], "edam:has_output": [ - { - "@id": "edam:data_1622" - }, { "@id": "edam:data_2884" }, { "@id": "edam:data_1636" + }, + { + "@id": "edam:data_1622" } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { @@ -61,18 +61,18 @@ "sc:description": "Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.", "sc:featureList": [ { - "@id": "edam:operation_2238" + "@id": "edam:operation_3233" }, { - "@id": "edam:operation_3233" + "@id": "edam:operation_2238" } ], "sc:license": "Artistic-2.0", "sc:name": "copynumber", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/copynumber.html", "sc:version": "1.14.0" diff --git a/data/copywriter/copywriterbioschemas.jsonld b/data/copywriter/copywriterbioschemas.jsonld index b1b7b6d38e05e..5f346aadd578d 100644 --- a/data/copywriter/copywriterbioschemas.jsonld +++ b/data/copywriter/copywriterbioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13059-015-0617-1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/copywriter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas Kuilman", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ { "@id": "https://doi.org/10.1186/s13059-015-0617-1" }, - "pmcid:PMC4396974", - "pubmed:25887352" + "pubmed:25887352", + "pmcid:PMC4396974" ], "sc:description": "This tool extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows extracting uniformly distributed copy number information, and it can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, this tool constitutes a widely applicable alternative to available copy number detection tools.", "sc:featureList": { @@ -35,12 +31,16 @@ "sc:license": "GPL-2.0", "sc:name": "CopywriteR", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CopywriteR.html", "sc:version": "2.6.0" + }, + { + "@id": "https://doi.org/10.1186/s13059-015-0617-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/coral/coralbioschemas.jsonld b/data/coral/coralbioschemas.jsonld index e433c21f99606..7d3f6b8fba0bd 100644 --- a/data/coral/coralbioschemas.jsonld +++ b/data/coral/coralbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An algorithm for ordering fingerprinted clones within contigs.", "sc:name": "CORAL (Contig Ordering Algorithm)", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.bcgsc.ca/platform/bioinfo/software/coral/" } \ No newline at end of file diff --git a/data/coraltbase/coraltbasebioschemas.jsonld b/data/coraltbase/coraltbasebioschemas.jsonld index 3a543dac36da1..997843a69428d 100644 --- a/data/coraltbase/coraltbasebioschemas.jsonld +++ b/data/coraltbase/coraltbasebioschemas.jsonld @@ -13,21 +13,21 @@ "@id": "https://bio.tools/CoralTBase", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Jianliang Xu", { "@id": "https://orcid.org/0000-0002-1541-9627" - }, - "Jianliang Xu" + } ], "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ + "pubmed:31101011", + "pmcid:PMC6525400", { "@id": "https://doi.org/10.1186/S12864-019-5744-8" - }, - "pmcid:PMC6525400", - "pubmed:31101011" + } ], "sc:description": "Transcriptomic database for 14 species of scleractinian corals.", "sc:featureList": [ @@ -35,28 +35,28 @@ "@id": "edam:operation_3258" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_3644" }, { - "@id": "edam:operation_3644" + "@id": "edam:operation_3431" } ], "sc:license": "Unlicense", "sc:name": "CoralTBase", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.comp.hkbu.edu.hk/~db/CoralTBase" }, - { - "@id": "https://doi.org/10.1186/S12864-019-5744-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0002-1541-9627", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/S12864-019-5744-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/corbi/corbibioschemas.jsonld b/data/corbi/corbibioschemas.jsonld index 7584d32f5112b..8dec50440825c 100644 --- a/data/corbi/corbibioschemas.jsonld +++ b/data/corbi/corbibioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1752-0509-7-S2-S6", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/corbi", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ling-Yun Wu", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:24565104", { "@id": "https://doi.org/10.1186/1752-0509-7-S2-S6" }, - "pmcid:PMC3851956", - "pubmed:24565104" + "pmcid:PMC3851956" ], "sc:description": "Biological network alignment and querying.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "Corbi", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://doc.aporc.org/wiki/Corbi" - }, - { - "@id": "https://doi.org/10.1186/1752-0509-7-S2-S6", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/core/corebioschemas.jsonld b/data/core/corebioschemas.jsonld index 506e842426763..61981b323b896 100644 --- a/data/core/corebioschemas.jsonld +++ b/data/core/corebioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-2.0", "sc:name": "CORE", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/package=CORE", "sc:version": "3.0" diff --git a/data/core_hunter/core_hunterbioschemas.jsonld b/data/core_hunter/core_hunterbioschemas.jsonld index 1c03e26e9991b..c8dd2b7574ef2 100644 --- a/data/core_hunter/core_hunterbioschemas.jsonld +++ b/data/core_hunter/core_hunterbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Herman De Beukelaer", "sc:additionalType": [ - "Desktop application", - "Library" + "Library", + "Desktop application" ], "sc:description": "Core Hunter is a flexible tool to sample diverse, representative subsets from large germplasm collections, with minimum redundancy. Such so-called core collections have applications in plant breeding and genetic resource management in general.In addition, CH3 is an improvement over CH2, with the option to use genetic marker data or phenotypic traits, or both, and improved speed.", "sc:license": "Apache-2.0", "sc:name": "Core Hunter", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.corehunter.org", "sc:version": "3.0" diff --git a/data/coregenes/coregenesbioschemas.jsonld b/data/coregenes/coregenesbioschemas.jsonld index 99d2465ed528a..2884091b0d512 100644 --- a/data/coregenes/coregenesbioschemas.jsonld +++ b/data/coregenes/coregenesbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1756-0500-6-140", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/coregenes", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:23566564", { "@id": "https://doi.org/10.1186/1756-0500-6-140" }, - "pubmed:23566564", "pmcid:PMC3630060" ], "sc:description": "A webserver for the determination of core genes from sets of viral and small bacterial genomes.", @@ -31,11 +27,15 @@ }, "sc:name": "CoreGenes3.5", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://binf.gmu.edu:8080/CoreGenes3.5/" + }, + { + "@id": "https://doi.org/10.1186/1756-0500-6-140", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/coregnet/coregnetbioschemas.jsonld b/data/coregnet/coregnetbioschemas.jsonld index ea638501dfcdf..a1904f000acbc 100644 --- a/data/coregnet/coregnetbioschemas.jsonld +++ b/data/coregnet/coregnetbioschemas.jsonld @@ -20,10 +20,10 @@ "Library" ], "sc:citation": [ + "pubmed:25979476", { "@id": "https://doi.org/10.1093/bioinformatics/btv305" }, - "pubmed:25979476", "pmcid:PMC4565029" ], "sc:description": "This package provides methods to identify active transcriptional programs, including methods and classes to import or infer large scale co-regulatory network from transcriptomic data. The specificity of the encoded networks is to model TF cooperation. External regulation evidences (TFBS, ChIP,...) can be integrated to assess the inferred network and refine it if necessary.", @@ -33,20 +33,20 @@ "sc:license": "GPL-3.0", "sc:name": "CoRegNet", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CoRegNet.html", "sc:version": "1.10.0" }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btv305", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0001-8084-1173", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv305", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/coremic/coremicbioschemas.jsonld b/data/coremic/coremicbioschemas.jsonld index 955febd981372..2aae460db7131 100644 --- a/data/coremic/coremicbioschemas.jsonld +++ b/data/coremic/coremicbioschemas.jsonld @@ -22,8 +22,8 @@ ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:29473009", "pmcid:PMC5816963", + "pubmed:29473009", { "@id": "https://doi.org/10.7717/peerj.4395" } @@ -34,9 +34,9 @@ }, "sc:name": "COREMIC", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://core-mic.com/", "sc:version": "2.0" diff --git a/data/coremine_medical/coremine_medicalbioschemas.jsonld b/data/coremine_medical/coremine_medicalbioschemas.jsonld index 781d7a5836f89..27bd4d8287a1b 100644 --- a/data/coremine_medical/coremine_medicalbioschemas.jsonld +++ b/data/coremine_medical/coremine_medicalbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:funder": "http://www.coremine.com/medical/helppages/HelpPages.html#5", "sc:name": "Coremine Medical", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "UiO", "sc:url": "http://www.coremine.com/medical", diff --git a/data/coremri/coremribioschemas.jsonld b/data/coremri/coremribioschemas.jsonld index 382f563666e15..a9f2d7a8b83ce 100644 --- a/data/coremri/coremribioschemas.jsonld +++ b/data/coremri/coremribioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-3786-3817", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/coreMRI", "@type": "sc:SoftwareApplication", @@ -24,11 +20,15 @@ "sc:license": "Unlicense", "sc:name": "coreMRI", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://www.coreMRI.org" + }, + { + "@id": "https://orcid.org/0000-0002-3786-3817", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/coreslicer/coreslicerbioschemas.jsonld b/data/coreslicer/coreslicerbioschemas.jsonld index 7cba3cdac83b5..59f6b61471b3a 100644 --- a/data/coreslicer/coreslicerbioschemas.jsonld +++ b/data/coreslicer/coreslicerbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12880-019-0316-6", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/CoreSlicer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Louis Mullie", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:citation": [ + "pmcid:PMC6371488", "pubmed:30744586", { "@id": "https://doi.org/10.1186/s12880-019-0316-6" - }, - "pmcid:PMC6371488" + } ], "sc:description": "Enables extraction of morphomic markers from CT images by non-technically skilled clinicians.", "sc:license": "MIT", @@ -33,10 +37,6 @@ "Linux" ], "sc:url": "https://coreslicer.com/" - }, - { - "@id": "https://doi.org/10.1186/s12880-019-0316-6", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/coretracker/coretrackerbioschemas.jsonld b/data/coretracker/coretrackerbioschemas.jsonld index 2e64f5a601c28..b2f455af64873 100644 --- a/data/coretracker/coretrackerbioschemas.jsonld +++ b/data/coretracker/coretrackerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Accurate codon reassignment prediction, applied to mitochondrial genomes.", "sc:name": "CoreTracker", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/UdeM-LBIT/CoreTracker" } \ No newline at end of file diff --git a/data/corgen/corgenbioschemas.jsonld b/data/corgen/corgenbioschemas.jsonld index 1bf113d8c27a5..6d8ef89aadada 100644 --- a/data/corgen/corgenbioschemas.jsonld +++ b/data/corgen/corgenbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Measures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.", "sc:name": "CorGen", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://corgen.molgen.mpg.de" diff --git a/data/corgi/corgibioschemas.jsonld b/data/corgi/corgibioschemas.jsonld index c3a79b01208f1..074d814ff7fab 100644 --- a/data/corgi/corgibioschemas.jsonld +++ b/data/corgi/corgibioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2539-x", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/CORGi", "@type": "sc:SoftwareApplication", @@ -20,27 +16,31 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:30577744", - "pmcid:PMC6302372", { "@id": "https://doi.org/10.1186/s12859-018-2539-x" - } + }, + "pmcid:PMC6302372" ], "sc:description": "CORGi (COmplex Rearrangement detection with Graph-search), a method for the detection and visualization of complex local genomic rearrangements.", "sc:featureList": [ { - "@id": "edam:operation_3185" + "@id": "edam:operation_0452" }, { - "@id": "edam:operation_0452" + "@id": "edam:operation_3185" } ], "sc:license": "Unlicense", "sc:name": "CORGi", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/zstephens/CORGi" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2539-x", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/corkoakdb/corkoakdbbioschemas.jsonld b/data/corkoakdb/corkoakdbbioschemas.jsonld index c6f93fa6c7436..91ecf3423da7f 100644 --- a/data/corkoakdb/corkoakdbbioschemas.jsonld +++ b/data/corkoakdb/corkoakdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Database of Cork Oak EST sequences from the Portuguese Cork Oak sequencing project.", "sc:name": "CorkOakDB", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "ELIXIR-PT", "sc:url": "http://corkoakdb.org/" diff --git a/data/cormotif/cormotifbioschemas.jsonld b/data/cormotif/cormotifbioschemas.jsonld index 8dc6f79f1fcaf..043e9b172b5c2 100644 --- a/data/cormotif/cormotifbioschemas.jsonld +++ b/data/cormotif/cormotifbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yingying Wei", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:28456158", "sc:description": "It fits correlation motif model to multiple studies to detect study specific differential expression patterns.", diff --git a/data/cormut/cormutbioschemas.jsonld b/data/cormut/cormutbioschemas.jsonld index 1ccf817dd6592..5dba7ee9775de 100644 --- a/data/cormut/cormutbioschemas.jsonld +++ b/data/cormut/cormutbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Zhenpeng Li", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Provides functions for computing kaks for individual sites or specific amino acids and detecting correlated mutations among them. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; Second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional.", "sc:license": "GPL-2.0", "sc:name": "CorMut", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CorMut.html", diff --git a/data/cornai/cornaibioschemas.jsonld b/data/cornai/cornaibioschemas.jsonld index ec3275d9c3513..b29a006060bb6 100644 --- a/data/cornai/cornaibioschemas.jsonld +++ b/data/cornai/cornaibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "coRNAi", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://bioconductor.org/packages/3.4/bioc/html/coRNAi.html", "sc:version": "1.24.0" diff --git a/data/cornet/cornetbioschemas.jsonld b/data/cornet/cornetbioschemas.jsonld index aa3bb74f6f5a8..19f6cf2712d0e 100644 --- a/data/cornet/cornetbioschemas.jsonld +++ b/data/cornet/cornetbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CORNET", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "http://gpcr.biocomp.unibo.it/cgi/predictors/cornet/pred_cmapcgi.cgi", diff --git a/data/cornet_arabidopsis/cornet_arabidopsisbioschemas.jsonld b/data/cornet_arabidopsis/cornet_arabidopsisbioschemas.jsonld index b62a3b833d4eb..4b8af6a43d4b2 100644 --- a/data/cornet_arabidopsis/cornet_arabidopsisbioschemas.jsonld +++ b/data/cornet_arabidopsis/cornet_arabidopsisbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This tool allows you to do co-expression analysis using either predefined or user-defined groups of micro array experiments.", "sc:name": "CorNet Arabidopsis", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ "VIB", diff --git a/data/cornet_maize/cornet_maizebioschemas.jsonld b/data/cornet_maize/cornet_maizebioschemas.jsonld index b79f1b51d70ea..644b78018b95b 100644 --- a/data/cornet_maize/cornet_maizebioschemas.jsonld +++ b/data/cornet_maize/cornet_maizebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CorNet Maize", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "PSB", "sc:url": "https://bioinformatics.psb.ugent.be/cornet_maize/", diff --git a/data/correct_bacode/correct_bacodebioschemas.jsonld b/data/correct_bacode/correct_bacodebioschemas.jsonld index a4d51f383b334..490b840178ab7 100644 --- a/data/correct_bacode/correct_bacodebioschemas.jsonld +++ b/data/correct_bacode/correct_bacodebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "correct_bacode", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/rikenbit/correct_barcode/" } \ No newline at end of file diff --git a/data/correlogo/correlogobioschemas.jsonld b/data/correlogo/correlogobioschemas.jsonld index d12723d8e63c4..9fbc40d8596dc 100644 --- a/data/correlogo/correlogobioschemas.jsonld +++ b/data/correlogo/correlogobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.", "sc:name": "CorreLogo", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://correlogo.abcc.ncifcrf.gov/" } \ No newline at end of file diff --git a/data/correp/bioconda_correp.yaml b/data/correp/bioconda_correp.yaml index 1fb71025fcc8e..4ebb8c6c06f51 100644 --- a/data/correp/bioconda_correp.yaml +++ b/data/correp/bioconda_correp.yaml @@ -4,7 +4,6 @@ description: Multivariate correlation estimation and statistical inference. See home: https://bioconductor.org/packages/3.10/bioc/html/CORREP.html identifiers: - biotools:correp -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-correp diff --git a/data/corrna/corrnabioschemas.jsonld b/data/corrna/corrnabioschemas.jsonld index a571426133ee0..971b299f679c5 100644 --- a/data/corrna/corrnabioschemas.jsonld +++ b/data/corrna/corrnabioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/corrna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jerome Waldispuhl", - "Error submission" + "Error submission", + "Jerome Waldispuhl" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:21596778", "sc:description": "corRna is a web server for predicting the multiple point deleterious mutations in structural RNAs. Users can apply search heuristics to improve the quality of the predictions.", "sc:name": "corRna", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://corrna.cs.mcgill.ca" } \ No newline at end of file diff --git a/data/corset/corsetbioschemas.jsonld b/data/corset/corsetbioschemas.jsonld index cd2022a8c10dc..ff967972fcbbc 100644 --- a/data/corset/corsetbioschemas.jsonld +++ b/data/corset/corsetbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Command-line software program to go from a de novo transcriptome assembly to gene-level counts. This software takes a set of reads that have been multi-mapped to the transcriptome and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq.", "sc:name": "Corset", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "unimelb.edu.au", "sc:url": "https://github.com/Oshlack/Corset/wiki", diff --git a/data/corum/corumbioschemas.jsonld b/data/corum/corumbioschemas.jsonld index 8bf768623744d..9ce0cdceb8782 100644 --- a/data/corum/corumbioschemas.jsonld +++ b/data/corum/corumbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkp914", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/corum", "@type": "sc:SoftwareApplication", @@ -30,10 +34,10 @@ ], "sc:citation": [ "pmcid:PMC2808912", + "pubmed:19884131", { "@id": "https://doi.org/10.1093/nar/gkp914" - }, - "pubmed:19884131" + } ], "sc:description": "Database which provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.", "sc:featureList": { @@ -41,16 +45,12 @@ }, "sc:name": "CORUM", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "Helmholtz Zentrum München-German Research Center for Environmental Health", "sc:url": "http://mips.gsf.de/genre/proj/corum" - }, - { - "@id": "https://doi.org/10.1093/nar/gkp914", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/coryneregnet/coryneregnetbioschemas.jsonld b/data/coryneregnet/coryneregnetbioschemas.jsonld index c2e91acbd8f2a..54df94a543602 100644 --- a/data/coryneregnet/coryneregnetbioschemas.jsonld +++ b/data/coryneregnet/coryneregnetbioschemas.jsonld @@ -21,29 +21,29 @@ }, "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:22080556", { "@id": "https://doi.org/10.1093/nar/gkr883" }, - "pmcid:PMC3245100" + "pmcid:PMC3245100", + "pubmed:22080556" ], "sc:description": "Reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.", "sc:featureList": [ { - "@id": "edam:operation_0338" + "@id": "edam:operation_2497" }, { "@id": "edam:operation_3439" }, { - "@id": "edam:operation_2497" + "@id": "edam:operation_0338" } ], "sc:name": "CoryneRegNet", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "bmb.sdu.dk", "sc:url": "http://www.coryneregnet.de" diff --git a/data/coseq/coseqbioschemas.jsonld b/data/coseq/coseqbioschemas.jsonld index 42d49fa2b0ecd..5a86afded0b69 100644 --- a/data/coseq/coseqbioschemas.jsonld +++ b/data/coseq/coseqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "coseq", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/coseq.html", diff --git a/data/cosims/cosimsbioschemas.jsonld b/data/cosims/cosimsbioschemas.jsonld index 1f3ae3758ee3c..98ce480752847 100644 --- a/data/cosims/cosimsbioschemas.jsonld +++ b/data/cosims/cosimsbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "CoSIMS", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ChristopherAMyers/CoSIMS" } \ No newline at end of file diff --git a/data/cosmic/cosmicbioschemas.jsonld b/data/cosmic/cosmicbioschemas.jsonld index b0ff6d75d5f4b..7861458a6321c 100644 --- a/data/cosmic/cosmicbioschemas.jsonld +++ b/data/cosmic/cosmicbioschemas.jsonld @@ -9,30 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/database/bar018", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://doi.org/10.1093/nar/gkp995", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cosmic", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Cosmic Support", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ + "pmcid:PMC3013785", { "@id": "https://doi.org/10.1093/database/bar018" }, - "pubmed:20952405", { - "@id": "https://doi.org/10.1093/nar/gkp995" + "@id": "https://doi.org/10.1093/nar/gkq929" }, "pmcid:PMC3263736", - "pubmed:21609966", { - "@id": "https://doi.org/10.1093/nar/gkq929" + "@id": "https://doi.org/10.1093/nar/gkp995" }, + "pubmed:21609966", + "pubmed:19906727", "pmcid:PMC2808858", - "pmcid:PMC3013785", - "pubmed:19906727" + "pubmed:20952405" ], "sc:description": "Catalogue Of Somatic Mutations In Cancer (COSMIC) - resource for exploring the impact of somatic mutations in human cancer.", "sc:featureList": [ @@ -40,35 +48,27 @@ "@id": "edam:operation_0477" }, { - "@id": "edam:operation_3202" + "@id": "edam:operation_2422" }, { "@id": "edam:operation_0306" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_3202" } ], "sc:license": "Other", "sc:name": "COSMIC", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.sanger.ac.uk/genetics/CGP/cosmic/" }, { "@id": "https://doi.org/10.1093/nar/gkq929", "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1093/nar/gkp995", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1093/database/bar018", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cosmiq/cosmiqbioschemas.jsonld b/data/cosmiq/cosmiqbioschemas.jsonld index ceddd36008bce..5868cf8bc0c97 100644 --- a/data/cosmiq/cosmiqbioschemas.jsonld +++ b/data/cosmiq/cosmiqbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/cosmiq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Christian Panse", - "David Fischer" + "David Fischer", + "Christian Panse" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Tool for the preprocessing of liquid/gas chromatography mass spectrometry (LCMS/GCMS) data, focusing on metabolomics or lipidomics applications. To improve the detection of low abundant signals, it generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately.", "sc:license": "GPL-3.0", "sc:name": "cosmiq", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cosmiq.html", "sc:version": "1.8.0" diff --git a/data/cosnet/cosnetbioschemas.jsonld b/data/cosnet/cosnetbioschemas.jsonld index ed6b3158e5753..4bb0bc3f2c750 100644 --- a/data/cosnet/cosnetbioschemas.jsonld +++ b/data/cosnet/cosnetbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "COSNet", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/COSNet.html", diff --git a/data/coss/cossbioschemas.jsonld b/data/coss/cossbioschemas.jsonld index e234e9f7b3e88..d7e868927bdf7 100644 --- a/data/coss/cossbioschemas.jsonld +++ b/data/coss/cossbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "COSS", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/compomics/COSS" } \ No newline at end of file diff --git a/data/costat/costatbioschemas.jsonld b/data/costat/costatbioschemas.jsonld index a0eca6c164996..5f824976c58f4 100644 --- a/data/costat/costatbioschemas.jsonld +++ b/data/costat/costatbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "CoStat is an easy-to-use program for data manipulation and statistical analysis.", "sc:name": "CoStat", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.cohort.com/costat.html", "sc:version": "6.4" diff --git a/data/couger/cougerbioschemas.jsonld b/data/couger/cougerbioschemas.jsonld index 71f864d43affb..83f78ace76007 100644 --- a/data/couger/cougerbioschemas.jsonld +++ b/data/couger/cougerbioschemas.jsonld @@ -15,15 +15,15 @@ "RALUCA GORDÂN" ], "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Framework for identifying co-factors associated with uniquely-bound genomic regions.", "sc:name": "COUGER", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://couger.oit.duke.edu" } \ No newline at end of file diff --git a/data/countclust/countclustbioschemas.jsonld b/data/countclust/countclustbioschemas.jsonld index 1196c93f64579..2c507c62cbe3d 100644 --- a/data/countclust/countclustbioschemas.jsonld +++ b/data/countclust/countclustbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Kushal Dey", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Fits grade of membership models (GoM, also known as admixture models) to cluster RNA-seq gene expression count data, identifies characteristic genes driving cluster memberships, and provides a visual summary of the cluster memberships.", "sc:license": "GPL-2.0", "sc:name": "CountClust", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CountClust.html", diff --git a/data/countnumber_parallel/countnumber_parallelbioschemas.jsonld b/data/countnumber_parallel/countnumber_parallelbioschemas.jsonld index ae94f465d4494..d67d8ad25b144 100644 --- a/data/countnumber_parallel/countnumber_parallelbioschemas.jsonld +++ b/data/countnumber_parallel/countnumber_parallelbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "countnumber_parallel", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/countreadgcpercent/countreadgcpercentbioschemas.jsonld b/data/countreadgcpercent/countreadgcpercentbioschemas.jsonld index e328bd8541933..62e11c74fa5a1 100644 --- a/data/countreadgcpercent/countreadgcpercentbioschemas.jsonld +++ b/data/countreadgcpercent/countreadgcpercentbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Count GC percent for each read against a genome.", "sc:name": "countreadgcpercent", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/countsimqc/countsimqcbioschemas.jsonld b/data/countsimqc/countsimqcbioschemas.jsonld index 695e732a3c04b..c79c9e8666179 100644 --- a/data/countsimqc/countsimqcbioschemas.jsonld +++ b/data/countsimqc/countsimqcbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/countsimqc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mark Robinson", - "Charlotte Soneson" + "Charlotte Soneson", + "Mark Robinson" ], "sc:additionalType": "Library", "sc:description": "Compare characteristic features of count data sets.", diff --git a/data/cov2html/cov2htmlbioschemas.jsonld b/data/cov2html/cov2htmlbioschemas.jsonld index 3a9bc7a497eef..3f40be34dde3c 100644 --- a/data/cov2html/cov2htmlbioschemas.jsonld +++ b/data/cov2html/cov2htmlbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "COV2HTML", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://mmonot.eu/COV2HTML" diff --git a/data/coval/covalbioschemas.jsonld b/data/coval/covalbioschemas.jsonld index ea6ad101bdce1..b12ca9f281773 100644 --- a/data/coval/covalbioschemas.jsonld +++ b/data/coval/covalbioschemas.jsonld @@ -26,8 +26,8 @@ }, "sc:name": "Coval", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sourceforge.net/projects/coval105/", "sc:version": "1.5" diff --git a/data/covalentdock_cloud/covalentdock_cloudbioschemas.jsonld b/data/covalentdock_cloud/covalentdock_cloudbioschemas.jsonld index b356a20d7b45e..61db88246c967 100644 --- a/data/covalentdock_cloud/covalentdock_cloudbioschemas.jsonld +++ b/data/covalentdock_cloud/covalentdock_cloudbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CovalentDock Cloud web server allows one to perform covalent docking experiments and analysis online. Input is the structure of both the ligand and the receptor.", "sc:name": "CovalentDock Cloud", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://docking.sce.ntu.edu.sg/" } \ No newline at end of file diff --git a/data/coveb/covebbioschemas.jsonld b/data/coveb/covebbioschemas.jsonld index 9787bf0adb5d3..c8998e8a267da 100644 --- a/data/coveb/covebbioschemas.jsonld +++ b/data/coveb/covebbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "covEB", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/covEB.html", "sc:version": "1.0.0" diff --git a/data/covenntree/covenntreebioschemas.jsonld b/data/covenntree/covenntreebioschemas.jsonld index ac23841620c0e..0374677db20ad 100644 --- a/data/covenntree/covenntreebioschemas.jsonld +++ b/data/covenntree/covenntreebioschemas.jsonld @@ -28,26 +28,26 @@ } ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3070" + "@id": "edam:topic_3174" }, { - "@id": "edam:topic_0092" + "@id": "edam:topic_3070" }, { - "@id": "edam:topic_3174" + "@id": "edam:topic_0092" } ], "sc:citation": [ - "pubmed:25750651", - "pmcid:PMC4335276", { "@id": "https://doi.org/10.3389/fgene.2015.00043" - } + }, + "pubmed:25750651", + "pmcid:PMC4335276" ], "sc:description": "It is developed to simultaneously compare up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. With the introduction of weighted Venn structures, the contents and relationships of various datasets can be correlated and simultaneously aggregated without losing information. It has been integrated into the Galaxy ToolShed and can be directly downloaded and integrated into the user instance.", "sc:featureList": [ diff --git a/data/coverageview/coverageviewbioschemas.jsonld b/data/coverageview/coverageviewbioschemas.jsonld index 8160657ec1561..be4fc7d9a9513 100644 --- a/data/coverageview/coverageviewbioschemas.jsonld +++ b/data/coverageview/coverageviewbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "CoverageView", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CoverageView.html", diff --git a/data/covrna/bioconda_covrna.yaml b/data/covrna/bioconda_covrna.yaml index fd9c53c3656e4..424b3b31f6273 100644 --- a/data/covrna/bioconda_covrna.yaml +++ b/data/covrna/bioconda_covrna.yaml @@ -4,7 +4,6 @@ description: This package provides the analysis methods fourthcorner and RLQ ana home: https://bioconductor.org/packages/3.10/bioc/html/covRNA.html identifiers: - biotools:covrna -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-covrna diff --git a/data/covrna/covrnabioschemas.jsonld b/data/covrna/covrnabioschemas.jsonld index c043be3471eef..090c4d3b9b2b2 100644 --- a/data/covrna/covrnabioschemas.jsonld +++ b/data/covrna/covrnabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lara Urban", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.", "sc:license": "GPL-2.0", "sc:name": "covRNA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/covRNA.html", "sc:version": "1.0.0" diff --git a/data/cowpi/cowpibioschemas.jsonld b/data/cowpi/cowpibioschemas.jsonld index 0ca3fd5e6a23d..08b37fdc9f4df 100644 --- a/data/cowpi/cowpibioschemas.jsonld +++ b/data/cowpi/cowpibioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3389/fmicb.2018.01095", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cowpi", "@type": "sc:SoftwareApplication", @@ -18,8 +22,8 @@ { "@id": "https://doi.org/10.3389/fmicb.2018.01095" }, - "pubmed:29887853", - "pmcid:PMC5981159" + "pmcid:PMC5981159", + "pubmed:29887853" ], "sc:description": "Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "GPL-3.0", "sc:name": "CowPI", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://www.cowpi.org/2018/03/welcome.html" - }, - { - "@id": "https://doi.org/10.3389/fmicb.2018.01095", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/coxpresdb/coxpresdbbioschemas.jsonld b/data/coxpresdb/coxpresdbbioschemas.jsonld index 17b1cb74c8286..a0ae8a850a237 100644 --- a/data/coxpresdb/coxpresdbbioschemas.jsonld +++ b/data/coxpresdb/coxpresdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "COXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly and nematoda, and addition of different layers of omics data into the integrated network of genes.", "sc:name": "COXPRESdb", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://coxpresdb.jp" } \ No newline at end of file diff --git a/data/cpag/cpagbioschemas.jsonld b/data/cpag/cpagbioschemas.jsonld index df24477b51f39..19137f699c527 100644 --- a/data/cpag/cpagbioschemas.jsonld +++ b/data/cpag/cpagbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "CPAG can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these results in the form of hierarchical clustering trees, heatmaps, and networks.", "sc:name": "CPAG", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://sourceforge.net/projects/cpag/", "sc:version": "0.2" diff --git a/data/cpbayes/cpbayesbioschemas.jsonld b/data/cpbayes/cpbayesbioschemas.jsonld index 791051839360b..cd0190d76cd0b 100644 --- a/data/cpbayes/cpbayesbioschemas.jsonld +++ b/data/cpbayes/cpbayesbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CPBayes", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/CPBayes/index.html" } \ No newline at end of file diff --git a/data/cpc/cpcbioschemas.jsonld b/data/cpc/cpcbioschemas.jsonld index 3936ea2170b2d..e6bd53499858c 100644 --- a/data/cpc/cpcbioschemas.jsonld +++ b/data/cpc/cpcbioschemas.jsonld @@ -9,38 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkm391", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/cpc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "CPC Team", + "Li-Ping Wei", "Ge Gao", - "Li-Ping Wei" + "CPC Team" ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:17631615", - "pmcid:PMC1933232", { "@id": "https://doi.org/10.1093/nar/gkm391" - } + }, + "pmcid:PMC1933232", + "pubmed:17631615" ], "sc:description": "Coding Potential Calculator (CPC) is a support vector machine-based classifier to assess the protein-coding potential of a transcript based on six biologically meaningful sequence features.", "sc:featureList": [ { - "@id": "edam:operation_0314" + "@id": "edam:operation_0256" }, { - "@id": "edam:operation_0235" + "@id": "edam:operation_0253" }, { "@id": "edam:operation_2995" }, { - "@id": "edam:operation_0253" + "@id": "edam:operation_0314" }, { - "@id": "edam:operation_0256" + "@id": "edam:operation_0235" } ], "sc:license": "GPL-2.0", @@ -51,10 +55,6 @@ "Mac" ], "sc:url": "http://cpc.cbi.pku.edu.cn/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkm391", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cpc2/cpc2bioschemas.jsonld b/data/cpc2/cpc2bioschemas.jsonld index 9858e9332650a..631e94702f156 100644 --- a/data/cpc2/cpc2bioschemas.jsonld +++ b/data/cpc2/cpc2bioschemas.jsonld @@ -16,8 +16,8 @@ "@id": "edam:data_3496" }, "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": [ "pubmed:28521017", @@ -29,16 +29,16 @@ "sc:description": "Coding Potential Calculator. Fast and accurate coding potential calculator based on sequence intrinsic features.", "sc:featureList": [ { - "@id": "edam:operation_0314" + "@id": "edam:operation_0253" }, { - "@id": "edam:operation_0256" + "@id": "edam:operation_0235" }, { - "@id": "edam:operation_0235" + "@id": "edam:operation_0314" }, { - "@id": "edam:operation_0253" + "@id": "edam:operation_0256" } ], "sc:name": "CPC2", diff --git a/data/cpdb/cpdbbioschemas.jsonld b/data/cpdb/cpdbbioschemas.jsonld index fba5e85156f01..91b99912f0e43 100644 --- a/data/cpdb/cpdbbioschemas.jsonld +++ b/data/cpdb/cpdbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways.", "sc:name": "cpdb", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://cpdb.molgen.mpg.de/", "sc:version": "1" diff --git a/data/cpgavas/cpgavasbioschemas.jsonld b/data/cpgavas/cpgavasbioschemas.jsonld index bce95ac63cea6..a5f4beaf8c04b 100644 --- a/data/cpgavas/cpgavasbioschemas.jsonld +++ b/data/cpgavas/cpgavasbioschemas.jsonld @@ -17,8 +17,8 @@ { "@id": "https://doi.org/10.1186/1471-2164-13-715" }, - "pubmed:23256920", - "pmcid:PMC3543216" + "pmcid:PMC3543216", + "pubmed:23256920" ], "sc:description": "CPGAVAS (Chloroplast Genome Annotation, Visualization, Analysis, and GenBank Submission) is a web server which allows accurate genome annotation, the generation of circular chloroplast genome maps, the provision of useful analysis results of the annotated genome, the creation of files that can be submitted to GenBank directly.", "sc:featureList": { diff --git a/data/cpgavas2/cpgavas2bioschemas.jsonld b/data/cpgavas2/cpgavas2bioschemas.jsonld index f78a247145263..b553c3b53a315 100644 --- a/data/cpgavas2/cpgavas2bioschemas.jsonld +++ b/data/cpgavas2/cpgavas2bioschemas.jsonld @@ -18,30 +18,30 @@ "Web application" ], "sc:citation": [ + "pubmed:31066451", "pmcid:PMC6602467", { "@id": "https://doi.org/10.1093/NAR/GKZ345" - }, - "pubmed:31066451" + } ], "sc:description": "Integrated plastome sequence annotator and analyzer.", "sc:featureList": [ { - "@id": "edam:operation_0484" + "@id": "edam:operation_0464" }, { - "@id": "edam:operation_0526" + "@id": "edam:operation_0484" }, { - "@id": "edam:operation_0464" + "@id": "edam:operation_0526" } ], "sc:license": "Unlicense", "sc:name": "CPGAVAS2", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.herbalgenomics.org/cpgavas2" }, diff --git a/data/cpgplot-ebi/cpgplot-ebibioschemas.jsonld b/data/cpgplot-ebi/cpgplot-ebibioschemas.jsonld index 5b575f3b4dd8a..662f3d39e4456 100644 --- a/data/cpgplot-ebi/cpgplot-ebibioschemas.jsonld +++ b/data/cpgplot-ebi/cpgplot-ebibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Identification of potential CpG islands.", "sc:name": "cpgplot (EBI)", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/", diff --git a/data/cpgplot/cpgplotbioschemas.jsonld b/data/cpgplot/cpgplotbioschemas.jsonld index 0efc731b78ba6..bd062ac584ada 100644 --- a/data/cpgplot/cpgplotbioschemas.jsonld +++ b/data/cpgplot/cpgplotbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK BBSRC", "Wellcome Trust", - "EMBOSS Contributors", "UK MRC", - "UK BBSRC" + "EMBOSS Contributors" ], "sc:description": "Identify and plot CpG islands in nucleotide sequence(s).", "sc:funder": [ - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "cpgplot", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/cpgplot.html", "sc:version": "r6" diff --git a/data/cpgreport/cpgreportbioschemas.jsonld b/data/cpgreport/cpgreportbioschemas.jsonld index b10eda2e6f09d..e7093de3052ef 100644 --- a/data/cpgreport/cpgreportbioschemas.jsonld +++ b/data/cpgreport/cpgreportbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "EMBOSS Contributors" ], "sc:description": "Identify and report CpG-rich regions in nucleotide sequence(s).", "sc:funder": [ @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "cpgreport", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/cphmodels/cphmodelsbioschemas.jsonld b/data/cphmodels/cphmodelsbioschemas.jsonld index 5ef86b7d98518..b473544521f68 100644 --- a/data/cphmodels/cphmodelsbioschemas.jsonld +++ b/data/cphmodels/cphmodelsbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkq535", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-7885-4311", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/cphmodels", "@type": "sc:SoftwareApplication", @@ -25,10 +17,10 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:20542909", { "@id": "https://doi.org/10.1093/nar/gkq535" }, - "pubmed:20542909", "pmcid:PMC2896139" ], "sc:description": "Protein homology modeling server.", @@ -38,6 +30,14 @@ "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/CPHmodels/", "sc:version": "3.2" + }, + { + "@id": "http://orcid.org/0000-0001-7885-4311", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gkq535", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cplexa/cplexabioschemas.jsonld b/data/cplexa/cplexabioschemas.jsonld index d305215db0c6e..c24be6802cfd9 100644 --- a/data/cplexa/cplexabioschemas.jsonld +++ b/data/cplexa/cplexabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions. The package is particularly suited to study gene expression at complex promoters controlled by multiple, local and distal, DNA binding sites for transcription factors.", "sc:name": "CplexA", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://cplexa.sourceforge.net/", diff --git a/data/cpmcglm/cpmcglmbioschemas.jsonld b/data/cpmcglm/cpmcglmbioschemas.jsonld index 466a19530b34a..d8cd0daeb12dc 100644 --- a/data/cpmcglm/cpmcglmbioschemas.jsonld +++ b/data/cpmcglm/cpmcglmbioschemas.jsonld @@ -27,9 +27,9 @@ "sc:license": "GPL-3.0", "sc:name": "CPMCGLM", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/package=CPMCGLM", "sc:version": "1.2" diff --git a/data/cpmd/cpmdbioschemas.jsonld b/data/cpmd/cpmdbioschemas.jsonld index cc5d9d87438c2..cf423bffeb57a 100644 --- a/data/cpmd/cpmdbioschemas.jsonld +++ b/data/cpmd/cpmdbioschemas.jsonld @@ -15,8 +15,8 @@ "CPMD contact" ], "sc:additionalType": [ - "Command-line tool", - "Workflow" + "Workflow", + "Command-line tool" ], "sc:description": "Parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.", "sc:name": "CPMD", diff --git a/data/cpndb/cpndbbioschemas.jsonld b/data/cpndb/cpndbbioschemas.jsonld index 505ae27ce31c2..fa18a30ff1d01 100644 --- a/data/cpndb/cpndbbioschemas.jsonld +++ b/data/cpndb/cpndbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. It is built and maintained with open source tools.", "sc:name": "cpnDB", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.cpndb.ca/" diff --git a/data/cpred/cpredbioschemas.jsonld b/data/cpred/cpredbioschemas.jsonld index 8f71667178f71..94968278dbbe2 100644 --- a/data/cpred/cpredbioschemas.jsonld +++ b/data/cpred/cpredbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "Cpred", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sarst.life.nthu.edu.tw/CPred" } \ No newline at end of file diff --git a/data/cpss/cpssbioschemas.jsonld b/data/cpss/cpssbioschemas.jsonld index 8fa4319730850..0e0c8369475e9 100644 --- a/data/cpss/cpssbioschemas.jsonld +++ b/data/cpss/cpssbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/cpss", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Qinghua Shi", - "Yuanwei Zhang" + "Yuanwei Zhang", + "Qinghua Shi" ], "sc:additionalType": "Web application", "sc:description": "Computational platform update for the analysis of small RNA sequencing data.", "sc:name": "CPSS", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://114.214.166.79/cpss2.0/", "sc:version": "2.0" diff --git a/data/cptra/cptrabioschemas.jsonld b/data/cptra/cptrabioschemas.jsonld index d1b953f53ffce..2c4a8be8fe162 100644 --- a/data/cptra/cptrabioschemas.jsonld +++ b/data/cptra/cptrabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Integrated transcriptome analysis from Sanger, 454, Solexa, SOLiD, etc reads.", "sc:name": "CPTRA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.mybiosoftware.com/cptra-20090207-cross-platform-transcriptome-analysis.html" } \ No newline at end of file diff --git a/data/cpvsnp/bioconda_cpvsnp.yaml b/data/cpvsnp/bioconda_cpvsnp.yaml index 232aea355d375..c1cf5e3a93928 100644 --- a/data/cpvsnp/bioconda_cpvsnp.yaml +++ b/data/cpvsnp/bioconda_cpvsnp.yaml @@ -9,7 +9,6 @@ description: Gene set analysis methods exist to combine SNP-level association p- home: https://bioconductor.org/packages/3.10/bioc/html/cpvSNP.html identifiers: - biotools:cpvsnp -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-cpvsnp summary: Gene set analysis methods for SNP association p-values that lie in genes diff --git a/data/cpvsnp/cpvsnpbioschemas.jsonld b/data/cpvsnp/cpvsnpbioschemas.jsonld index 11f6298f7c7dc..cf65cc4911994 100644 --- a/data/cpvsnp/cpvsnpbioschemas.jsonld +++ b/data/cpvsnp/cpvsnpbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Caitlin McHugh", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package implements two methods to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. These methods require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs.", "sc:license": "Artistic-2.0", "sc:name": "cpvSNP", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cpvSNP.html", "sc:version": "1.6.0" diff --git a/data/cqn/cqnbioschemas.jsonld b/data/cqn/cqnbioschemas.jsonld index aff561ce68ab0..8d2d0c37e56fa 100644 --- a/data/cqn/cqnbioschemas.jsonld +++ b/data/cqn/cqnbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-0086-0687", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/cqn", "@type": "sc:SoftwareApplication", @@ -16,15 +20,15 @@ "@id": "http://orcid.org/0000-0003-0086-0687" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pmcid:PMC3297825", "pubmed:22285995", { "@id": "https://doi.org/10.1093/biostatistics/kxr054" - } + }, + "pmcid:PMC3297825" ], "sc:description": "A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.", "sc:featureList": [ @@ -39,8 +43,8 @@ "sc:name": "cqn", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cqn.html", "sc:version": "1.20.0" @@ -48,10 +52,6 @@ { "@id": "https://doi.org/10.1093/biostatistics/kxr054", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-0086-0687", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/cr-est/cr-estbioschemas.jsonld b/data/cr-est/cr-estbioschemas.jsonld index 14253b05658e2..621c0dfeecb6f 100644 --- a/data/cr-est/cr-estbioschemas.jsonld +++ b/data/cr-est/cr-estbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "CR-EST", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://apex.ipk-gatersleben.de/apex/f?p=CREST" } \ No newline at end of file diff --git a/data/cra_toolbox/cra_toolboxbioschemas.jsonld b/data/cra_toolbox/cra_toolboxbioschemas.jsonld index 9f6e1a012f268..02d6fb28581ff 100644 --- a/data/cra_toolbox/cra_toolboxbioschemas.jsonld +++ b/data/cra_toolbox/cra_toolboxbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Software package for conditional robustness analysis of cancer systems biology models in MATLAB.", "sc:name": "CRA toolbox", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://gitlab.ict4life.com/SysBiOThe/CRA-Matlab" diff --git a/data/crac/cracbioschemas.jsonld b/data/crac/cracbioschemas.jsonld index 1192251cc996b..54e1f01c7e0f1 100644 --- a/data/crac/cracbioschemas.jsonld +++ b/data/crac/cracbioschemas.jsonld @@ -17,32 +17,32 @@ "@id": "https://bio.tools/crac", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "For questions, comments, remarks on the algorithm or the article", - "For question regarding the software" + "For question regarding the software", + "For questions, comments, remarks on the algorithm or the article" ], "sc:additionalType": "Command-line tool", "sc:citation": [ { - "@id": "https://doi.org/10.1186/gb-2013-14-3-r30" + "@id": "https://doi.org/10.1038/nmeth.4106" }, - "pmcid:PMC5792058", + "pubmed:23537109", "pmcid:PMC4053775", + "pubmed:27941783", { - "@id": "https://doi.org/10.1038/nmeth.4106" + "@id": "https://doi.org/10.1186/gb-2013-14-3-r30" }, - "pubmed:23537109", - "pubmed:27941783" + "pmcid:PMC5792058" ], "sc:description": "CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read.", "sc:featureList": [ { - "@id": "edam:operation_3211" + "@id": "edam:operation_3800" }, { "@id": "edam:operation_3198" }, { - "@id": "edam:operation_3800" + "@id": "edam:operation_3211" } ], "sc:license": "CECILL-2.0", diff --git a/data/cracle/craclebioschemas.jsonld b/data/cracle/craclebioschemas.jsonld index 4af42fec5ffd4..6d6e2958f7f0b 100644 --- a/data/cracle/craclebioschemas.jsonld +++ b/data/cracle/craclebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "cRacle", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.github.com/rsh249/cRacle" } \ No newline at end of file diff --git a/data/crambled/crambledbioschemas.jsonld b/data/crambled/crambledbioschemas.jsonld index 7e269c08d9050..984516f5d634e 100644 --- a/data/crambled/crambledbioschemas.jsonld +++ b/data/crambled/crambledbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.7453.1", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-7876-7338", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/crambled", "@type": "sc:SoftwareApplication", @@ -16,15 +24,15 @@ "@id": "http://orcid.org/0000-0002-7876-7338" }, "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:citation": [ - "pubmed:26962434", "pmcid:PMC4765721", { "@id": "https://doi.org/10.12688/F1000RESEARCH.7453.1" - } + }, + "pubmed:26962434" ], "sc:description": "Part of the crambled-seg pipeline. It allows to interactively explore the cellularity, depth of coverage and clonality of tumour samples that have gone for whole-genome sequencing. In particular, it allows the user to assess the competing solutions for such data that can arise from using different packages.", "sc:featureList": { @@ -33,14 +41,6 @@ "sc:license": "GPL-2.0", "sc:name": "Crambled", "sc:url": "https://github.com/dralynch/crambled" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.7453.1", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-7876-7338", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/crc64/crc64bioschemas.jsonld b/data/crc64/crc64bioschemas.jsonld index ad8f286047ffc..f6a59bf957188 100644 --- a/data/crc64/crc64bioschemas.jsonld +++ b/data/crc64/crc64bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "CRC64", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfadmin.cs.ucl.ac.uk/downloads/crc64/", "sc:version": "2006" diff --git a/data/crcrpred/crcrpredbioschemas.jsonld b/data/crcrpred/crcrpredbioschemas.jsonld index fb2b917081d3d..1849982067879 100644 --- a/data/crcrpred/crcrpredbioschemas.jsonld +++ b/data/crcrpred/crcrpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "CRCRpred", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://webs.iiitd.edu.in/raghava/crcrpred" } \ No newline at end of file diff --git a/data/crcview/crcviewbioschemas.jsonld b/data/crcview/crcviewbioschemas.jsonld index 00d83beb1c8f7..d98c2a2013a77 100644 --- a/data/crcview/crcviewbioschemas.jsonld +++ b/data/crcview/crcviewbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "CRCView is a web-based microarray data analysis and visualization system. CRCView is powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm", "sc:name": "CRCView", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://crcview.hegroup.org/", diff --git a/data/createcontrolsubset/createcontrolsubsetbioschemas.jsonld b/data/createcontrolsubset/createcontrolsubsetbioschemas.jsonld index 4bedeb80a4e50..bbb242a2db0fd 100644 --- a/data/createcontrolsubset/createcontrolsubsetbioschemas.jsonld +++ b/data/createcontrolsubset/createcontrolsubsetbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Preprocess ChIP-seq aligned reads before calling FindPeaks: Filter out dulpicates from the SAMPLE (optional) and create a CONTROL dataset w/o duplicates with the same number of reads as in the SAMPLE. Only eland, sam and bam files are accepted.", "sc:name": "createcontrolsubset", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.htslib.org/", "sc:version": "1.0" diff --git a/data/cregulome/cregulomebioschemas.jsonld b/data/cregulome/cregulomebioschemas.jsonld index 69ccd4b69dd0b..3291e7ee22b2c 100644 --- a/data/cregulome/cregulomebioschemas.jsonld +++ b/data/cregulome/cregulomebioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:30867986", { "@id": "https://doi.org/10.7717/peerj.6509" }, - "pmcid:PMC6410695" + "pmcid:PMC6410695", + "pubmed:30867986" ], "sc:description": "R package for accessing microRNA and transcription factor-gene expression correlations in cancer.", "sc:featureList": [ @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "cRegulome", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/package=cRegulome" }, diff --git a/data/creme/cremebioschemas.jsonld b/data/creme/cremebioschemas.jsonld index ac7b468f41637..86e3ba3cb9d40 100644 --- a/data/creme/cremebioschemas.jsonld +++ b/data/creme/cremebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.", "sc:name": "CREME", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://creme.dcode.org/" } \ No newline at end of file diff --git a/data/crh/crhbioschemas.jsonld b/data/crh/crhbioschemas.jsonld index 7a449b1af5be8..1bfbf6e8d4d16 100644 --- a/data/crh/crhbioschemas.jsonld +++ b/data/crh/crhbioschemas.jsonld @@ -15,8 +15,8 @@ "Ian Sillitoe" ], "sc:additionalType": [ - "Suite", - "Command-line tool" + "Command-line tool", + "Suite" ], "sc:description": "cath-resolve-hits (CRH)- tool that resolves domain matches suspiciously quickly.", "sc:license": "GPL-3.0", diff --git a/data/crimage/crimagebioschemas.jsonld b/data/crimage/crimagebioschemas.jsonld index 6562dbd205f21..4d53b30bb87a3 100644 --- a/data/crimage/crimagebioschemas.jsonld +++ b/data/crimage/crimagebioschemas.jsonld @@ -22,8 +22,8 @@ "sc:license": "Artistic-2.0", "sc:name": "CRImage", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CRImage.html", diff --git a/data/crispi/crispibioschemas.jsonld b/data/crispi/crispibioschemas.jsonld index 464c300ba0829..efc94ce6657c0 100644 --- a/data/crispi/crispibioschemas.jsonld +++ b/data/crispi/crispibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Crispi", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "GenOuest", "sc:url": "http://crispi.genouest.org/" diff --git a/data/crispr-era/crispr-erabioschemas.jsonld b/data/crispr-era/crispr-erabioschemas.jsonld index 48af5096fd161..7e4c8a9ef8a73 100644 --- a/data/crispr-era/crispr-erabioschemas.jsonld +++ b/data/crispr-era/crispr-erabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "CRISPR-ERA", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://crispr-era.stanford.edu/" } \ No newline at end of file diff --git a/data/crispr-focus/crispr-focusbioschemas.jsonld b/data/crispr-focus/crispr-focusbioschemas.jsonld index b0ed6307ab411..d5e9617eca0e8 100644 --- a/data/crispr-focus/crispr-focusbioschemas.jsonld +++ b/data/crispr-focus/crispr-focusbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0184281", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/crispr-focus", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "X. Shirley Liu", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5584922", + "pubmed:28873439", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0184281" }, - "pubmed:28873439" + "pmcid:PMC5584922" ], "sc:description": "A web server for designing focused CRISPR screening experiments.", "sc:featureList": { @@ -31,6 +27,10 @@ }, "sc:name": "CRISPR-FOCUS", "sc:url": "http://cistrome.org/crispr-focus/" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0184281", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/crispr-ge/crispr-gebioschemas.jsonld b/data/crispr-ge/crispr-gebioschemas.jsonld index d3225856aea22..04e56d939c933 100644 --- a/data/crispr-ge/crispr-gebioschemas.jsonld +++ b/data/crispr-ge/crispr-gebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CRISPR-GE", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://skl.scau.edu.cn/home/" } \ No newline at end of file diff --git a/data/crispr-p/crispr-pbioschemas.jsonld b/data/crispr-p/crispr-pbioschemas.jsonld index c00478d8d3846..c2b3306c728da 100644 --- a/data/crispr-p/crispr-pbioschemas.jsonld +++ b/data/crispr-p/crispr-pbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Unlicense", "sc:name": "CRISPR-P", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://crispr.hzau.edu.cn/CRISPR2/", diff --git a/data/crisprcasfinder/crisprcasfinderbioschemas.jsonld b/data/crisprcasfinder/crisprcasfinderbioschemas.jsonld index d5ed3d459132e..f9bd14372642a 100644 --- a/data/crisprcasfinder/crisprcasfinderbioschemas.jsonld +++ b/data/crisprcasfinder/crisprcasfinderbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/CRISPRCasFinder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "David Couvin", "Marie Touchon", + "David Couvin", "Christine Pourcel" ], "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:citation": "pubmed:29790974", "sc:description": "Easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program with improved specificity and indication on the CRISPR orientation. MacSyFinder is used to identify cas genes, the CRISPR-Cas type and subtype.", "sc:name": "CRISPRCasFinder", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index", "sc:version": "1.0.5 - I2BC" diff --git a/data/crisprdirect/crisprdirectbioschemas.jsonld b/data/crisprdirect/crisprdirectbioschemas.jsonld index 30e3441912117..01168e516f4ac 100644 --- a/data/crisprdirect/crisprdirectbioschemas.jsonld +++ b/data/crisprdirect/crisprdirectbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CRISPRdirect", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://crispr.dbcls.jp/" } \ No newline at end of file diff --git a/data/crisprfinder/crisprfinderbioschemas.jsonld b/data/crisprfinder/crisprfinderbioschemas.jsonld index 7a695fa0f34a2..4b74eff42fa1b 100644 --- a/data/crisprfinder/crisprfinderbioschemas.jsonld +++ b/data/crisprfinder/crisprfinderbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "CRISPRFinder", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index" } \ No newline at end of file diff --git a/data/crisprmap/crisprmapbioschemas.jsonld b/data/crisprmap/crisprmapbioschemas.jsonld index 00eae9f447675..a7614f3a4cf92 100644 --- a/data/crisprmap/crisprmapbioschemas.jsonld +++ b/data/crisprmap/crisprmapbioschemas.jsonld @@ -20,40 +20,40 @@ ], "sc:additionalType": "Web application", "sc:author": [ + "Sita Saunders", { "@id": "http://orcid.org/0000-0001-8231-3323" - }, - "Sita Saunders" + } ], "sc:citation": [ "pubmed:25161238", + "pubmed:23863837", + "pmcid:PMC4147912", { "@id": "https://doi.org/10.1093/bioinformatics/btu459" - }, - "pmcid:PMC4147912", - "pubmed:23863837" + } ], "sc:description": "Prediction of CRISPR RNA by repeat conservation.", "sc:name": "CRISPRmap web server", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": [ - "University Freiburg", - "rnateam" + "rnateam", + "University Freiburg" ], "sc:url": "http://rna.informatik.uni-freiburg.de/CRISPRmap/", "sc:version": "2.1.3" }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btu459", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0001-8231-3323", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btu459", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/crisprseek/crisprseekbioschemas.jsonld b/data/crisprseek/crisprseekbioschemas.jsonld index 417d2bc8d94b3..d3d5ae3f69eab 100644 --- a/data/crisprseek/crisprseekbioschemas.jsonld +++ b/data/crisprseek/crisprseekbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0108424", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/crisprseek", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ "Command-line tool" ], "sc:citation": [ + "pmcid:PMC4172692", "pubmed:25247697", { "@id": "https://doi.org/10.1371/journal.pone.0108424" - }, - "pmcid:PMC4172692" + } ], "sc:description": "The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not.", "sc:featureList": { @@ -32,15 +36,11 @@ "sc:name": "CRISPRseek", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CRISPRseek.html", "sc:version": "1.14.0" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0108424", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/crisprseekplus/crisprseekplusbioschemas.jsonld b/data/crisprseekplus/crisprseekplusbioschemas.jsonld index 5e0ab54986e09..807b982a9d710 100644 --- a/data/crisprseekplus/crisprseekplusbioschemas.jsonld +++ b/data/crisprseekplus/crisprseekplusbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "crisprseekplus", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/crisprseekplus.html", diff --git a/data/crisprvariants/crisprvariantsbioschemas.jsonld b/data/crisprvariants/crisprvariantsbioschemas.jsonld index 00f384cf2bdbc..4a5f7d054c9d0 100644 --- a/data/crisprvariants/crisprvariantsbioschemas.jsonld +++ b/data/crisprvariants/crisprvariantsbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "CrispRVariants", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CrispRVariants.html", "sc:version": "1.2.0" diff --git a/data/crispulator/crispulatorbioschemas.jsonld b/data/crispulator/crispulatorbioschemas.jsonld index 534f08754d990..6cc41a5a33a09 100644 --- a/data/crispulator/crispulatorbioschemas.jsonld +++ b/data/crispulator/crispulatorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Discrete simulation tool for designing pooled genetic screens.", "sc:name": "CRISPulator", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://crispulator.ucsf.edu/" diff --git a/data/crlmm/crlmmbioschemas.jsonld b/data/crlmm/crlmmbioschemas.jsonld index 13c5121de3b00..faa118bca68e2 100644 --- a/data/crlmm/crlmmbioschemas.jsonld +++ b/data/crlmm/crlmmbioschemas.jsonld @@ -9,19 +9,15 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-7383-0609", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/crlmm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Benilton S Carvalho", + "Robert Scharpf", { "@id": "http://orcid.org/0000-0002-7383-0609" }, - "Robert Scharpf" + "Benilton S Carvalho" ], "sc:additionalType": [ "Library", @@ -35,12 +31,16 @@ "sc:license": "Artistic-2.0", "sc:name": "crlmm", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/crlmm.html", "sc:version": "1.32.0" + }, + { + "@id": "http://orcid.org/0000-0002-7383-0609", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/crmb/crmbbioschemas.jsonld b/data/crmb/crmbbioschemas.jsonld index a6104b0f1c930..cd85e7b8d2f24 100644 --- a/data/crmb/crmbbioschemas.jsonld +++ b/data/crmb/crmbbioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Nolan A. Wages", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5799912", { "@id": "https://doi.org/10.1186/s12885-018-4038-x" }, + "pmcid:PMC5799912", "pubmed:29402249" ], "sc:description": "Simulate operating characteristics of the Bayesian CRM.", diff --git a/data/crnpred/crnpredbioschemas.jsonld b/data/crnpred/crnpredbioschemas.jsonld index ecd64dec95f29..e9c3921d96b44 100644 --- a/data/crnpred/crnpredbioschemas.jsonld +++ b/data/crnpred/crnpredbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "CRNPRED is a program that predicts secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO) of a native protein structure from its amino acid sequence.", "sc:name": "CRNPRED", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bioinformatics.org/crnpred/wiki/", "sc:version": "1.1" diff --git a/data/croco/crocobioschemas.jsonld b/data/croco/crocobioschemas.jsonld index f39a0009a814c..1831c49b62aac 100644 --- a/data/croco/crocobioschemas.jsonld +++ b/data/croco/crocobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Khalid Belkhir", - "Maximilian Telford", - "Paul Simion" + "Paul Simion", + "Maximilian Telford" ], "sc:additionalType": "Command-line tool", "sc:description": "A program to detect potential cross contaminations in HTS assembled transcriptomes using expression level quantification.", "sc:name": "CroCo", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://gitlab.mbb.univ-montp2.fr/mbb/CroCo" } \ No newline at end of file diff --git a/data/crop/cropbioschemas.jsonld b/data/crop/cropbioschemas.jsonld index 9be119e6b7eec..8ffda901a6e33 100644 --- a/data/crop/cropbioschemas.jsonld +++ b/data/crop/cropbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A clustering tool which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU).", "sc:name": "crop", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://code.google.com/archive/p/crop-tingchenlab/", "sc:version": "1.33" diff --git a/data/cropcircdb/cropcircdbbioschemas.jsonld b/data/cropcircdb/cropcircdbbioschemas.jsonld index 83b54f4c02f14..ff6a8f5d8d986 100644 --- a/data/cropcircdb/cropcircdbbioschemas.jsonld +++ b/data/cropcircdb/cropcircdbbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/DATABASE/BAZ053", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/CropCircDB", "@type": "sc:SoftwareApplication", @@ -25,10 +21,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:31058278", - "pmcid:PMC6501434", { "@id": "https://doi.org/10.1093/DATABASE/BAZ053" - } + }, + "pmcid:PMC6501434" ], "sc:description": "Comprehensive circular RNA resource for crops in response to abiotic stress.", "sc:featureList": { @@ -43,6 +39,10 @@ ], "sc:url": "http://deepbiology.cn/crop/" }, + { + "@id": "https://doi.org/10.1093/DATABASE/BAZ053", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0002-2425-3526", "@type": "schema:Person" diff --git a/data/croppal/croppalbioschemas.jsonld b/data/croppal/croppalbioschemas.jsonld index ab865bc722c11..a60c1a386124f 100644 --- a/data/croppal/croppalbioschemas.jsonld +++ b/data/croppal/croppalbioschemas.jsonld @@ -19,13 +19,13 @@ "sc:name": "cropPAL", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ + "unimelb.edu.au", "ARC Centre of Excellence in Plant Energy Biology", - "The University of Western Australia", - "unimelb.edu.au" + "The University of Western Australia" ], "sc:url": "http://crop-pal.org/" } \ No newline at end of file diff --git a/data/cropper/cropperbioschemas.jsonld b/data/cropper/cropperbioschemas.jsonld index c4c1a91c4d12e..e23e62f8830fd 100644 --- a/data/cropper/cropperbioschemas.jsonld +++ b/data/cropper/cropperbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "T. Haller", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:30634901", "pmcid:PMC6330393", { "@id": "https://doi.org/10.1186/s12859-019-2600-4" - } + }, + "pubmed:30634901" ], "sc:description": "GUI application for viewing and handling Manhattan Plots. The user can zoom, select and crop Manhattan Plots and generate output both in the graphical and numerical format.", "sc:featureList": [ @@ -33,9 +33,9 @@ "sc:license": "GPL-3.0", "sc:name": "Cropper", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://www.geenivaramu.ee/en/tools/cropper" }, diff --git a/data/crossalive/crossalivebioschemas.jsonld b/data/crossalive/crossalivebioschemas.jsonld index c933b769da20c..f5552ec3f8a8a 100644 --- a/data/crossalive/crossalivebioschemas.jsonld +++ b/data/crossalive/crossalivebioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Gian Tartaglia", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:description": "Web server for predicting the in vivo structure of RNA molecules.", "sc:license": "Unlicense", diff --git a/data/crosscheck/crosscheckbioschemas.jsonld b/data/crosscheck/crosscheckbioschemas.jsonld index 6ac23f8ae9dbe..28b3859aca64e 100644 --- a/data/crosscheck/crosscheckbioschemas.jsonld +++ b/data/crosscheck/crosscheckbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CrossCheck", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://proteinguru.com/toolbox/crosscheck/" } \ No newline at end of file diff --git a/data/crosshub/crosshubbioschemas.jsonld b/data/crosshub/crosshubbioschemas.jsonld index 2dc5b5f1ab50f..1cff7f911bc75 100644 --- a/data/crosshub/crosshubbioschemas.jsonld +++ b/data/crosshub/crosshubbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Dmitriev AA", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:26773058", "pmcid:PMC4838350", { "@id": "https://doi.org/10.1093/NAR/GKV1478" - }, - "pubmed:26773058" + } ], "sc:description": "A tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "CrossHub", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/crosshub/" } diff --git a/data/crosslinkwgcna/crosslinkwgcnabioschemas.jsonld b/data/crosslinkwgcna/crosslinkwgcnabioschemas.jsonld index ad09f37153738..a56ac74e51492 100644 --- a/data/crosslinkwgcna/crosslinkwgcnabioschemas.jsonld +++ b/data/crosslinkwgcna/crosslinkwgcnabioschemas.jsonld @@ -14,10 +14,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Workflow", "sc:citation": [ - "pubmed:19114008", { "@id": "https://doi.org/10.1186/1471-2105-9-559" }, + "pubmed:19114008", "pmcid:PMC2631488" ], "sc:description": "The crosslinkWGCNA web tool provides a user-friendly interface to the popular Weighted Gene Co-expression Network Analysis (WGCNA) R package. Users are able to upload their data sets and subsequently apply the standard workflow steps using a project-based structure and an easy to navigate interface. Along the way, the tool provides multiple familiar visualizations such as the hierarchically clustered genes with color-coded clusters, a similar tree for the samples and sample traits, module-trait correlations, and more. In addition, the tool allows for integrating multiple WGCNA projects using a correlation-based approach. Both data and visualizations can be exported", diff --git a/data/crossmeta/crossmetabioschemas.jsonld b/data/crossmeta/crossmetabioschemas.jsonld index 9bd159390c7bc..56724b810e408 100644 --- a/data/crossmeta/crossmetabioschemas.jsonld +++ b/data/crossmeta/crossmetabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "MIT", "sc:name": "crossmeta", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/crossmeta.html", "sc:version": "1.0.1" diff --git a/data/crosstalkdb/crosstalkdbbioschemas.jsonld b/data/crosstalkdb/crosstalkdbbioschemas.jsonld index f8dd288ff0c43..e42f3f4b6710d 100644 --- a/data/crosstalkdb/crosstalkdbbioschemas.jsonld +++ b/data/crosstalkdb/crosstalkdbbioschemas.jsonld @@ -15,8 +15,8 @@ "Ole Nørregaard Jensen" ], "sc:additionalType": [ - "Web application", "Database portal", + "Web application", "Web API" ], "sc:description": "Repository and statistical tools for directly determined PTM crosstalk based on long peptides measured by mass spectrometry. Focus on histone proteins.", diff --git a/data/crowdbreaks/crowdbreaksbioschemas.jsonld b/data/crowdbreaks/crowdbreaksbioschemas.jsonld index 605459264123a..6926d3cf91fa7 100644 --- a/data/crowdbreaks/crowdbreaksbioschemas.jsonld +++ b/data/crowdbreaks/crowdbreaksbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "Crowdbreaks", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://www.crowdbreaks.org/" diff --git a/data/crp/crpbioschemas.jsonld b/data/crp/crpbioschemas.jsonld index b38a0b7d013ea..8d039aa92f15e 100644 --- a/data/crp/crpbioschemas.jsonld +++ b/data/crp/crpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.", "sc:name": "CRP", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://fasta.bioch.virginia.edu/crp/" } \ No newline at end of file diff --git a/data/crunch/crunchbioschemas.jsonld b/data/crunch/crunchbioschemas.jsonld index 0ab70a8960c15..206c597217e97 100644 --- a/data/crunch/crunchbioschemas.jsonld +++ b/data/crunch/crunchbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A completely automated pipe-line for ChIP-seq data analysis, starting from raw sequencing reads, through quality filtering, read mapping, fragment size estimation, peak calling, peak annotation and comprehensive regulatory motif analysis. It runs with data from human (hg19), mouse (mm9) or drosophila (dm3).", "sc:name": "CRUNCH", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://crunch.unibas.ch" diff --git a/data/crusview/crusviewbioschemas.jsonld b/data/crusview/crusviewbioschemas.jsonld index 739b66c0b5800..cc1241ec65584 100644 --- a/data/crusview/crusviewbioschemas.jsonld +++ b/data/crusview/crusviewbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Xiangfeng (Bryan) Wang", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:23898041", "pmcid:PMC3762655", { "@id": "https://doi.org/10.1104/PP.113.219444" - }, - "pubmed:23898041" + } ], "sc:description": "Visualization platform for comparative genomics analyses in Brassicaceae species.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "CrusView", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.cmbb.arizona.edu/?page_id=250" diff --git a/data/cryfa/cryfabioschemas.jsonld b/data/cryfa/cryfabioschemas.jsonld index cfc55573a4461..74356a1a0f4b1 100644 --- a/data/cryfa/cryfabioschemas.jsonld +++ b/data/cryfa/cryfabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Cryfa", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/cobilab/cryfa" } \ No newline at end of file diff --git a/data/cryptodb/cryptodbbioschemas.jsonld b/data/cryptodb/cryptodbbioschemas.jsonld index 0f30056128f84..5956ecd02ed2e 100644 --- a/data/cryptodb/cryptodbbioschemas.jsonld +++ b/data/cryptodb/cryptodbbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Genomic-scale dataset associated with the eukaryotic pathogens Cryptosporidium.", "sc:name": "Cryptosporidium genome resources CryptoDB", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "University of Georgia", diff --git a/data/crysalis/crysalisbioschemas.jsonld b/data/crysalis/crysalisbioschemas.jsonld index cdf393f524ae7..6be99f4eb3f36 100644 --- a/data/crysalis/crysalisbioschemas.jsonld +++ b/data/crysalis/crysalisbioschemas.jsonld @@ -34,8 +34,8 @@ }, "sc:name": "Crysalis", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://nmrcen.xmu.edu.cn/crysalis/" diff --git a/data/crysol/crysolbioschemas.jsonld b/data/crysol/crysolbioschemas.jsonld index b5c7b5dd4c50a..578bf245e0238 100644 --- a/data/crysol/crysolbioschemas.jsonld +++ b/data/crysol/crysolbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Predict the X-ray solution scattering curve of a known structure, given the atomic coordinates in a PDB file, and fit to an experimental scattering curve.", "sc:name": "Crysol", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://www.embl-hamburg.de/ExternalInfo/Research/Sax/crysol.html", diff --git a/data/crysplot/crysplotbioschemas.jsonld b/data/crysplot/crysplotbioschemas.jsonld index 5cf72916039d4..ca327fdaedf9d 100644 --- a/data/crysplot/crysplotbioschemas.jsonld +++ b/data/crysplot/crysplotbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "CRYSPLOT", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://crysplot.crystalsolutions.eu" diff --git a/data/crystfel/crystfelbioschemas.jsonld b/data/crystfel/crystfelbioschemas.jsonld index ab0ee773f97b2..a9f64ab638f5e 100644 --- a/data/crystfel/crystfelbioschemas.jsonld +++ b/data/crystfel/crystfelbioschemas.jsonld @@ -9,27 +9,27 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1107/S205979831801238X", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/CrystFEL", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas White", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6400257", "pubmed:30821710", { "@id": "https://doi.org/10.1107/S205979831801238X" - }, - "pmcid:PMC6400257" + } ], "sc:description": "Software for processing serial crystallography data from an X-ray free-electron laser or a synchrotron light source.", "sc:license": "GPL-3.0", "sc:name": "CrystFEL", "sc:operatingSystem": "Linux", "sc:url": "http://www.desy.de/~twhite/crystfel/" + }, + { + "@id": "https://doi.org/10.1107/S205979831801238X", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cs-rosetta3/cs-rosetta3bioschemas.jsonld b/data/cs-rosetta3/cs-rosetta3bioschemas.jsonld index bbe49d10654a1..5cba6494e69cf 100644 --- a/data/cs-rosetta3/cs-rosetta3bioschemas.jsonld +++ b/data/cs-rosetta3/cs-rosetta3bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Protocol which generates 3D models of proteins, using only the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts as input.", "sc:name": "CS-ROSETTA3", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://haddock.science.uu.nl/enmr/services/CS-ROSETTA3/" } \ No newline at end of file diff --git a/data/cs23d/cs23dbioschemas.jsonld b/data/cs23d/cs23dbioschemas.jsonld index 415fd2cab46a9..89240a3d8a8cb 100644 --- a/data/cs23d/cs23dbioschemas.jsonld +++ b/data/cs23d/cs23dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Chemical Shift to 3D Structure is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input.", "sc:name": "CS23D", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.cs23d.ca" } \ No newline at end of file diff --git a/data/cs2bp2-plot/cs2bp2-plotbioschemas.jsonld b/data/cs2bp2-plot/cs2bp2-plotbioschemas.jsonld index a6790b97a5ad8..e7aadc1d54286 100644 --- a/data/cs2bp2-plot/cs2bp2-plotbioschemas.jsonld +++ b/data/cs2bp2-plot/cs2bp2-plotbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-019-2902-6", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0003-1100-646X", "@type": "schema:Person" @@ -21,11 +25,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31142266", + "pmcid:PMC6542128", { "@id": "https://doi.org/10.1186/S12859-019-2902-6" - }, - "pubmed:31142266", - "pmcid:PMC6542128" + } ], "sc:description": "Pairwise visual comparison of small RNA secondary structures with base pair probabilities.", "sc:featureList": [ @@ -47,10 +51,6 @@ "Linux" ], "sc:url": "https://nrcmonsrv01.nrc.ca/cs2bp2plot" - }, - { - "@id": "https://doi.org/10.1186/S12859-019-2902-6", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/csa/csabioschemas.jsonld b/data/csa/csabioschemas.jsonld index 256a3426b84b0..8760d8ff3574d 100644 --- a/data/csa/csabioschemas.jsonld +++ b/data/csa/csabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Comparative Structural Alignment (CSA) is a webserver for computing and comparing protein structure alignments. Different scoring schemes are used to compute score-optimal alignments. Input is two PDB files.", "sc:name": "CSA", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://csa.project.cwi.nl" } \ No newline at end of file diff --git a/data/csar/csarbioschemas.jsonld b/data/csar/csarbioschemas.jsonld index 1eea7b9f254b2..bfcd08858271d 100644 --- a/data/csar/csarbioschemas.jsonld +++ b/data/csar/csarbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "http://orcid.org/0000-0002-6403-7262", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/1746-4811-7-11", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/csar", "@type": "sc:SoftwareApplication", @@ -27,8 +31,8 @@ { "@id": "https://doi.org/10.1186/1746-4811-7-11" }, - "pmcid:PMC3114017", - "pubmed:21554688" + "pubmed:21554688", + "pmcid:PMC3114017" ], "sc:description": "Statistical tools for ChIP-seq data analysis. Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.", "sc:featureList": { @@ -37,16 +41,12 @@ "sc:license": "Artistic-2.0", "sc:name": "CSAR", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CSAR.html", "sc:version": "1.26.0" - }, - { - "@id": "https://doi.org/10.1186/1746-4811-7-11", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/csar_scaffolding/csar_scaffoldingbioschemas.jsonld b/data/csar_scaffolding/csar_scaffoldingbioschemas.jsonld index 1c159ada6bd27..cdb6c5692e17f 100644 --- a/data/csar_scaffolding/csar_scaffoldingbioschemas.jsonld +++ b/data/csar_scaffolding/csar_scaffoldingbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/csar_scaffolding", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hsien-Tai Chiu", - "Chin Lung Lu" + "Chin Lung Lu", + "Hsien-Tai Chiu" ], "sc:additionalType": "Command-line tool", "sc:description": "A contig scaffolding tool using algebraic rearrangements.", diff --git a/data/csaw/csawbioschemas.jsonld b/data/csaw/csawbioschemas.jsonld index e148c71ccb6ca..1c096ad14fa84 100644 --- a/data/csaw/csawbioschemas.jsonld +++ b/data/csaw/csawbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1093/nar/gku351", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0002-3564-4813", + "@type": "schema:Person" }, { "@id": "https://bio.tools/csaw", @@ -27,10 +27,10 @@ "@id": "edam:data_2884" }, { - "@id": "edam:data_2012" + "@id": "edam:data_0867" }, { - "@id": "edam:data_0867" + "@id": "edam:data_2012" } ], "sc:additionalType": [ @@ -39,13 +39,13 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3168" + "@id": "edam:topic_3511" }, { - "@id": "edam:topic_0092" + "@id": "edam:topic_3168" }, { - "@id": "edam:topic_3511" + "@id": "edam:topic_0092" }, { "@id": "edam:topic_3169" @@ -73,8 +73,8 @@ "sc:version": "1.8.0" }, { - "@id": "http://orcid.org/0000-0002-3564-4813", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/nar/gku351", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cscan/cscanbioschemas.jsonld b/data/cscan/cscanbioschemas.jsonld index ebf9f4dfce82e..c7c718c72e0a3 100644 --- a/data/cscan/cscanbioschemas.jsonld +++ b/data/cscan/cscanbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "Cscan", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-ITA-MILANO", "sc:url": "http://www.beaconlab.it/cscan", diff --git a/data/cscape/cscapebioschemas.jsonld b/data/cscape/cscapebioschemas.jsonld index 46182e34de155..bf9a5450ba703 100644 --- a/data/cscape/cscapebioschemas.jsonld +++ b/data/cscape/cscapebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mark F. Rogers", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Predicts the oncogenic status (disease-driver or neutral) of somatic point mutations in the coding and non-coding regions of the cancer genome. Enter a mutation or list of mutations (one per line) into the form below using the format chromosome,position,reference,mutant (see Help for more details). Mutations uploaded from a file should use the VCF format with a minimum of five columns (chromosome, position, id, reference, mutant).", "sc:license": "CC-BY-4.0", "sc:name": "CScape", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://cscape.biocompute.org.uk/" } \ No newline at end of file diff --git a/data/csdeconv/csdeconvbioschemas.jsonld b/data/csdeconv/csdeconvbioschemas.jsonld index 2aaa1b222acef..b699a5b4cfdd0 100644 --- a/data/csdeconv/csdeconvbioschemas.jsonld +++ b/data/csdeconv/csdeconvbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "CSDeconv maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach", "sc:name": "CSDeconv", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://crab.rutgers.edu/~dslun/csdeconv/index.html", "sc:version": "1.03" diff --git a/data/csesa/csesabioschemas.jsonld b/data/csesa/csesabioschemas.jsonld index 02631ad900ecd..394f2cb49300f 100644 --- a/data/csesa/csesabioschemas.jsonld +++ b/data/csesa/csesabioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:31029079", "pmcid:PMC6486994", { "@id": "https://doi.org/10.1186/s12859-019-2806-5" - } + }, + "pubmed:31029079" ], "sc:description": "R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR.", "sc:featureList": [ @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "CSESA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://cran.r-project.org/package=CSESA", "sc:version": "1.2.0" diff --git a/data/cshl_fastx_artifacts_filter/cshl_fastx_artifacts_filterbioschemas.jsonld b/data/cshl_fastx_artifacts_filter/cshl_fastx_artifacts_filterbioschemas.jsonld index 4a36f6aad2170..fe408cf7f27a1 100644 --- a/data/cshl_fastx_artifacts_filter/cshl_fastx_artifacts_filterbioschemas.jsonld +++ b/data/cshl_fastx_artifacts_filter/cshl_fastx_artifacts_filterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool filters sequencing artifacts (reads with all but 3 identical bases).", "sc:name": "cshl_fastx_artifacts_filter", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://hannonlab.cshl.edu/fastx_toolkit/", diff --git a/data/cshl_fastx_collapser/cshl_fastx_collapserbioschemas.jsonld b/data/cshl_fastx_collapser/cshl_fastx_collapserbioschemas.jsonld index 8f6f48dfbd3f6..1291e7e4e5913 100644 --- a/data/cshl_fastx_collapser/cshl_fastx_collapserbioschemas.jsonld +++ b/data/cshl_fastx_collapser/cshl_fastx_collapserbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool collapses identical sequences in a FASTA file into a single sequence.", "sc:name": "cshl_fastx_collapser", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://hannonlab.cshl.edu/fastx_toolkit/", "sc:version": "1.0.0" diff --git a/data/cshl_fastx_nucleotides_distribution/cshl_fastx_nucleotides_distributionbioschemas.jsonld b/data/cshl_fastx_nucleotides_distribution/cshl_fastx_nucleotides_distributionbioschemas.jsonld index 8040c83f9812e..ed6f7be115d14 100644 --- a/data/cshl_fastx_nucleotides_distribution/cshl_fastx_nucleotides_distributionbioschemas.jsonld +++ b/data/cshl_fastx_nucleotides_distribution/cshl_fastx_nucleotides_distributionbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "cshl_fastx_nucleotides_distribution", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://hannonlab.cshl.edu/fastx_toolkit/", "sc:version": "1.0.0" diff --git a/data/cshl_fastx_renamer/cshl_fastx_renamerbioschemas.jsonld b/data/cshl_fastx_renamer/cshl_fastx_renamerbioschemas.jsonld index e1e6845dca0d5..3361181a2152b 100644 --- a/data/cshl_fastx_renamer/cshl_fastx_renamerbioschemas.jsonld +++ b/data/cshl_fastx_renamer/cshl_fastx_renamerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Rename the sequence identifiers in a FASTQ/A file.", "sc:name": "cshl_fastx_renamer", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://hannonlab.cshl.edu/fastx_toolkit/", "sc:version": "0.0.11" diff --git a/data/cshl_fastx_reverse_complement/cshl_fastx_reverse_complementbioschemas.jsonld b/data/cshl_fastx_reverse_complement/cshl_fastx_reverse_complementbioschemas.jsonld index 073cbd7203cee..5b30086bc827e 100644 --- a/data/cshl_fastx_reverse_complement/cshl_fastx_reverse_complementbioschemas.jsonld +++ b/data/cshl_fastx_reverse_complement/cshl_fastx_reverse_complementbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Reverse-complement each sequence in a library. If the library is a FASTQ, the quality-scores are also reversed.", "sc:name": "cshl_fastx_reverse_complement", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://hannonlab.cshl.edu/fastx_toolkit/", "sc:version": "1.0.0" diff --git a/data/cshl_fastx_trimmer/cshl_fastx_trimmerbioschemas.jsonld b/data/cshl_fastx_trimmer/cshl_fastx_trimmerbioschemas.jsonld index c29f7f5e7cd94..c47977d0f33d6 100644 --- a/data/cshl_fastx_trimmer/cshl_fastx_trimmerbioschemas.jsonld +++ b/data/cshl_fastx_trimmer/cshl_fastx_trimmerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Trim (cut bases from) sequences in a FASTA/Q file.", "sc:name": "cshl_fastx_trimmer", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://hannonlab.cshl.edu/fastx_toolkit/", "sc:version": "1.0.0" diff --git a/data/cshl_princeton_fastx_barcode_splitter/cshl_princeton_fastx_barcode_splitterbioschemas.jsonld b/data/cshl_princeton_fastx_barcode_splitter/cshl_princeton_fastx_barcode_splitterbioschemas.jsonld index 77fd74ebae930..8b79ad0d11d14 100644 --- a/data/cshl_princeton_fastx_barcode_splitter/cshl_princeton_fastx_barcode_splitterbioschemas.jsonld +++ b/data/cshl_princeton_fastx_barcode_splitter/cshl_princeton_fastx_barcode_splitterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Split a FASTQ or FASTA file into several files, using barcodes as the split criteria.", "sc:name": "cshl_princeton_fastx_barcode_splitter", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://hannonlab.cshl.edu/fastx_toolkit/", "sc:version": "1.1" diff --git a/data/cshmm/cshmmbioschemas.jsonld b/data/cshmm/cshmmbioschemas.jsonld index 5250b2bbee107..b95ced9d5e6e2 100644 --- a/data/cshmm/cshmmbioschemas.jsonld +++ b/data/cshmm/cshmmbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "CSHMM", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.andrew.cmu.edu/user/chiehl1/CSHMM/" } \ No newline at end of file diff --git a/data/csm-lig/csm-ligbioschemas.jsonld b/data/csm-lig/csm-ligbioschemas.jsonld index 9829dd4528236..10687023ec70e 100644 --- a/data/csm-lig/csm-ligbioschemas.jsonld +++ b/data/csm-lig/csm-ligbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKW390", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/csm-lig", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Douglas Eduardo Valente Pires", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4987933", "pubmed:27151202", { "@id": "https://doi.org/10.1093/NAR/GKW390" - } + }, + "pmcid:PMC4987933" ], "sc:description": "Web server for assessing and comparing protein–small molecule affinities.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "CSM-lig", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://biosig.unimelb.edu.au/csm_lig/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKW390", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/csm/csmbioschemas.jsonld b/data/csm/csmbioschemas.jsonld index 258820e0d4ecf..87b88c1e03438 100644 --- a/data/csm/csmbioschemas.jsonld +++ b/data/csm/csmbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "CSM", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://homepages.dcc.ufmg.br/~dpires/csm/index.html" } \ No newline at end of file diff --git a/data/csmetapred/csmetapredbioschemas.jsonld b/data/csmetapred/csmetapredbioschemas.jsonld index c26972f067d20..2a8aa10ca2f18 100644 --- a/data/csmetapred/csmetapredbioschemas.jsonld +++ b/data/csmetapred/csmetapredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CSmetaPred", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://14.139.227.206/csmetapred/" } \ No newline at end of file diff --git a/data/csnap/csnapbioschemas.jsonld b/data/csnap/csnapbioschemas.jsonld index 767647f960e8f..8bf2880774cf2 100644 --- a/data/csnap/csnapbioschemas.jsonld +++ b/data/csnap/csnapbioschemas.jsonld @@ -14,10 +14,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:25826798", { "@id": "https://doi.org/10.1371/journal.pcbi.1004153" }, - "pubmed:25826798", "pmcid:PMC4380459" ], "sc:description": "CSNAP is a computational approach for compound target identification based on network similarity graphs. Query and reference compounds are populated on the network connectivity map and a graph-based neighbor counting method is applied to rank the consensus targets among the neighborhood of each query ligand. The CSNAP approach can facilitate high-throughput target discovery and off-target prediction for any compound set identified from phenotype-based or cell-based chemical screens.", @@ -26,9 +26,9 @@ }, "sc:name": "CSNAP", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://services.mbi.ucla.edu/CSNAP/", "sc:version": "1.0" diff --git a/data/cspritz/cspritzbioschemas.jsonld b/data/cspritz/cspritzbioschemas.jsonld index 8920bb9a972c4..57490aca5cf71 100644 --- a/data/cspritz/cspritzbioschemas.jsonld +++ b/data/cspritz/cspritzbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "CSpritz", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/cspritz/", diff --git a/data/csq/csqbioschemas.jsonld b/data/csq/csqbioschemas.jsonld index 2f2b8ec062db8..2191b468eee0f 100644 --- a/data/csq/csqbioschemas.jsonld +++ b/data/csq/csqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "fast program for haplotype-aware consequence calling which can take into account known phase.", "sc:name": "csq", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://samtools.github.io/bcftools/" } \ No newline at end of file diff --git a/data/css/cssbioschemas.jsonld b/data/css/cssbioschemas.jsonld index 3d87b15d6baf4..1300c0e9c1bc7 100644 --- a/data/css/cssbioschemas.jsonld +++ b/data/css/cssbioschemas.jsonld @@ -13,9 +13,9 @@ "biotools:primaryContact": "Nick Furnham", "sc:additionalType": "Web application", "sc:author": [ - "James Torrance", + "Thornton Group", "Nick Furnham", - "Thornton Group" + "James Torrance" ], "sc:contributor": "Craig Porter", "sc:description": "Search a protein structure for likely catalytic sites.", diff --git a/data/cssp/csspbioschemas.jsonld b/data/cssp/csspbioschemas.jsonld index 03b236412f6c6..fe53da9734adc 100644 --- a/data/cssp/csspbioschemas.jsonld +++ b/data/cssp/csspbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chandler Zuo", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.", "sc:license": "GPL-2.0", "sc:name": "CSSP", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CSSP.html", "sc:version": "1.12.0" diff --git a/data/cstea/csteabioschemas.jsonld b/data/cstea/csteabioschemas.jsonld index b0e498fb272dc..67b18f082388f 100644 --- a/data/cstea/csteabioschemas.jsonld +++ b/data/cstea/csteabioschemas.jsonld @@ -9,43 +9,39 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-6316-2734", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/cstea", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Prof. Xing-Ming Zhao", { "@id": "http://orcid.org/0000-0001-6316-2734" - } + }, + "Prof. Xing-Ming Zhao" ], "sc:additionalType": [ - "Suite", - "Web application" + "Web application", + "Suite" ], "sc:citation": [ + "pubmed:28486666", "pmcid:PMC5570201", { "@id": "https://doi.org/10.1093/nar/gkx402" - }, - "pubmed:28486666" + } ], "sc:description": "Cell State Transition Expression Atlas. Organize, analyze and visualize the time-course gene expression data during cell differentiation, cellular reprogramming and trans-differentiation in human and mouse. In particular, it defines gene signatures for uncharacterized stages during cell state transitions.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_3223" }, { - "@id": "edam:operation_3223" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_0314" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_0314" } ], "sc:name": "CSTEA", @@ -54,6 +50,10 @@ { "@id": "https://doi.org/10.1093/nar/gkx402", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-6316-2734", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/ctc/bioconda_ctc.yaml b/data/ctc/bioconda_ctc.yaml index 2e53389b033c0..0d386d76ed31d 100644 --- a/data/ctc/bioconda_ctc.yaml +++ b/data/ctc/bioconda_ctc.yaml @@ -4,7 +4,6 @@ description: Tools for export and import classification trees and clusters to ot home: https://bioconductor.org/packages/3.10/bioc/html/ctc.html identifiers: - biotools:ctc -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-ctc diff --git a/data/ctc/ctcbioschemas.jsonld b/data/ctc/ctcbioschemas.jsonld index c64df851eccff..31ebc4acd5676 100644 --- a/data/ctc/ctcbioschemas.jsonld +++ b/data/ctc/ctcbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Antoine Lucas", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Tools for export and import classification trees and clusters to other programs.", "sc:license": "GPL-2.0", "sc:name": "ctc", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ctc.html", "sc:version": "1.48.0" diff --git a/data/ctd/ctdbioschemas.jsonld b/data/ctd/ctdbioschemas.jsonld index aa4276686b363..bef924dd20b76 100644 --- a/data/ctd/ctdbioschemas.jsonld +++ b/data/ctd/ctdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Curated database about the interaction of environmental chemicals with gene products, and their effects on human health. New features include statistical analyses and analytical tools, including GeneComps and ChemComps, enriched Gene Ontology terms associated with chemicals, statistically ranked chemical-disease inferences, Venn diagram tools to discover overlapping and unique attributes of any set of chemicals, genes or disease, and enhanced gene pathway data content, among other features.", "sc:name": "The Comparative Toxicogenomics Database (CTD)", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://ctd.mdibl.org" } \ No newline at end of file diff --git a/data/ctdquerier/ctdquerierbioschemas.jsonld b/data/ctdquerier/ctdquerierbioschemas.jsonld index ae61fc26bca03..0dde202528bbb 100644 --- a/data/ctdquerier/ctdquerierbioschemas.jsonld +++ b/data/ctdquerier/ctdquerierbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Comparative Toxicogenomics Database data extraction, visualization and enrichment of environmental and toxicological studies.", "sc:name": "CTDquerier", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/isglobal-brge/CTDquerier" } \ No newline at end of file diff --git a/data/ctk_clip/ctk_clipbioschemas.jsonld b/data/ctk_clip/ctk_clipbioschemas.jsonld index 03dc1c1b7d941..1c1f054acadbd 100644 --- a/data/ctk_clip/ctk_clipbioschemas.jsonld +++ b/data/ctk_clip/ctk_clipbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btw653", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ctk_clip", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chaolin Zhang", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27797762", { "@id": "https://doi.org/10.1093/bioinformatics/btw653" }, - "pmcid:PMC6041811", - "pubmed:27797762" + "pmcid:PMC6041811" ], "sc:description": "The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive UV cross-linking and immunoprecipitation (CLIP) data analysis.", "sc:featureList": { @@ -37,6 +33,10 @@ ], "sc:url": "https://github.com/chaolinzhanglab/ctk", "sc:version": "v1.1.2" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btw653", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ctsge/ctsgebioschemas.jsonld b/data/ctsge/ctsgebioschemas.jsonld index 74a83b624d67e..2a381ab728d13 100644 --- a/data/ctsge/ctsgebioschemas.jsonld +++ b/data/ctsge/ctsgebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "ctsGE", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ctsGE.html", "sc:version": "1.0.0" diff --git a/data/cube-db/cube-dbbioschemas.jsonld b/data/cube-db/cube-dbbioschemas.jsonld index 9c2328dbd6047..f52c661a5843f 100644 --- a/data/cube-db/cube-dbbioschemas.jsonld +++ b/data/cube-db/cube-dbbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "CUBE-DB", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html" } \ No newline at end of file diff --git a/data/cuda-ec/cuda-ecbioschemas.jsonld b/data/cuda-ec/cuda-ecbioschemas.jsonld index 41c186236003e..b52e17b2866b2 100644 --- a/data/cuda-ec/cuda-ecbioschemas.jsonld +++ b/data/cuda-ec/cuda-ecbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A scalable parallel algorithm for correcting sequencing errors in high-throughput short-read data so that error-free reads can be available before DNA fragment assembly.", "sc:name": "CUDA-EC", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.nvidia.com/object/bio_info_life_sciences.html" } \ No newline at end of file diff --git a/data/cuffcompare/cuffcomparebioschemas.jsonld b/data/cuffcompare/cuffcomparebioschemas.jsonld index c5661b42bfb10..3bce02e0564b2 100644 --- a/data/cuffcompare/cuffcomparebioschemas.jsonld +++ b/data/cuffcompare/cuffcomparebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "cuffcompare", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://cole-trapnell-lab.github.io/cufflinks/", "sc:version": "2.2.1.0" diff --git a/data/cuffdiff/cuffdiffbioschemas.jsonld b/data/cuffdiff/cuffdiffbioschemas.jsonld index 80c5dc425b6ea..43be3fbe2c5eb 100644 --- a/data/cuffdiff/cuffdiffbioschemas.jsonld +++ b/data/cuffdiff/cuffdiffbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Galaxy Support Team", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC3146043", - "pubmed:20436464", { "@id": "https://doi.org/10.1038/nbt.1621" - } + }, + "pubmed:20436464", + "pmcid:PMC3146043" ], "sc:description": "Find significant changes in transcript expression, splicing, and promoter use.", "sc:name": "cuffdiff", diff --git a/data/cufflinks/cufflinksbioschemas.jsonld b/data/cufflinks/cufflinksbioschemas.jsonld index 6ccc884a49a90..850d487bbbc23 100644 --- a/data/cufflinks/cufflinksbioschemas.jsonld +++ b/data/cufflinks/cufflinksbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Cole Trapnell Lab", "sc:additionalType": [ - "Suite", - "Command-line tool" + "Command-line tool", + "Suite" ], "sc:citation": "pubmed:20436464", "sc:description": "Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.", "sc:license": "BSL-1.0", "sc:name": "Cufflinks", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://cole-trapnell-lab.github.io/cufflinks" } \ No newline at end of file diff --git a/data/cummerbund/cummerbundbioschemas.jsonld b/data/cummerbund/cummerbundbioschemas.jsonld index 5bcc727091708..c87a8f411b026 100644 --- a/data/cummerbund/cummerbundbioschemas.jsonld +++ b/data/cummerbund/cummerbundbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Loyal A. Goff", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.", "sc:license": "Artistic-2.0", "sc:name": "cummeRbund", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cummeRbund.html", diff --git a/data/cuneiform/cuneiformbioschemas.jsonld b/data/cuneiform/cuneiformbioschemas.jsonld index f269ffe2d6531..5cc6f0dcff67a 100644 --- a/data/cuneiform/cuneiformbioschemas.jsonld +++ b/data/cuneiform/cuneiformbioschemas.jsonld @@ -21,12 +21,12 @@ "sc:license": "Apache-2.0", "sc:name": "Cuneiform", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "Humboldt-Universität zu Berlin", - "hu-berlin.de" + "hu-berlin.de", + "Humboldt-Universität zu Berlin" ], "sc:url": "http://www.cuneiform-lang.org", "sc:version": "2.0.3" diff --git a/data/cupsat/cupsatbioschemas.jsonld b/data/cupsat/cupsatbioschemas.jsonld index 4cc9f2c8a792c..6d0416dfe7112 100644 --- a/data/cupsat/cupsatbioschemas.jsonld +++ b/data/cupsat/cupsatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.", "sc:name": "CUPSAT", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://cupsat.tu-bs.de/" } \ No newline at end of file diff --git a/data/curves/curvesbioschemas.jsonld b/data/curves/curvesbioschemas.jsonld index a0393f417b264..6a7b711a3d0b3 100644 --- a/data/curves/curvesbioschemas.jsonld +++ b/data/curves/curvesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Curves+ is a web server for the analysis and visualization of the helical backbone and groove parameters of nucleic acid structures.", "sc:name": "CURVES+", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://gbio-pbil.ibcp.fr/cgi/Curves_plus/" } \ No newline at end of file diff --git a/data/cushaw3/cushaw3bioschemas.jsonld b/data/cushaw3/cushaw3bioschemas.jsonld index 0f2d76edd0aef..9ee4dc965258c 100644 --- a/data/cushaw3/cushaw3bioschemas.jsonld +++ b/data/cushaw3/cushaw3bioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Yongchao Li", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:24466273", + "pmcid:PMC3899341", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0086869" - }, - "pubmed:24466273", - "pmcid:PMC3899341" + } ], "sc:description": "Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding.", "sc:featureList": { diff --git a/data/cusp/cuspbioschemas.jsonld b/data/cusp/cuspbioschemas.jsonld index 1f7922d13f3e7..255941dd507ba 100644 --- a/data/cusp/cuspbioschemas.jsonld +++ b/data/cusp/cuspbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Create a codon usage table from nucleotide sequence(s).", "sc:funder": [ - "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "cusp", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/customprodb/customprodbbioschemas.jsonld b/data/customprodb/customprodbbioschemas.jsonld index a17580eaecf63..69f8e7a6262b9 100644 --- a/data/customprodb/customprodbbioschemas.jsonld +++ b/data/customprodb/customprodbbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "xiaojing wang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Generate customized protein sequence database from RNA-Seq data for proteomics search.", "sc:license": "Artistic-2.0", "sc:name": "customProDB", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/customProDB.html", "sc:version": "1.14.0" diff --git a/data/cutadapt/cutadaptbioschemas.jsonld b/data/cutadapt/cutadaptbioschemas.jsonld index 34bb455df5273..633be4114c493 100644 --- a/data/cutadapt/cutadaptbioschemas.jsonld +++ b/data/cutadapt/cutadaptbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "Cutadapt", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://pypi.python.org/pypi/cutadapt" } \ No newline at end of file diff --git a/data/cutgextract/cutgextractbioschemas.jsonld b/data/cutgextract/cutgextractbioschemas.jsonld index 7bf3665d71390..4836b880dff27 100644 --- a/data/cutgextract/cutgextractbioschemas.jsonld +++ b/data/cutgextract/cutgextractbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "EMBOSS Contributors", "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:description": "Extract codon usage tables from CUTG database.", "sc:funder": [ "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "cutgextract", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/cuticledb/cuticledbbioschemas.jsonld b/data/cuticledb/cuticledbbioschemas.jsonld index dbe1243e3f628..f84f9e08c0ebc 100644 --- a/data/cuticledb/cuticledbbioschemas.jsonld +++ b/data/cuticledb/cuticledbbioschemas.jsonld @@ -29,10 +29,10 @@ }, "sc:citation": [ "pmcid:PMC522807", + "pubmed:15453918", { "@id": "https://doi.org/10.1186/1471-2105-5-138" - }, - "pubmed:15453918" + } ], "sc:description": "A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif responsible for chitin binding in Arthropod cuticle.", "sc:featureList": { @@ -40,13 +40,13 @@ }, "sc:name": "CuticleDB", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": [ - "University of Athens", - "University of Georgia" + "University of Georgia", + "University of Athens" ], "sc:url": "http://biophysics.biol.uoa.gr/cuticleDB/" } diff --git a/data/cutpointsoehr/cutpointsoehrbioschemas.jsonld b/data/cutpointsoehr/cutpointsoehrbioschemas.jsonld index a3c4043c5f77d..3655229d7310b 100644 --- a/data/cutpointsoehr/cutpointsoehrbioschemas.jsonld +++ b/data/cutpointsoehr/cutpointsoehrbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12874-019-0738-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0002-1123-5556", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/S12874-019-0738-4", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/CutpointsOEHR", "@type": "sc:SoftwareApplication", @@ -34,18 +34,18 @@ "sc:description": "Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model.", "sc:featureList": [ { - "@id": "edam:operation_3659" + "@id": "edam:operation_0490" }, { - "@id": "edam:operation_0490" + "@id": "edam:operation_3659" } ], "sc:license": "GPL-3.0", "sc:name": "CutpointsOEHR", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/package=CutpointsOEHR" } diff --git a/data/cutseq/cutseqbioschemas.jsonld b/data/cutseq/cutseqbioschemas.jsonld index 4859e69563799..52316255e322d 100644 --- a/data/cutseq/cutseqbioschemas.jsonld +++ b/data/cutseq/cutseqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", + "EMBOSS Contributors", "Wellcome Trust", - "EMBOSS Contributors" + "UK BBSRC", + "UK MRC" ], "sc:description": "Remove a section from a sequence.", "sc:funder": [ - "UK BBSRC", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "cutseq", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/cutseq.html", "sc:version": "r6" diff --git a/data/cve/cvebioschemas.jsonld b/data/cve/cvebioschemas.jsonld index 20b66587d1a09..74e3df386c4e7 100644 --- a/data/cve/cvebioschemas.jsonld +++ b/data/cve/cvebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "CVE", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CVE.html", "sc:version": "1.0.0" diff --git a/data/cwdprnp/cwdprnpbioschemas.jsonld b/data/cwdprnp/cwdprnpbioschemas.jsonld index 2f66e6fb7ac74..681b7fe9938b8 100644 --- a/data/cwdprnp/cwdprnpbioschemas.jsonld +++ b/data/cwdprnp/cwdprnpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Unified framework for analyzing prion protein gene variability and spatial structure.", "sc:name": "CWDPRNP", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://ecosystems.psu.edu/research/labs/walter-lab/additional-labs/population-genetics-lab" } \ No newline at end of file diff --git a/data/cyana/cyanabioschemas.jsonld b/data/cyana/cyanabioschemas.jsonld index 13e7da728fac9..72193571a5ad8 100644 --- a/data/cyana/cyanabioschemas.jsonld +++ b/data/cyana/cyanabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "CYANA", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://www.cyana.org/wiki/index.php/Main_Page", diff --git a/data/cyanimator/cyanimatorbioschemas.jsonld b/data/cyanimator/cyanimatorbioschemas.jsonld index 6ede6860d66a5..6a4421a10af90 100644 --- a/data/cyanimator/cyanimatorbioschemas.jsonld +++ b/data/cyanimator/cyanimatorbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.6852.2", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-0290-7979", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/cyanimator", "@type": "sc:SoftwareApplication", @@ -36,14 +44,6 @@ ], "sc:url": "http://www.cgl.ucsf.edu/cytoscape/CyAnimator/index.shtml", "sc:version": "2.1.0" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.6852.2", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-0290-7979", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/cyanobase/cyanobasebioschemas.jsonld b/data/cyanobase/cyanobasebioschemas.jsonld index dc558cbe53126..db9cfe2361385 100644 --- a/data/cyanobase/cyanobasebioschemas.jsonld +++ b/data/cyanobase/cyanobasebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "CyanoBase", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://genome.kazusa.or.jp/cyanobase" } \ No newline at end of file diff --git a/data/cyanolyase/cyanolyasebioschemas.jsonld b/data/cyanolyase/cyanolyasebioschemas.jsonld index 2ae7ca109ae57..e264c890ac9a9 100644 --- a/data/cyanolyase/cyanolyasebioschemas.jsonld +++ b/data/cyanolyase/cyanolyasebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Manually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases.", "sc:name": "CyanoLyase", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "GenOuest", "sc:url": "http://cyanolyase.genouest.org/" diff --git a/data/cycle/cyclebioschemas.jsonld b/data/cycle/cyclebioschemas.jsonld index 664a779ed17ce..d2947fa940035 100644 --- a/data/cycle/cyclebioschemas.jsonld +++ b/data/cycle/cyclebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-6245-8071", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/cycle", "@type": "sc:SoftwareApplication", @@ -34,6 +30,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cycle.html", "sc:version": "1.28.0" + }, + { + "@id": "http://orcid.org/0000-0002-6245-8071", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/cyclebase/cyclebasebioschemas.jsonld b/data/cyclebase/cyclebasebioschemas.jsonld index 3c3a782ca3187..63b3fcca53915 100644 --- a/data/cyclebase/cyclebasebioschemas.jsonld +++ b/data/cyclebase/cyclebasebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/cyclebase", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rasmus Wernersson", "Lars Juhl Jensen", + "Rasmus Wernersson", "Alberto Santos" ], "sc:additionalType": "Database portal", @@ -20,9 +20,9 @@ "sc:description": "Online resource of cell-cycle-related experiments. It provides an easy-to-use web interface that facilitates visualization and download of genome-wide cell-cycle data and analysis results. Data from different experiments are normalized to a common timescale and are complimented with key cell-cycle information and derived analysis results. Included is information on cyclin-dependent kinase (CDK) substrates, predicted degradation signals and loss-of-function phenotypes from genome-wide screens.", "sc:name": "Cyclebase", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cyclebase.org/" } \ No newline at end of file diff --git a/data/cyclops/cyclopsbioschemas.jsonld b/data/cyclops/cyclopsbioschemas.jsonld index 792dc8eec2337..05fe7aa25c378 100644 --- a/data/cyclops/cyclopsbioschemas.jsonld +++ b/data/cyclops/cyclopsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "CycloPsWeb generates structures for and displays properties of cyclised and linear peptides. Information includes solid-phase peptide synthesis feasibility, Octanol-water partition coefficient, and drug-like properties Structural representations are available in 1D SMILES, 2D .png image, and 3D .sdf formats Functionality for generating libraries of cyclised peptides, including commercially available non-natural amino acids is available in the standalone CycloPs client.", "sc:name": "CycloPs", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioware.ucd.ie/~cyclops/cgi-bin/webpep.cgi", diff --git a/data/cyclum/cyclumbioschemas.jsonld b/data/cyclum/cyclumbioschemas.jsonld index 05461d58035a3..dbfbdc496aa2d 100644 --- a/data/cyclum/cyclumbioschemas.jsonld +++ b/data/cyclum/cyclumbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "Cyclum", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/KChen-lab/cyclum" diff --git a/data/cyclus3d/cyclus3dbioschemas.jsonld b/data/cyclus3d/cyclus3dbioschemas.jsonld index ff25c9d3eb790..9791f456a15fb 100644 --- a/data/cyclus3d/cyclus3dbioschemas.jsonld +++ b/data/cyclus3d/cyclus3dbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Cytoscape plugin for identifying functional modules in integrated networks composed of multiple interaction types.", "sc:name": "CyClus3D", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "ugent.be", diff --git a/data/cydar/cydarbioschemas.jsonld b/data/cydar/cydarbioschemas.jsonld index 33932f7c97505..91b4b43c430f2 100644 --- a/data/cydar/cydarbioschemas.jsonld +++ b/data/cydar/cydarbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "cydar", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cydar.html" } \ No newline at end of file diff --git a/data/cygenexpi/cygenexpibioschemas.jsonld b/data/cygenexpi/cygenexpibioschemas.jsonld index c17e6b4d4b6ef..f11c17cae5c70 100644 --- a/data/cygenexpi/cygenexpibioschemas.jsonld +++ b/data/cygenexpi/cygenexpibioschemas.jsonld @@ -24,14 +24,14 @@ "sc:license": "LGPL-3.0", "sc:name": "CyGenexpi", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/cas-bioinf/genexpi/wiki/CyGenexpi", "sc:version": [ - "1.3.0", - "1.4.2" + "1.4.2", + "1.3.0" ] }, { diff --git a/data/cylofold/cylofoldbioschemas.jsonld b/data/cylofold/cylofoldbioschemas.jsonld index f641e36356e9c..1fee47f28b1a3 100644 --- a/data/cylofold/cylofoldbioschemas.jsonld +++ b/data/cylofold/cylofoldbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/cylofold", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Eckart Bindewald", + "Bruce A. Shapiro", "Wojciech Kasprzak", - "Bruce A. Shapiro" + "Eckart Bindewald" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:20501603", "sc:description": "CyloFold is a web tool for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity.", "sc:name": "CyloFold", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cylofold.ncifcrf.gov" } \ No newline at end of file diff --git a/data/cynetsvm/cynetsvmbioschemas.jsonld b/data/cynetsvm/cynetsvmbioschemas.jsonld index 6f2997502030c..edd7b82ddf8be 100644 --- a/data/cynetsvm/cynetsvmbioschemas.jsonld +++ b/data/cynetsvm/cynetsvmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool that is integrated as a Cytoscape APP to predict clinical outcome and identify network bio-markers by integrating gene expression data and PPI data.", "sc:name": "CyNetSVM", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://sourceforge.net/projects/netsvmjava/" } \ No newline at end of file diff --git a/data/cyrest/cyrestbioschemas.jsonld b/data/cyrest/cyrestbioschemas.jsonld index ee552d62d5c49..c7b53d978d805 100644 --- a/data/cyrest/cyrestbioschemas.jsonld +++ b/data/cyrest/cyrestbioschemas.jsonld @@ -9,41 +9,41 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.6767.1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/cyrest", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web service", "sc:citation": [ - "pmcid:PMC4670004", "pubmed:26672762", { "@id": "https://doi.org/10.12688/F1000RESEARCH.6767.1" - } + }, + "pmcid:PMC4670004" ], "sc:description": "Turbocharging Cytoscape Access for External Tools via a RESTful API. It is a technology that powers Cytoscape Automation, which enables you to create reproducible workflows executed entirely within Cytoscape or by external tools (e.g., Jupyter, R, GenomeSpace, etc). This enables Cytoscape to scale to large collections of datasets and larger more complex workflows than is practical via keyboard and mouse.", "sc:featureList": [ - { - "@id": "edam:operation_3760" - }, { "@id": "edam:operation_0337" }, { "@id": "edam:operation_0335" + }, + { + "@id": "edam:operation_3760" } ], "sc:license": "MIT", "sc:name": "CyREST", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://apps.cytoscape.org/apps/cyrest" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.6767.1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cyrface/cyrfacebioschemas.jsonld b/data/cyrface/cyrfacebioschemas.jsonld index c140eb9a47fe1..4c13d5eea00e9 100644 --- a/data/cyrface/cyrfacebioschemas.jsonld +++ b/data/cyrface/cyrfacebioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/cyrface", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", - "Plug-in" + "Plug-in", + "Library" ], "sc:description": "Establishes an interface between R and Cytoscape by using different Java-R libraries, e.g. Rserve, RCaller. It can be used as a plug-in, e.g. to run R commands or to be used as a library to allow your plug-in to connect to R.", "sc:name": "Cyrface", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/saezrodriguez/cyrface/" } \ No newline at end of file diff --git a/data/cytodx/cytodxbioschemas.jsonld b/data/cytodx/cytodxbioschemas.jsonld index 623e65bc7bee4..93ef6c1323f51 100644 --- a/data/cytodx/cytodxbioschemas.jsonld +++ b/data/cytodx/cytodxbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "CytoDx", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/CytoDx.html", "sc:version": "1.0.0" diff --git a/data/cytof_workflow/cytof_workflowbioschemas.jsonld b/data/cytof_workflow/cytof_workflowbioschemas.jsonld index 97dcb1b5da15c..e6d165b0c14f6 100644 --- a/data/cytof_workflow/cytof_workflowbioschemas.jsonld +++ b/data/cytof_workflow/cytof_workflowbioschemas.jsonld @@ -18,10 +18,10 @@ "sc:additionalType": "Workflow", "sc:citation": [ "pmcid:PMC5473464", - "pubmed:28663787", { "@id": "https://doi.org/10.12688/F1000RESEARCH.11622.3" - } + }, + "pubmed:28663787" ], "sc:description": "Differential discovery in high-throughput high-dimensional cytometry datasets.", "sc:featureList": [ @@ -38,19 +38,19 @@ "sc:license": "Unlicense", "sc:name": "CyTOF workflow", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow" }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.11622.3", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0002-3048-5518", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.11622.3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/cytofkit/cytofkitbioschemas.jsonld b/data/cytofkit/cytofkitbioschemas.jsonld index 45347c09b993b..8ed6a1b842c8c 100644 --- a/data/cytofkit/cytofkitbioschemas.jsonld +++ b/data/cytofkit/cytofkitbioschemas.jsonld @@ -11,12 +11,12 @@ "@id": "https://bio.tools/cytofkit", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hao Chen", - "Jinmiao Chen" + "Jinmiao Chen", + "Hao Chen" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:26074076", "sc:contributor": "Evan Newell", @@ -24,9 +24,9 @@ "sc:license": "Artistic-2.0", "sc:name": "cytofkit", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cytofkit.html", "sc:version": "1.6.1" diff --git a/data/cytogps/cytogpsbioschemas.jsonld b/data/cytogps/cytogpsbioschemas.jsonld index b53d9f980c166..ebdecb2cffd53 100644 --- a/data/cytogps/cytogpsbioschemas.jsonld +++ b/data/cytogps/cytogpsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "CytoGPS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://cytogps.org/", diff --git a/data/cytolib/cytolibbioschemas.jsonld b/data/cytolib/cytolibbioschemas.jsonld index 96f0780b427c4..a565b1ab71a34 100644 --- a/data/cytolib/cytolibbioschemas.jsonld +++ b/data/cytolib/cytolibbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "cytolib", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/cytolib.html", "sc:version": "1.2.0" diff --git a/data/cytomine/cytominebioschemas.jsonld b/data/cytomine/cytominebioschemas.jsonld index dd97c8b5acb6a..652ef2f31fe73 100644 --- a/data/cytomine/cytominebioschemas.jsonld +++ b/data/cytomine/cytominebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Apache-2.0", "sc:name": "Cytomine", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://cytomine.be/" } \ No newline at end of file diff --git a/data/cytoml/cytomlbioschemas.jsonld b/data/cytoml/cytomlbioschemas.jsonld index 103dba78f338c..311eafbb86308 100644 --- a/data/cytoml/cytomlbioschemas.jsonld +++ b/data/cytoml/cytomlbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mike Jiang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.", "sc:license": "Artistic-2.0", diff --git a/data/cytopacq/cytopacqbioschemas.jsonld b/data/cytopacq/cytopacqbioschemas.jsonld index 3f0952a7f83a4..9295b3a794ae1 100644 --- a/data/cytopacq/cytopacqbioschemas.jsonld +++ b/data/cytopacq/cytopacqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "CytoPacq", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://cbia.fi.muni.cz/simulator" diff --git a/data/cytosaddlesum/cytosaddlesumbioschemas.jsonld b/data/cytosaddlesum/cytosaddlesumbioschemas.jsonld index 6eb5f430ea57d..99631e4b67943 100644 --- a/data/cytosaddlesum/cytosaddlesumbioschemas.jsonld +++ b/data/cytosaddlesum/cytosaddlesumbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "CytoSaddleSum", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/mn/enrich/index.html", "sc:version": "1.5" diff --git a/data/cytoscape/cytoscapebioschemas.jsonld b/data/cytoscape/cytoscapebioschemas.jsonld index d630bce81e98d..2ed558726f36d 100644 --- a/data/cytoscape/cytoscapebioschemas.jsonld +++ b/data/cytoscape/cytoscapebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Cytoscape", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cytoscape.org/", "sc:version": "3.7.1" diff --git a/data/cytoscape_web/cytoscape_webbioschemas.jsonld b/data/cytoscape_web/cytoscape_webbioschemas.jsonld index 1f8e9c68c168f..7adfd2c1ffd15 100644 --- a/data/cytoscape_web/cytoscape_webbioschemas.jsonld +++ b/data/cytoscape_web/cytoscape_webbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-based network visualization tool-modeled after Cytoscape-which is open source, interactive, customizable and easily integrated into web sites.", "sc:name": "Cytoscape Web", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://cytoscapeweb.cytoscape.org/" } \ No newline at end of file diff --git a/data/cytotrace/cytotracebioschemas.jsonld b/data/cytotrace/cytotracebioschemas.jsonld index 3a7706d9b26b8..a61eef53abec2 100644 --- a/data/cytotrace/cytotracebioschemas.jsonld +++ b/data/cytotrace/cytotracebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "CytoTRACE", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://cytotrace.stanford.edu" diff --git a/data/cyvcf2/cyvcf2bioschemas.jsonld b/data/cyvcf2/cyvcf2bioschemas.jsonld index 48d2182d1cf71..2a29de035c422 100644 --- a/data/cyvcf2/cyvcf2bioschemas.jsonld +++ b/data/cyvcf2/cyvcf2bioschemas.jsonld @@ -21,15 +21,15 @@ "Brent S Pedersen" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:28165109", "pmcid:PMC5870853", { "@id": "https://doi.org/10.1093/bioinformatics/btx057" - } + }, + "pubmed:28165109" ], "sc:description": "Library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility.", "sc:featureList": { diff --git a/data/d-genies/d-geniesbioschemas.jsonld b/data/d-genies/d-geniesbioschemas.jsonld index 37f03455ea9d8..ae14368b0420a 100644 --- a/data/d-genies/d-geniesbioschemas.jsonld +++ b/data/d-genies/d-geniesbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.7717/peerj.4958", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/d-genies", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christophe Klopp", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5991294", - "pubmed:29888139", { "@id": "https://doi.org/10.7717/peerj.4958" - } + }, + "pmcid:PMC5991294", + "pubmed:29888139" ], "sc:description": "Dotplot large Genomes in an Interactive, Efficient and Simple way.", "sc:featureList": { @@ -33,6 +29,10 @@ "sc:name": "D-GENIES", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/genotoul-bioinfo/dgenies" + }, + { + "@id": "https://doi.org/10.7717/peerj.4958", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/d3e/d3ebioschemas.jsonld b/data/d3e/d3ebioschemas.jsonld index 132c880e6c64c..afd25c5c5a94a 100644 --- a/data/d3e/d3ebioschemas.jsonld +++ b/data/d3e/d3ebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/D3E", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Identification of differentially-expressed genes in single-cell RNA sequencing data.", "sc:license": "GPL-3.0", "sc:name": "D3E", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://www.sanger.ac.uk/science/tools/discrete-distributional-differential-expression-d3e" } \ No newline at end of file diff --git a/data/dad-is/dad-isbioschemas.jsonld b/data/dad-is/dad-isbioschemas.jsonld index fa40e9383f00c..87ed3d0b8339a 100644 --- a/data/dad-is/dad-isbioschemas.jsonld +++ b/data/dad-is/dad-isbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Not licensed", "sc:name": "DAD-IS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.fao.org/dad-is/en/" } \ No newline at end of file diff --git a/data/dada2/dada2bioschemas.jsonld b/data/dada2/dada2bioschemas.jsonld index 68b3cb7397a76..1d1e1dee16f42 100644 --- a/data/dada2/dada2bioschemas.jsonld +++ b/data/dada2/dada2bioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/nmeth.3869", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dada2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Benjamin Callahan", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC4927377", "pubmed:27214047", { "@id": "https://doi.org/10.1038/nmeth.3869" - }, - "pmcid:PMC4927377" + } ], "sc:description": "This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.", "sc:featureList": { @@ -35,12 +31,16 @@ "sc:license": "GPL-3.0", "sc:name": "dada2", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/dada2.html", "sc:version": "1.2.1" + }, + { + "@id": "https://doi.org/10.1038/nmeth.3869", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/daglogo/daglogobioschemas.jsonld b/data/daglogo/daglogobioschemas.jsonld index 22b64714cd9b7..1d0e62fdaf041 100644 --- a/data/daglogo/daglogobioschemas.jsonld +++ b/data/daglogo/daglogobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jianhong Ou", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Visualize significant conserved amino acid sequence pattern in groups based on probability theory.", "sc:license": "GPL-2.0", diff --git a/data/dali/dalibioschemas.jsonld b/data/dali/dalibioschemas.jsonld index 5d7ecae70c931..78d3e8f96c4eb 100644 --- a/data/dali/dalibioschemas.jsonld +++ b/data/dali/dalibioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Dali", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://ekhidna.biocenter.helsinki.fi/dali_server" } \ No newline at end of file diff --git a/data/dalilite/dalilitebioschemas.jsonld b/data/dalilite/dalilitebioschemas.jsonld index 5ab39f37a6d6c..3a8283e9a5118 100644 --- a/data/dalilite/dalilitebioschemas.jsonld +++ b/data/dalilite/dalilitebioschemas.jsonld @@ -13,19 +13,19 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "Web Production", - "Liisa Holm" + "Liisa Holm", + "Web Production" ], "sc:description": "Pairwise structure alignment.", "sc:name": "DaliLite", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBL-EBI", - "University of Helsinki" + "University of Helsinki", + "EMBL-EBI" ], "sc:url": "http://www.ebi.ac.uk/Tools/structure/dalilite/", "sc:version": "1" diff --git a/data/dama/damabioschemas.jsonld b/data/dama/damabioschemas.jsonld index 2153058527796..9be67b8614366 100644 --- a/data/dama/damabioschemas.jsonld +++ b/data/dama/damabioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jobst Landgrebe", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data.", "sc:license": "GPL-2.0", diff --git a/data/dambe/dambebioschemas.jsonld b/data/dambe/dambebioschemas.jsonld index 0f4666ba9305c..f166a1758bf30 100644 --- a/data/dambe/dambebioschemas.jsonld +++ b/data/dambe/dambebioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/molbev/msy073", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/dambe", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xuhua Xia", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:29669107", - "pmcid:PMC5967572", { "@id": "https://doi.org/10.1093/molbev/msy073" - } + }, + "pmcid:PMC5967572", + "pubmed:29669107" ], "sc:description": "Comprehensive software package for genomic and phylogenetic data analysis.", "sc:featureList": [ @@ -37,10 +41,6 @@ "Linux" ], "sc:url": "http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx" - }, - { - "@id": "https://doi.org/10.1093/molbev/msy073", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/damidseq_pipeline/damidseq_pipelinebioschemas.jsonld b/data/damidseq_pipeline/damidseq_pipelinebioschemas.jsonld index 0211f7d32c117..2c8cbbd567220 100644 --- a/data/damidseq_pipeline/damidseq_pipelinebioschemas.jsonld +++ b/data/damidseq_pipeline/damidseq_pipelinebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btv386", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/damidseq_pipeline", "@type": "sc:SoftwareApplication", @@ -35,11 +39,11 @@ } ], "sc:citation": [ + "pmcid:PMC4595905", "pubmed:26112292", { "@id": "https://doi.org/10.1093/bioinformatics/btv386" - }, - "pmcid:PMC4595905" + } ], "sc:description": "Single script that automatically handles sequence alignment, read extension, binned counts, normalisation, pseudocount addition and final ratio file generation.", "sc:featureList": [ @@ -47,10 +51,10 @@ "@id": "edam:operation_3435" }, { - "@id": "edam:operation_3222" + "@id": "edam:operation_3798" }, { - "@id": "edam:operation_3798" + "@id": "edam:operation_3222" } ], "sc:license": "GPL-2.0", @@ -60,10 +64,6 @@ "Mac" ], "sc:url": "http://owenjm.github.io/damidseq_pipeline/" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btv386", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/damirseq/damirseqbioschemas.jsonld b/data/damirseq/damirseqbioschemas.jsonld index e4a2b9011605e..de040c4964cd1 100644 --- a/data/damirseq/damirseqbioschemas.jsonld +++ b/data/damirseq/damirseqbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/damirseq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Luca Piacentini", - "Mattia Chiesa" + "Mattia Chiesa", + "Luca Piacentini" ], "sc:additionalType": "Library", "sc:description": "Tidy pipeline of data mining\nprocedures to identify transcriptional biomarkers and exploit\nthem for both binary and multi-class classification purposes.", diff --git a/data/dammit/dammitbioschemas.jsonld b/data/dammit/dammitbioschemas.jsonld index 2fe613c5356f2..0e99aef9031dd 100644 --- a/data/dammit/dammitbioschemas.jsonld +++ b/data/dammit/dammitbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-2-Clause", "sc:name": "dammit", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/dib-lab/dammit/" diff --git a/data/dampd/dampdbioschemas.jsonld b/data/dampd/dampdbioschemas.jsonld index aba54f8151734..5021bb2e738cc 100644 --- a/data/dampd/dampdbioschemas.jsonld +++ b/data/dampd/dampdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Manually curated database of known and putative antimicrobial peptides.", "sc:name": "DAMPD", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://apps.sanbi.ac.za/dampd/" } \ No newline at end of file diff --git a/data/dan/danbioschemas.jsonld b/data/dan/danbioschemas.jsonld index 66b162c8e850f..ab27398e7ff98 100644 --- a/data/dan/danbioschemas.jsonld +++ b/data/dan/danbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK MRC", "UK BBSRC", + "Wellcome Trust", "EMBOSS Contributors" ], "sc:description": "Calculate nucleic acid melting temperature.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", + "Wellcome Trust", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "dan", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dan.html", "sc:version": "r6" diff --git a/data/danpos/danposbioschemas.jsonld b/data/danpos/danposbioschemas.jsonld index 654c627fa7e4d..459e1c70c6484 100644 --- a/data/danpos/danposbioschemas.jsonld +++ b/data/danpos/danposbioschemas.jsonld @@ -32,13 +32,13 @@ "sc:url": "https://sites.google.com/site/danposdoc/", "sc:version": "2.2.2" }, - { - "@id": "http://orcid.org/0000-0001-9931-5990", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1038/ng.3385", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-9931-5990", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dante/dantebioschemas.jsonld b/data/dante/dantebioschemas.jsonld index d40b767b6e65f..f3645c3d4ae73 100644 --- a/data/dante/dantebioschemas.jsonld +++ b/data/dante/dantebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Protein quantitation, statistical analysis and visualization.", "sc:name": "DAnTE", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://omics.pnl.gov/software/DAnTE.php" } \ No newline at end of file diff --git a/data/darc_site/darc_sitebioschemas.jsonld b/data/darc_site/darc_sitebioschemas.jsonld index 46d01740d2de8..3a9bb89168738 100644 --- a/data/darc_site/darc_sitebioschemas.jsonld +++ b/data/darc_site/darc_sitebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A database of aligned ribosomal complexes. Houses available cryo-EM maps and atomic coordinates of ribosomal particles from the Electron Microscopy Data Bank and Protein Data Bank aligned within a common system.", "sc:name": "DARC site", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://darcsite.genzentrum.lmu.de/darc/" } \ No newline at end of file diff --git a/data/dario/dariobioschemas.jsonld b/data/dario/dariobioschemas.jsonld index 5368a4a870e81..8e2b781641248 100644 --- a/data/dario/dariobioschemas.jsonld +++ b/data/dario/dariobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "DARIO", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://dario.bioinf.uni-leipzig.de/" } \ No newline at end of file diff --git a/data/dart/dartbioschemas.jsonld b/data/dart/dartbioschemas.jsonld index 0f23c5cace344..ee08565870136 100644 --- a/data/dart/dartbioschemas.jsonld +++ b/data/dart/dartbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2407-10-604", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/dart", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Charles Shijie Zheng", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pubmed:21050467", + "pmcid:PMC2991308", { "@id": "https://doi.org/10.1186/1471-2407-10-604" - }, - "pmcid:PMC2991308" + } ], "sc:description": "Denoising Algorithm based on Relevance network Topology is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples.", "sc:featureList": { @@ -31,16 +35,12 @@ "sc:license": "GPL-2.0", "sc:name": "DART", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DART.html", "sc:version": "1.22.0" - }, - { - "@id": "https://doi.org/10.1186/1471-2407-10-604", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/das-tmfilter/das-tmfilterbioschemas.jsonld b/data/das-tmfilter/das-tmfilterbioschemas.jsonld index 00e038860bdf8..a8ec90a5aef7c 100644 --- a/data/das-tmfilter/das-tmfilterbioschemas.jsonld +++ b/data/das-tmfilter/das-tmfilterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "DAS (Dense Alignment Surface) is based on low-stringency dot-plots of the query sequence against a set of library sequences - non-homologous membrane proteins - using a previously derived, special scoring matrix. The method provides a high precision hyrdophobicity profile for the query from which the location of the potential transmembrane segments can be obtained. The novelty of the DAS-TMfilter algorithm is a second prediction cycle to predict TM segments in the sequences of the TM-library.", "sc:name": "DAS-TMfilter", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://mendel.imp.ac.at/sat/DAS/DAS.html" diff --git a/data/das/dasbioschemas.jsonld b/data/das/dasbioschemas.jsonld index 20919ea8e28b6..cefab5a5c47fe 100644 --- a/data/das/dasbioschemas.jsonld +++ b/data/das/dasbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "DAS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "bils.se", diff --git a/data/dasir/dasirbioschemas.jsonld b/data/dasir/dasirbioschemas.jsonld index a7135933998b4..5d08bc9d351f8 100644 --- a/data/dasir/dasirbioschemas.jsonld +++ b/data/dasir/dasirbioschemas.jsonld @@ -12,19 +12,19 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ricard Illa", "sc:additionalType": [ - "Command-line tool", - "Plug-in" + "Plug-in", + "Command-line tool" ], "sc:author": [ - "Oscar Flores", - "Anna Mantsoki" + "Anna Mantsoki", + "Oscar Flores" ], "sc:description": "R package for programmatic retrieval of information from DAS servers.", "sc:name": "DASiR", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "BioConductor", "sc:url": "http://www.bioconductor.org/packages//2.13/bioc/html/DASiR.html", diff --git a/data/dasmiweb/dasmiwebbioschemas.jsonld b/data/dasmiweb/dasmiwebbioschemas.jsonld index b1074b46228a9..333f5c30a91c2 100644 --- a/data/dasmiweb/dasmiwebbioschemas.jsonld +++ b/data/dasmiweb/dasmiwebbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server that allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can support incorporation of user data.", "sc:name": "DASMIweb", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.dasmiweb.de" } \ No newline at end of file diff --git a/data/dasty/dastybioschemas.jsonld b/data/dasty/dastybioschemas.jsonld index 87d1cd9577ec0..39e6ca2a12e31 100644 --- a/data/dasty/dastybioschemas.jsonld +++ b/data/dasty/dastybioschemas.jsonld @@ -17,8 +17,8 @@ "sc:additionalType": "Web application", "sc:author": "Jose Villaveces", "sc:contributor": [ - "Rafael C Jimenez", - "Leyla J Garcia" + "Leyla J Garcia", + "Rafael C Jimenez" ], "sc:description": "Visualization and integration of protein sequence feature annotations via DAS.", "sc:name": "DASty", diff --git a/data/data_information_system_daisy/data_information_system_daisybioschemas.jsonld b/data/data_information_system_daisy/data_information_system_daisybioschemas.jsonld index 9fa5651991810..a3e91ba9c8b3f 100644 --- a/data/data_information_system_daisy/data_information_system_daisybioschemas.jsonld +++ b/data/data_information_system_daisy/data_information_system_daisybioschemas.jsonld @@ -9,18 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-2224-0780", - "@type": "schema:Person" - }, { "@id": "https://orcid.org/0000-0001-6501-0806", "@type": "schema:Person" }, - { - "@id": "https://orcid.org/0000-0002-6532-5880", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/Data_Information_System_DAISY", "@type": "sc:SoftwareApplication", @@ -33,22 +25,22 @@ "sc:additionalType": "Web application", "sc:author": [ "Yohan Jarosz", + "Kavita Rege", + "Jacek Lebioda", { "@id": "https://orcid.org/0000-0001-6501-0806" - }, - "Kavita Rege", - "Jacek Lebioda" + } ], "sc:contributor": [ - "Vilem Ded", { "@id": "https://orcid.org/0000-0002-8278-1618" }, + "Sandrine Munoz", { "@id": "https://orcid.org/0000-0002-6532-5880" }, - "Christophe Trefois", - "Sandrine Munoz" + "Vilem Ded", + "Christophe Trefois" ], "sc:description": "DAISY is an open-source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement.", "sc:license": "AGPL-3.0", @@ -64,6 +56,14 @@ { "@id": "https://orcid.org/0000-0002-8278-1618", "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0002-6532-5880", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0002-2224-0780", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/database_for_bacterial_group_2_introns/database_for_bacterial_group_2_intronsbioschemas.jsonld b/data/database_for_bacterial_group_2_introns/database_for_bacterial_group_2_intronsbioschemas.jsonld index 3288d6a4e9e27..494fa91ecbf4c 100644 --- a/data/database_for_bacterial_group_2_introns/database_for_bacterial_group_2_intronsbioschemas.jsonld +++ b/data/database_for_bacterial_group_2_introns/database_for_bacterial_group_2_intronsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database for Bacterial Group 2 Introns: a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. General info on group 2 intron properties, structures and classification. Lists info for individual introns (insertion sites, DNA sequences, intron-encoded protein sequences, RNA secondary structure models). Tools fo ridentification and analysis of intron sequences.", "sc:name": "Database for Bacterial Group 2 Introns", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://webapps2.ucalgary.ca/~groupii/" } \ No newline at end of file diff --git a/data/database_manager/database_managerbioschemas.jsonld b/data/database_manager/database_managerbioschemas.jsonld index f68a634602e52..9ca1691a8042a 100644 --- a/data/database_manager/database_managerbioschemas.jsonld +++ b/data/database_manager/database_managerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Sequence database manager, including random database generation.", "sc:name": "Database Manager", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://pappso.inra.fr/bioinfo/pdm/" } \ No newline at end of file diff --git a/data/datacube_explorer/datacube_explorerbioschemas.jsonld b/data/datacube_explorer/datacube_explorerbioschemas.jsonld index 5d3f910e4ae06..1816c8fca77a0 100644 --- a/data/datacube_explorer/datacube_explorerbioschemas.jsonld +++ b/data/datacube_explorer/datacube_explorerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "Datacube Explorer", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.amolf.nl/download/datacubeexplorer/" } \ No newline at end of file diff --git a/data/datasets2tools/datasets2toolsbioschemas.jsonld b/data/datasets2tools/datasets2toolsbioschemas.jsonld index 5cf008c85c6c5..f75d62e093297 100644 --- a/data/datasets2tools/datasets2toolsbioschemas.jsonld +++ b/data/datasets2tools/datasets2toolsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "Datasets2Tools", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://amp.pharm.mssm.edu/datasets2tools/" } \ No newline at end of file diff --git a/data/datastorr/datastorrbioschemas.jsonld b/data/datastorr/datastorrbioschemas.jsonld index 8c714ec15cbf2..13f144424275a 100644 --- a/data/datastorr/datastorrbioschemas.jsonld +++ b/data/datastorr/datastorrbioschemas.jsonld @@ -13,26 +13,22 @@ "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ035", "@type": "sc:CreativeWork" }, - { - "@id": "https://orcid.org/0000-0002-9814-092X", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/Datastorr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rich FitzJohn", { "@id": "https://orcid.org/0000-0002-9814-092X" - } + }, + "Rich FitzJohn" ], "sc:additionalType": "Workflow", "sc:citation": [ + "pmcid:PMC6506717", "pubmed:31042286", { "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ035" - }, - "pmcid:PMC6506717" + } ], "sc:description": "Workflow and package for delivering successive versions of 'evolving data' directly into R.", "sc:featureList": { @@ -41,11 +37,15 @@ "sc:license": "MIT", "sc:name": "Datastorr", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://github.com/ropenscilabs/datastorr" + }, + { + "@id": "https://orcid.org/0000-0002-9814-092X", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dataup/dataupbioschemas.jsonld b/data/dataup/dataupbioschemas.jsonld index 956fe14421da3..e165dfcb17b05 100644 --- a/data/dataup/dataupbioschemas.jsonld +++ b/data/dataup/dataupbioschemas.jsonld @@ -9,27 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.3-6.V2", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-9592-2339", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/dataup", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Plug-in" + "Plug-in", + "Web application" ], "sc:citation": [ - "pubmed:25653834", "pmcid:PMC4304223", { "@id": "https://doi.org/10.12688/F1000RESEARCH.3-6.V2" - } + }, + "pubmed:25653834" ], "sc:contributor": { "@id": "http://orcid.org/0000-0001-9592-2339" @@ -37,10 +29,10 @@ "sc:description": "Describe and share tabular data. It includes three components: (1) the Excel add-in; (2) the public web client; and (3) the private web service that mediates between the add-in and client and the ONEShare repository", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_0337" }, { "@id": "edam:operation_3431" @@ -50,6 +42,14 @@ "sc:name": "DataUp", "sc:operatingSystem": "Windows", "sc:url": "https://zenodo.org/record/7639#.W45ZrC0rzfZ" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.3-6.V2", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-9592-2339", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/datf/datfbioschemas.jsonld b/data/datf/datfbioschemas.jsonld index cdc7af47c5ab3..184ef5e15ef00 100644 --- a/data/datf/datfbioschemas.jsonld +++ b/data/datf/datfbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DATF", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://datf.cbi.pku.edu.cn" } \ No newline at end of file diff --git a/data/david_bioinformatics_resources/david_bioinformatics_resourcesbioschemas.jsonld b/data/david_bioinformatics_resources/david_bioinformatics_resourcesbioschemas.jsonld index bf6a52d152fd8..322bb70360240 100644 --- a/data/david_bioinformatics_resources/david_bioinformatics_resourcesbioschemas.jsonld +++ b/data/david_bioinformatics_resources/david_bioinformatics_resourcesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.", "sc:name": "DAVID Bioinformatics Resources", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://david.abcc.ncifcrf.gov/home.jsp" } \ No newline at end of file diff --git a/data/david_ws/david_wsbioschemas.jsonld b/data/david_ws/david_wsbioschemas.jsonld index e424fae33cc3d..c7c6deb9265d3 100644 --- a/data/david_ws/david_wsbioschemas.jsonld +++ b/data/david_ws/david_wsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Bioinformatics resources which consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists.", "sc:name": "DAVID WS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html", diff --git a/data/davidquery/davidquerybioschemas.jsonld b/data/davidquery/davidquerybioschemas.jsonld index fc6e8a2e6bda3..dd12e24dc64fb 100644 --- a/data/davidquery/davidquerybioschemas.jsonld +++ b/data/davidquery/davidquerybioschemas.jsonld @@ -12,19 +12,19 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Roger Day", "sc:additionalType": [ - "Command-line tool", - "Plug-in" + "Plug-in", + "Command-line tool" ], "sc:author": [ - "Alex Lisovich", - "Roger Day" + "Roger Day", + "Alex Lisovich" ], "sc:description": "An R package for retrieving data from DAVID, the Database for Annotation, Visualization and Integrated Discovery", "sc:license": "GPL-2.0", "sc:name": "DAVIDQuery", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "BioConductor", diff --git a/data/dbass/dbassbioschemas.jsonld b/data/dbass/dbassbioschemas.jsonld index 299f75875e9de..a32194c3b34ed 100644 --- a/data/dbass/dbassbioschemas.jsonld +++ b/data/dbass/dbassbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Comprehensive repositories of new exon boundaries induced by pathogenic mutations in human disease genes. Aberrant 5’- and 3’-splice sites were activated either by mutations in the consensus sequences of natural exon-intron junctions or elsewhere. Data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the algorithm-estimated splice-site strength.", "sc:name": "DBASS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.dbass.org.uk/" } \ No newline at end of file diff --git a/data/dbbqs/dbbqsbioschemas.jsonld b/data/dbbqs/dbbqsbioschemas.jsonld index c6fc314ef0061..c63e0400ee0d6 100644 --- a/data/dbbqs/dbbqsbioschemas.jsonld +++ b/data/dbbqs/dbbqsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The database of bacterial quality scores.", "sc:name": "dBBQs", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://arc-gem.uams.edu/dbbqs/" diff --git a/data/dbcan/dbcanbioschemas.jsonld b/data/dbcan/dbcanbioschemas.jsonld index 7b77bdf91498c..813585161a302 100644 --- a/data/dbcan/dbcanbioschemas.jsonld +++ b/data/dbcan/dbcanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "dbCAN provides automated carbohydrate-active enzyme signature domain-based annotation for a set of proteins. Each carbohydrate-active enzyme has an assigned signature domain.", "sc:name": "dbCAN", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://csbl.bmb.uga.edu/dbCAN/annotate.php" } \ No newline at end of file diff --git a/data/dbchip/dbchipbioschemas.jsonld b/data/dbchip/dbchipbioschemas.jsonld index 4f7303c0e1577..d3a4734343497 100644 --- a/data/dbchip/dbchipbioschemas.jsonld +++ b/data/dbchip/dbchipbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Kun Liang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.", "sc:license": "GPL-2.0", diff --git a/data/dbd/dbdbioschemas.jsonld b/data/dbd/dbdbioschemas.jsonld index 0a1cada3cd985..4fec7dcca0085 100644 --- a/data/dbd/dbdbioschemas.jsonld +++ b/data/dbd/dbdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predicted transcription factors in completely sequenced genomes.", "sc:name": "Transcription factor prediction database (DBD)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.transcriptionfactor.org/index.cgi" } \ No newline at end of file diff --git a/data/dbdnv/dbdnvbioschemas.jsonld b/data/dbdnv/dbdnvbioschemas.jsonld index 8718a3b21b69d..d125cec0317c6 100644 --- a/data/dbdnv/dbdnvbioschemas.jsonld +++ b/data/dbdnv/dbdnvbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304,110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates.", "sc:name": "dbDNV", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://goods.ibms.sinica.edu.tw/DNVs/" } \ No newline at end of file diff --git a/data/dbest/dbestbioschemas.jsonld b/data/dbest/dbestbioschemas.jsonld index 0e3ce89a3316d..cf398ab938755 100644 --- a/data/dbest/dbestbioschemas.jsonld +++ b/data/dbest/dbestbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Division of GenBank that contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.", "sc:name": "dbEST database of EST sequences", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "NCBI", "sc:url": "http://www.ncbi.nlm.nih.gov/dbEST/" diff --git a/data/dbeth/dbethbioschemas.jsonld b/data/dbeth/dbethbioschemas.jsonld index 5ef9bd16599ef..80dce32ef63db 100644 --- a/data/dbeth/dbethbioschemas.jsonld +++ b/data/dbeth/dbethbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DBETH", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.hpppi.iicb.res.in/btox/" } \ No newline at end of file diff --git a/data/dbfetch/dbfetchbioschemas.jsonld b/data/dbfetch/dbfetchbioschemas.jsonld index 329bbb1b00dfd..e41223d8d8a3e 100644 --- a/data/dbfetch/dbfetchbioschemas.jsonld +++ b/data/dbfetch/dbfetchbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "dbfetch", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ebi.ac.uk/Tools/dbfetch/", "sc:version": "1" diff --git a/data/dbgap/dbgapbioschemas.jsonld b/data/dbgap/dbgapbioschemas.jsonld index a472b90e4aec6..b87e519b162f0 100644 --- a/data/dbgap/dbgapbioschemas.jsonld +++ b/data/dbgap/dbgapbioschemas.jsonld @@ -18,33 +18,33 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Feolo", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ - "pmcid:PMC3965052", "pubmed:24297256", { "@id": "https://doi.org/10.1093/nar/gkt1211" - } + }, + "pmcid:PMC3965052" ], "sc:description": "The Database of Genotypes and Phenotypes (dbGAP) is a National Institutes of Health-sponsored repository charged to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in humans. Information in dbGaP is organized as a hierarchical structure and includes the accessioned objects, phenotypes (as variables and datasets), various molecular assay data (SNP and Expression Array data, Sequence and Epigenomic marks), analyses and documents.", "sc:featureList": [ - { - "@id": "edam:operation_3196" - }, { "@id": "edam:operation_2422" }, { "@id": "edam:operation_3431" + }, + { + "@id": "edam:operation_3196" } ], "sc:name": "dbGAP", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/gap" } diff --git a/data/dbiblast/dbiblastbioschemas.jsonld b/data/dbiblast/dbiblastbioschemas.jsonld index 4216ae9065daf..5be348451cf87 100644 --- a/data/dbiblast/dbiblastbioschemas.jsonld +++ b/data/dbiblast/dbiblastbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "EMBOSS Contributors", "UK BBSRC", "UK MRC", - "Wellcome Trust", - "EMBOSS Contributors" + "Wellcome Trust" ], "sc:description": "Index a BLAST database.", "sc:funder": [ - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "dbiblast", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dbiblast.html", "sc:version": "r6" diff --git a/data/dbifasta/dbifastabioschemas.jsonld b/data/dbifasta/dbifastabioschemas.jsonld index 098a603ddfe61..7dbf8f7a85500 100644 --- a/data/dbifasta/dbifastabioschemas.jsonld +++ b/data/dbifasta/dbifastabioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK MRC", "EMBOSS Contributors", "Wellcome Trust", - "UK MRC", "UK BBSRC" ], "sc:description": "Index a fasta file database.", "sc:funder": [ - "UK BBSRC", "UK MRC", + "UK BBSRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "dbifasta", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/dbiflat/dbiflatbioschemas.jsonld b/data/dbiflat/dbiflatbioschemas.jsonld index b2e45e1a1af84..7f06fdd01ec1a 100644 --- a/data/dbiflat/dbiflatbioschemas.jsonld +++ b/data/dbiflat/dbiflatbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "Wellcome Trust", "UK MRC", + "Wellcome Trust", + "UK BBSRC", "EMBOSS Contributors" ], "sc:description": "Index a flat file database.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", + "Wellcome Trust", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "dbiflat", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ diff --git a/data/dbigcg/dbigcgbioschemas.jsonld b/data/dbigcg/dbigcgbioschemas.jsonld index 028d9256760eb..839b830a33e51 100644 --- a/data/dbigcg/dbigcgbioschemas.jsonld +++ b/data/dbigcg/dbigcgbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", - "UK MRC", "EMBOSS Contributors", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:description": "Index a GCG formatted database.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "dbigcg", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/dbindr/dbindrbioschemas.jsonld b/data/dbindr/dbindrbioschemas.jsonld index 5db379137becf..57886ceb8f119 100644 --- a/data/dbindr/dbindrbioschemas.jsonld +++ b/data/dbindr/dbindrbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "DBindR is a web server for prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature", "sc:name": "DBindR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.cbi.seu.edu.cn/DBindR/DBindR.htm" } \ No newline at end of file diff --git a/data/dbmae/dbmaebioschemas.jsonld b/data/dbmae/dbmaebioschemas.jsonld index 9b4ddd9f1e025..d1311f3596fd2 100644 --- a/data/dbmae/dbmaebioschemas.jsonld +++ b/data/dbmae/dbmaebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkv1106", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/dbmae", "@type": "sc:SoftwareApplication", @@ -17,35 +21,31 @@ "Web application" ], "sc:citation": [ + "pubmed:26503248", + "pmcid:PMC4702807", { "@id": "https://doi.org/10.1093/nar/gkv1106" - }, - "pmcid:PMC4702807", - "pubmed:26503248" + } ], "sc:description": "Database of autosomal monoallelic expression for investigating whether the gene/gene class of interest is inferred or measured to be monoallelic in mouse or human tissues.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_2495" }, { "@id": "edam:operation_3431" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3196" } ], "sc:name": "dbMAE", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://mae.hms.harvard.edu/aboutmae.php" - }, - { - "@id": "https://doi.org/10.1093/nar/gkv1106", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dbnp/dbnpbioschemas.jsonld b/data/dbnp/dbnpbioschemas.jsonld index 7bdd375f26599..a509c35d91d1a 100644 --- a/data/dbnp/dbnpbioschemas.jsonld +++ b/data/dbnp/dbnpbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Nutritional Phenotype Database (dbnp)", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-NL", "sc:url": "http://dbnp.org/", diff --git a/data/dbnsfp/dbnsfpbioschemas.jsonld b/data/dbnsfp/dbnsfpbioschemas.jsonld index 783d23738f97e..d18f1b7bac3f3 100644 --- a/data/dbnsfp/dbnsfpbioschemas.jsonld +++ b/data/dbnsfp/dbnsfpbioschemas.jsonld @@ -14,23 +14,23 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xiaoming Liu", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ "pmcid:PMC4752381", - "pubmed:26555599", { "@id": "https://doi.org/10.1002/humu.22932" - } + }, + "pubmed:26555599" ], "sc:description": "Database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs) in the human genome. It also facilitates the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome-sequencing study.", "sc:license": "Unlicense", "sc:name": "dbNSFP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://sites.google.com/site/jpopgen/dbNSFP", "sc:version": "3.0" diff --git a/data/dbptm/dbptmbioschemas.jsonld b/data/dbptm/dbptmbioschemas.jsonld index 8e8936e7c1184..dc9ecdd9242b5 100644 --- a/data/dbptm/dbptmbioschemas.jsonld +++ b/data/dbptm/dbptmbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkj083", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/dbptm", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ "Web application" ], "sc:citation": [ - "pmcid:PMC1347446", + "pubmed:16381945", { "@id": "https://doi.org/10.1093/nar/gkj083" }, - "pubmed:16381945" + "pmcid:PMC1347446" ], "sc:description": "An informative resource for protein post-translational modifications (PTMs).", "sc:featureList": { @@ -30,16 +34,12 @@ }, "sc:name": "dbPTM", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://dbptm.mbc.nctu.edu.tw", "sc:version": "3.0" - }, - { - "@id": "https://doi.org/10.1093/nar/gkj083", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dbsnp-q/dbsnp-qbioschemas.jsonld b/data/dbsnp-q/dbsnp-qbioschemas.jsonld index 13cb6955d87bc..3887c2a379955 100644 --- a/data/dbsnp-q/dbsnp-qbioschemas.jsonld +++ b/data/dbsnp-q/dbsnp-qbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "dbSNP-Q is a web application for working with the dbSNP relational database. dbSNP is a source of information on single nucleotide polymorphisms (SNPs) and other genetic variation for many different organisms, including humans. dbSNP-Q can be used to query human data from dbSNP for a variety tasks such as genomic mapping, SNP/gene functional properties, allele frequency data and information on the underlying experiments. It also includes documentation and download tools.", "sc:name": "dbSNP-Q", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://cgsmd.isi.edu/dbsnpq" } \ No newline at end of file diff --git a/data/dbsnp/dbsnpbioschemas.jsonld b/data/dbsnp/dbsnpbioschemas.jsonld index 1fca6849af6a3..d8054730bc849 100644 --- a/data/dbsnp/dbsnpbioschemas.jsonld +++ b/data/dbsnp/dbsnpbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/dbsnp", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "Database of single nucleotide polymorphism (dbSNP) contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.", "sc:name": "dbSNP", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "NCBI", "sc:url": "http://www.ncbi.nlm.nih.gov/SNP/" diff --git a/data/dbsts/dbstsbioschemas.jsonld b/data/dbsts/dbstsbioschemas.jsonld index 9291d517663af..5567a0687c75d 100644 --- a/data/dbsts/dbstsbioschemas.jsonld +++ b/data/dbsts/dbstsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.", "sc:name": "NCBI database of sequence tagged sites", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/dbSTS/" } \ No newline at end of file diff --git a/data/dbsuper/dbsuperbioschemas.jsonld b/data/dbsuper/dbsuperbioschemas.jsonld index 01500a764c970..7118fc7a677c9 100644 --- a/data/dbsuper/dbsuperbioschemas.jsonld +++ b/data/dbsuper/dbsuperbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKV1002", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dbsuper", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Database portal", "sc:citation": [ "pmcid:PMC4702767", + "pubmed:26438538", { "@id": "https://doi.org/10.1093/NAR/GKV1002" - }, - "pubmed:26438538" + } ], "sc:description": "A database of super-enhancers in mouse and human genome.", "sc:featureList": { @@ -36,6 +32,10 @@ "Mac" ], "sc:url": "http://asntech.org/dbsuper/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKV1002", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dbtell/dbtellbioschemas.jsonld b/data/dbtell/dbtellbioschemas.jsonld index 9e6baf766176d..33e3becd7914b 100644 --- a/data/dbtell/dbtellbioschemas.jsonld +++ b/data/dbtell/dbtellbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "Wellcome Trust", "EMBOSS Contributors", + "Wellcome Trust", + "UK MRC", "UK BBSRC" ], "sc:description": "Display information about a public database.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "dbtell", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/dbtl/dbtlbioschemas.jsonld b/data/dbtl/dbtlbioschemas.jsonld index d938770b8f392..245fa0c5cd2ec 100644 --- a/data/dbtl/dbtlbioschemas.jsonld +++ b/data/dbtl/dbtlbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "DBTL", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://panoramaweb.org/DBTL-ML-for-dodencanol-production-in-e-coli.url" } \ No newline at end of file diff --git a/data/dbtoolkit/dbtoolkitbioschemas.jsonld b/data/dbtoolkit/dbtoolkitbioschemas.jsonld index c2d70ec4baa12..7aa1a7a7d09f3 100644 --- a/data/dbtoolkit/dbtoolkitbioschemas.jsonld +++ b/data/dbtoolkit/dbtoolkitbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lennart Martens", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:citation": "pubmed:16030071", "sc:description": "Easy-to-use environment for customized fasta database manipulations.", "sc:name": "dbtoolkit", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://code.google.com/p/dbtoolkit/", diff --git a/data/dbxcompress/dbxcompressbioschemas.jsonld b/data/dbxcompress/dbxcompressbioschemas.jsonld index 814deb1fdb25b..8bc7182a24dd6 100644 --- a/data/dbxcompress/dbxcompressbioschemas.jsonld +++ b/data/dbxcompress/dbxcompressbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK BBSRC", + "UK MRC", "EMBOSS Contributors", - "UK MRC" + "Wellcome Trust" ], "sc:description": "Compress an uncompressed dbx index.", "sc:funder": [ + "UK BBSRC", "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "dbxcompress", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dbxcompress.html", "sc:version": "r6" diff --git a/data/dbxedam/dbxedambioschemas.jsonld b/data/dbxedam/dbxedambioschemas.jsonld index ec298b436d47d..af97e4b5aa1ec 100644 --- a/data/dbxedam/dbxedambioschemas.jsonld +++ b/data/dbxedam/dbxedambioschemas.jsonld @@ -14,8 +14,8 @@ "sc:contributor": [ "UK BBSRC", "EMBOSS Contributors", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:description": "Index the EDAM ontology using b+tree indices.", "sc:funder": [ @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "dbxedam", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dbxedam.html", "sc:version": "r6" diff --git a/data/dbxfasta/dbxfastabioschemas.jsonld b/data/dbxfasta/dbxfastabioschemas.jsonld index 9635e44599f8f..91c1569eafcd5 100644 --- a/data/dbxfasta/dbxfastabioschemas.jsonld +++ b/data/dbxfasta/dbxfastabioschemas.jsonld @@ -13,14 +13,14 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK MRC", - "Wellcome Trust", + "EMBOSS Contributors", "UK BBSRC", - "EMBOSS Contributors" + "Wellcome Trust" ], "sc:description": "Index a fasta file database using b+tree indices.", "sc:funder": [ - "UK MRC", "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", diff --git a/data/dbxflat/dbxflatbioschemas.jsonld b/data/dbxflat/dbxflatbioschemas.jsonld index 8da6a21129d79..fae4360a86c6f 100644 --- a/data/dbxflat/dbxflatbioschemas.jsonld +++ b/data/dbxflat/dbxflatbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "Wellcome Trust", + "EMBOSS Contributors", "UK BBSRC", - "EMBOSS Contributors" + "UK MRC", + "Wellcome Trust" ], "sc:description": "Index a flat file database using b+tree indices.", "sc:funder": [ - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "dbxflat", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ diff --git a/data/dbxgcg/dbxgcgbioschemas.jsonld b/data/dbxgcg/dbxgcgbioschemas.jsonld index 72f769fc2f0aa..d8dc8085cbc9b 100644 --- a/data/dbxgcg/dbxgcgbioschemas.jsonld +++ b/data/dbxgcg/dbxgcgbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "EMBOSS Contributors" ], "sc:description": "Index a GCG formatted database using b+tree indices.", "sc:funder": [ + "UK BBSRC", "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "dbxgcg", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/dbxobo/dbxobobioschemas.jsonld b/data/dbxobo/dbxobobioschemas.jsonld index ab236820f8636..67f96513ebdb9 100644 --- a/data/dbxobo/dbxobobioschemas.jsonld +++ b/data/dbxobo/dbxobobioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "UK BBSRC", + "UK MRC", "EMBOSS Contributors", - "UK MRC" + "UK BBSRC" ], "sc:description": "Index an obo ontology using b+tree indices.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "dbxobo", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dbxobo.html", "sc:version": "r6" diff --git a/data/dbxreport/dbxreportbioschemas.jsonld b/data/dbxreport/dbxreportbioschemas.jsonld index 2ff1e959b741d..7bebc9ab3259a 100644 --- a/data/dbxreport/dbxreportbioschemas.jsonld +++ b/data/dbxreport/dbxreportbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "UK MRC", + "EMBOSS Contributors", "Wellcome Trust", - "EMBOSS Contributors" + "UK BBSRC" ], "sc:description": "Validate index and report internals for dbx databases.", "sc:funder": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "dbxreport", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dbxreport.html", "sc:version": "r6" diff --git a/data/dbxresource/dbxresourcebioschemas.jsonld b/data/dbxresource/dbxresourcebioschemas.jsonld index d40c77f338e4f..300b8a2626bd7 100644 --- a/data/dbxresource/dbxresourcebioschemas.jsonld +++ b/data/dbxresource/dbxresourcebioschemas.jsonld @@ -27,12 +27,12 @@ "sc:name": "dbxresource", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dbxresource.html", "sc:version": "r6" diff --git a/data/dbxstat/dbxstatbioschemas.jsonld b/data/dbxstat/dbxstatbioschemas.jsonld index 2a7713d59914b..2ed9604d98a2f 100644 --- a/data/dbxstat/dbxstatbioschemas.jsonld +++ b/data/dbxstat/dbxstatbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "EMBOSS Contributors", - "UK BBSRC", - "Wellcome Trust" + "UK MRC", + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Dump statistics for dbx databases.", "sc:funder": [ @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "dbxstat", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/dbxtax/dbxtaxbioschemas.jsonld b/data/dbxtax/dbxtaxbioschemas.jsonld index ee89eb3654c5e..cdb7141238b35 100644 --- a/data/dbxtax/dbxtaxbioschemas.jsonld +++ b/data/dbxtax/dbxtaxbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK BBSRC", "EMBOSS Contributors", - "UK MRC" + "UK BBSRC", + "UK MRC", + "Wellcome Trust" ], "sc:description": "Index NCBI taxonomy using b+tree indices.", "sc:funder": [ - "UK MRC", "Wellcome Trust", + "UK MRC", "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "dbxtax", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dbxtax.html", "sc:version": "r6" diff --git a/data/dbxuncompress/dbxuncompressbioschemas.jsonld b/data/dbxuncompress/dbxuncompressbioschemas.jsonld index 046c66651b7e3..1dfa890da14af 100644 --- a/data/dbxuncompress/dbxuncompressbioschemas.jsonld +++ b/data/dbxuncompress/dbxuncompressbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "Wellcome Trust", + "UK MRC", + "EMBOSS Contributors" ], "sc:description": "Uncompress a compressed dbx index.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", + "UK BBSRC", "UK MRC" ], "sc:license": "GPL-3.0", @@ -31,8 +31,8 @@ "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dbxuncompress.html", "sc:version": "r6" diff --git a/data/dca/dcabioschemas.jsonld b/data/dca/dcabioschemas.jsonld index 6b873d8a2062f..23165bfb8a956 100644 --- a/data/dca/dcabioschemas.jsonld +++ b/data/dca/dcabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Apache-2.0", "sc:name": "DCA", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/theislab/dca" diff --git a/data/dcell/dcellbioschemas.jsonld b/data/dcell/dcellbioschemas.jsonld index 98208b82b34df..5203e616952c9 100644 --- a/data/dcell/dcellbioschemas.jsonld +++ b/data/dcell/dcellbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "DCell", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://d-cell.ucsd.edu/" } \ No newline at end of file diff --git a/data/dcgl/dcglbioschemas.jsonld b/data/dcgl/dcglbioschemas.jsonld index fa717483feb49..468faf75b6bb7 100644 --- a/data/dcgl/dcglbioschemas.jsonld +++ b/data/dcgl/dcglbioschemas.jsonld @@ -28,8 +28,8 @@ "sc:name": "DCGL", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/DCGL/index.html", "sc:version": "2.0" diff --git a/data/dcgor/dcgorbioschemas.jsonld b/data/dcgor/dcgorbioschemas.jsonld index 75f16d2650bd7..794a875e360df 100644 --- a/data/dcgor/dcgorbioschemas.jsonld +++ b/data/dcgor/dcgorbioschemas.jsonld @@ -15,19 +15,19 @@ "biotools:primaryContact": "Hai Fang", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC4214615", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003929" }, - "pubmed:25356683" + "pubmed:25356683", + "pmcid:PMC4214615" ], "sc:description": "An R Package for Analysing Ontologies and Protein Domain Annotations.", "sc:featureList": [ { - "@id": "edam:operation_3352" + "@id": "edam:operation_0361" }, { - "@id": "edam:operation_0361" + "@id": "edam:operation_3352" } ], "sc:name": "dcGOR", diff --git a/data/dcgsa/bioconda_dcgsa.yaml b/data/dcgsa/bioconda_dcgsa.yaml index b51586f3b66fa..21b8d19877a96 100644 --- a/data/dcgsa/bioconda_dcgsa.yaml +++ b/data/dcgsa/bioconda_dcgsa.yaml @@ -9,7 +9,6 @@ description: Distance-correlation based Gene Set Analysis for longitudinal gene home: https://bioconductor.org/packages/3.10/bioc/html/dcGSA.html identifiers: - biotools:dcgsa -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-dcgsa diff --git a/data/dcgsa/dcgsabioschemas.jsonld b/data/dcgsa/dcgsabioschemas.jsonld index c58c3dec62758..49c7f10251cf5 100644 --- a/data/dcgsa/dcgsabioschemas.jsonld +++ b/data/dcgsa/dcgsabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jiehuan sun", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles. In longitudinal studies, the gene expression profiles were collected at each visit from each subject and hence there are multiple measurements of the gene expression profiles for each subject. The package could be used to assess the associations between gene sets and clinical outcomes of interest by fully taking advantage of the longitudinal nature of both the gene expression profiles and clinical outcomes.", "sc:license": "GPL-2.0", "sc:name": "dcGSA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/dcGSA.html", "sc:version": "1.2.0" diff --git a/data/dchiprep/dchiprepbioschemas.jsonld b/data/dchiprep/dchiprepbioschemas.jsonld index 353e8656bb2bb..c090f86cff6dd 100644 --- a/data/dchiprep/dchiprepbioschemas.jsonld +++ b/data/dchiprep/dchiprepbioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.7717/peerj.1981", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dchiprep", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bernd Klaus", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pmcid:PMC4860309", @@ -35,12 +31,16 @@ "sc:license": "MIT", "sc:name": "DChIPRep", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DChIPRep.html", "sc:version": "1.4.0" + }, + { + "@id": "https://doi.org/10.7717/peerj.1981", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dclip/dclipbioschemas.jsonld b/data/dclip/dclipbioschemas.jsonld index fd20cf681fb77..b2ec858398780 100644 --- a/data/dclip/dclipbioschemas.jsonld +++ b/data/dclip/dclipbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Yang Xie", - "Guanghua Xiao", "Bo Yao", + "Guanghua Xiao", "Contact Address" ], "sc:additionalType": "Command-line tool", diff --git a/data/dcmf/dcmfbioschemas.jsonld b/data/dcmf/dcmfbioschemas.jsonld index 17c187a3a36b5..7f1d45274694d 100644 --- a/data/dcmf/dcmfbioschemas.jsonld +++ b/data/dcmf/dcmfbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "DCMF", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.slimsuite.unsw.edu.au/research/dcmf/" } \ No newline at end of file diff --git a/data/dcon/dconbioschemas.jsonld b/data/dcon/dconbioschemas.jsonld index 4f065606a0192..cf8f274bbadf7 100644 --- a/data/dcon/dconbioschemas.jsonld +++ b/data/dcon/dconbioschemas.jsonld @@ -12,14 +12,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Piero Fariselli", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Predictor of Disulfide Connectivity in Proteins.", "sc:name": "DCON", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", diff --git a/data/ddap/ddapbioschemas.jsonld b/data/ddap/ddapbioschemas.jsonld index ffd8bfa6bee5e..474b15f7e8826 100644 --- a/data/ddap/ddapbioschemas.jsonld +++ b/data/ddap/ddapbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/DDAP", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Database portal" + "Database portal", + "Command-line tool" ], "sc:description": "Docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.", "sc:license": "MIT", "sc:name": "DDAP", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://tylii.github.io/ddap" } \ No newline at end of file diff --git a/data/ddbj/ddbjbioschemas.jsonld b/data/ddbj/ddbjbioschemas.jsonld index e0d6d7d5d02eb..112fbd10732b1 100644 --- a/data/ddbj/ddbjbioschemas.jsonld +++ b/data/ddbj/ddbjbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. A new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Other improvements include improved content of the patent sequence, released a new submission tool of the Sequence Read Archive (DRA) and the Read Annotation Pipeline.", "sc:name": "DDBJ", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ddbj.nig.ac.jp" } \ No newline at end of file diff --git a/data/ddbrna/ddbrnabioschemas.jsonld b/data/ddbrna/ddbrnabioschemas.jsonld index b7967541eb98f..3fa7d43639d0c 100644 --- a/data/ddbrna/ddbrnabioschemas.jsonld +++ b/data/ddbrna/ddbrnabioschemas.jsonld @@ -24,8 +24,8 @@ "sc:description": "Software for detection of conserved secondary structures in multiple alignments.", "sc:name": "ddbRNA", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://dibernardo.tigem.it/softwares/ddbrna" diff --git a/data/ddct/bioconda_ddct.yaml b/data/ddct/bioconda_ddct.yaml index 8194bc9b64a95..cfaa8ad3cc29a 100644 --- a/data/ddct/bioconda_ddct.yaml +++ b/data/ddct/bioconda_ddct.yaml @@ -11,7 +11,6 @@ description: The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to d home: https://bioconductor.org/packages/3.10/bioc/html/ddCt.html identifiers: - biotools:ddct -- doi:10.1038/nmeth.3252 license: LGPL-3 license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-ddct diff --git a/data/ddct/ddctbioschemas.jsonld b/data/ddct/ddctbioschemas.jsonld index 8d09e183eee83..b3130982a36c9 100644 --- a/data/ddct/ddctbioschemas.jsonld +++ b/data/ddct/ddctbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "ddCt", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ddCt.html", "sc:version": "1.30.0" diff --git a/data/ddecon/ddeconbioschemas.jsonld b/data/ddecon/ddeconbioschemas.jsonld index dffb26e7e8b39..7520d588d6840 100644 --- a/data/ddecon/ddeconbioschemas.jsonld +++ b/data/ddecon/ddeconbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-3161-8802", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/ddecon", "@type": "sc:SoftwareApplication", @@ -30,19 +34,15 @@ "sc:license": "Other", "sc:name": "DDecon", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://www.scripps.edu/fowler/ddecon/" }, { "@id": "https://doi.org/10.1111/jmi.12456", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-3161-8802", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/ddgraph/ddgraphbioschemas.jsonld b/data/ddgraph/ddgraphbioschemas.jsonld index c5778b5984e58..2e7cb053bc638 100644 --- a/data/ddgraph/ddgraphbioschemas.jsonld +++ b/data/ddgraph/ddgraphbioschemas.jsonld @@ -9,25 +9,29 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-4588-7867", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/ddgraph", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Robert Stojnic", { "@id": "http://orcid.org/0000-0003-4588-7867" - }, - "Robert Stojnic" + } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:23144600", + "pmcid:PMC3493460", { "@id": "https://doi.org/10.1371/journal.pcbi.1002725" }, - "pmcid:PMC3493460" + "pubmed:23144600" ], "sc:description": "Distinguish direct from indirect interactions in gene regulation and infer combinatorial code from highly correlated variables such as transcription factor binding profiles. The package implements the Neighbourhood Consistent PC algorithm (NCPC) and draws Direct Dependence Graphs to represent dependence structure around a target variable. The package also provides a unified interface to other Graphical Modelling (Bayesian Network) packages for distinguishing direct and indirect interactions.", "sc:featureList": { @@ -36,17 +40,13 @@ "sc:license": "GPL-3.0", "sc:name": "ddgraph", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ddgraph.html", "sc:version": "1.18.0" }, - { - "@id": "http://orcid.org/0000-0003-4588-7867", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1371/journal.pcbi.1002725", "@type": "sc:CreativeWork" diff --git a/data/ddi-cpi/ddi-cpibioschemas.jsonld b/data/ddi-cpi/ddi-cpibioschemas.jsonld index f1c4352ee62a6..92b3ce47582eb 100644 --- a/data/ddi-cpi/ddi-cpibioschemas.jsonld +++ b/data/ddi-cpi/ddi-cpibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "DDI-CPI, is a web server that predicts Drug-Drug Interactions through implementing the Chemical-Protein Interactome.", "sc:name": "DDI-CPI", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://cpi.bio-x.cn/ddi/" } \ No newline at end of file diff --git a/data/ddpcr/ddpcrbioschemas.jsonld b/data/ddpcr/ddpcrbioschemas.jsonld index 7bb35d7636616..ba32701105c3e 100644 --- a/data/ddpcr/ddpcrbioschemas.jsonld +++ b/data/ddpcr/ddpcrbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/f1000research.9022.1", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-6983-2759", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/ddpcr", "@type": "sc:SoftwareApplication", @@ -42,10 +34,18 @@ "sc:name": "ddpcr", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://daattali.com/shiny/ddpcr/" + }, + { + "@id": "http://orcid.org/0000-0002-6983-2759", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.12688/f1000research.9022.1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ddpcrclust/ddpcrclustbioschemas.jsonld b/data/ddpcrclust/ddpcrclustbioschemas.jsonld index d9c402ceec4c4..2c14f82bfdb4c 100644 --- a/data/ddpcrclust/ddpcrclustbioschemas.jsonld +++ b/data/ddpcrclust/ddpcrclustbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Benedikt G Brink", "sc:additionalType": [ - "Library", - "Web application" + "Web application", + "Library" ], "sc:description": "Automated quantification of non-orthogonal, multiplexed ddPCR data.", "sc:license": "Artistic-2.0", "sc:name": "ddPCRclust", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/bgbrink/ddPCRclust", "sc:version": "1.0.1" diff --git a/data/ddt/ddtbioschemas.jsonld b/data/ddt/ddtbioschemas.jsonld index 17d75d7f07938..008c70cc9f090 100644 --- a/data/ddt/ddtbioschemas.jsonld +++ b/data/ddt/ddtbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "DDT", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://sites.google.com/site/vittoriolimongelli/downloads" } \ No newline at end of file diff --git a/data/debrowser/debrowserbioschemas.jsonld b/data/debrowser/debrowserbioschemas.jsonld index df70c91a594ed..2b10ddd2be90a 100644 --- a/data/debrowser/debrowserbioschemas.jsonld +++ b/data/debrowser/debrowserbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "debrowser", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/debrowser.html", "sc:version": "1.2.3" diff --git a/data/deca/decabioschemas.jsonld b/data/deca/decabioschemas.jsonld index 476851fe27e5f..5e1f0956e909e 100644 --- a/data/deca/decabioschemas.jsonld +++ b/data/deca/decabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Species disambiguation system for biological named entities. The system will identify protein entities and disambiguate them according to species, by assigning NCBI Taxonomy organism IDs.", "sc:name": "DECA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.nactem.ac.uk/deca_details/start.cgi" } \ No newline at end of file diff --git a/data/decipher/decipherbioschemas.jsonld b/data/decipher/decipherbioschemas.jsonld index 511edd7499fcc..9999cbc9c2ae8 100644 --- a/data/decipher/decipherbioschemas.jsonld +++ b/data/decipher/decipherbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "DECIPHER", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DECIPHER.html", "sc:version": "2.2.0" diff --git a/data/decipher_rare_disease/decipher_rare_diseasebioschemas.jsonld b/data/decipher_rare_disease/decipher_rare_diseasebioschemas.jsonld index 6c69e9a37b023..5dc93d956797b 100644 --- a/data/decipher_rare_disease/decipher_rare_diseasebioschemas.jsonld +++ b/data/decipher_rare_disease/decipher_rare_diseasebioschemas.jsonld @@ -9,42 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1002/humu.22842", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/DECIPHER_rare_disease", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:26220709", { "@id": "https://doi.org/10.1002/humu.22842" }, + "pubmed:26220709", "pmcid:PMC4832335" ], "sc:description": "Web-based platform for secure deposition, analysis, and sharing of plausibly pathogenic genomic variants from well-phenotyped patients suffering from genetic disorders.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_3226" }, { "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3226" + "@id": "edam:operation_3431" } ], "sc:license": "Other", "sc:name": "DECIPHER", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://decipher.sanger.ac.uk/", "sc:version": "9.29" - }, - { - "@id": "https://doi.org/10.1002/humu.22842", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/decoad/decoadbioschemas.jsonld b/data/decoad/decoadbioschemas.jsonld index c02ddb037dc40..92c52b8286697 100644 --- a/data/decoad/decoadbioschemas.jsonld +++ b/data/decoad/decoadbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S13104-015-1211-Z", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/decoad", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mehdi Bagheri Hamaneh", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:26047952", + "pmcid:PMC4467632", { "@id": "https://doi.org/10.1186/S13104-015-1211-Z" }, - "pmcid:PMC4467632" + "pubmed:26047952" ], "sc:description": "Determining correlations among diseases using protein interaction networks.", "sc:featureList": [ @@ -37,10 +41,6 @@ "Mac" ], "sc:url": "https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/mn/DeCoaD/" - }, - { - "@id": "https://doi.org/10.1186/S13104-015-1211-Z", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/decode/decodebioschemas.jsonld b/data/decode/decodebioschemas.jsonld index 2e9c382493a15..8156dfb00ee1f 100644 --- a/data/decode/decodebioschemas.jsonld +++ b/data/decode/decodebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "deCODE", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/cgi-bin/decode/decode.cgi", diff --git a/data/decomptumor2sig/decomptumor2sigbioschemas.jsonld b/data/decomptumor2sig/decomptumor2sigbioschemas.jsonld index d6ba3ae4465a7..6f9e32d49bd1a 100644 --- a/data/decomptumor2sig/decomptumor2sigbioschemas.jsonld +++ b/data/decomptumor2sig/decomptumor2sigbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2688-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/decompTumor2Sig", "@type": "sc:SoftwareApplication", @@ -20,30 +16,34 @@ "sc:additionalType": "Library", "sc:author": "Prof. Dr. Rosario M. Piro", "sc:citation": [ - "pubmed:30999866", - "pmcid:PMC6472187", { "@id": "https://doi.org/10.1186/s12859-019-2688-6" - } + }, + "pubmed:30999866", + "pmcid:PMC6472187" ], "sc:description": "R package for identification of mutational signatures active in individual tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor.", "sc:featureList": [ { - "@id": "edam:operation_0239" + "@id": "edam:operation_1812" }, { - "@id": "edam:operation_1812" + "@id": "edam:operation_0239" } ], "sc:license": "GPL-2.0", "sc:name": "decompTumor2Sig", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://rmpiro.net/decompTumor2Sig/", "sc:version": "2.0.0" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2688-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/deconmsn/deconmsnbioschemas.jsonld b/data/deconmsn/deconmsnbioschemas.jsonld index 2b5b436973523..120a372757726 100644 --- a/data/deconmsn/deconmsnbioschemas.jsonld +++ b/data/deconmsn/deconmsnbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for accurate precursor ion monoisotopic mass determination for tandem mass spectra.", "sc:name": "DeconMSn", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://omics.pnl.gov/software/DeconMSn.php" } \ No newline at end of file diff --git a/data/deconrnaseq/deconrnaseqbioschemas.jsonld b/data/deconrnaseq/deconrnaseqbioschemas.jsonld index 4a66186c6782a..423a573718080 100644 --- a/data/deconrnaseq/deconrnaseqbioschemas.jsonld +++ b/data/deconrnaseq/deconrnaseqbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "DeconRNASeq", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DeconRNASeq.html", "sc:version": "1.16.0" diff --git a/data/deconseq/deconseqbioschemas.jsonld b/data/deconseq/deconseqbioschemas.jsonld index b592f1731e76b..0aef3bdfcdde0 100644 --- a/data/deconseq/deconseqbioschemas.jsonld +++ b/data/deconseq/deconseqbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/deconseq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Q&A Site", - "Rob Edwards" + "Rob Edwards", + "Q&A Site" ], "sc:additionalType": "Web service", "sc:citation": "pubmed:21408061", @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "DeconSeq", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://edwards.sdsu.edu/deconseq" } \ No newline at end of file diff --git a/data/deconstruct/deconstructbioschemas.jsonld b/data/deconstruct/deconstructbioschemas.jsonld index ac24b3267859c..e88326769f3d6 100644 --- a/data/deconstruct/deconstructbioschemas.jsonld +++ b/data/deconstruct/deconstructbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "deconSTRUCT web server interfaces with a protein database search engine and can be used for the detection of similar protein (sub)structures.", "sc:name": "deconSTRUCT", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://epsf.bmad.bii.a-star.edu.sg/struct_server.html" diff --git a/data/decontaminer/decontaminerbioschemas.jsonld b/data/decontaminer/decontaminerbioschemas.jsonld index a6e8decda593f..2839ab169a527 100644 --- a/data/decontaminer/decontaminerbioschemas.jsonld +++ b/data/decontaminer/decontaminerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "DecontaMiner", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www-labgtp.na.icar.cnr.it/decontaminer" } \ No newline at end of file diff --git a/data/decontools/decontoolsbioschemas.jsonld b/data/decontools/decontoolsbioschemas.jsonld index 6f6510ae61954..edcf76556a0ef 100644 --- a/data/decontools/decontoolsbioschemas.jsonld +++ b/data/decontools/decontoolsbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/decontools", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": "pubmed:10757168", "sc:description": "Advanced peak picking of MS and LC-MS(/MS) data using THRASH and other algorithms.", "sc:name": "DeconTools", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://omics.pnl.gov/software/DeconTools.php" } \ No newline at end of file diff --git a/data/decostar/decostarbioschemas.jsonld b/data/decostar/decostarbioschemas.jsonld index 87e2aa6837789..792d2d82f3528 100644 --- a/data/decostar/decostarbioschemas.jsonld +++ b/data/decostar/decostarbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/gbe/evx069", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/decostar", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5441342", - "pubmed:28402423", { "@id": "https://doi.org/10.1093/gbe/evx069" - } + }, + "pubmed:28402423" ], "sc:description": "Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.", "sc:featureList": { @@ -31,10 +35,6 @@ "Mac" ], "sc:url": "http://pbil.univ-lyon1.fr/software/DeCoSTAR/" - }, - { - "@id": "https://doi.org/10.1093/gbe/evx069", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/decoydeveloper/decoydeveloperbioschemas.jsonld b/data/decoydeveloper/decoydeveloperbioschemas.jsonld index 3c7c70505792d..196e41b3ba263 100644 --- a/data/decoydeveloper/decoydeveloperbioschemas.jsonld +++ b/data/decoydeveloper/decoydeveloperbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "DecoyDeveloper", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://glycopro.chem.ku.edu/JHome.php" } \ No newline at end of file diff --git a/data/decrease_redundancy/decrease_redundancybioschemas.jsonld b/data/decrease_redundancy/decrease_redundancybioschemas.jsonld index 9c65261604615..e54e1398324b0 100644 --- a/data/decrease_redundancy/decrease_redundancybioschemas.jsonld +++ b/data/decrease_redundancy/decrease_redundancybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Redundancy reduction in a set of aligned or unaligned sequences", "sc:name": "Decrease redundancy", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://web.expasy.org/decrease_redundancy/" } \ No newline at end of file diff --git a/data/decres/decresbioschemas.jsonld b/data/decres/decresbioschemas.jsonld index 3a24bddb51bfd..cb17688901cdd 100644 --- a/data/decres/decresbioschemas.jsonld +++ b/data/decres/decresbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "DEep learning for identifying Cis-Regulatory ElementS is an extension of the Deep Learning Tutorials developped by LISA lab (www.deeplearning.net/tutorial/). Although it is developped for the identification of CREs, it can also be used for other applications.", "sc:name": "DECRES", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/yifeng-li/DECRES" } \ No newline at end of file diff --git a/data/decryptor/decryptorbioschemas.jsonld b/data/decryptor/decryptorbioschemas.jsonld index e8a64979c22f5..27b43ac597625 100644 --- a/data/decryptor/decryptorbioschemas.jsonld +++ b/data/decryptor/decryptorbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/decryptor", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jana Vrbková", - "Decryptor support" + "Decryptor support", + "Jana Vrbková" ], "sc:additionalType": "Web application", "sc:description": "Tandem mass spectrometry data analysis of human proteome for presence of point alterations. Subsequently, deduces DNA/mRNA alterations whenever possible.", "sc:name": "Decryptor", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "Palacky University Olomouc", "sc:url": "http://decryptor.imtm.cz/", diff --git a/data/dedal/dedalbioschemas.jsonld b/data/dedal/dedalbioschemas.jsonld index ce30558057c52..b36173ecb2bd2 100644 --- a/data/dedal/dedalbioschemas.jsonld +++ b/data/dedal/dedalbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "DeDaL", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinfo-out.curie.fr/projects/dedal/" } \ No newline at end of file diff --git a/data/deds/dedsbioschemas.jsonld b/data/deds/dedsbioschemas.jsonld index 45508cb97808c..5110936835b87 100644 --- a/data/deds/dedsbioschemas.jsonld +++ b/data/deds/dedsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yuanyuan Xiao", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F and B statistics. It also implements a new methodology called Differential Expression via Distance Summary, which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.", "sc:license": "GPL-3.0", diff --git a/data/deep/deepbioschemas.jsonld b/data/deep/deepbioschemas.jsonld index 2dd726eaf9d9d..5d28c96c5f5d8 100644 --- a/data/deep/deepbioschemas.jsonld +++ b/data/deep/deepbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).", "sc:name": "DEEP", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.bioinf.med.uni-goettingen.de/services/deep/" } \ No newline at end of file diff --git a/data/deepbase/deepbasebioschemas.jsonld b/data/deepbase/deepbasebioschemas.jsonld index e5e1915dc52c1..a052c1508573c 100644 --- a/data/deepbase/deepbasebioschemas.jsonld +++ b/data/deepbase/deepbasebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, C. intestinalis, D. melanogaster, C. elegans and A. thaliana. It facilitates the comprehensive annotation and discovery of small RNAs from transcriptomic data such as ncRNA-associated small RNAs (nasRNAs), promoter-associated small RNAs (pasRNAs), exon-associated small RNAs (easRNAs), repeat-associated small RNAs (rasRNAs) and miRNA and snoRNA candidates.", "sc:name": "deepBase", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://rna.sysu.edu.cn/deepBase/" } \ No newline at end of file diff --git a/data/deepblue/deepbluebioschemas.jsonld b/data/deepblue/deepbluebioschemas.jsonld index 508d83dc5bc0f..52548e701b4a1 100644 --- a/data/deepblue/deepbluebioschemas.jsonld +++ b/data/deepblue/deepbluebioschemas.jsonld @@ -12,14 +12,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Felipe Albrecht", "sc:additionalType": [ + "Web application", "Web API", - "Database portal", - "Web application" + "Database portal" ], "sc:author": "Felipe Albrecht", "sc:contributor": [ - "EU grant No. HEALTH-F5-2011-282510 (BLUEPRINT project)", - "German Science Ministry Grant No.01KU1216A (DEEP project)" + "German Science Ministry Grant No.01KU1216A (DEEP project)", + "EU grant No. HEALTH-F5-2011-282510 (BLUEPRINT project)" ], "sc:description": "Provides a central data access hub for large collections of epigenomic data. It organizes the data from different sources using controlled vocabularies and ontologies. The data is stored in our server, where the users can access the data programmatically or by our web interface. It contains a set of commands designed to perform operations on the epigenomic data. Users can execute all operations in a pipeline fashion in the server and transfer only meaningful data.", "sc:funder": [ @@ -30,8 +30,8 @@ "sc:name": "DeepBlue Epigenomic Data Server", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "Max Planck Institute for Informatics", diff --git a/data/deepbluer/deepbluerbioschemas.jsonld b/data/deepbluer/deepbluerbioschemas.jsonld index a1e6548dde6bf..947410a9ab214 100644 --- a/data/deepbluer/deepbluerbioschemas.jsonld +++ b/data/deepbluer/deepbluerbioschemas.jsonld @@ -9,22 +9,26 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btx099", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/deepbluer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Felipe Albrecht", { "@id": "http://orcid.org/0000-0002-0941-4168" - } + }, + "Felipe Albrecht" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:28334349", "pmcid:PMC5870546", + "pubmed:28334349", { "@id": "https://doi.org/10.1093/bioinformatics/btx099" } @@ -46,10 +50,6 @@ { "@id": "http://orcid.org/0000-0002-0941-4168", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btx099", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/deepcircode/deepcircodebioschemas.jsonld b/data/deepcircode/deepcircodebioschemas.jsonld index 5012c559211d0..67899a5cae5b9 100644 --- a/data/deepcircode/deepcircodebioschemas.jsonld +++ b/data/deepcircode/deepcircodebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/DeepCirCode", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Liangjiang Wang", - "Jun Wang" + "Jun Wang", + "Liangjiang Wang" ], "sc:additionalType": "Library", "sc:citation": "pubmed:31077303", @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "DeepCirCode", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/BioDataLearning/DeepCirCode" } \ No newline at end of file diff --git a/data/deepdr/deepdrbioschemas.jsonld b/data/deepdr/deepdrbioschemas.jsonld index 0742d365f36fc..666834835bae6 100644 --- a/data/deepdr/deepdrbioschemas.jsonld +++ b/data/deepdr/deepdrbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Unlicense", "sc:name": "deepDR", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ChengF-Lab/deepDR" } \ No newline at end of file diff --git a/data/deepefflux/deepeffluxbioschemas.jsonld b/data/deepefflux/deepeffluxbioschemas.jsonld index 75cf92ed18b39..41bcc530563dc 100644 --- a/data/deepefflux/deepeffluxbioschemas.jsonld +++ b/data/deepefflux/deepeffluxbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "2D convolutional neural network model for identifying families of efflux proteins in transporters.", "sc:name": "DeepEfflux", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://140.138.155.216/deepefflux/" } \ No newline at end of file diff --git a/data/deeploc/deeplocbioschemas.jsonld b/data/deeploc/deeplocbioschemas.jsonld index 0b95fb28bfdad..0266d5cd097aa 100644 --- a/data/deeploc/deeplocbioschemas.jsonld +++ b/data/deeploc/deeplocbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "DeepLoc", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.cbs.dtu.dk/services/DeepLoc/", "sc:version": "1.0" diff --git a/data/deeppvp/deeppvpbioschemas.jsonld b/data/deeppvp/deeppvpbioschemas.jsonld index a2a8bdaf4af09..01a5397c025af 100644 --- a/data/deeppvp/deeppvpbioschemas.jsonld +++ b/data/deeppvp/deeppvpbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2633-8", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/DeepPVP", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bio-Ontology Research Group", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:30727941", { "@id": "https://doi.org/10.1186/s12859-019-2633-8" }, - "pubmed:30727941", "pmcid:PMC6364462" ], "sc:description": "Phenotype-based variant prioritization method that combined automated inference with deep neural networks to identify the likely causative variants in whole exome or whole genome sequence data.", @@ -40,10 +44,6 @@ "Linux" ], "sc:url": "https://github.com/bio-ontology-research-group/phenomenet-vp" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2633-8", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/deepred/deepredbioschemas.jsonld b/data/deepred/deepredbioschemas.jsonld index 8882d4169168c..d4a42eec4c9ad 100644 --- a/data/deepred/deepredbioschemas.jsonld +++ b/data/deepred/deepredbioschemas.jsonld @@ -17,15 +17,15 @@ "@id": "https://bio.tools/DEEPred", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Volkan Atalay", - "Tunca DoÄŸan" + "Tunca DoÄŸan", + "Volkan Atalay" ], "sc:additionalType": "Script", "sc:citation": [ + "pmcid:PMC6517386", { "@id": "https://doi.org/10.1038/S41598-019-43708-3" }, - "pmcid:PMC6517386", "pubmed:31089211" ], "sc:description": "Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks.", @@ -35,8 +35,8 @@ "sc:license": "GPL-3.0", "sc:name": "DEEPred", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/cansyl/DEEPred" diff --git a/data/deepsig/deepsigbioschemas.jsonld b/data/deepsig/deepsigbioschemas.jsonld index 676a3df4f353a..6243e93f050b4 100644 --- a/data/deepsig/deepsigbioschemas.jsonld +++ b/data/deepsig/deepsigbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Prediction of secretory signal peptides in protein sequences", "sc:name": "DeepSig", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "https://deepsig.biocomp.unibo.it", diff --git a/data/deepsnv/deepsnvbioschemas.jsonld b/data/deepsnv/deepsnvbioschemas.jsonld index 8164bafbd68ce..c901e13ff2083 100644 --- a/data/deepsnv/deepsnvbioschemas.jsonld +++ b/data/deepsnv/deepsnvbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btt750", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/deepsnv", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC3998123", "pubmed:24443148", { "@id": "https://doi.org/10.1093/bioinformatics/btt750" - } + }, + "pmcid:PMC3998123" ], "sc:description": "This package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages are integrated to provide a wide range of tools for gene expression analysis.", "sc:featureList": { @@ -31,16 +35,12 @@ "sc:license": "GPL-3.0", "sc:name": "deepSNV", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/deepSNV.html", "sc:version": "1.20.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btt750", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/deepsplice/deepsplicebioschemas.jsonld b/data/deepsplice/deepsplicebioschemas.jsonld index 37886d1bd2c63..19677a96bfcce 100644 --- a/data/deepsplice/deepsplicebioschemas.jsonld +++ b/data/deepsplice/deepsplicebioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Yi Zhang", "sc:additionalType": "Script", "sc:citation": [ - "pubmed:30591034", - "pmcid:PMC6307148", { "@id": "https://doi.org/10.1186/s12864-018-5350-1" - } + }, + "pmcid:PMC6307148", + "pubmed:30591034" ], "sc:description": "Deep learning based splice junction sequence classifier.", "sc:featureList": [ @@ -27,17 +27,17 @@ "@id": "edam:operation_0446" }, { - "@id": "edam:operation_0433" + "@id": "edam:operation_0264" }, { - "@id": "edam:operation_0264" + "@id": "edam:operation_0433" } ], "sc:license": "Unlicense", "sc:name": "DeepSplice", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/zhangyimc/DeepSplice" }, diff --git a/data/deepsynergy/deepsynergybioschemas.jsonld b/data/deepsynergy/deepsynergybioschemas.jsonld index f8be944ae8174..cf3742fa41e5b 100644 --- a/data/deepsynergy/deepsynergybioschemas.jsonld +++ b/data/deepsynergy/deepsynergybioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Predicting anti-cancer drug synergy with Deep Learning.", "sc:name": "DeepSynergy", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.bioinf.jku.at/software/DeepSynergy/" } \ No newline at end of file diff --git a/data/deeptools/deeptoolsbioschemas.jsonld b/data/deeptools/deeptoolsbioschemas.jsonld index 02dc97e912f1d..34d43c211bb1d 100644 --- a/data/deeptools/deeptoolsbioschemas.jsonld +++ b/data/deeptools/deeptoolsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "DeepTools", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://deeptools.readthedocs.io/en/latest/" } \ No newline at end of file diff --git a/data/deeptype/deeptypebioschemas.jsonld b/data/deeptype/deeptypebioschemas.jsonld index 2bbf13db3ebe2..05465597e7f3e 100644 --- a/data/deeptype/deeptypebioschemas.jsonld +++ b/data/deeptype/deeptypebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "DeepType", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.acsu.buffalo.edu/~yijunsun/lab/DeepType.html" } \ No newline at end of file diff --git a/data/deepubi/deepubibioschemas.jsonld b/data/deepubi/deepubibioschemas.jsonld index eba575f05a685..c6ec75299601b 100644 --- a/data/deepubi/deepubibioschemas.jsonld +++ b/data/deepubi/deepubibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "DeepUbi", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/Sunmile/DeepUbi" } \ No newline at end of file diff --git a/data/defcom/defcombioschemas.jsonld b/data/defcom/defcombioschemas.jsonld index 179391c7987eb..6a19b6901420d 100644 --- a/data/defcom/defcombioschemas.jsonld +++ b/data/defcom/defcombioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/defcom", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Terry Furey", - "Bryan Quach" + "Bryan Quach", + "Terry Furey" ], "sc:additionalType": "Library", "sc:citation": "pubmed:27993786", diff --git a/data/deformats/bioconda_deformats.yaml b/data/deformats/bioconda_deformats.yaml index 20a5175eb5faf..c9b2a34327272 100644 --- a/data/deformats/bioconda_deformats.yaml +++ b/data/deformats/bioconda_deformats.yaml @@ -4,7 +4,6 @@ description: Convert between different data formats used by differential gene ex home: https://bioconductor.org/packages/3.10/bioc/html/DEFormats.html identifiers: - biotools:deformats -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-deformats diff --git a/data/deformats/deformatsbioschemas.jsonld b/data/deformats/deformatsbioschemas.jsonld index be3b6d9bec2d6..d209395cde3ce 100644 --- a/data/deformats/deformatsbioschemas.jsonld +++ b/data/deformats/deformatsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Andrzej Oleś", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Covert between different data formats used by differential gene expression analysis tools.", "sc:license": "GPL-3.0", "sc:name": "DEFormats", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DEFormats.html", "sc:version": "1.2.0" diff --git a/data/defume/defumebioschemas.jsonld b/data/defume/defumebioschemas.jsonld index 558c0873c8a55..b6a3f5829b303 100644 --- a/data/defume/defumebioschemas.jsonld +++ b/data/defume/defumebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13104-015-1281-y", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/defume", "@type": "sc:SoftwareApplication", @@ -18,10 +22,10 @@ ], "sc:additionalType": "Web service", "sc:citation": [ - "pmcid:PMC4520277", { "@id": "https://doi.org/10.1186/s13104-015-1281-y" }, + "pmcid:PMC4520277", "pubmed:26227142" ], "sc:description": "Assemble Sanger sequencing reads, identify ORFs and blast these as well as annotating them with InterPro.", @@ -30,16 +34,12 @@ }, "sc:name": "deFUME", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.cbs.dtu.dk/services/deFUME/", "sc:version": "1.0" - }, - { - "@id": "https://doi.org/10.1186/s13104-015-1281-y", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/defuse/defusebioschemas.jsonld b/data/defuse/defusebioschemas.jsonld index f6b95df9f1fed..7d1c896f3d5f6 100644 --- a/data/defuse/defusebioschemas.jsonld +++ b/data/defuse/defusebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries.", "sc:name": "DeFuse", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://shahlab.ca/projects/defuse/" } \ No newline at end of file diff --git a/data/degapseq/degapseqbioschemas.jsonld b/data/degapseq/degapseqbioschemas.jsonld index b15bc8df6a251..713996b0c1092 100644 --- a/data/degapseq/degapseqbioschemas.jsonld +++ b/data/degapseq/degapseqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", + "EMBOSS Contributors", "Wellcome Trust", "UK MRC", - "EMBOSS Contributors" + "UK BBSRC" ], "sc:description": "Remove non-alphabetic (e.g. gap) characters from sequences.", "sc:funder": [ - "UK BBSRC", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "degapseq", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/degapseq.html", "sc:version": "r6" diff --git a/data/degps/degpsbioschemas.jsonld b/data/degps/degpsbioschemas.jsonld index 87169dd40190f..b3cadc004f387 100644 --- a/data/degps/degpsbioschemas.jsonld +++ b/data/degps/degpsbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC4465298", - "pubmed:26070955", { "@id": "https://doi.org/10.1186/s12864-015-1676-0" - } + }, + "pubmed:26070955" ], "sc:description": "deGPS is a tool for detecting differential expression in RNA-Seq data.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "Other", "sc:name": "deGPS", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/LL-LAB-MCW/deGPS" } diff --git a/data/degraph/degraphbioschemas.jsonld b/data/degraph/degraphbioschemas.jsonld index e3b2bbb22939f..2e64c672fc1df 100644 --- a/data/degraph/degraphbioschemas.jsonld +++ b/data/degraph/degraphbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laurent Jacob", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Implements recent hypothesis testing methods to assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches. These recent methods consider the topology of the network to yield more powerful detection procedures. It provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.", "sc:license": "GPL-3.0", "sc:name": "DEGraph", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DEGraph.html", "sc:version": "1.26.0" diff --git a/data/degreport/bioconda_degreport.yaml b/data/degreport/bioconda_degreport.yaml index d1834162d84e6..3826a7ed5a25e 100644 --- a/data/degreport/bioconda_degreport.yaml +++ b/data/degreport/bioconda_degreport.yaml @@ -6,7 +6,6 @@ description: Creation of a HTML report of differential expression analyses of co home: https://bioconductor.org/packages/3.10/bioc/html/DEGreport.html identifiers: - biotools:degreport -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-degreport diff --git a/data/degreport/degreportbioschemas.jsonld b/data/degreport/degreportbioschemas.jsonld index 25ab12216aab9..ad95c8dfe6d2b 100644 --- a/data/degreport/degreportbioschemas.jsonld +++ b/data/degreport/degreportbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lorena Pantano", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.", "sc:license": "MIT", diff --git a/data/degseq/degseqbioschemas.jsonld b/data/degseq/degseqbioschemas.jsonld index db986917132ee..d980a14aeb1fb 100644 --- a/data/degseq/degseqbioschemas.jsonld +++ b/data/degseq/degseqbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Likun Wang", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "R package to identify differentially expressed genes from RNA-Seq data.", "sc:license": "GPL-2.0", "sc:name": "DEGseq", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DEGseq.html", "sc:version": "1.28.0" diff --git a/data/delayedarray/delayedarraybioschemas.jsonld b/data/delayedarray/delayedarraybioschemas.jsonld index 7214d53257457..850be1731d6d4 100644 --- a/data/delayedarray/delayedarraybioschemas.jsonld +++ b/data/delayedarray/delayedarraybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "DelayedArray", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DelayedArray.html", diff --git a/data/delayedmatrixstats/delayedmatrixstatsbioschemas.jsonld b/data/delayedmatrixstats/delayedmatrixstatsbioschemas.jsonld index 59bf22e5c16cc..41cdb341de166 100644 --- a/data/delayedmatrixstats/delayedmatrixstatsbioschemas.jsonld +++ b/data/delayedmatrixstats/delayedmatrixstatsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "DelayedMatrixStats", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DelayedMatrixStats.html", "sc:version": "1.2.0" diff --git a/data/delly2/delly2bioschemas.jsonld b/data/delly2/delly2bioschemas.jsonld index 40d5190e92d81..888194db65b16 100644 --- a/data/delly2/delly2bioschemas.jsonld +++ b/data/delly2/delly2bioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/bts378", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/delly2", "@type": "sc:SoftwareApplication", @@ -20,33 +16,37 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:22962449", + "pmcid:PMC3436805", { "@id": "https://doi.org/10.1093/bioinformatics/bts378" - }, - "pmcid:PMC3436805" + } ], "sc:description": "Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.", "sc:featureList": [ { - "@id": "edam:operation_3227" + "@id": "edam:operation_0452" }, { - "@id": "edam:operation_2480" + "@id": "edam:operation_3227" }, { - "@id": "edam:operation_0452" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3211" + "@id": "edam:operation_2480" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3211" } ], "sc:license": "GPL-3.0", "sc:name": "Delly2", "sc:operatingSystem": "Linux", "sc:url": "http://www.korbel.embl.de/software.html" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/bts378", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/delphi_force/delphi_forcebioschemas.jsonld b/data/delphi_force/delphi_forcebioschemas.jsonld index 8ae984d778e0e..c8a2fff047024 100644 --- a/data/delphi_force/delphi_forcebioschemas.jsonld +++ b/data/delphi_force/delphi_forcebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Calculate the electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, etc.", "sc:name": "DelPhi Force", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://compbio.clemson.edu/delphi-force/" } \ No newline at end of file diff --git a/data/delphiforce/delphiforcebioschemas.jsonld b/data/delphiforce/delphiforcebioschemas.jsonld index 6009d0a8aacc2..44c868ba350d1 100644 --- a/data/delphiforce/delphiforcebioschemas.jsonld +++ b/data/delphiforce/delphiforcebioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1002/jcc.24715", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/delphiforce", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Emil Alexov", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5315605", "pubmed:28130775", { "@id": "https://doi.org/10.1002/jcc.24715" - } + }, + "pmcid:PMC5315605" ], "sc:description": "DelPhi-based script, allowing to calculate the electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, etc.", "sc:featureList": [ { - "@id": "edam:operation_0262" + "@id": "edam:operation_0250" }, { - "@id": "edam:operation_0250" + "@id": "edam:operation_0262" } ], "sc:name": "DelPhiForce", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://compbio.clemson.edu/delphi-force/" + }, + { + "@id": "https://doi.org/10.1002/jcc.24715", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/delta_mass/delta_massbioschemas.jsonld b/data/delta_mass/delta_massbioschemas.jsonld index 9f089fabf3a7b..653883ee89045 100644 --- a/data/delta_mass/delta_massbioschemas.jsonld +++ b/data/delta_mass/delta_massbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The ABRF database of protein post-translational modifications.", "sc:name": "Delta Mass", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.abrf.org/index.cfm/dm.home" } \ No newline at end of file diff --git a/data/deltag_prediction/deltag_predictionbioschemas.jsonld b/data/deltag_prediction/deltag_predictionbioschemas.jsonld index 4bf0d22927d11..f6a5140ff6904 100644 --- a/data/deltag_prediction/deltag_predictionbioschemas.jsonld +++ b/data/deltag_prediction/deltag_predictionbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "DeltaG prediction", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "bils.se", "sc:url": "http://dgpred.cbr.su.se/", diff --git a/data/deltamass/deltamassbioschemas.jsonld b/data/deltamass/deltamassbioschemas.jsonld index 78538aa416e67..a6d4718fefbe2 100644 --- a/data/deltamass/deltamassbioschemas.jsonld +++ b/data/deltamass/deltamassbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "DeltaMass", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/chhh/deltamass", diff --git a/data/deltanet/deltanetbioschemas.jsonld b/data/deltanet/deltanetbioschemas.jsonld index 535e30933989e..cf9c24703d65b 100644 --- a/data/deltanet/deltanetbioschemas.jsonld +++ b/data/deltanet/deltanetbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "DeltaNet is a network analysis tool for predicting genetic perturbations from gene expression data.", "sc:name": "DeltaNet", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cabsel.ethz.ch/tools/DeltaNet", "sc:version": "1.0" diff --git a/data/demand/bioconda_demand.yaml b/data/demand/bioconda_demand.yaml index 585b2d185553c..f0756d5b444b9 100644 --- a/data/demand/bioconda_demand.yaml +++ b/data/demand/bioconda_demand.yaml @@ -6,7 +6,6 @@ description: DEMAND predicts Drug MoA by interrogating a cell context specific r home: https://bioconductor.org/packages/3.10/bioc/html/DeMAND.html identifiers: - biotools:demand -- doi:10.1038/nmeth.3252 license: file LICENSE license_file: LICENSE name: bioconductor-demand diff --git a/data/demand/demandbioschemas.jsonld b/data/demand/demandbioschemas.jsonld index 4daab6ffb1031..7033f420ad509 100644 --- a/data/demand/demandbioschemas.jsonld +++ b/data/demand/demandbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/demand", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jung Hoon Woo", - "Mariano Alvarez" + "Mariano Alvarez", + "Jung Hoon Woo" ], "sc:additionalType": [ "Library", @@ -21,8 +21,8 @@ "sc:description": "This software predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.", "sc:name": "DeMAND", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DeMAND.html", diff --git a/data/demuxlet/demuxletbioschemas.jsonld b/data/demuxlet/demuxletbioschemas.jsonld index 75bf6f3c3bdc6..bdc0dc9adf0dd 100644 --- a/data/demuxlet/demuxletbioschemas.jsonld +++ b/data/demuxlet/demuxletbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Apache-2.0", "sc:name": "demuxlet", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/statgen/demuxlet" diff --git a/data/den-im/den-imbioschemas.jsonld b/data/den-im/den-imbioschemas.jsonld index 7d03c5d36f2bb..b6a9616062fbc 100644 --- a/data/den-im/den-imbioschemas.jsonld +++ b/data/den-im/den-imbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "DEN-IM", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/B-UMMI/DEN-IM" } \ No newline at end of file diff --git a/data/dendrix/dendrixbioschemas.jsonld b/data/dendrix/dendrixbioschemas.jsonld index 0b04b5d8d0677..1b1742ccbd5fa 100644 --- a/data/dendrix/dendrixbioschemas.jsonld +++ b/data/dendrix/dendrixbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/dendrix", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Plug-in" + "Plug-in", + "Command-line tool" ], "sc:description": "De novo Driver Exclusivity is an algorithm to discover mutated driver pathways in cancer using only mutation data. It finds sets of genes, domains, or nucleotides whose mutations exhibit both high coverage and high exclusivity in the analyzed samples.", "sc:name": "Dendrix", diff --git a/data/dendroscope3/dendroscope3bioschemas.jsonld b/data/dendroscope3/dendroscope3bioschemas.jsonld index f5c54fee5280e..2d2ea2a80de4b 100644 --- a/data/dendroscope3/dendroscope3bioschemas.jsonld +++ b/data/dendroscope3/dendroscope3bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "Dendroscope3", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://dendroscope.org" } \ No newline at end of file diff --git a/data/dendrosplit/dendrosplitbioschemas.jsonld b/data/dendrosplit/dendrosplitbioschemas.jsonld index 6d22db3c59e53..81deaa425625d 100644 --- a/data/dendrosplit/dendrosplitbioschemas.jsonld +++ b/data/dendrosplit/dendrosplitbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Jesse M. Zhang", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:29523077", - "pmcid:PMC5845381", { "@id": "https://doi.org/10.1186/s12859-018-2092-7" - } + }, + "pubmed:29523077", + "pmcid:PMC5845381" ], "sc:description": "An interpretable framework for clustering single-cell RNA-Seq datasets.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "DendroSplit", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/jessemzhang/dendrosplit" } diff --git a/data/denovo_pipeline/denovo_pipelinebioschemas.jsonld b/data/denovo_pipeline/denovo_pipelinebioschemas.jsonld index b6508cc4e8959..4d3d57276bf0c 100644 --- a/data/denovo_pipeline/denovo_pipelinebioschemas.jsonld +++ b/data/denovo_pipeline/denovo_pipelinebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "DeNovo Pipeline performes protein identification by de novo interpretation by coupling the PepNovo software for sequencing and the Fasta tool for homology searching.", "sc:name": "DeNovo Pipeline", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://pappso.inra.fr/bioinfo/denovopipeline/", "sc:version": "1.5" diff --git a/data/denovogui/denovoguibioschemas.jsonld b/data/denovogui/denovoguibioschemas.jsonld index 692fa9a193fac..d8e615b95e166 100644 --- a/data/denovogui/denovoguibioschemas.jsonld +++ b/data/denovogui/denovoguibioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/denovogui", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Graphical user interface for de novo sequencing of tandem mass spectra.", "sc:license": "Apache-2.0", "sc:name": "Denovogui", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://compomics.github.io/projects/denovogui.html", diff --git a/data/density/densitybioschemas.jsonld b/data/density/densitybioschemas.jsonld index 79fd997b657fb..c1d9eace257f2 100644 --- a/data/density/densitybioschemas.jsonld +++ b/data/density/densitybioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "EMBOSS Contributors", + "UK BBSRC", "UK MRC", - "UK BBSRC" + "EMBOSS Contributors", + "Wellcome Trust" ], "sc:description": "Draw a nucleic acid density plot.", "sc:funder": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "density", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/densityserver/densityserverbioschemas.jsonld b/data/densityserver/densityserverbioschemas.jsonld index 05cde283bf579..6972645bf493b 100644 --- a/data/densityserver/densityserverbioschemas.jsonld +++ b/data/densityserver/densityserverbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DensityServer", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://density.litemol.org", "sc:version": "0.9.4" diff --git a/data/deogen2/deogen2bioschemas.jsonld b/data/deogen2/deogen2bioschemas.jsonld index 1b3d04c8bca3d..46eeb4635ba93 100644 --- a/data/deogen2/deogen2bioschemas.jsonld +++ b/data/deogen2/deogen2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-7470-4324", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/DEOGEN2", "@type": "sc:SoftwareApplication", @@ -24,10 +28,6 @@ "sc:description": "Sequence-based predictor of deleteriousness of amino acid variants in human proteins", "sc:name": "DEOGEN2", "sc:url": "http://deogen2.mutaframe.com/" - }, - { - "@id": "https://orcid.org/0000-0001-7470-4324", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dep/depbioschemas.jsonld b/data/dep/depbioschemas.jsonld index e91ea0b6ab5c8..211a2aa2364d9 100644 --- a/data/dep/depbioschemas.jsonld +++ b/data/dep/depbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DEP", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DEP.html", "sc:version": "1.2.0" diff --git a/data/dependency/dependencybioschemas.jsonld b/data/dependency/dependencybioschemas.jsonld index f3a62a163d5d1..883a7cba02eb1 100644 --- a/data/dependency/dependencybioschemas.jsonld +++ b/data/dependency/dependencybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A program using Multiple Interdependency to detect functional interactions between amino acids in proteins.", "sc:name": "Dependency", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.uhnresearch.ca/labs/tillier/software.htm#2", "sc:version": "2.1" diff --git a/data/depib/depibbioschemas.jsonld b/data/depib/depibbioschemas.jsonld index 882f1b3e65b5d..af28342b22493 100644 --- a/data/depib/depibbioschemas.jsonld +++ b/data/depib/depibbioschemas.jsonld @@ -9,20 +9,28 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-8689-2083", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0003-3237-7382", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/DEPIB", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Eric Charpentier", "sc:additionalType": "Workflow", "sc:author": [ + { + "@id": "https://orcid.org/0000-0002-8689-2083" + }, "Erwan Delage", - "Eric Charpentier", { "@id": "https://orcid.org/0000-0003-3237-7382" }, - { - "@id": "https://orcid.org/0000-0002-8689-2083" - } + "Eric Charpentier" ], "sc:citation": "pubmed:30977188", "sc:contributor": "Damien Vintache", @@ -31,14 +39,6 @@ "sc:provider": "BiRD", "sc:url": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipeline", "sc:version": "1.0" - }, - { - "@id": "https://orcid.org/0000-0003-3237-7382", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0002-8689-2083", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/deploid/deploidbioschemas.jsonld b/data/deploid/deploidbioschemas.jsonld index 140ef305c50ee..6d430de98378a 100644 --- a/data/deploid/deploidbioschemas.jsonld +++ b/data/deploid/deploidbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/deploid", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Gil McVean", - "Sha Joe Zhu" + "Sha Joe Zhu", + "Gil McVean" ], "sc:additionalType": "Command-line tool", "sc:description": "Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data .", diff --git a/data/depot/depotbioschemas.jsonld b/data/depot/depotbioschemas.jsonld index 42f7f67a484d2..fdcd09f206c95 100644 --- a/data/depot/depotbioschemas.jsonld +++ b/data/depot/depotbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0217410", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/DEPOT", "@type": "sc:SoftwareApplication", @@ -18,8 +22,8 @@ "Database portal" ], "sc:citation": [ - "pubmed:31120982", "pmcid:PMC6532897", + "pubmed:31120982", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0217410" } @@ -29,14 +33,10 @@ "sc:name": "DEPOT", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://depot.tbportals.niaid.nih.gov" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0217410", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/depth/depthbioschemas.jsonld b/data/depth/depthbioschemas.jsonld index d5c19871944ca..60123642198e2 100644 --- a/data/depth/depthbioschemas.jsonld +++ b/data/depth/depthbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "DEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.", "sc:name": "DEPTH", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://mspc.bii.a-star.edu.sg/depth" diff --git a/data/deqor/deqorbioschemas.jsonld b/data/deqor/deqorbioschemas.jsonld index bc1a6ff99bef9..9713fb7b44d3f 100644 --- a/data/deqor/deqorbioschemas.jsonld +++ b/data/deqor/deqorbioschemas.jsonld @@ -15,32 +15,32 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:15215362", + "pmcid:PMC441546", { "@id": "https://doi.org/10.1093/nar/gkh408" - }, - "pmcid:PMC441546" + } ], "sc:description": "Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.", "sc:featureList": [ { - "@id": "edam:operation_3218" + "@id": "edam:operation_2428" }, { - "@id": "edam:operation_2428" + "@id": "edam:operation_3180" }, { "@id": "edam:operation_2008" }, { - "@id": "edam:operation_3180" + "@id": "edam:operation_3218" } ], "sc:license": "Unlicense", "sc:name": "DEQOR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://144.76.155.9/deqor_new/input.html", "sc:version": "3" diff --git a/data/derfinder/derfinderbioschemas.jsonld b/data/derfinder/derfinderbioschemas.jsonld index a8b1e56de20ed..a1705d1c28079 100644 --- a/data/derfinder/derfinderbioschemas.jsonld +++ b/data/derfinder/derfinderbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-2873-2671", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/derfinder", "@type": "sc:SoftwareApplication", @@ -36,11 +32,11 @@ "@id": "edam:topic_3170" }, "sc:citation": [ + "pubmed:24398039", "pmcid:PMC4059460", { "@id": "https://doi.org/10.1093/biostatistics/kxt053" - }, - "pubmed:24398039" + } ], "sc:description": "This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.", "sc:featureList": [ @@ -54,9 +50,9 @@ "sc:license": "Artistic-2.0", "sc:name": "derfinder", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/derfinder.html", "sc:version": "1.8.0" @@ -64,6 +60,10 @@ { "@id": "https://doi.org/10.1093/biostatistics/kxt053", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-2873-2671", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/derfinderhelper/derfinderhelperbioschemas.jsonld b/data/derfinderhelper/derfinderhelperbioschemas.jsonld index 26e1ec37489b7..e92346f0816df 100644 --- a/data/derfinderhelper/derfinderhelperbioschemas.jsonld +++ b/data/derfinderhelper/derfinderhelperbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkw852", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/derfinderhelper", "@type": "sc:SoftwareApplication", @@ -28,10 +32,10 @@ }, "sc:citation": [ "pmcid:PMC5314792", - "pubmed:27694310", { "@id": "https://doi.org/10.1093/nar/gkw852" - } + }, + "pubmed:27694310" ], "sc:description": "Helper package for speeding up the derfinder package when using multiple cores.", "sc:featureList": { @@ -41,15 +45,11 @@ "sc:name": "derfinderHelper", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/derfinderHelper.html", "sc:version": "1.8.0" - }, - { - "@id": "https://doi.org/10.1093/nar/gkw852", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/derfinderplot/derfinderplotbioschemas.jsonld b/data/derfinderplot/derfinderplotbioschemas.jsonld index efe30d892f669..7d8271ee2e8ad 100644 --- a/data/derfinderplot/derfinderplotbioschemas.jsonld +++ b/data/derfinderplot/derfinderplotbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkw852", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/derfinderplot", "@type": "sc:SoftwareApplication", @@ -31,11 +27,11 @@ "@id": "edam:topic_0092" }, "sc:citation": [ - "pmcid:PMC5314792", + "pubmed:27694310", { "@id": "https://doi.org/10.1093/nar/gkw852" }, - "pubmed:27694310" + "pmcid:PMC5314792" ], "sc:description": "This package provides plotting functions for results from the derfinder package.", "sc:featureList": { @@ -44,12 +40,16 @@ "sc:license": "Artistic-2.0", "sc:name": "derfinderPlot", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/derfinderPlot.html", "sc:version": "1.8.0" + }, + { + "@id": "https://doi.org/10.1093/nar/gkw852", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/descan2/descan2bioschemas.jsonld b/data/descan2/descan2bioschemas.jsonld index 681f6c4f6e528..ec9efdf46e475 100644 --- a/data/descan2/descan2bioschemas.jsonld +++ b/data/descan2/descan2bioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "DEScan2", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DEScan2.html", diff --git a/data/descfold/descfoldbioschemas.jsonld b/data/descfold/descfoldbioschemas.jsonld index 730313740754e..763c68c26262e 100644 --- a/data/descfold/descfoldbioschemas.jsonld +++ b/data/descfold/descfoldbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "DescFold is a web server for protein fold recognition,which can predict a protein’s fold type from its amino acid sequence.", "sc:name": "DescFold", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://protein.cau.edu.cn/DescFold/" } \ No newline at end of file diff --git a/data/descseq/descseqbioschemas.jsonld b/data/descseq/descseqbioschemas.jsonld index 7f8d0cf99e63f..5808061d4fd21 100644 --- a/data/descseq/descseqbioschemas.jsonld +++ b/data/descseq/descseqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK MRC", "UK BBSRC", "Wellcome Trust", - "UK MRC", "EMBOSS Contributors" ], "sc:description": "Alter the name or description of a sequence.", "sc:funder": [ + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "descseq", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/descseq.html", "sc:version": "r6" diff --git a/data/deseq/deseqbioschemas.jsonld b/data/deseq/deseqbioschemas.jsonld index eb0297d4f88fa..1e1b8eca9c2fb 100644 --- a/data/deseq/deseqbioschemas.jsonld +++ b/data/deseq/deseqbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/gb-2010-11-10-r106", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-4868-1805", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/deseq", "@type": "sc:SoftwareApplication", @@ -24,26 +16,34 @@ "@id": "http://orcid.org/0000-0003-4868-1805" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pubmed:20979621", { "@id": "https://doi.org/10.1186/gb-2010-11-10-r106" }, - "pmcid:PMC3218662", - "pubmed:20979621" + "pmcid:PMC3218662" ], "sc:description": "Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.", "sc:license": "GPL-3.0", "sc:name": "DESeq", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DESeq.html", "sc:version": "1.26.0" + }, + { + "@id": "http://orcid.org/0000-0003-4868-1805", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/gb-2010-11-10-r106", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/deseq2/deseq2bioschemas.jsonld b/data/deseq2/deseq2bioschemas.jsonld index 3d08326101693..98d71e0b53c3e 100644 --- a/data/deseq2/deseq2bioschemas.jsonld +++ b/data/deseq2/deseq2bioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Wolfgang Huber", "Michael Love", - "Simon Anders" + "Simon Anders", + "Wolfgang Huber" ], "sc:description": "R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.", "sc:license": "LGPL-2.1", diff --git a/data/designsignatures/designsignaturesbioschemas.jsonld b/data/designsignatures/designsignaturesbioschemas.jsonld index c2872330d32c3..bf7614c7a5d36 100644 --- a/data/designsignatures/designsignaturesbioschemas.jsonld +++ b/data/designsignatures/designsignaturesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "DesignSignatures", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www2.decipher.codes/DesignSignatures.html" } \ No newline at end of file diff --git a/data/desingle/desinglebioschemas.jsonld b/data/desingle/desinglebioschemas.jsonld index 7a1b20e86ab62..bdd2c66751aea 100644 --- a/data/desingle/desinglebioschemas.jsonld +++ b/data/desingle/desinglebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "DEsingle", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DEsingle.html", "sc:version": "1.0.4" diff --git a/data/destiny/destinybioschemas.jsonld b/data/destiny/destinybioschemas.jsonld index 27db678d7f0c2..6b0484f4ab487 100644 --- a/data/destiny/destinybioschemas.jsonld +++ b/data/destiny/destinybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "destiny", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/destiny.html", "sc:version": "2.0.3" diff --git a/data/desubs/desubsbioschemas.jsonld b/data/desubs/desubsbioschemas.jsonld index 67bbb3702fdf7..3b1029bccb538 100644 --- a/data/desubs/desubsbioschemas.jsonld +++ b/data/desubs/desubsbioschemas.jsonld @@ -15,8 +15,8 @@ "Anastasios Bezerianos" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:27542770", "sc:description": "A network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features.", diff --git a/data/detect/detectbioschemas.jsonld b/data/detect/detectbioschemas.jsonld index d0fb1b9c9fabd..5421268ff15be 100644 --- a/data/detect/detectbioschemas.jsonld +++ b/data/detect/detectbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DETECT", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.compsysbio.org/projects/DETECT/" } \ No newline at end of file diff --git a/data/detectir/detectirbioschemas.jsonld b/data/detectir/detectirbioschemas.jsonld index 9d4a59b3e18e8..b03100c35aca9 100644 --- a/data/detectir/detectirbioschemas.jsonld +++ b/data/detectir/detectirbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Script", "sc:citation": [ "pmcid:PMC4237412", + "pubmed:25409465", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0113349" - }, - "pubmed:25409465" + } ], "sc:description": "A tool for detecting perfect and imperfect inverted repeats in genomes.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:license": "CC-BY-NC-SA-3.0", "sc:name": "detectIR", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sourceforge.net/projects/detectir/" } diff --git a/data/detector/detectorbioschemas.jsonld b/data/detector/detectorbioschemas.jsonld index 5e7f4ffcd0ab7..ec37d75caafb3 100644 --- a/data/detector/detectorbioschemas.jsonld +++ b/data/detector/detectorbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "DeTECTOR", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-ITA-CRS4", "sc:url": "http://detector.bioinformatica.crs4.it/", diff --git a/data/determ/determbioschemas.jsonld b/data/determ/determbioschemas.jsonld index 8ff037877bdde..b0a98aced451d 100644 --- a/data/determ/determbioschemas.jsonld +++ b/data/determ/determbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "DeTerm", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://bitbucket.org/skibbe/DeTerm/wiki/Home" } \ No newline at end of file diff --git a/data/deus/deusbioschemas.jsonld b/data/deus/deusbioschemas.jsonld index a4f78a60be23a..025346e42aea9 100644 --- a/data/deus/deusbioschemas.jsonld +++ b/data/deus/deusbioschemas.jsonld @@ -21,9 +21,9 @@ "sc:license": "GPL-3.0", "sc:name": "DEUS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ibis.helmholtz-muenchen.de/deus/" } \ No newline at end of file diff --git a/data/deuterater/deuteraterbioschemas.jsonld b/data/deuterater/deuteraterbioschemas.jsonld index 4bebffa741774..bc1014ff1be26 100644 --- a/data/deuterater/deuteraterbioschemas.jsonld +++ b/data/deuterater/deuteraterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Quantifying peptide isotope precision and kinetic proteomics.", "sc:name": "DeuteRater", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/JC-Price/DeuteRater" } \ No newline at end of file diff --git a/data/deuteros/deuterosbioschemas.jsonld b/data/deuteros/deuterosbioschemas.jsonld index cc6ab90501a96..33073abd30cb2 100644 --- a/data/deuteros/deuterosbioschemas.jsonld +++ b/data/deuteros/deuterosbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "Deuteros", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/andymlau/Deuteros" } \ No newline at end of file diff --git a/data/devis/devisbioschemas.jsonld b/data/devis/devisbioschemas.jsonld index 55d4d05343e3a..52f4edd9a4b60 100644 --- a/data/devis/devisbioschemas.jsonld +++ b/data/devis/devisbioschemas.jsonld @@ -19,8 +19,8 @@ "biotools:primaryContact": "Adam Price", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:30832568", "pmcid:PMC6399874", + "pubmed:30832568", { "@id": "https://doi.org/10.1186/s12859-019-2702-z" } @@ -28,20 +28,20 @@ "sc:description": "R package for aggregation and visualization of differential expression data.", "sc:featureList": [ { - "@id": "edam:operation_3436" + "@id": "edam:operation_3741" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3741" + "@id": "edam:operation_2495" } ], "sc:license": "LGPL-2.0", "sc:name": "DEvis", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://cran.r-project.org/package=DEVis" diff --git a/data/dewe_differential_expression_workflow_executor/dewe_differential_expression_workflow_executorbioschemas.jsonld b/data/dewe_differential_expression_workflow_executor/dewe_differential_expression_workflow_executorbioschemas.jsonld index 4d19662212bc7..feb52a9b6d97b 100644 --- a/data/dewe_differential_expression_workflow_executor/dewe_differential_expression_workflow_executorbioschemas.jsonld +++ b/data/dewe_differential_expression_workflow_executor/dewe_differential_expression_workflow_executorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "DEWE: Differential Expression Workflow Executor", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.sing-group.org/dewe/", "sc:version": "1.2.0" diff --git a/data/dexseq/dexseqbioschemas.jsonld b/data/dexseq/dexseqbioschemas.jsonld index 604639f6504cf..f9d9953795d53 100644 --- a/data/dexseq/dexseqbioschemas.jsonld +++ b/data/dexseq/dexseqbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-8717-6612", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1073/pnas.1307202110", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dexseq", "@type": "sc:SoftwareApplication", @@ -24,34 +16,42 @@ "@id": "http://orcid.org/0000-0001-8717-6612" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pmcid:PMC3780897", { "@id": "https://doi.org/10.1073/pnas.1307202110" }, - "pmcid:PMC3780897", "pubmed:24003148" ], "sc:description": "The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.", "sc:featureList": [ { - "@id": "edam:operation_0446" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_0446" } ], "sc:license": "GPL-3.0", "sc:name": "DEXSeq", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DEXSeq.html", "sc:version": "1.20.1" + }, + { + "@id": "http://orcid.org/0000-0001-8717-6612", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1073/pnas.1307202110", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dexus/dexusbioschemas.jsonld b/data/dexus/dexusbioschemas.jsonld index f7fe8a91abbe6..83bc94f98c921 100644 --- a/data/dexus/dexusbioschemas.jsonld +++ b/data/dexus/dexusbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-2861-5552", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gkt834", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/dexus", "@type": "sc:SoftwareApplication", @@ -16,8 +24,8 @@ "@id": "http://orcid.org/0000-0003-2861-5552" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ { @@ -39,14 +47,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/dexus.html", "sc:version": "1.14.0" - }, - { - "@id": "https://doi.org/10.1093/nar/gkt834", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-2861-5552", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dfast/dfastbioschemas.jsonld b/data/dfast/dfastbioschemas.jsonld index 79a90740790b4..201a47884648e 100644 --- a/data/dfast/dfastbioschemas.jsonld +++ b/data/dfast/dfastbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yasukazu Nakamura", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Flexible prokaryotic genome annotation pipeline for faster genome publication.", "sc:license": "GPL-3.0", diff --git a/data/dfp/bioconda_dfp.yaml b/data/dfp/bioconda_dfp.yaml index 2eae76c44b4d9..15de95439f1d7 100644 --- a/data/dfp/bioconda_dfp.yaml +++ b/data/dfp/bioconda_dfp.yaml @@ -6,7 +6,6 @@ description: This package provides a supervised technique able to identify diffe home: https://bioconductor.org/packages/3.10/bioc/html/DFP.html identifiers: - biotools:dfp -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-dfp diff --git a/data/dfp/dfpbioschemas.jsonld b/data/dfp/dfpbioschemas.jsonld index ee72e2fa90d57..1d7d88faa7e64 100644 --- a/data/dfp/dfpbioschemas.jsonld +++ b/data/dfp/dfpbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Rodrigo Alvarez-Glez", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \\emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.", "sc:license": "GPL-2.0", "sc:name": "DFP", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DFP.html", "sc:version": "1.32.0" diff --git a/data/dgca/dgcabioschemas.jsonld b/data/dgca/dgcabioschemas.jsonld index 9a9c55842d5aa..3e0a87cf6ba77 100644 --- a/data/dgca/dgcabioschemas.jsonld +++ b/data/dgca/dgcabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DGCA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/DGCA/index.html" } \ No newline at end of file diff --git a/data/dgd/dgdbioschemas.jsonld b/data/dgd/dgdbioschemas.jsonld index 4c4aa939f11d7..87c1ad1dd658a 100644 --- a/data/dgd/dgdbioschemas.jsonld +++ b/data/dgd/dgdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Provides a list of groups of co-located and duplicated genes.", "sc:name": "DGD", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "GenOuest", "sc:url": "http://dgd.genouest.org/" diff --git a/data/dgva/dgvabioschemas.jsonld b/data/dgva/dgvabioschemas.jsonld index e6dd9b7b0cb6b..dc90daafd39d0 100644 --- a/data/dgva/dgvabioschemas.jsonld +++ b/data/dgva/dgvabioschemas.jsonld @@ -18,33 +18,33 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "DGVa Helpdesk", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ { "@id": "https://doi.org/10.1093/nar/gks1213" }, - "pubmed:23193291", - "pmcid:PMC3531204" + "pmcid:PMC3531204", + "pubmed:23193291" ], "sc:description": "The Database of Genomic Variants archive ((DGVa) is a repository that provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species.", "sc:featureList": [ - { - "@id": "edam:operation_3431" - }, { "@id": "edam:operation_2422" }, { "@id": "edam:operation_3228" + }, + { + "@id": "edam:operation_3431" } ], "sc:name": "DGVa", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ebi.ac.uk/dgva" } diff --git a/data/dgw/dgwbioschemas.jsonld b/data/dgw/dgwbioschemas.jsonld index ec2419bfdac92..8f924d02a683f 100644 --- a/data/dgw/dgwbioschemas.jsonld +++ b/data/dgw/dgwbioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:28105912", - "pmcid:PMC5249015", { "@id": "https://doi.org/10.1186/s12859-016-1306-0" - } + }, + "pmcid:PMC5249015" ], "sc:description": "DGW is an open source software package for simultaneous alignment and clustering of multiple epigenomic marks.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "DGW", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://lukauskas.co.uk/dgw/", "sc:version": "0.1.0" diff --git a/data/dhcl/dhclbioschemas.jsonld b/data/dhcl/dhclbioschemas.jsonld index 9b0b1e06f84b9..376d7b59d665c 100644 --- a/data/dhcl/dhclbioschemas.jsonld +++ b/data/dhcl/dhclbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "DHcL", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://cropnet.pl/dhcl/" } \ No newline at end of file diff --git a/data/dia-db/dia-dbbioschemas.jsonld b/data/dia-db/dia-dbbioschemas.jsonld index 61965e1283b94..159c83fc39e71 100644 --- a/data/dia-db/dia-dbbioschemas.jsonld +++ b/data/dia-db/dia-dbbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3390/MOLECULES24102002", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0003-4468-7898", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/DIA-DB", "@type": "sc:SoftwareApplication", @@ -32,10 +40,10 @@ "@id": "edam:operation_0394" }, { - "@id": "edam:operation_3216" + "@id": "edam:operation_0482" }, { - "@id": "edam:operation_0482" + "@id": "edam:operation_3216" } ], "sc:license": "CC-BY-NC-4.0", @@ -46,14 +54,6 @@ "Mac" ], "sc:url": "http://bio-hpc.ucam.edu/dia-db/" - }, - { - "@id": "https://doi.org/10.3390/MOLECULES24102002", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0003-4468-7898", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dia-umpire/dia-umpirebioschemas.jsonld b/data/dia-umpire/dia-umpirebioschemas.jsonld index 2028bd40e8d4e..143fc44582953 100644 --- a/data/dia-umpire/dia-umpirebioschemas.jsonld +++ b/data/dia-umpire/dia-umpirebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Apache-2.0", "sc:name": "DIA-Umpire", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://sourceforge.net/projects/diaumpire/", "sc:version": "2.0" diff --git a/data/dial/dialbioschemas.jsonld b/data/dial/dialbioschemas.jsonld index e69ece51057ec..68bde79bafe89 100644 --- a/data/dial/dialbioschemas.jsonld +++ b/data/dial/dialbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "DIAL", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinformatics.bc.edu/clotelab/DIAL/" } \ No newline at end of file diff --git a/data/dialign-tx/dialign-txbioschemas.jsonld b/data/dialign-tx/dialign-txbioschemas.jsonld index de2a06f4435b6..5aec709b281f5 100644 --- a/data/dialign-tx/dialign-txbioschemas.jsonld +++ b/data/dialign-tx/dialign-txbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "DIALIGN-TX is an update to DIALIGN. It combines the greedy heuristic method of DIALIGN with a traditional progressive method.", "sc:name": "DIALIGN-TX", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://dialign-tx.gobics.de/" diff --git a/data/dialign/dialignbioschemas.jsonld b/data/dialign/dialignbioschemas.jsonld index 926cf60e281fc..3ba099ae9bc14 100644 --- a/data/dialign/dialignbioschemas.jsonld +++ b/data/dialign/dialignbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.", "sc:name": "DIALIGN", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://dialign.gobics.de" } \ No newline at end of file diff --git a/data/dials/dialsbioschemas.jsonld b/data/dials/dialsbioschemas.jsonld index d8e6806ba601e..550fe31ae9abe 100644 --- a/data/dials/dialsbioschemas.jsonld +++ b/data/dials/dialsbioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1107/S2059798317017235", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dials", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5947772", "pubmed:29533234", + "pmcid:PMC5947772", { "@id": "https://doi.org/10.1107/S2059798317017235" } @@ -35,6 +31,10 @@ "Mac" ], "sc:url": "https://dials.github.io/" + }, + { + "@id": "https://doi.org/10.1107/S2059798317017235", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/diana-lncbase/diana-lncbasebioschemas.jsonld b/data/diana-lncbase/diana-lncbasebioschemas.jsonld index 31c62b11b02ad..b6164d5498f44 100644 --- a/data/diana-lncbase/diana-lncbasebioschemas.jsonld +++ b/data/diana-lncbase/diana-lncbasebioschemas.jsonld @@ -10,7 +10,7 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1093/nar/gks1246", + "@id": "https://doi.org/10.1093/nar/gkv1270", "@type": "sc:CreativeWork" }, { @@ -18,16 +18,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:23193281", "pmcid:PMC3531175", { "@id": "https://doi.org/10.1093/nar/gkv1270" }, + "pubmed:26612864", + "pubmed:23193281", { "@id": "https://doi.org/10.1093/nar/gks1246" }, - "pmcid:PMC4702897", - "pubmed:26612864" + "pmcid:PMC4702897" ], "sc:description": "Incorporates an extensive collection of miRNA:lncRNA interactions. The database includes more than 70,000 low and high-throughput, (in)direct miRNA:lncRNA experimentally supported interactions, derived from manually curated publications and the analysis of 153 AGO CLIP-Seq libraries. LncBase v2 hosts in silico predicted miRNA targets on lncRNAs, identified with the DIANA-microT algorithm.", "sc:featureList": { @@ -35,14 +35,14 @@ }, "sc:name": "DIANA-LNCBase", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.microrna.gr/LncBase/" }, { - "@id": "https://doi.org/10.1093/nar/gkv1270", + "@id": "https://doi.org/10.1093/nar/gks1246", "@type": "sc:CreativeWork" } ] diff --git a/data/diana-microt/diana-microtbioschemas.jsonld b/data/diana-microt/diana-microtbioschemas.jsonld index e237f98a9f59b..5cfa9c13b1ee5 100644 --- a/data/diana-microt/diana-microtbioschemas.jsonld +++ b/data/diana-microt/diana-microtbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Dedicated to miRNA target prediction and functional analysis and is widely used since 2009 from the scientific community. \nIt predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser. Updates include sophisticated workflows.", "sc:name": "DIANA-microT v5.0", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=MicroT_CDS/index" } \ No newline at end of file diff --git a/data/diana-mirextra/diana-mirextrabioschemas.jsonld b/data/diana-mirextra/diana-mirextrabioschemas.jsonld index 7b03732cb0576..bb00df03816cc 100644 --- a/data/diana-mirextra/diana-mirextrabioschemas.jsonld +++ b/data/diana-mirextra/diana-mirextrabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0009171", + "@type": "sc:CreativeWork" + }, { "@id": "https://doi.org/10.1093/nar/gkw455", "@type": "sc:CreativeWork" @@ -18,43 +22,39 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web service", "sc:citation": [ + { + "@id": "https://doi.org/10.1093/nar/gkw455" + }, { "@id": "https://doi.org/10.1371/journal.pone.0009171" }, - "pubmed:27207881", - "pubmed:20161787", "pmcid:PMC2820085", + "pubmed:27207881", "pmcid:PMC4987956", - { - "@id": "https://doi.org/10.1093/nar/gkw455" - } + "pubmed:20161787" ], "sc:description": "Performs a combined Differential expression analysis(DEA) of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0.", "sc:featureList": [ - { - "@id": "edam:operation_0361" - }, { "@id": "edam:operation_2495" }, { "@id": "edam:operation_3680" }, + { + "@id": "edam:operation_0361" + }, { "@id": "edam:operation_2403" } ], "sc:name": "DIANA-mirExTra", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.microrna.gr/mirextrav2" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0009171", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/diana-mirgen/diana-mirgenbioschemas.jsonld b/data/diana-mirgen/diana-mirgenbioschemas.jsonld index 3502fd082afdd..201aa108dab46 100644 --- a/data/diana-mirgen/diana-mirgenbioschemas.jsonld +++ b/data/diana-mirgen/diana-mirgenbioschemas.jsonld @@ -10,15 +10,11 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1093/nar/gkp888", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1093/nar/gkv1254", + "@id": "https://doi.org/10.1093/nar/gkl904", "@type": "sc:CreativeWork" }, { - "@id": "https://doi.org/10.1093/nar/gkl904", + "@id": "https://doi.org/10.1093/nar/gkp888", "@type": "sc:CreativeWork" }, { @@ -26,21 +22,21 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:26586797", + "pubmed:17108354", { "@id": "https://doi.org/10.1093/nar/gkl904" }, - { - "@id": "https://doi.org/10.1093/nar/gkp888" - }, - "pubmed:19850714", - "pubmed:17108354", - "pmcid:PMC2808909", { "@id": "https://doi.org/10.1093/nar/gkv1254" }, + "pmcid:PMC2808909", "pmcid:PMC4702888", - "pmcid:PMC1669779" + "pubmed:26586797", + "pubmed:19850714", + "pmcid:PMC1669779", + { + "@id": "https://doi.org/10.1093/nar/gkp888" + } ], "sc:description": "Provides accurate cell-line-specific miRNA gene transcription start sites, coupled with genome-wide maps of transcription factor binding sites in order to unveil the mechanisms of miRNA transcription regulation. The database schema and web interface facilitates user interaction, provides advanced queries and innate connection with other DIANA resources for miRNA target identification and pathway analysis.", "sc:featureList": { @@ -48,11 +44,15 @@ }, "sc:name": "DIANA-miRGen", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.microrna.gr/mirgen" + }, + { + "@id": "https://doi.org/10.1093/nar/gkv1254", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/diana-mirpath/diana-mirpathbioschemas.jsonld b/data/diana-mirpath/diana-mirpathbioschemas.jsonld index a73a53c935aa4..271dca633678e 100644 --- a/data/diana-mirpath/diana-mirpathbioschemas.jsonld +++ b/data/diana-mirpath/diana-mirpathbioschemas.jsonld @@ -19,24 +19,24 @@ "biotools:primaryContact": "Ioannis S Vlachos", "sc:additionalType": "Web service", "sc:citation": [ - "pubmed:19435746", { "@id": "https://doi.org/10.1093/nar/gkv403" }, - "pubmed:22649059", - "pmcid:PMC4489228", - "pmcid:PMC3394305", - "pubmed:25977294", { "@id": "https://doi.org/10.1093/nar/gks494" - } + }, + "pmcid:PMC4489228", + "pubmed:25977294", + "pubmed:22649059", + "pmcid:PMC3394305", + "pubmed:19435746" ], "sc:description": "Dedicated to the assessment of miRNA regulatory roles and the identification of controlled pathways. It support all analyses for KEGG molecular pathways, as well as multiple slices of Gene Ontology (GO) in seven species. A unique feature of DIANA-miRPath v3.0 is its redesigned Reverse Search module, which enables users to identify and visualize miRNAs significantly controlling selected pathways or belonging to specific GO categories based on in silico or experimental data.", "sc:name": "DIANA-mirPath", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.microrna.gr/miRPathv3" }, diff --git a/data/diana_mirpath/diana_mirpathbioschemas.jsonld b/data/diana_mirpath/diana_mirpathbioschemas.jsonld index c1fbc81a92919..57714f7fbf5c6 100644 --- a/data/diana_mirpath/diana_mirpathbioschemas.jsonld +++ b/data/diana_mirpath/diana_mirpathbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web-based computational tool that identifies potentially altered molecular pathways by the expression of a single or multiple microRNAs.", "sc:name": "DIANA miRPath", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://snf-515788.vm.okeanos.grnet.gr/" diff --git a/data/dianna/diannabioschemas.jsonld b/data/dianna/diannabioschemas.jsonld index 81981ba025f9a..258f389e31172 100644 --- a/data/dianna/diannabioschemas.jsonld +++ b/data/dianna/diannabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.", "sc:name": "DiANNA", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinformatics.bc.edu/clotelab/DiANNA/" } \ No newline at end of file diff --git a/data/diark/diarkbioschemas.jsonld b/data/diark/diarkbioschemas.jsonld index af30b2967c574..40d33c3b1428e 100644 --- a/data/diark/diarkbioschemas.jsonld +++ b/data/diark/diarkbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database driven web application that is designed to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes.", "sc:name": "diArk - a resource for eukaryotic genome research", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.diark.org/" } \ No newline at end of file diff --git a/data/dicer/dicerbioschemas.jsonld b/data/dicer/dicerbioschemas.jsonld index a2e848207c63d..f27f5c393fd5d 100644 --- a/data/dicer/dicerbioschemas.jsonld +++ b/data/dicer/dicerbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Derek Chiu", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:29334888", + "pmcid:PMC5769335", { "@id": "https://doi.org/10.1186/s12859-017-1996-y" }, - "pmcid:PMC5769335" + "pubmed:29334888" ], "sc:description": "Performs cluster analysis using an ensemble clustering framework. Results from a diverse set of algorithms are pooled together using methods such as majority voting, K-Modes, LinkCluE, and CSPA.", "sc:featureList": { diff --git a/data/dichromatch/dichromatchbioschemas.jsonld b/data/dichromatch/dichromatchbioschemas.jsonld index 477917ebf62ba..61f71bedcd9d7 100644 --- a/data/dichromatch/dichromatchbioschemas.jsonld +++ b/data/dichromatch/dichromatchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "DichroMatch webserver identifies proteins with similar spectral characteristics as a way to detect possible structurally and functionally related proteins and homologues. Users input a query spectrum which is searched against the protein circular dichromism data bank or a user provided data set.", "sc:name": "DichroMatch", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://dichromatch.cryst.bbk.ac.uk" } \ No newline at end of file diff --git a/data/dichroweb/dichrowebbioschemas.jsonld b/data/dichroweb/dichrowebbioschemas.jsonld index 2c2befb249266..caf2c20b2581c 100644 --- a/data/dichroweb/dichrowebbioschemas.jsonld +++ b/data/dichroweb/dichrowebbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.", "sc:name": "DICHROWEB", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://dichroweb.cryst.bbk.ac.uk/html/home.shtml" diff --git a/data/dictybase/dictybasebioschemas.jsonld b/data/dictybase/dictybasebioschemas.jsonld index 02184c433fd51..1d332ac0d0e20 100644 --- a/data/dictybase/dictybasebioschemas.jsonld +++ b/data/dictybase/dictybasebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Database for the biology and genomics of the social amoeba Dictyostelium discoideum.", "sc:name": "dictyBase", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "Center for Genetic Medicine, Northwestern University", "sc:url": "http://dictybase.org/" diff --git a/data/dictybase_update_2011/dictybase_update_2011bioschemas.jsonld b/data/dictybase_update_2011/dictybase_update_2011bioschemas.jsonld index 5a59260c756cc..a420d2354b4c1 100644 --- a/data/dictybase_update_2011/dictybase_update_2011bioschemas.jsonld +++ b/data/dictybase_update_2011/dictybase_update_2011bioschemas.jsonld @@ -9,30 +9,30 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkq1103", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dictybase_update_2011", "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC3013695", { "@id": "https://doi.org/10.1093/nar/gkq1103" }, - "pubmed:21087999" + "pubmed:21087999", + "pmcid:PMC3013695" ], "sc:description": "Database for the biology and genomics of the social amoeba Dictyostelium discoideum. It provides well integrated, high quality data and tools for Dictyostelium discoideum and related species. It houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a reference genome in the Amoebozoa clade.", "sc:name": "dictyBase update 2011", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "Center for Genetic Medicine, Northwestern University", "sc:url": "http://www.dictybase.org" + }, + { + "@id": "https://doi.org/10.1093/nar/gkq1103", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dictyexpress/dictyexpressbioschemas.jsonld b/data/dictyexpress/dictyexpressbioschemas.jsonld index 0e84cdeddfc17..7016dffe180f2 100644 --- a/data/dictyexpress/dictyexpressbioschemas.jsonld +++ b/data/dictyexpress/dictyexpressbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "dictyExpress", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://dictyexpress.biolab.si/", "sc:version": "1.5" diff --git a/data/dida/didabioschemas.jsonld b/data/dida/didabioschemas.jsonld index d2fe6813bbd28..1bbbbec7105c4 100644 --- a/data/dida/didabioschemas.jsonld +++ b/data/dida/didabioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkv1068", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0003-3645-1455", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/dida", "@type": "sc:SoftwareApplication", @@ -20,40 +28,32 @@ "Database portal" ], "sc:citation": [ + "pubmed:26481352", + "pmcid:PMC4702791", { "@id": "https://doi.org/10.1093/nar/gkv1068" - }, - "pubmed:26481352", - "pmcid:PMC4702791" + } ], "sc:description": "Digenic Diseases Database (DiDA) provides detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.", "sc:featureList": [ { - "@id": "edam:operation_3661" + "@id": "edam:operation_2421" }, { "@id": "edam:operation_3197" }, { - "@id": "edam:operation_2421" + "@id": "edam:operation_3661" } ], "sc:name": "Digenic Diseases Database (DIDA)", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "Interuniversity Institute of Bioinformatics in Brussels", "sc:url": "http://dida.ibsquare.be" - }, - { - "@id": "https://doi.org/10.1093/nar/gkv1068", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0003-3645-1455", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/diffany/diffanybioschemas.jsonld b/data/diffany/diffanybioschemas.jsonld index fcf7297c19247..ab3a1891a899a 100644 --- a/data/diffany/diffanybioschemas.jsonld +++ b/data/diffany/diffanybioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Open-source toolbox for calculating and visualizing differential networks.", "sc:name": "Diffany", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/", diff --git a/data/diffatonce/diffatoncebioschemas.jsonld b/data/diffatonce/diffatoncebioschemas.jsonld index 5a59700a2e9f1..680e3b597f475 100644 --- a/data/diffatonce/diffatoncebioschemas.jsonld +++ b/data/diffatonce/diffatoncebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Proprietary", "sc:name": "DiffAtOnce", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.diffatonce.com/" } \ No newline at end of file diff --git a/data/diffbind/diffbindbioschemas.jsonld b/data/diffbind/diffbindbioschemas.jsonld index 94e3a84eab655..3f3adfdf8f761 100644 --- a/data/diffbind/diffbindbioschemas.jsonld +++ b/data/diffbind/diffbindbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/bcr3664", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/diffbind", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Library" ], "sc:citation": [ - "pubmed:24886537", - "pmcid:PMC4076632", { "@id": "https://doi.org/10.1186/bcr3664" - } + }, + "pubmed:24886537", + "pmcid:PMC4076632" ], "sc:description": "Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.", "sc:featureList": { @@ -35,12 +31,16 @@ "sc:license": "Artistic-2.0", "sc:name": "DiffBind", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DiffBind.html", "sc:version": "2.2.6" + }, + { + "@id": "https://doi.org/10.1186/bcr3664", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/diffcoexp/diffcoexpbioschemas.jsonld b/data/diffcoexp/diffcoexpbioschemas.jsonld index ada766ab64900..07031501d83ac 100644 --- a/data/diffcoexp/diffcoexpbioschemas.jsonld +++ b/data/diffcoexp/diffcoexpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "diffcoexp", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/diffcoexp.html", "sc:version": "1.0.0" diff --git a/data/diffcyt/diffcytbioschemas.jsonld b/data/diffcyt/diffcytbioschemas.jsonld index c99eb0c39d03e..faa65b9a1c90f 100644 --- a/data/diffcyt/diffcytbioschemas.jsonld +++ b/data/diffcyt/diffcytbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "diffcyt", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/diffcyt.html", diff --git a/data/diffexpress/diffexpressbioschemas.jsonld b/data/diffexpress/diffexpressbioschemas.jsonld index 6302a6f865d19..c0ca3582739af 100644 --- a/data/diffexpress/diffexpressbioschemas.jsonld +++ b/data/diffexpress/diffexpressbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3389/FGENE.2019.00356", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/DiffExpress", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ ], "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31139204", + "pmcid:PMC6527599", { "@id": "https://doi.org/10.3389/FGENE.2019.00356" - }, - "pmcid:PMC6527599", - "pubmed:31139204" + } ], "sc:description": "Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis.", "sc:featureList": [ @@ -34,20 +30,24 @@ "@id": "edam:operation_3680" }, { - "@id": "edam:operation_3223" + "@id": "edam:operation_3800" }, { - "@id": "edam:operation_3800" + "@id": "edam:operation_3223" } ], "sc:license": "Unlicense", "sc:name": "DiffExpress", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://simplicity.nsilico.com/dea" + }, + { + "@id": "https://doi.org/10.3389/FGENE.2019.00356", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/diffgeneanalysis/bioconda_diffgeneanalysis.yaml b/data/diffgeneanalysis/bioconda_diffgeneanalysis.yaml index ba773cec18bde..fa72e9c42d8a4 100644 --- a/data/diffgeneanalysis/bioconda_diffgeneanalysis.yaml +++ b/data/diffgeneanalysis/bioconda_diffgeneanalysis.yaml @@ -3,7 +3,6 @@ description: Analyze microarray data home: https://bioconductor.org/packages/3.10/bioc/html/diffGeneAnalysis.html identifiers: - biotools:diffgeneanalysis -- doi:10.1038/nmeth.3252 license: GPL license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-diffgeneanalysis diff --git a/data/diffgeneanalysis/diffgeneanalysisbioschemas.jsonld b/data/diffgeneanalysis/diffgeneanalysisbioschemas.jsonld index 0a1c176a563b1..ee01c21b49d1d 100644 --- a/data/diffgeneanalysis/diffgeneanalysisbioschemas.jsonld +++ b/data/diffgeneanalysis/diffgeneanalysisbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "diffGeneAnalysis", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/diffGeneAnalysis.html", "sc:version": "1.56.0" diff --git a/data/diffhic/diffhicbioschemas.jsonld b/data/diffhic/diffhicbioschemas.jsonld index b68e5ecaffefd..10b74a3a441af 100644 --- a/data/diffhic/diffhicbioschemas.jsonld +++ b/data/diffhic/diffhicbioschemas.jsonld @@ -32,26 +32,26 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3168" + "@id": "edam:topic_3391" }, { - "@id": "edam:topic_3391" + "@id": "edam:topic_3168" } ], "sc:citation": [ - "pubmed:26283514", + "pmcid:PMC4539688", { "@id": "https://doi.org/10.1186/s12859-015-0683-0" }, - "pmcid:PMC4539688" + "pubmed:26283514" ], "sc:description": "Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.", "sc:featureList": [ { - "@id": "edam:operation_3435" + "@id": "edam:operation_3432" }, { - "@id": "edam:operation_3432" + "@id": "edam:operation_3435" } ], "sc:license": "GPL-3.0", @@ -64,13 +64,13 @@ "sc:url": "http://bioconductor.org/packages/release/bioc/html/diffHic.html", "sc:version": "1.6.0" }, - { - "@id": "https://doi.org/10.1186/s12859-015-0683-0", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-3564-4813", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/s12859-015-0683-0", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/difflogo/difflogobioschemas.jsonld b/data/difflogo/difflogobioschemas.jsonld index 288f26d9b5605..a00e594813228 100644 --- a/data/difflogo/difflogobioschemas.jsonld +++ b/data/difflogo/difflogobioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-8032-9890", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/s12859-015-0767-x", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/difflogo", "@type": "sc:SoftwareApplication", @@ -17,24 +25,24 @@ }, "edam:has_input": [ { - "@id": "edam:data_2082" + "@id": "edam:data_3494" }, { - "@id": "edam:data_3494" + "@id": "edam:data_3495" }, { - "@id": "edam:data_2976" + "@id": "edam:data_2082" }, { - "@id": "edam:data_3495" + "@id": "edam:data_2976" } ], "edam:has_output": { "@id": "edam:data_2884" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": { "@id": "edam:topic_0622" @@ -43,8 +51,8 @@ { "@id": "https://doi.org/10.1186/s12859-015-0767-x" }, - "pubmed:26577052", - "pmcid:PMC4650857" + "pmcid:PMC4650857", + "pubmed:26577052" ], "sc:description": "Easy-to-use tool to visualize motif differences.", "sc:featureList": { @@ -53,20 +61,12 @@ "sc:license": "GPL-2.0", "sc:name": "DiffLogo", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DiffLogo.html", "sc:version": "1.4.0" - }, - { - "@id": "https://doi.org/10.1186/s12859-015-0767-x", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-8032-9890", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/diffloop/diffloopbioschemas.jsonld b/data/diffloop/diffloopbioschemas.jsonld index 72c97781b6b22..2e2aadd77f390 100644 --- a/data/diffloop/diffloopbioschemas.jsonld +++ b/data/diffloop/diffloopbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Caleb Lareau", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A suite of tools for subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments or other assays that infer chromatin loops.", "sc:license": "MIT", "sc:name": "diffloop", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/diffloop.html", "sc:version": "1.2.1" diff --git a/data/diffreps/diffrepsbioschemas.jsonld b/data/diffreps/diffrepsbioschemas.jsonld index 2ba6e1560a12c..5d471cd2990df 100644 --- a/data/diffreps/diffrepsbioschemas.jsonld +++ b/data/diffreps/diffrepsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr. Li Shen", "sc:additionalType": [ - "Command-line tool", - "Script" + "Script", + "Command-line tool" ], "sc:citation": "pubmed:23762400", "sc:description": "This software is developed to find different peaks in ChIP-seq. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. It takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especiallly for in vivo brain tissues.", diff --git a/data/diffseq/diffseqbioschemas.jsonld b/data/diffseq/diffseqbioschemas.jsonld index 4f1fc6239af23..ab8b508ee4332 100644 --- a/data/diffseq/diffseqbioschemas.jsonld +++ b/data/diffseq/diffseqbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:description": "Compare and report features of two similar sequences.", "sc:funder": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "diffseq", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/diffslc/diffslcbioschemas.jsonld b/data/diffslc/diffslcbioschemas.jsonld index 8ec055932726b..17c6049a02db5 100644 --- a/data/diffslc/diffslcbioschemas.jsonld +++ b/data/diffslc/diffslcbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Graph centrality method to detect essential proteins of a protein-protein interaction network.", "sc:name": "DiffSLC", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/divyamistry/diffslc-py" diff --git a/data/diffustats/diffustatsbioschemas.jsonld b/data/diffustats/diffustatsbioschemas.jsonld index 6fee0c62411e1..533c3ec53f17f 100644 --- a/data/diffustats/diffustatsbioschemas.jsonld +++ b/data/diffustats/diffustatsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-6426-8204", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/diffustats", "@type": "sc:SoftwareApplication", @@ -24,6 +20,10 @@ "sc:license": "GPL-3.0", "sc:name": "diffuStats", "sc:url": "https://bioconductor.org/packages/release/bioc/html/diffuStats.html" + }, + { + "@id": "https://orcid.org/0000-0002-6426-8204", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/digchem/digchembioschemas.jsonld b/data/digchem/digchembioschemas.jsonld index b22c06f91a121..71b64e361c287 100644 --- a/data/digchem/digchembioschemas.jsonld +++ b/data/digchem/digchembioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1007022", "@type": "sc:CreativeWork" }, - { - "@id": "https://orcid.org/0000-0003-2389-7183", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/DigChem", "@type": "sc:SoftwareApplication", @@ -25,32 +21,36 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31091224", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1007022" }, - "pubmed:31091224", "pmcid:PMC6519793" ], "sc:description": "Identification of disease-gene-chemical relationships from Medline abstracts.", "sc:featureList": [ - { - "@id": "edam:operation_3280" - }, { "@id": "edam:operation_2422" }, { "@id": "edam:operation_3625" + }, + { + "@id": "edam:operation_3280" } ], "sc:license": "Unlicense", "sc:name": "DigChem", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://gcancer.org/digchem" + }, + { + "@id": "https://orcid.org/0000-0003-2389-7183", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/digenome-seq/digenome-seqbioschemas.jsonld b/data/digenome-seq/digenome-seqbioschemas.jsonld index 6d40eba6ebe25..3c90a1c212e0f 100644 --- a/data/digenome-seq/digenome-seqbioschemas.jsonld +++ b/data/digenome-seq/digenome-seqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Digenome-seq web tool", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.rgenome.net/digenome-js/#!" } \ No newline at end of file diff --git a/data/diggit/diggitbioschemas.jsonld b/data/diggit/diggitbioschemas.jsonld index bbfed62f8c984..3b92ed7524235 100644 --- a/data/diggit/diggitbioschemas.jsonld +++ b/data/diggit/diggitbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Inference of Genetic Variants Driving Cellullar Phenotypes by the DIGGIT algorithm.", "sc:name": "diggit", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/diggit.html", "sc:version": "1.6.0" diff --git a/data/digsee/digseebioschemas.jsonld b/data/digsee/digseebioschemas.jsonld index b21f85be77108..465e92221dde4 100644 --- a/data/digsee/digseebioschemas.jsonld +++ b/data/digsee/digseebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "DigSee", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://gcancer.org/digsee" diff --git a/data/dilimot/dilimotbioschemas.jsonld b/data/dilimot/dilimotbioschemas.jsonld index eeccbc6511983..003866099b1bf 100644 --- a/data/dilimot/dilimotbioschemas.jsonld +++ b/data/dilimot/dilimotbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/dilimot", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rob Russell (questions, comments or bug reports)", - "Matthew Betts (problems with the server)" + "Matthew Betts (problems with the server)", + "Rob Russell (questions, comments or bug reports)" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:16279839", diff --git a/data/dimm-sc/dimm-scbioschemas.jsonld b/data/dimm-sc/dimm-scbioschemas.jsonld index b98e9197e516e..6f15fcb5d8066 100644 --- a/data/dimm-sc/dimm-scbioschemas.jsonld +++ b/data/dimm-sc/dimm-scbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/dimm-sc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wei Chen", - "Ming Hu" + "Ming Hu", + "Wei Chen" ], "sc:additionalType": "Library", "sc:description": "Dirichlet mixture model for clustering droplet-based single cell transcriptomic data.", diff --git a/data/dinamo/dinamobioschemas.jsonld b/data/dinamo/dinamobioschemas.jsonld index b023b60790813..e547a3bfcf852 100644 --- a/data/dinamo/dinamobioschemas.jsonld +++ b/data/dinamo/dinamobioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "DiNAMO", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/bonsai-team/DiNAMO" diff --git a/data/dinc/dincbioschemas.jsonld b/data/dinc/dincbioschemas.jsonld index 0a36e8391de82..5eb6319bd6122 100644 --- a/data/dinc/dincbioschemas.jsonld +++ b/data/dinc/dincbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1472-6807-13-S1-S11", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dinc", "@type": "sc:SoftwareApplication", @@ -31,11 +27,15 @@ }, "sc:name": "DINC", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://dinc.kavrakilab.org/" + }, + { + "@id": "https://doi.org/10.1186/1472-6807-13-S1-S11", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dinies/diniesbioschemas.jsonld b/data/dinies/diniesbioschemas.jsonld index 409bd3f8792ed..8d22d25ed061b 100644 --- a/data/dinies/diniesbioschemas.jsonld +++ b/data/dinies/diniesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool based on Supervised analysis enables the prediction of potential interactions between drug molecules and target proteins, based on drug data and omics-scale protein data. The users can use any data as the input, as long as they are represented as the tab-delimited matrices or profiles.", "sc:name": "DINIES", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.genome.jp/tools/dinies/" } \ No newline at end of file diff --git a/data/dinosaur/dinosaurbioschemas.jsonld b/data/dinosaur/dinosaurbioschemas.jsonld index 959e86f58e5aa..06052c8c681d9 100644 --- a/data/dinosaur/dinosaurbioschemas.jsonld +++ b/data/dinosaur/dinosaurbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1021/acs.jproteome.6b00016", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dinosaur", "@type": "sc:SoftwareApplication", @@ -28,30 +24,34 @@ }, "sc:citation": [ "pmcid:PMC4933939", - "pubmed:27224449", { "@id": "https://doi.org/10.1021/acs.jproteome.6b00016" - } + }, + "pubmed:27224449" ], "sc:description": "Peptide feature detector for LC-MS data", "sc:featureList": [ { - "@id": "edam:operation_3634" + "@id": "edam:operation_3704" }, { - "@id": "edam:operation_3704" + "@id": "edam:operation_3634" } ], "sc:isAccessibleForFree": true, "sc:license": "Apache-2.0", "sc:name": "Dinosaur", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/fickludd/dinosaur/", "sc:version": "1.1.4" + }, + { + "@id": "https://doi.org/10.1021/acs.jproteome.6b00016", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dintor/dintorbioschemas.jsonld b/data/dintor/dintorbioschemas.jsonld index 3da7e887ab972..95a436da19304 100644 --- a/data/dintor/dintorbioschemas.jsonld +++ b/data/dintor/dintorbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12864-015-2279-5", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/dintor", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christian Weichenberger", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4687148", + "pubmed:26691694", { "@id": "https://doi.org/10.1186/S12864-015-2279-5" }, - "pubmed:26691694" + "pmcid:PMC4687148" ], "sc:description": "Functional annotation of genomic and proteomic data.", "sc:featureList": { @@ -31,15 +35,11 @@ "sc:license": "MIT", "sc:name": "Dintor", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://dintor.eurac.edu/" - }, - { - "@id": "https://doi.org/10.1186/S12864-015-2279-5", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dip/dipbioschemas.jsonld b/data/dip/dipbioschemas.jsonld index cb69a995fe68c..7952a8a35e148 100644 --- a/data/dip/dipbioschemas.jsonld +++ b/data/dip/dipbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Database of interacting proteins (DIP)", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://dip.doe-mbi.ucla.edu/" } \ No newline at end of file diff --git a/data/dipole/dipolebioschemas.jsonld b/data/dipole/dipolebioschemas.jsonld index 2373d7db7cac4..f4f9e318eab3a 100644 --- a/data/dipole/dipolebioschemas.jsonld +++ b/data/dipole/dipolebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.", "sc:name": "Protein Dipole Server", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioportal.weizmann.ac.il/dipol/" diff --git a/data/dire/direbioschemas.jsonld b/data/dire/direbioschemas.jsonld index 306abf2ddfa38..638be0104b8a7 100644 --- a/data/dire/direbioschemas.jsonld +++ b/data/dire/direbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.", "sc:name": "DiRE", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://dire.dcode.org" } \ No newline at end of file diff --git a/data/director/bioconda_director.yaml b/data/director/bioconda_director.yaml index e6d12e15656b1..f76bdf4d2cfff 100644 --- a/data/director/bioconda_director.yaml +++ b/data/director/bioconda_director.yaml @@ -11,7 +11,6 @@ description: Director is an R package designed to streamline the visualization o home: https://bioconductor.org/packages/3.10/bioc/html/Director.html identifiers: - biotools:director -- doi:10.1038/nmeth.3252 license: GPL-3 + file LICENSE license_file: LICENSE name: bioconductor-director diff --git a/data/director/directorbioschemas.jsonld b/data/director/directorbioschemas.jsonld index 8b55650c6745a..e7fc5768ed6fd 100644 --- a/data/director/directorbioschemas.jsonld +++ b/data/director/directorbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "Director", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Director.html", "sc:version": "1.0.0" diff --git a/data/dirichletmultinomial/dirichletmultinomialbioschemas.jsonld b/data/dirichletmultinomial/dirichletmultinomialbioschemas.jsonld index 130865f49d087..5d268cbd13844 100644 --- a/data/dirichletmultinomial/dirichletmultinomialbioschemas.jsonld +++ b/data/dirichletmultinomial/dirichletmultinomialbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Martin Morgan", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data.", "sc:license": "GPL-3.0", "sc:name": "DirichletMultinomial", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DirichletMultinomial.html", "sc:version": "1.16.0" diff --git a/data/disambiguate/disambiguatebioschemas.jsonld b/data/disambiguate/disambiguatebioschemas.jsonld index 2e420070b2b3b..31dc2c1c8334f 100644 --- a/data/disambiguate/disambiguatebioschemas.jsonld +++ b/data/disambiguate/disambiguatebioschemas.jsonld @@ -9,23 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-9091-7773", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/disambiguate", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pmcid:PMC5130069", - "pubmed:27990269", { "@id": "https://doi.org/10.12688/f1000research.10082.2" - } + }, + "pubmed:27990269", + "pmcid:PMC5130069" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-9091-7773" @@ -46,6 +42,10 @@ { "@id": "https://doi.org/10.12688/f1000research.10082.2", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-9091-7773", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/disco_segmentation/disco_segmentationbioschemas.jsonld b/data/disco_segmentation/disco_segmentationbioschemas.jsonld index b3b62f9b38325..adc23bfc99568 100644 --- a/data/disco_segmentation/disco_segmentationbioschemas.jsonld +++ b/data/disco_segmentation/disco_segmentationbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Framework for using the physical constraints imposed by microfluidic traps, the shape based morphological constraints of budding yeast and temporal information about cell growth and motion to allow tracking and segmentation of cells in microfluidic devices.", "sc:name": "DISCO", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/pswain/segmentation-software" } \ No newline at end of file diff --git a/data/discordant/discordantbioschemas.jsonld b/data/discordant/discordantbioschemas.jsonld index 2653f53d89433..83c1be0f54b33 100644 --- a/data/discordant/discordantbioschemas.jsonld +++ b/data/discordant/discordantbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btv633", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/discordant", "@type": "sc:SoftwareApplication", @@ -32,12 +28,16 @@ "sc:license": "GPL-2.0", "sc:name": "discordant", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/discordant.html", "sc:version": "1.4.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv633", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/discovar/discovarbioschemas.jsonld b/data/discovar/discovarbioschemas.jsonld index bf34abb05e187..6337261ee16a4 100644 --- a/data/discovar/discovarbioschemas.jsonld +++ b/data/discovar/discovarbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Variant caller designed for state-of-the-art data. It can call variants on a region by region basis, potentially tiling an entire large genome. Its variant calling is under active development and transitioning to VCF.", "sc:name": "DISCOVAR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.broadinstitute.org/software/discovar/blog/" } \ No newline at end of file diff --git a/data/discoversl/discoverslbioschemas.jsonld b/data/discoversl/discoverslbioschemas.jsonld index 736364b1a495b..643ff90e248b9 100644 --- a/data/discoversl/discoverslbioschemas.jsonld +++ b/data/discoversl/discoverslbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "DiscoverSL", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/shaoli86/DiscoverSL/releases/tag/V1.0", "sc:version": "1.0" diff --git a/data/discovery_environment/discovery_environmentbioschemas.jsonld b/data/discovery_environment/discovery_environmentbioschemas.jsonld index f074ca7cbfdf2..1a328fcc2f39f 100644 --- a/data/discovery_environment/discovery_environmentbioschemas.jsonld +++ b/data/discovery_environment/discovery_environmentbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Numerous methods for expression and promoter analysis.", "sc:name": "Discovery Environment", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.cyverse.org/discovery-environment" diff --git a/data/discromark/discromarkbioschemas.jsonld b/data/discromark/discromarkbioschemas.jsonld index d5bc7a20c46c6..6fc109f3f0b92 100644 --- a/data/discromark/discromarkbioschemas.jsonld +++ b/data/discromark/discromarkbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sereina Rutschmann", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:citation": "pubmed:27454666", "sc:description": "Discovery of Markers. Identify conserved regions and design primers based on multiple sequence alignments of putative orthologous sequences from whole‐genome or whole‐transcriptome data.", diff --git a/data/disease_ontology/disease_ontologybioschemas.jsonld b/data/disease_ontology/disease_ontologybioschemas.jsonld index 654dacd5ac53a..3e94a595acf98 100644 --- a/data/disease_ontology/disease_ontologybioschemas.jsonld +++ b/data/disease_ontology/disease_ontologybioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkr972", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/disease_ontology", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Web application" ], "sc:citation": [ - "pubmed:22080554", + "pmcid:PMC3245088", { "@id": "https://doi.org/10.1093/nar/gkr972" }, - "pmcid:PMC3245088" + "pubmed:22080554" ], "sc:description": "The Disease Ontology (DO) has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.", "sc:featureList": [ @@ -34,10 +30,10 @@ "@id": "edam:operation_3352" }, { - "@id": "edam:operation_0226" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_0226" }, { "@id": "edam:operation_3559" @@ -46,11 +42,15 @@ "sc:license": "CC-BY-1.0", "sc:name": "DO", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://disease-ontology.org/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkr972", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/diseasecard/diseasecardbioschemas.jsonld b/data/diseasecard/diseasecardbioschemas.jsonld index 59107ea1f1da9..51486a0802c62 100644 --- a/data/diseasecard/diseasecardbioschemas.jsonld +++ b/data/diseasecard/diseasecardbioschemas.jsonld @@ -11,21 +11,21 @@ "@id": "https://bio.tools/diseasecard", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "José Luis Oliveira", - "Pedro Lopes" + "Pedro Lopes", + "José Luis Oliveira" ], "sc:additionalType": [ - "Web application", + "Database portal", "Web API", - "Database portal" + "Web application" ], "sc:citation": "pubmed:23973272", "sc:description": "Information retrieval tool for accessing and integrating genetic and medical information for health applications. Resorting to this integrated environment, clinicians are able to access and relate diseases data already available in the Internet, scattered along multiple databases.", "sc:name": "Diseasecard", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinformatics.ua.pt/diseasecard/" } \ No newline at end of file diff --git a/data/diseaseconnect/diseaseconnectbioschemas.jsonld b/data/diseaseconnect/diseaseconnectbioschemas.jsonld index 45448e76dfc9c..b03c31ddc8bbf 100644 --- a/data/diseaseconnect/diseaseconnectbioschemas.jsonld +++ b/data/diseaseconnect/diseaseconnectbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.", "sc:name": "DiseaseConnect", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://disease-connect.org" } \ No newline at end of file diff --git a/data/diseasemeth/diseasemethbioschemas.jsonld b/data/diseasemeth/diseasemethbioschemas.jsonld index a7a862dacaa9b..d83d56bb1d294 100644 --- a/data/diseasemeth/diseasemethbioschemas.jsonld +++ b/data/diseasemeth/diseasemethbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A web based resource focused on the aberrant methylomes of human diseases.", "sc:name": "DiseaseMeth", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioinfo.hrbmu.edu.cn/diseasemeth" diff --git a/data/diseases/diseasesbioschemas.jsonld b/data/diseases/diseasesbioschemas.jsonld index 50c3c2b6e3f7e..330d6ecd89eff 100644 --- a/data/diseases/diseasesbioschemas.jsonld +++ b/data/diseases/diseasesbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "DISEASES", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://diseases.jensenlab.org/" } \ No newline at end of file diff --git a/data/disembl_ws_jabaws/disembl_ws_jabawsbioschemas.jsonld b/data/disembl_ws_jabaws/disembl_ws_jabawsbioschemas.jsonld index 8978eb3f25f7e..b6caaddebf4d8 100644 --- a/data/disembl_ws_jabaws/disembl_ws_jabawsbioschemas.jsonld +++ b/data/disembl_ws_jabaws/disembl_ws_jabawsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Disembl WS (jabaws)", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.compbio.dundee.ac.uk/jabaws/", "sc:version": "1" diff --git a/data/disentangler/disentanglerbioschemas.jsonld b/data/disentangler/disentanglerbioschemas.jsonld index c873df6227d19..2c567d33787c6 100644 --- a/data/disentangler/disentanglerbioschemas.jsonld +++ b/data/disentangler/disentanglerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers.", "sc:name": "disentangler", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://kumasakanatsuhiko.jp/projects/disentangler/", "sc:version": "20111001" diff --git a/data/disgenet/disgenetbioschemas.jsonld b/data/disgenet/disgenetbioschemas.jsonld index 906b364e94a38..25e55ed2a5559 100644 --- a/data/disgenet/disgenetbioschemas.jsonld +++ b/data/disgenet/disgenetbioschemas.jsonld @@ -9,12 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-2846-6174", + "@type": "schema:Person" + }, { "@id": "https://orcid.org/0000-0002-9383-528X", "@type": "schema:Person" }, { - "@id": "https://orcid.org/0000-0002-2846-6174", + "@id": "http://orcid.org/0000-0002-7534-7661", "@type": "schema:Person" }, { @@ -25,45 +29,41 @@ }, "sc:additionalType": [ "Plug-in", - "Web API", - "SPARQL endpoint", "Web application", - "Database portal" + "SPARQL endpoint", + "Database portal", + "Web API" ], "sc:author": [ { "@id": "https://orcid.org/0000-0002-2846-6174" }, - "Janet Piñero", - "Núria Queralt Rosinach" + "Núria Queralt Rosinach", + "Janet Piñero" ], "sc:contributor": [ + "Núria Queralt Rosinach", { "@id": "http://orcid.org/0000-0002-7534-7661" }, - "Janet Piñero", - "Núria Queralt Rosinach" + "Janet Piñero" ], "sc:description": "DisGeNET is a discovery platform containing one of the largest publicly available collections of genes and variants associated to human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype–phenotype relationships.\n\nThe current version of DisGeNET (v6.0) contains 628,685 gene-disease associations (GDAs), between 17,549 genes and 24,166 diseases, disorders, traits, and clinical or abnormal human phenotypes, and 210,498 variant-disease associations (VDAs), between 117,337 variants and 10,358 diseases, traits, and phenotypes.", "sc:license": "CC-BY-NC-SA-4.0", "sc:name": "DisGeNET", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.disgenet.org/", "sc:version": [ - "disgenet2r R package Version: 0.0.9", - "Database version 6.0", "Platform v1.1.0", "DisGeNET RDF release 5.0", - "REST API v1.0.0" + "Database version 6.0", + "REST API v1.0.0", + "disgenet2r R package Version: 0.0.9" ] - }, - { - "@id": "http://orcid.org/0000-0002-7534-7661", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dislocate/dislocatebioschemas.jsonld b/data/dislocate/dislocatebioschemas.jsonld index 53db4e90c836b..a96f572f28b53 100644 --- a/data/dislocate/dislocatebioschemas.jsonld +++ b/data/dislocate/dislocatebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Prediction of cysteine connectivity patterns in a protein chain.", "sc:name": "DisLocate", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "http://dislocate.biocomp.unibo.it/dislocate/default/index", diff --git a/data/dismiss/dismissbioschemas.jsonld b/data/dismiss/dismissbioschemas.jsonld index ec6930d1aa098..b89022d7614ae 100644 --- a/data/dismiss/dismissbioschemas.jsonld +++ b/data/dismiss/dismissbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-016-1158-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/dismiss", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Martin T. Swain", "sc:additionalType": [ - "Plug-in", - "Command-line tool" + "Command-line tool", + "Plug-in" ], "sc:citation": [ "pmcid:PMC4966778", + "pubmed:27473283", { "@id": "https://doi.org/10.1186/s12859-016-1158-7" - }, - "pubmed:27473283" + } ], "sc:description": "DISMISS is a new software package that detects strand-associated DNA methylation from existing MeDIP-Seq analyses", "sc:featureList": { @@ -32,14 +36,10 @@ "sc:name": "DISMISS", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://uhkniazi.github.io/dismiss/" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1158-7", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/disnor/disnorbioschemas.jsonld b/data/disnor/disnorbioschemas.jsonld index 4dd43715612a9..bf4195141ec62 100644 --- a/data/disnor/disnorbioschemas.jsonld +++ b/data/disnor/disnorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "CC-BY-NC-4.0", "sc:name": "DISNOR", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy", "sc:url": "https://disnor.uniroma2.it/" diff --git a/data/disprot/disprotbioschemas.jsonld b/data/disprot/disprotbioschemas.jsonld index 4d8db62064bdc..5a81ec6d6cb85 100644 --- a/data/disprot/disprotbioschemas.jsonld +++ b/data/disprot/disprotbioschemas.jsonld @@ -17,13 +17,13 @@ }, "edam:has_input": [ { - "@id": "edam:data_3021" + "@id": "edam:data_2723" }, { "@id": "edam:data_1009" }, { - "@id": "edam:data_2723" + "@id": "edam:data_3021" } ], "edam:has_output": [ @@ -35,9 +35,9 @@ } ], "sc:additionalType": [ - "Web application", "Database portal", - "Web API" + "Web API", + "Web application" ], "sc:applicationSubCategory": { "@id": "edam:topic_3538" @@ -52,30 +52,30 @@ "sc:description": "Database of protein disorder. It is a community resource annotating protein sequences for intrinsically disordered regions from the literature.", "sc:featureList": [ { - "@id": "edam:operation_3092" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_3092" } ], "sc:license": "CC-BY-NC-1.0", "sc:name": "Database of protein disorder (DisProt)", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", "sc:url": "http://www.disprot.org/", "sc:version": "7.0" }, - { - "@id": "https://doi.org/10.1093/nar/gkw1279", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0003-4525-7793", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gkw1279", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/disqover/disqoverbioschemas.jsonld b/data/disqover/disqoverbioschemas.jsonld index 3825df0a8d539..7914379194bc3 100644 --- a/data/disqover/disqoverbioschemas.jsonld +++ b/data/disqover/disqoverbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/disqover", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", + "Web API", "Database portal", - "Web API" + "Web application" ], "sc:description": "DISQOVER is a data integration platform for public, licensed and internal data. The Data Ingestion Engine enables transforming data into Linked Data which can be searched, navigated and analysed via the user interface and the API. The publicly accessible DISQOVER platform contains 140+ public data sources in life sciences and related domains.", "sc:license": "Unlicense", diff --git a/data/distancep/distancepbioschemas.jsonld b/data/distancep/distancepbioschemas.jsonld index 42494959fa2d0..7803085ec18b5 100644 --- a/data/distancep/distancepbioschemas.jsonld +++ b/data/distancep/distancepbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-5823-4000", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/distancep", "@type": "sc:SoftwareApplication", @@ -32,6 +28,10 @@ "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/DistanceP", "sc:version": "1.0" + }, + { + "@id": "http://orcid.org/0000-0001-5823-4000", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/distild/distildbioschemas.jsonld b/data/distild/distildbioschemas.jsonld index 3d9d23237e2ce..88ea51ca4e7f3 100644 --- a/data/distild/distildbioschemas.jsonld +++ b/data/distild/distildbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Diseases and traits in linkage disequilibrium (LD) blocks. Data from HapMap Project is used to partition chromosomal regions which are associated with a disease into LD blocks. This allows researchers to answer the question of which SNPs associated with diseases are in LD with a gene of interest?", "sc:name": "DistiLD", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://distild.jensenlab.org/" } \ No newline at end of file diff --git a/data/distiller/distillerbioschemas.jsonld b/data/distiller/distillerbioschemas.jsonld index d121ed152d97d..783c4158d6849 100644 --- a/data/distiller/distillerbioschemas.jsonld +++ b/data/distiller/distillerbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/distiller", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Data integration system to identify links in expression regulation.", "sc:name": "DISTILLER", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Lemmens_2008/Index.html", diff --git a/data/distmap/distmapbioschemas.jsonld b/data/distmap/distmapbioschemas.jsonld index 5621faaabd1c5..3c3b56cec93f6 100644 --- a/data/distmap/distmapbioschemas.jsonld +++ b/data/distmap/distmapbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Christian Schlötterer", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC3751911", - "pubmed:24009693", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0072614" - } + }, + "pmcid:PMC3751911", + "pubmed:24009693" ], "sc:description": "A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster.", "sc:featureList": { diff --git a/data/distmat/distmatbioschemas.jsonld b/data/distmat/distmatbioschemas.jsonld index 276492d9b55ea..81928c71c8b11 100644 --- a/data/distmat/distmatbioschemas.jsonld +++ b/data/distmat/distmatbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", + "UK BBSRC", "EMBOSS Contributors", "UK MRC", - "UK BBSRC" + "Wellcome Trust" ], "sc:description": "Create a distance matrix from a multiple sequence alignment.", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "distmat", diff --git a/data/distnet/distnetbioschemas.jsonld b/data/distnet/distnetbioschemas.jsonld index 88e0fc0580a12..9731c9c7a5d7e 100644 --- a/data/distnet/distnetbioschemas.jsonld +++ b/data/distnet/distnetbioschemas.jsonld @@ -24,21 +24,21 @@ "sc:description": "R package for interactive checking of dimension-reduction visualizations.", "sc:featureList": [ { - "@id": "edam:operation_2937" + "@id": "edam:operation_2939" }, { - "@id": "edam:operation_3432" + "@id": "edam:operation_2937" }, { - "@id": "edam:operation_2939" + "@id": "edam:operation_3432" } ], "sc:license": "LGPL-3.0", "sc:name": "distnet", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/simon-anders/distnet" }, diff --git a/data/disulfind/disulfindbioschemas.jsonld b/data/disulfind/disulfindbioschemas.jsonld index 918bd8fc5afa9..0e3ea714a1d29 100644 --- a/data/disulfind/disulfindbioschemas.jsonld +++ b/data/disulfind/disulfindbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.", "sc:name": "DISULFIND", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://disulfind.dsi.unifi.it/" } \ No newline at end of file diff --git a/data/disv-hpv16/disv-hpv16bioschemas.jsonld b/data/disv-hpv16/disv-hpv16bioschemas.jsonld index d76b54809fc47..6075fbca97508 100644 --- a/data/disv-hpv16/disv-hpv16bioschemas.jsonld +++ b/data/disv-hpv16/disv-hpv16bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "DisV-HPV16", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ybq1204/DisV-HPV16" } \ No newline at end of file diff --git a/data/disvis/disvisbioschemas.jsonld b/data/disvis/disvisbioschemas.jsonld index 34a5d91b25641..48c676a640155 100644 --- a/data/disvis/disvisbioschemas.jsonld +++ b/data/disvis/disvisbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Visualize and quantify the information content of distance restraints between macromolecular complexes. A full and systematic 6 dimensional search of the three translational and rotational degrees of freedom to determine the number of complexes consistent with the restraints. It outputs the percentage of restraints being violated and a density that represents the center-of-mass position of the scanning chain corresponding to the highest number of consistent restraints at every position in space.", "sc:name": "DisVis", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Utrecht University", "sc:url": "http://milou.science.uu.nl/services/DISVIS", diff --git a/data/divenn/divennbioschemas.jsonld b/data/divenn/divennbioschemas.jsonld index 29ff1211394e6..2a1624446e1bf 100644 --- a/data/divenn/divennbioschemas.jsonld +++ b/data/divenn/divennbioschemas.jsonld @@ -13,8 +13,8 @@ "@id": "https://bio.tools/DiVenn", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yinbing Ge", "Zach Robinson", + "Yinbing Ge", "Liang Sun" ], "sc:additionalType": "Web application", @@ -31,17 +31,17 @@ "@id": "edam:operation_3501" }, { - "@id": "edam:operation_0533" + "@id": "edam:operation_0277" }, { - "@id": "edam:operation_0277" + "@id": "edam:operation_0533" } ], "sc:license": "GPL-3.0", "sc:name": "DiVenn", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://divenn.noble.org/" diff --git a/data/diversitycollection/diversitycollectionbioschemas.jsonld b/data/diversitycollection/diversitycollectionbioschemas.jsonld index d801af94b80b3..e4ac26d08f33a 100644 --- a/data/diversitycollection/diversitycollectionbioschemas.jsonld +++ b/data/diversitycollection/diversitycollectionbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-1980-3148", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/DiversityCollection", "@type": "sc:SoftwareApplication", @@ -16,8 +20,8 @@ "@id": "https://orcid.org/0000-0003-1980-3148" }, "sc:additionalType": [ - "Desktop application", - "Web service" + "Web service", + "Desktop application" ], "sc:description": "DiversityCollection (DWB-DC) is an application of the Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DC is designed for data describing collection events, collections, collection vouchers and specimens, parts of specimens, as well as observation and occurrence data with assigned multimedia objects and documents. It is processing any action concerning the gathering, storage, transaction and treatment of specimens in a collection and is also appropriate to store observation data with analyses added. DC is unique among collection management systems by its focus on biological relations between organisms linked together as one or more specimens or observations (e. g., host, parasite, hyperparasite, symbionts, etc.) and by its interoperability through internal and external services.", "sc:funder": "Deutsche Forschungsgemeinschaft (DFG)", @@ -26,10 +30,6 @@ "sc:operatingSystem": "Windows", "sc:provider": "SNSB IT Center", "sc:url": "https://diversityworkbench.net/Portal/DiversityCollection" - }, - { - "@id": "https://orcid.org/0000-0003-1980-3148", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/diversityexsiccatae/diversityexsiccataebioschemas.jsonld b/data/diversityexsiccatae/diversityexsiccataebioschemas.jsonld index 1ad103f3fae81..e7b78ed5f4597 100644 --- a/data/diversityexsiccatae/diversityexsiccataebioschemas.jsonld +++ b/data/diversityexsiccatae/diversityexsiccataebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-1980-3148", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/DiversityExsiccatae", "@type": "sc:SoftwareApplication", @@ -20,9 +16,9 @@ "@id": "https://orcid.org/0000-0003-1980-3148" }, "sc:additionalType": [ - "Desktop application", "Database portal", - "Web service" + "Web service", + "Desktop application" ], "sc:description": "DiversityExsiccatae (DWB-DE) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DE is currently used in a core installation at the SNSB, Botanische Staatssammlung München to manage bibliographic information and standardized abbreviations of botanical and mycological exsiccatae in a global index. Exsiccatae are series of specimen collections which are distributed as a publication together with assigned printed matters. They are usually available in multiple copies worldwide. This standard list for Exsiccatal series with unique and stable series identifers is increasing the efficiency of the digitization of botanical and mycological collections.", "sc:funder": "Deutsche Forschungsgemeinschaft (DFG)", @@ -31,6 +27,10 @@ "sc:operatingSystem": "Windows", "sc:provider": "SNSB IT Center", "sc:url": "https://diversityworkbench.net/Portal/DiversityExsiccatae" + }, + { + "@id": "https://orcid.org/0000-0003-1980-3148", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/diversityprojects/diversityprojectsbioschemas.jsonld b/data/diversityprojects/diversityprojectsbioschemas.jsonld index d3ad7226e9405..f6500909fffad 100644 --- a/data/diversityprojects/diversityprojectsbioschemas.jsonld +++ b/data/diversityprojects/diversityprojectsbioschemas.jsonld @@ -16,8 +16,8 @@ "@id": "https://orcid.org/0000-0003-1980-3148" }, "sc:additionalType": [ - "Web service", - "Desktop application" + "Desktop application", + "Web service" ], "sc:description": "DiversityProjects (DWB-DP) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DP is focused on the management of (research) projects, data collections, processed by the other DWB modules. It is managing metadata , labels, descriptors, and descriptions of projects, including data package-specific settings for a metadata standard-compliant publication. DP is organising the storage of (legal) documents, permits, information on publications and multimedia resources. DP is handling roles of persons and organisations involved in collection and research projects. The tool is organising project classification and hierarchy in relation to sister and umbrella projects as well as the storage of each type of stable identifier related to data packages. DP is managing issues on web presentation of data collections.", "sc:funder": "Deutsche Forschungsgemeinschaft (DFG)", diff --git a/data/diversityscientificterms/diversityscientifictermsbioschemas.jsonld b/data/diversityscientificterms/diversityscientifictermsbioschemas.jsonld index 56ef26e70b587..3dc0dcf3e955a 100644 --- a/data/diversityscientificterms/diversityscientifictermsbioschemas.jsonld +++ b/data/diversityscientificterms/diversityscientifictermsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-1980-3148", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/DiversityScientificTerms", "@type": "sc:SoftwareApplication", @@ -27,6 +23,10 @@ "sc:operatingSystem": "Windows", "sc:provider": "SNSB IT Center", "sc:url": "https://diversityworkbench.net/Portal/DiversityScientificTerms" + }, + { + "@id": "https://orcid.org/0000-0003-1980-3148", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/diversitytaxonnames/diversitytaxonnamesbioschemas.jsonld b/data/diversitytaxonnames/diversitytaxonnamesbioschemas.jsonld index 0abcafde5d9a9..101e68d087a4b 100644 --- a/data/diversitytaxonnames/diversitytaxonnamesbioschemas.jsonld +++ b/data/diversitytaxonnames/diversitytaxonnamesbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-1980-3148", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/DiversityTaxonNames", "@type": "sc:SoftwareApplication", @@ -31,6 +27,10 @@ "sc:operatingSystem": "Windows", "sc:provider": "SNSB IT Center", "sc:url": "https://diversityworkbench.net/Portal/DiversityTaxonNames" + }, + { + "@id": "https://orcid.org/0000-0003-1980-3148", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dizzy-beats/dizzy-beatsbioschemas.jsonld b/data/dizzy-beats/dizzy-beatsbioschemas.jsonld index ea10b604e0184..bdb6041402ad6 100644 --- a/data/dizzy-beats/dizzy-beatsbioschemas.jsonld +++ b/data/dizzy-beats/dizzy-beatsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "Dizzy-Beats", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/p/bayesevidence/home/Home/" } \ No newline at end of file diff --git a/data/dks/dksbioschemas.jsonld b/data/dks/dksbioschemas.jsonld index 0c49ba3f35f7f..87d7b9d550c94 100644 --- a/data/dks/dksbioschemas.jsonld +++ b/data/dks/dksbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jeffrey T. Leek", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package consists of a set of diagnostic functions for multiple testing methods. The functions can be used to determine if the p-values produced by a multiple testing procedure are correct. These functions are designed to be applied to simulated data. The functions require the entire set of p-values from multiple simulated studies, so that the joint distribution can be evaluated.", "sc:license": "GPL-3.0", "sc:name": "dks", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/dks.html", "sc:version": "1.20.0" diff --git a/data/dlocalmotif/dlocalmotifbioschemas.jsonld b/data/dlocalmotif/dlocalmotifbioschemas.jsonld index 3e5597d54d141..08e457989374b 100644 --- a/data/dlocalmotif/dlocalmotifbioschemas.jsonld +++ b/data/dlocalmotif/dlocalmotifbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "DLocalMotif is a discriminitive motif discovery web service specifically designed to discover local motifs in protein sequences that are aligned relative to a defined sequence landmark. It uses three discriminitive scoring features, motif spatial confinement (MSC), motif over-representation (MOR) and motif relative entropy (MRE). These features establish if a motif is positioned in a constrained sequence interval in positive data set and absent in negative data set.", "sc:name": "DLocalMotif", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioinf.scmb.uq.edu.au/dlocalmotif/" diff --git a/data/dmchmm/dmchmmbioschemas.jsonld b/data/dmchmm/dmchmmbioschemas.jsonld index de9fb54152012..de632214d85bc 100644 --- a/data/dmchmm/dmchmmbioschemas.jsonld +++ b/data/dmchmm/dmchmmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "DMCHMM", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DMCHMM.html", diff --git a/data/dmdtoolkit/dmdtoolkitbioschemas.jsonld b/data/dmdtoolkit/dmdtoolkitbioschemas.jsonld index b1e5b31601322..008c86932f969 100644 --- a/data/dmdtoolkit/dmdtoolkitbioschemas.jsonld +++ b/data/dmdtoolkit/dmdtoolkitbioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Shiwen Wu", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:28152980", { "@id": "https://doi.org/10.1186/S12859-017-1504-4" }, + "pubmed:28152980", "pmcid:PMC5290630" ], "sc:description": "Tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD.", @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "DMDtoolkit", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/zhoujp111/DMDtoolkit" } diff --git a/data/dminda/dmindabioschemas.jsonld b/data/dminda/dmindabioschemas.jsonld index abf7b954438d3..3f4f9fc1b42dd 100644 --- a/data/dminda/dmindabioschemas.jsonld +++ b/data/dminda/dmindabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "DMINDA: An integrated web server for DNA motif identification and analyses.", "sc:name": "DMINDA", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://csbl.bmb.uga.edu/DMINDA/" } \ No newline at end of file diff --git a/data/dmpy/dmpybioschemas.jsonld b/data/dmpy/dmpybioschemas.jsonld index db4981f6add07..6101624013ed1 100644 --- a/data/dmpy/dmpybioschemas.jsonld +++ b/data/dmpy/dmpybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Automated mathematical model construction of large-scale metabolic systems.", "sc:name": "DMPy", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://gitlab.com/wurssb/DMPy" } \ No newline at end of file diff --git a/data/dmrcaller/dmrcallerbioschemas.jsonld b/data/dmrcaller/dmrcallerbioschemas.jsonld index 9bbc98e8be2c6..ef09254e0e125 100644 --- a/data/dmrcaller/dmrcallerbioschemas.jsonld +++ b/data/dmrcaller/dmrcallerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "DMRcaller", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DMRcaller.html", "sc:version": "1.6.0" diff --git a/data/dmrcate/dmrcatebioschemas.jsonld b/data/dmrcate/dmrcatebioschemas.jsonld index 41d3d2092a7a0..5a10c22944b97 100644 --- a/data/dmrcate/dmrcatebioschemas.jsonld +++ b/data/dmrcate/dmrcatebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1756-8935-8-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dmrcate", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Library" ], "sc:citation": [ + "pubmed:25972926", { "@id": "https://doi.org/10.1186/1756-8935-8-6" }, - "pmcid:PMC4429355", - "pubmed:25972926" + "pmcid:PMC4429355" ], "sc:description": "De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulphite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.", "sc:featureList": { @@ -34,12 +30,16 @@ }, "sc:name": "DMRcate", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DMRcate.html", "sc:version": "1.10.1" + }, + { + "@id": "https://doi.org/10.1186/1756-8935-8-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dmrfinder/dmrfinderbioschemas.jsonld b/data/dmrfinder/dmrfinderbioschemas.jsonld index 2a23ac388818f..1ad1730b446bc 100644 --- a/data/dmrfinder/dmrfinderbioschemas.jsonld +++ b/data/dmrfinder/dmrfinderbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "John M. Gaspar", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:29187143", + "pmcid:PMC5817627", { "@id": "https://doi.org/10.1186/s12859-017-1909-0" - }, - "pubmed:29187143", - "pmcid:PMC5817627" + } ], "sc:description": "Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data.", "sc:featureList": { diff --git a/data/dmrforpairs/dmrforpairsbioschemas.jsonld b/data/dmrforpairs/dmrforpairsbioschemas.jsonld index a9e7f01f414aa..45519bdf879d3 100644 --- a/data/dmrforpairs/dmrforpairsbioschemas.jsonld +++ b/data/dmrforpairs/dmrforpairsbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1186/1471-2105-15-141", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0002-2528-8077", + "@type": "schema:Person" }, { "@id": "https://bio.tools/dmrforpairs", @@ -24,15 +24,15 @@ }, "edam:has_output": [ { - "@id": "edam:data_1255" + "@id": "edam:data_2884" }, { - "@id": "edam:data_2884" + "@id": "edam:data_1255" } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { @@ -46,34 +46,34 @@ } ], "sc:citation": [ - "pmcid:PMC4046028", + "pubmed:24884391", { "@id": "https://doi.org/10.1186/1471-2105-15-141" }, - "pubmed:24884391" + "pmcid:PMC4046028" ], "sc:description": "This tool compares n>=2 unique samples regarding their methylation profile in either single CpG locus or region based analysis, defining regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional classes and differential methylation is evaluated by comparing the methylation values within each region between individual samples.", "sc:featureList": [ { - "@id": "edam:operation_0256" + "@id": "edam:operation_3204" }, { - "@id": "edam:operation_3204" + "@id": "edam:operation_0256" } ], "sc:license": "GPL-2.0", "sc:name": "DMRforPairs", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DMRforPairs.html", "sc:version": "1.10.0" }, { - "@id": "http://orcid.org/0000-0002-2528-8077", - "@type": "schema:Person" + "@id": "https://doi.org/10.1186/1471-2105-15-141", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dmrscan/dmrscanbioschemas.jsonld b/data/dmrscan/dmrscanbioschemas.jsonld index 801adadcac575..e50f0f7c6499c 100644 --- a/data/dmrscan/dmrscanbioschemas.jsonld +++ b/data/dmrscan/dmrscanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "DMRScan", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DMRScan.html", "sc:version": "1.6.0" diff --git a/data/dmu/dmubioschemas.jsonld b/data/dmu/dmubioschemas.jsonld index ef691814888f6..ba5d84f339033 100644 --- a/data/dmu/dmubioschemas.jsonld +++ b/data/dmu/dmubioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Proprietary", "sc:name": "DMU", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://dmu.agrsci.dk/", "sc:version": "v6-R5-2" diff --git a/data/dnaasm-link/dnaasm-linkbioschemas.jsonld b/data/dnaasm-link/dnaasm-linkbioschemas.jsonld index 380130532af75..0c8117df24e82 100644 --- a/data/dnaasm-link/dnaasm-linkbioschemas.jsonld +++ b/data/dnaasm-link/dnaasm-linkbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "LGPL-3.0", "sc:name": "dnaasm-link", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://dnaasm.sourceforge.net" } \ No newline at end of file diff --git a/data/dnaasm/dnaasmbioschemas.jsonld b/data/dnaasm/dnaasmbioschemas.jsonld index ea4fb5f3e9323..5f8813d3aba0f 100644 --- a/data/dnaasm/dnaasmbioschemas.jsonld +++ b/data/dnaasm/dnaasmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "LGPL-3.0", "sc:name": "dnaasm", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://dnaasm.sourceforge.net/" } \ No newline at end of file diff --git a/data/dnabarcodecompatibility/dnabarcodecompatibilitybioschemas.jsonld b/data/dnabarcodecompatibility/dnabarcodecompatibilitybioschemas.jsonld index 5cafd06c381a7..ce619fe7c28c9 100644 --- a/data/dnabarcodecompatibility/dnabarcodecompatibilitybioschemas.jsonld +++ b/data/dnabarcodecompatibility/dnabarcodecompatibilitybioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Céline Trébeau", "sc:additionalType": [ - "Desktop application", - "Library" + "Library", + "Desktop application" ], "sc:citation": [ + "pmcid:PMC6662285", + "pubmed:30576403", { "@id": "https://doi.org/10.1093/bioinformatics/bty1030" - }, - "pubmed:30576403", - "pmcid:PMC6662285" + } ], "sc:description": "R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments.", "sc:featureList": [ @@ -34,18 +34,18 @@ "@id": "edam:operation_3200" }, { - "@id": "edam:operation_3745" + "@id": "edam:operation_3192" }, { - "@id": "edam:operation_3192" + "@id": "edam:operation_3745" } ], "sc:license": "GPL-2.0", "sc:name": "DNABarcodeCompatibility", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/comoto-pasteur-fr" } diff --git a/data/dnabarcodes/dnabarcodesbioschemas.jsonld b/data/dnabarcodes/dnabarcodesbioschemas.jsonld index edfcc58cf34ff..9b239253618a2 100644 --- a/data/dnabarcodes/dnabarcodesbioschemas.jsonld +++ b/data/dnabarcodes/dnabarcodesbioschemas.jsonld @@ -14,14 +14,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Tilo Buschmann", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC3853030", { "@id": "https://doi.org/10.1186/1471-2105-14-272" }, - "pmcid:PMC3853030", "pubmed:24021088" ], "sc:description": "The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.", @@ -31,8 +31,8 @@ "sc:license": "GPL-2.0", "sc:name": "DNABarcodes", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DNABarcodes.html", diff --git a/data/dnacopy/bioconda_dnacopy.yaml b/data/dnacopy/bioconda_dnacopy.yaml index 075842bf98920..d60b0a4ba795c 100644 --- a/data/dnacopy/bioconda_dnacopy.yaml +++ b/data/dnacopy/bioconda_dnacopy.yaml @@ -4,7 +4,6 @@ description: Implements the circular binary segmentation (CBS) algorithm to segm home: https://bioconductor.org/packages/3.10/bioc/html/DNAcopy.html identifiers: - biotools:dnacopy -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-dnacopy diff --git a/data/dnacopy/dnacopybioschemas.jsonld b/data/dnacopy/dnacopybioschemas.jsonld index 000a773f64b70..8ecc136439a4a 100644 --- a/data/dnacopy/dnacopybioschemas.jsonld +++ b/data/dnacopy/dnacopybioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Venkatraman E. Seshan", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.", "sc:license": "GPL-2.0", diff --git a/data/dnamate/dnamatebioschemas.jsonld b/data/dnamate/dnamatebioschemas.jsonld index 9096dcfc0258e..b5e2d08954e48 100644 --- a/data/dnamate/dnamatebioschemas.jsonld +++ b/data/dnamate/dnamatebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "dnaMATE", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://melolab.org/dnaMATE/" } \ No newline at end of file diff --git a/data/dnaplotter/dnaplotterbioschemas.jsonld b/data/dnaplotter/dnaplotterbioschemas.jsonld index 50de07d826832..588a05540c15c 100644 --- a/data/dnaplotter/dnaplotterbioschemas.jsonld +++ b/data/dnaplotter/dnaplotterbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "DNAPlotter is a collaborative project between Jemboss and Artemis. It makes use of the existing circular plot in Jemboss and the Artemis sequence libraries.", "sc:name": "DNAPlotter", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.sanger.ac.uk/science/tools/dnaplotter", "sc:version": "1.11" diff --git a/data/dnas/dnasbioschemas.jsonld b/data/dnas/dnasbioschemas.jsonld index 42c2cf2a6bb2e..d568f373e2418 100644 --- a/data/dnas/dnasbioschemas.jsonld +++ b/data/dnas/dnasbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web service providing assignment of nucleic acid conformers used in bioinformatic analysis of nucleic acids and protein/DNA interfaces.", "sc:name": "DNAS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ELIXIR-CZ", "sc:url": "http://www.structbio.org/dnas", diff --git a/data/dnascan/dnascanbioschemas.jsonld b/data/dnascan/dnascanbioschemas.jsonld index 290575091f406..19059a3b4d088 100644 --- a/data/dnascan/dnascanbioschemas.jsonld +++ b/data/dnascan/dnascanbioschemas.jsonld @@ -9,33 +9,29 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2791-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/DNAscan", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "KCL IoPPN: NIHR BRC-MH Bioinformatics Group", "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC6487045", - "pubmed:31029080", { "@id": "https://doi.org/10.1186/s12859-019-2791-8" - } + }, + "pubmed:31029080", + "pmcid:PMC6487045" ], "sc:contributor": [ - "Dr Alfredo Iacoangeli", - "Dr Stephen J Newhouse" + "Dr Stephen J Newhouse", + "Dr Alfredo Iacoangeli" ], "sc:description": "Personal computer compatible NGS analysis, annotation and visualisation.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_3196" }, { "@id": "edam:operation_3227" @@ -44,11 +40,15 @@ "sc:license": "MIT", "sc:name": "DNAscan", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/KHP-Informatics/DNAscan" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2791-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dnaser/dnaserbioschemas.jsonld b/data/dnaser/dnaserbioschemas.jsonld index 6af1d0240b0f8..314b5fd3b8b51 100644 --- a/data/dnaser/dnaserbioschemas.jsonld +++ b/data/dnaser/dnaserbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-2.0", "sc:name": "DNaseR", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.riken.jp/packages/2.14/bioc/html/DNaseR.html" } \ No newline at end of file diff --git a/data/dnashaper/dnashaperbioschemas.jsonld b/data/dnashaper/dnashaperbioschemas.jsonld index bfcec9f577143..44dd2d64bc05e 100644 --- a/data/dnashaper/dnashaperbioschemas.jsonld +++ b/data/dnashaper/dnashaperbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Tsu-Pei Chiu", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pmcid:PMC4824130", "pubmed:26668005", { "@id": "https://doi.org/10.1093/bioinformatics/btv735" - }, - "pmcid:PMC4824130" + } ], "sc:description": "R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.", "sc:featureList": { @@ -35,8 +35,8 @@ "sc:license": "GPL-2.0", "sc:name": "DNAshapeR", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DNAshapeR.html", "sc:version": "1.2.0" diff --git a/data/dnatco/dnatcobioschemas.jsonld b/data/dnatco/dnatcobioschemas.jsonld index 85c6dfb7230fe..72bcf52f367f5 100644 --- a/data/dnatco/dnatcobioschemas.jsonld +++ b/data/dnatco/dnatcobioschemas.jsonld @@ -15,8 +15,8 @@ "Command-line tool" ], "sc:author": [ - "Jiří Černý", - "Bohdan Schneider" + "Bohdan Schneider", + "Jiří Černý" ], "sc:description": "A web service providing assignment of nucleic acid conformers used in bioinformatic analysis of nucleic acids and protein/DNA interfaces.", "sc:name": "DNATCO", diff --git a/data/dnatools/dnatoolsbioschemas.jsonld b/data/dnatools/dnatoolsbioschemas.jsonld index 1f79fc6947572..5079be8789cbb 100644 --- a/data/dnatools/dnatoolsbioschemas.jsonld +++ b/data/dnatools/dnatoolsbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "DNAtools", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://pongor.itk.ppke.hu/?q=bioinfoservices" } \ No newline at end of file diff --git a/data/dnatraffic/dnatrafficbioschemas.jsonld b/data/dnatraffic/dnatrafficbioschemas.jsonld index 132249f1b389d..f532489344458 100644 --- a/data/dnatraffic/dnatrafficbioschemas.jsonld +++ b/data/dnatraffic/dnatrafficbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database dedicated to comprehensive and rich annotations of genome dynamics during cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study.", "sc:name": "DNAtraffic", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://dnatraffic.ibb.waw.pl/" } \ No newline at end of file diff --git a/data/dnazip/dnazipbioschemas.jsonld b/data/dnazip/dnazipbioschemas.jsonld index 5d6534beaba86..52cb2750cd72e 100644 --- a/data/dnazip/dnazipbioschemas.jsonld +++ b/data/dnazip/dnazipbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Other", "sc:name": "DNAzip", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ics.uci.edu/%7Ednazip/" } \ No newline at end of file diff --git a/data/dnenrich/dnenrichbioschemas.jsonld b/data/dnenrich/dnenrichbioschemas.jsonld index 7b1a9c8374b34..87da78ba62868 100644 --- a/data/dnenrich/dnenrichbioschemas.jsonld +++ b/data/dnenrich/dnenrichbioschemas.jsonld @@ -21,8 +21,8 @@ { "@id": "https://doi.org/10.1038/nature12929" }, - "pmcid:PMC4237002", - "pubmed:24463507" + "pubmed:24463507", + "pmcid:PMC4237002" ], "sc:description": "Statistical software package for calculating gene set enrichment for de novo mutations (typically detected by exome sequencing) of a disease cohort.", "sc:featureList": { diff --git a/data/do-ms/do-msbioschemas.jsonld b/data/do-ms/do-msbioschemas.jsonld index c5a5a2644e7e0..8d55b98dfbb98 100644 --- a/data/do-ms/do-msbioschemas.jsonld +++ b/data/do-ms/do-msbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "MIT", "sc:name": "DO-MS", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://do-ms.slavovlab.net" } \ No newline at end of file diff --git a/data/do_x3dna/do_x3dnabioschemas.jsonld b/data/do_x3dna/do_x3dnabioschemas.jsonld index 1baeae032a349..59f3ce63f9da5 100644 --- a/data/do_x3dna/do_x3dnabioschemas.jsonld +++ b/data/do_x3dna/do_x3dnabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "do_x3dna", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/rjdkmr/do_x3dna" } \ No newline at end of file diff --git a/data/doc2hpo/doc2hpobioschemas.jsonld b/data/doc2hpo/doc2hpobioschemas.jsonld index 695a52196c986..4f6d78bd7b41d 100644 --- a/data/doc2hpo/doc2hpobioschemas.jsonld +++ b/data/doc2hpo/doc2hpobioschemas.jsonld @@ -21,18 +21,18 @@ "@id": "https://bio.tools/Doc2Hpo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kai Wang", { "@id": "https://orcid.org/0000-0002-9624-0214" - } + }, + "Kai Wang" ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31106327", { "@id": "https://doi.org/10.1093/NAR/GKZ386" }, - "pmcid:PMC6602487" + "pmcid:PMC6602487", + "pubmed:31106327" ], "sc:description": "Web application for efficient and accurate Human Phenotype Ontology (HPO) concept curation.", "sc:featureList": [ @@ -49,8 +49,8 @@ "sc:license": "Unlicense", "sc:name": "Doc2Hpo", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://impact2.dbmi.columbia.edu/doc2hpo/" diff --git a/data/docker4seq/docker4seqbioschemas.jsonld b/data/docker4seq/docker4seqbioschemas.jsonld index 48366f87b42e1..839d4f6f918c6 100644 --- a/data/docker4seq/docker4seqbioschemas.jsonld +++ b/data/docker4seq/docker4seqbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-6125-9460", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/docker4seq", "@type": "sc:SoftwareApplication", @@ -26,11 +22,15 @@ "sc:license": "GPL-3.0", "sc:name": "docker4seq", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/kendomaniac/docker4seq", "sc:version": "2.2.9" + }, + { + "@id": "https://orcid.org/0000-0001-6125-9460", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dockscore/dockscorebioschemas.jsonld b/data/dockscore/dockscorebioschemas.jsonld index 4220cad8ee904..2bfe809c12a59 100644 --- a/data/dockscore/dockscorebioschemas.jsonld +++ b/data/dockscore/dockscorebioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4414291", - "pubmed:25902779", { "@id": "https://doi.org/10.1186/S12859-015-0572-6" - } + }, + "pmcid:PMC4414291", + "pubmed:25902779" ], "sc:description": "A webserver for ranking protein-protein docked poses.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "DOCKSCORE", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://caps.ncbs.res.in/dockscore/" } diff --git a/data/dockstore/dockstorebioschemas.jsonld b/data/dockstore/dockstorebioschemas.jsonld index bca481d84cf87..f07dcfc5665ee 100644 --- a/data/dockstore/dockstorebioschemas.jsonld +++ b/data/dockstore/dockstorebioschemas.jsonld @@ -26,18 +26,18 @@ "sc:description": "Brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within.", "sc:featureList": [ { - "@id": "edam:operation_2409" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_2409" } ], "sc:license": "Apache-2.0", "sc:name": "Dockstore", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://dockstore.org" }, diff --git a/data/doe_joint_genome_institute_genome_portal/doe_joint_genome_institute_genome_portalbioschemas.jsonld b/data/doe_joint_genome_institute_genome_portal/doe_joint_genome_institute_genome_portalbioschemas.jsonld index 9cae1dce3289a..aa6521d846f28 100644 --- a/data/doe_joint_genome_institute_genome_portal/doe_joint_genome_institute_genome_portalbioschemas.jsonld +++ b/data/doe_joint_genome_institute_genome_portal/doe_joint_genome_institute_genome_portalbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.", "sc:name": "DOE Joint Genome Institute Genome Portal", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://genome.jgi-psf.org/" } \ No newline at end of file diff --git a/data/doelan/doelanbioschemas.jsonld b/data/doelan/doelanbioschemas.jsonld index 08483c0ba6863..7b6d63808cb91 100644 --- a/data/doelan/doelanbioschemas.jsonld +++ b/data/doelan/doelanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Doelan is an tool designed to monitor the quality of DNA microarray production.", "sc:name": "Doelan", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.transcriptome.ens.fr/doelan/" } \ No newline at end of file diff --git a/data/doestrare/doestrarebioschemas.jsonld b/data/doestrare/doestrarebioschemas.jsonld index d71fe08b3c5d9..e388879c565f7 100644 --- a/data/doestrare/doestrarebioschemas.jsonld +++ b/data/doestrare/doestrarebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "DoEstRare", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/DoEstRare/index.html" diff --git a/data/dogma/dogmabioschemas.jsonld b/data/dogma/dogmabioschemas.jsonld index 16087ef9857cc..1853a10555c5d 100644 --- a/data/dogma/dogmabioschemas.jsonld +++ b/data/dogma/dogmabioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKZ366", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-2416-9842", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/DOGMA", "@type": "sc:SoftwareApplication", @@ -16,14 +24,14 @@ "@id": "https://orcid.org/0000-0002-2416-9842" }, "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:citation": [ + "pmcid:PMC6602495", { "@id": "https://doi.org/10.1093/NAR/GKZ366" }, - "pmcid:PMC6602495", "pubmed:31076763" ], "sc:description": "Domain-based transcriptome and proteome quality assessment.", @@ -33,19 +41,11 @@ "sc:license": "Unlicense", "sc:name": "DOGMA", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://domainworld-services.uni-muenster.de/dogma/" - }, - { - "@id": "https://orcid.org/0000-0002-2416-9842", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ366", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dognet/dognetbioschemas.jsonld b/data/dognet/dognetbioschemas.jsonld index a44fd6c286d19..b778a9b55cbf3 100644 --- a/data/dognet/dognetbioschemas.jsonld +++ b/data/dognet/dognetbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://orcid.org/0000-0002-4264-8572", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1007012", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/DoGNet", "@type": "sc:SoftwareApplication", @@ -25,8 +21,8 @@ }, "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC6533009", "pubmed:31083649", + "pmcid:PMC6533009", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1007012" } @@ -38,11 +34,15 @@ "sc:license": "GPL-3.0", "sc:name": "DoGNet", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/kulikovv/dognet" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1007012", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dogsitescorer/dogsitescorerbioschemas.jsonld b/data/dogsitescorer/dogsitescorerbioschemas.jsonld index 1a5ab80c97916..f55c56c1cfaef 100644 --- a/data/dogsitescorer/dogsitescorerbioschemas.jsonld +++ b/data/dogsitescorer/dogsitescorerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Automated pocket detection and analysis tool enabling the identification of potential binding pockets and subpockets in protein structures. Additionally, global properties, describing size, shape and chemical features of the predicted (sub)pockets, are calculated. Per default, a simple druggability score is provided for each (sub)pocket, based on a linear combination of the three descriptors describing volume, hydrophobicity and enclosure.", "sc:name": "DoGSiteScorer", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "University of Hamburg - Center for Bioinformatics", "sc:url": "http://proteinsplus.zbh.uni-hamburg.de/#dogsite" diff --git a/data/dolce/dolcebioschemas.jsonld b/data/dolce/dolcebioschemas.jsonld index e5786b703790e..756199fe183b9 100644 --- a/data/dolce/dolcebioschemas.jsonld +++ b/data/dolce/dolcebioschemas.jsonld @@ -11,11 +11,11 @@ "@id": "https://bio.tools/dolce", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jiří Černý", - "Petr Cech", "Bohdan Schneider", "Daniel Svozil", - "Filip Lankaš" + "Filip Lankaš", + "Jiří Černý", + "Petr Cech" ], "sc:additionalType": "Database portal", "sc:description": "Database of local biomolecular conformers, stores DNA structural data including the information about DNA local spatial arrangement.", diff --git a/data/domaination/domainationbioschemas.jsonld b/data/domaination/domainationbioschemas.jsonld index 0484f45604429..66e5101eb3132 100644 --- a/data/domaination/domainationbioschemas.jsonld +++ b/data/domaination/domainationbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Method to identify domains in a protein sequence from similarity searches using PSI-BLAST. The identified domains are used in individual PSI-BLAST searches to improve detection of distant homologous sequences. The tool iterates until no new domains are found.", "sc:name": "DOMAINATION_Domain_Prediction", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ibi.vu.nl/programs/domainationwww/", "sc:version": "1" diff --git a/data/domainsignatures/domainsignaturesbioschemas.jsonld b/data/domainsignatures/domainsignaturesbioschemas.jsonld index 35f1838083ac7..66edc3891a472 100644 --- a/data/domainsignatures/domainsignaturesbioschemas.jsonld +++ b/data/domainsignatures/domainsignaturesbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Florian Hahne", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure.", "sc:license": "Artistic-2.0", "sc:name": "domainsignatures", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/domainsignatures.html", diff --git a/data/domine/dominebioschemas.jsonld b/data/domine/dominebioschemas.jsonld index 3a70c52b23e91..53b9a90d0db13 100644 --- a/data/domine/dominebioschemas.jsonld +++ b/data/domine/dominebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources. The updated version includes 2285 new domain-domain interactions (DDIs) inferred from experimentally characterized high-resolution three-dimensional structures, and about 3500 novel predictions by five computational approaches published over the last 3 years. New features include a new classification scheme to assign confidence levels to predicted DDIs.", "sc:name": "DOMINE", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://domine.utdallas.edu" diff --git a/data/domino/dominobioschemas.jsonld b/data/domino/dominobioschemas.jsonld index 5f482fa106b18..0439a193e75c3 100644 --- a/data/domino/dominobioschemas.jsonld +++ b/data/domino/dominobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6839-9148", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/domino", "@type": "sc:SoftwareApplication", @@ -27,10 +31,6 @@ "Mac" ], "sc:url": "http://www.ub.edu/softevol/domino/" - }, - { - "@id": "http://orcid.org/0000-0002-6839-9148", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dommino/domminobioschemas.jsonld b/data/dommino/domminobioschemas.jsonld index b93dc006e0363..028c8443b72f2 100644 --- a/data/dommino/domminobioschemas.jsonld +++ b/data/dommino/domminobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of Macromolecular interactions. Includes interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.", "sc:name": "DOMMINO", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://orion.rnet.missouri.edu/~nz953/DOMMINO/" } \ No newline at end of file diff --git a/data/doppelgangr/doppelgangrbioschemas.jsonld b/data/doppelgangr/doppelgangrbioschemas.jsonld index 6bd9fa29c285d..0e60107e64118 100644 --- a/data/doppelgangr/doppelgangrbioschemas.jsonld +++ b/data/doppelgangr/doppelgangrbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "doppelgangR", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/doppelgangR.html", "sc:version": "1.2.0" diff --git a/data/doqtl/doqtlbioschemas.jsonld b/data/doqtl/doqtlbioschemas.jsonld index 977bc01284f4d..609d0e873ecfa 100644 --- a/data/doqtl/doqtlbioschemas.jsonld +++ b/data/doqtl/doqtlbioschemas.jsonld @@ -23,10 +23,10 @@ ], "sc:citation": [ "pubmed:25237114", + "pmcid:PMC4169154", { "@id": "https://doi.org/10.1534/g3.114.013748" - }, - "pmcid:PMC4169154" + } ], "sc:description": "Quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, it can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.", "sc:featureList": { @@ -35,9 +35,9 @@ "sc:license": "GPL-3.0", "sc:name": "DOQTL", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DOQTL.html", "sc:version": "1.10.0" diff --git a/data/dorina/dorinabioschemas.jsonld b/data/dorina/dorinabioschemas.jsonld index 3bdde7b6d23f3..91a30dd0dc2da 100644 --- a/data/dorina/dorinabioschemas.jsonld +++ b/data/dorina/dorinabioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-0468-0117", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gku1180", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/dorina", "@type": "sc:SoftwareApplication", @@ -31,11 +39,11 @@ } ], "sc:citation": [ - "pubmed:25416797", { "@id": "https://doi.org/10.1093/nar/gku1180" }, - "pmcid:PMC4383974" + "pmcid:PMC4383974", + "pubmed:25416797" ], "sc:description": "A database of RNA interactions in post-transcriptional regulation.", "sc:featureList": { @@ -45,12 +53,12 @@ "sc:name": "doRiNA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "Max Delbrück Centre for Molecular Medicine", - "rnateam" + "rnateam", + "Max Delbrück Centre for Molecular Medicine" ], "sc:softwareHelp": [ { @@ -61,14 +69,6 @@ } ], "sc:url": "http://dorina.mdc-berlin.de/" - }, - { - "@id": "http://orcid.org/0000-0002-0468-0117", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/nar/gku1180", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dose/dosebioschemas.jsonld b/data/dose/dosebioschemas.jsonld index 15adc1ca07fa4..c4eb1995f42cd 100644 --- a/data/dose/dosebioschemas.jsonld +++ b/data/dose/dosebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6485-8781", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/dose", "@type": "sc:SoftwareApplication", @@ -16,8 +20,8 @@ "@id": "http://orcid.org/0000-0002-6485-8781" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:25677125", "sc:description": "This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.", @@ -30,10 +34,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DOSE.html", "sc:version": "3.0.9" - }, - { - "@id": "http://orcid.org/0000-0002-6485-8781", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dotlet/dotletbioschemas.jsonld b/data/dotlet/dotletbioschemas.jsonld index 261ad17afd553..64d69546f2fc3 100644 --- a/data/dotlet/dotletbioschemas.jsonld +++ b/data/dotlet/dotletbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Dotlet", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://myhits.isb-sib.ch/cgi-bin/dotlet" } \ No newline at end of file diff --git a/data/dotmatcher/dotmatcherbioschemas.jsonld b/data/dotmatcher/dotmatcherbioschemas.jsonld index 155e8551f2da9..22761f9b3a046 100644 --- a/data/dotmatcher/dotmatcherbioschemas.jsonld +++ b/data/dotmatcher/dotmatcherbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "Wellcome Trust", + "EMBOSS Contributors", "UK MRC", - "EMBOSS Contributors" + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Draw a threshold dotplot of two sequences.", "sc:funder": [ "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "dotmatcher", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dotmatcher.html", "sc:version": "r6" diff --git a/data/dotmatcher_ws_husar/dotmatcher_ws_husarbioschemas.jsonld b/data/dotmatcher_ws_husar/dotmatcher_ws_husarbioschemas.jsonld index 7fa918dd2f362..7bd098d54d7e0 100644 --- a/data/dotmatcher_ws_husar/dotmatcher_ws_husarbioschemas.jsonld +++ b/data/dotmatcher_ws_husar/dotmatcher_ws_husarbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Displays a thresholded dotplot of two sequences.", "sc:name": "dotmatcher_WS (husar)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/dotmatcher.html", "sc:version": "1" diff --git a/data/dotpath/dotpathbioschemas.jsonld b/data/dotpath/dotpathbioschemas.jsonld index d37b069398e07..5a96540651057 100644 --- a/data/dotpath/dotpathbioschemas.jsonld +++ b/data/dotpath/dotpathbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK MRC", + "EMBOSS Contributors", "UK BBSRC", - "EMBOSS Contributors" + "Wellcome Trust" ], "sc:description": "Draw a non-overlapping wordmatch dotplot of two sequences.", "sc:funder": [ - "Wellcome Trust", + "UK BBSRC", "UK MRC", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "dotpath", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dotpath.html", "sc:version": "r6" diff --git a/data/dotter/dotterbioschemas.jsonld b/data/dotter/dotterbioschemas.jsonld index 011554866d320..7699ce3983aa4 100644 --- a/data/dotter/dotterbioschemas.jsonld +++ b/data/dotter/dotterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis.", "sc:name": "Dotter", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://sonnhammer.sbc.su.se/Dotter.html", diff --git a/data/dottup/dottupbioschemas.jsonld b/data/dottup/dottupbioschemas.jsonld index d109765607e70..02354a6d80068 100644 --- a/data/dottup/dottupbioschemas.jsonld +++ b/data/dottup/dottupbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "EMBOSS Contributors", + "UK MRC", "UK BBSRC", - "UK MRC" + "EMBOSS Contributors" ], "sc:description": "Display a wordmatch dotplot of two sequences.", "sc:funder": [ - "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "dottup", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/dottup_ws_husar/dottup_ws_husarbioschemas.jsonld b/data/dottup_ws_husar/dottup_ws_husarbioschemas.jsonld index c36cfe8d4de36..8c207bdb7d7cf 100644 --- a/data/dottup_ws_husar/dottup_ws_husarbioschemas.jsonld +++ b/data/dottup_ws_husar/dottup_ws_husarbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Displays a wordmatch dotplot of two sequences.", "sc:name": "dottup_WS (husar)", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/dottup.html", "sc:version": "1" diff --git a/data/doubletdetection/doubletdetectionbioschemas.jsonld b/data/doubletdetection/doubletdetectionbioschemas.jsonld index acd7fd10f1c12..1b4b15e7faca9 100644 --- a/data/doubletdetection/doubletdetectionbioschemas.jsonld +++ b/data/doubletdetection/doubletdetectionbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "DoubletDetection", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/JonathanShor/DoubletDetection" } \ No newline at end of file diff --git a/data/doutfinder/doutfinderbioschemas.jsonld b/data/doutfinder/doutfinderbioschemas.jsonld index 73cb6e2ee47aa..9f8fba15b5fde 100644 --- a/data/doutfinder/doutfinderbioschemas.jsonld +++ b/data/doutfinder/doutfinderbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for facilitating protein domain detection among remotely related protein sequences.", "sc:name": "DOUTfinder", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://mendel.imp.ac.at/dout/" } \ No newline at end of file diff --git a/data/dove/dovebioschemas.jsonld b/data/dove/dovebioschemas.jsonld index f50f340db7264..4cabfe09d4828 100644 --- a/data/dove/dovebioschemas.jsonld +++ b/data/dove/dovebioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1002/mgg3.510", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/DOVE", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mitch Bailey", "sc:additionalType": "Web service", "sc:citation": [ - "pmcid:PMC6382494", - "pubmed:30450799", { "@id": "https://doi.org/10.1002/mgg3.510" - } + }, + "pubmed:30450799", + "pmcid:PMC6382494" ], "sc:description": "DMD Open-access Variant Explorer (DOVE) - web-based aid for DMD variant interpretation which additionally reports variant-specific predicted molecular eligibility for therapy.", "sc:featureList": [ @@ -33,14 +37,10 @@ "sc:license": "Unlicense", "sc:name": "DOVE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.dmd.nl/DOVE" - }, - { - "@id": "https://doi.org/10.1002/mgg3.510", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dpubchem/dpubchembioschemas.jsonld b/data/dpubchem/dpubchembioschemas.jsonld index d937ba49b26fe..27dff73c8978c 100644 --- a/data/dpubchem/dpubchembioschemas.jsonld +++ b/data/dpubchem/dpubchembioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DPubChem", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.cbrc.kaust.edu.sa/dpubchem/" } \ No newline at end of file diff --git a/data/dpvweb/dpvwebbioschemas.jsonld b/data/dpvweb/dpvwebbioschemas.jsonld index 4883893f5a42a..0637c220c2553 100644 --- a/data/dpvweb/dpvwebbioschemas.jsonld +++ b/data/dpvweb/dpvwebbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Information about viruses, viroids and satellites of plants, fungi and protozoa, with some additional data on related animal viruses.", "sc:name": "DPVweb database of plant viruses", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "Rothamsted Research", "sc:url": "http://www.dpvweb.net/" diff --git a/data/dragonfly/dragonflybioschemas.jsonld b/data/dragonfly/dragonflybioschemas.jsonld index dbf84b71ae4f3..d2b200414817c 100644 --- a/data/dragonfly/dragonflybioschemas.jsonld +++ b/data/dragonfly/dragonflybioschemas.jsonld @@ -9,14 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1107/S1600576716008165", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/dragonfly", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "N. Duane Loh", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27504078", "pmcid:PMC4970497", + "pubmed:27504078", { "@id": "https://doi.org/10.1107/S1600576716008165" } @@ -29,14 +33,10 @@ "sc:name": "Dragonfly", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://duaneloh.github.io/Dragonfly/" - }, - { - "@id": "https://doi.org/10.1107/S1600576716008165", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/drap/drapbioschemas.jsonld b/data/drap/drapbioschemas.jsonld index 4177257d6ebc1..c197de81f1499 100644 --- a/data/drap/drapbioschemas.jsonld +++ b/data/drap/drapbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5316280", "pubmed:28224052", { "@id": "https://doi.org/10.7717/peerj.2988" - }, - "pmcid:PMC5316280" + } ], "sc:description": "De novo RNA-Seq Assembly Pipeline.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:license": "GPL-3.0", "sc:name": "DRAP", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.sigenae.org/drap/" } diff --git a/data/drar-cpi/drar-cpibioschemas.jsonld b/data/drar-cpi/drar-cpibioschemas.jsonld index d95ae24203dbd..97589ebdf928d 100644 --- a/data/drar-cpi/drar-cpibioschemas.jsonld +++ b/data/drar-cpi/drar-cpibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "DRAR-CPI is a web server for the identification of drug repositioning and adverse drug reactions using mining of a chemical-protein interactome.", "sc:name": "DRAR-CPI", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cpi.bio-x.cn/drar/" } \ No newline at end of file diff --git a/data/drawid/drawidbioschemas.jsonld b/data/drawid/drawidbioschemas.jsonld index 581dfda395733..927e4ea7a6d09 100644 --- a/data/drawid/drawidbioschemas.jsonld +++ b/data/drawid/drawidbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Ilya Kirov", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC5740402", "pubmed:29302295", { "@id": "https://doi.org/10.3897/CompCytogen.v11i4.20830" - }, - "pmcid:PMC5740402" + } ], "sc:description": "Chromosome analysis and idiogram construction.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "DRAWID", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.drawid.xyz/" } diff --git a/data/drawproteins/drawproteinsbioschemas.jsonld b/data/drawproteins/drawproteinsbioschemas.jsonld index de5989e150156..076a5553752a6 100644 --- a/data/drawproteins/drawproteinsbioschemas.jsonld +++ b/data/drawproteins/drawproteinsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "drawProteins", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/drawProteins.html", "sc:version": "1.0.0" diff --git a/data/drcancer/drcancerbioschemas.jsonld b/data/drcancer/drcancerbioschemas.jsonld index b590325cf8066..25680fd82ebf7 100644 --- a/data/drcancer/drcancerbioschemas.jsonld +++ b/data/drcancer/drcancerbioschemas.jsonld @@ -17,19 +17,19 @@ }, "edam:has_input": [ { - "@id": "edam:data_2974" + "@id": "edam:data_2563" }, { - "@id": "edam:data_3021" + "@id": "edam:data_2974" }, { - "@id": "edam:data_1016" + "@id": "edam:data_1176" }, { - "@id": "edam:data_2563" + "@id": "edam:data_1016" }, { - "@id": "edam:data_1176" + "@id": "edam:data_3021" } ], "edam:has_output": { @@ -64,22 +64,22 @@ "sc:isAccessibleForFree": true, "sc:name": "DrCancer", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:softwareHelp": { "@id": "http://snps.biofold.org/drcancer/pages/DrCancer_Help.html" }, "sc:url": "http://snps.biofold.org/drcancer" }, - { - "@id": "http://orcid.org/0000-0002-2323-0963", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1016/j.ygeno.2011.06.010", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-2323-0963", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dreamtools/dreamtoolsbioschemas.jsonld b/data/dreamtools/dreamtoolsbioschemas.jsonld index 78502109768f2..3a34a9901aa97 100644 --- a/data/dreamtools/dreamtoolsbioschemas.jsonld +++ b/data/dreamtools/dreamtoolsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/f1000research.7118.2", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0001-6286-1138", "@type": "schema:Person" @@ -21,11 +25,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4837986", - "pubmed:27134723", { "@id": "https://doi.org/10.12688/f1000research.7118.2" - } + }, + "pubmed:27134723", + "pmcid:PMC4837986" ], "sc:description": "DREAMTools is a Python package for evaluating DREAM challenge scoring metrics. DREAMTools provides a command line interface that enables researchers to test new methods on past challenges, as well as a framework for scoring new challenges.", "sc:featureList": { @@ -34,15 +38,11 @@ "sc:license": "BSD-3-Clause", "sc:name": "DREAMTools", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/dreamtools/dreamtools" - }, - { - "@id": "https://doi.org/10.12688/f1000research.7118.2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dreg/dregbioschemas.jsonld b/data/dreg/dregbioschemas.jsonld index 2dc07715eea09..5a17ae6168bd1 100644 --- a/data/dreg/dregbioschemas.jsonld +++ b/data/dreg/dregbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", + "Wellcome Trust", "UK BBSRC", "EMBOSS Contributors", - "Wellcome Trust" + "UK MRC" ], "sc:description": "Regular expression search of nucleotide sequence(s).", "sc:funder": [ - "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "dreg", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/dreg.html", "sc:version": "r6" diff --git a/data/drep/drepbioschemas.jsonld b/data/drep/drepbioschemas.jsonld index 63336d914fd77..2441c0b91e558 100644 --- a/data/drep/drepbioschemas.jsonld +++ b/data/drep/drepbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.", "sc:name": "dRep", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/MrOlm/drep" } \ No newline at end of file diff --git a/data/drexplorer/drexplorerbioschemas.jsonld b/data/drexplorer/drexplorerbioschemas.jsonld index f658ed9d94063..0834709a054a7 100644 --- a/data/drexplorer/drexplorerbioschemas.jsonld +++ b/data/drexplorer/drexplorerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "drexplorer", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/nickytong/drexplorer" } \ No newline at end of file diff --git a/data/drfinddata/drfinddatabioschemas.jsonld b/data/drfinddata/drfinddatabioschemas.jsonld index fd4738a467551..92bf9638d2b71 100644 --- a/data/drfinddata/drfinddatabioschemas.jsonld +++ b/data/drfinddata/drfinddatabioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "Wellcome Trust", + "UK BBSRC", "EMBOSS Contributors", - "UK BBSRC" + "UK MRC" ], "sc:description": "Find public databases by data type.", "sc:funder": [ "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "drfinddata", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/drfinddata.html", "sc:version": "r6" diff --git a/data/drfindformat/drfindformatbioschemas.jsonld b/data/drfindformat/drfindformatbioschemas.jsonld index 75a8ccf2eb829..9ee9d196eb3da 100644 --- a/data/drfindformat/drfindformatbioschemas.jsonld +++ b/data/drfindformat/drfindformatbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "Wellcome Trust", "UK BBSRC", + "Wellcome Trust", + "EMBOSS Contributors", "UK MRC" ], "sc:description": "Find public databases by format.", "sc:funder": [ - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "drfindformat", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ diff --git a/data/drfindid/drfindidbioschemas.jsonld b/data/drfindid/drfindidbioschemas.jsonld index 48d43a529f1bf..62a967d20a831 100644 --- a/data/drfindid/drfindidbioschemas.jsonld +++ b/data/drfindid/drfindidbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", + "EMBOSS Contributors", "Wellcome Trust", - "UK BBSRC", - "EMBOSS Contributors" + "UK MRC", + "UK BBSRC" ], "sc:description": "Find public databases by identifier.", "sc:funder": [ "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "drfindid", @@ -31,8 +31,8 @@ "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/drfindid.html", "sc:version": "r6" diff --git a/data/drfindresource/drfindresourcebioschemas.jsonld b/data/drfindresource/drfindresourcebioschemas.jsonld index 0a3ec9c52ad4b..8ca0ce19920ef 100644 --- a/data/drfindresource/drfindresourcebioschemas.jsonld +++ b/data/drfindresource/drfindresourcebioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Find public databases by resource.", "sc:funder": [ - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "drfindresource", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/drfindresource.html", "sc:version": "r6" diff --git a/data/drfit/drfitbioschemas.jsonld b/data/drfit/drfitbioschemas.jsonld index 40cfbd93ea622..3ffb339b45c1c 100644 --- a/data/drfit/drfitbioschemas.jsonld +++ b/data/drfit/drfitbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "DRfit", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.structuralchemistry.org/pcsb/drfit.php" diff --git a/data/drgap/drgapbioschemas.jsonld b/data/drgap/drgapbioschemas.jsonld index ce9fef15a3292..29659265c3c60 100644 --- a/data/drgap/drgapbioschemas.jsonld +++ b/data/drgap/drgapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A Powerful Tool for Identifying Driver Genes and Pathways in Cancer Sequencing Studies.", "sc:name": "DrGaP", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://code.google.com/archive/p/drgap/" } \ No newline at end of file diff --git a/data/drget/drgetbioschemas.jsonld b/data/drget/drgetbioschemas.jsonld index 28f339121c2a0..582b513ad7ee7 100644 --- a/data/drget/drgetbioschemas.jsonld +++ b/data/drget/drgetbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK MRC", "UK BBSRC", "Wellcome Trust", - "EMBOSS Contributors", - "UK MRC" + "EMBOSS Contributors" ], "sc:description": "Get data resource entries.", "sc:funder": [ "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "drget", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/drget.html", "sc:version": "r6" diff --git a/data/drimpute/drimputebioschemas.jsonld b/data/drimpute/drimputebioschemas.jsonld index 1bd6289abb4d4..717b412365a88 100644 --- a/data/drimpute/drimputebioschemas.jsonld +++ b/data/drimpute/drimputebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DrImpute", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/gongx030/DrImpute." } \ No newline at end of file diff --git a/data/drimseq/drimseqbioschemas.jsonld b/data/drimseq/drimseqbioschemas.jsonld index 0c0a024beddfe..a3c85a9be8424 100644 --- a/data/drimseq/drimseqbioschemas.jsonld +++ b/data/drimseq/drimseqbioschemas.jsonld @@ -14,8 +14,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Malgorzata Nowicka", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pubmed:28105305", @@ -32,8 +32,8 @@ "sc:name": "DRIMSeq", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DRIMSeq.html", "sc:version": "1.2.0" diff --git a/data/drivernet/drivernetbioschemas.jsonld b/data/drivernet/drivernetbioschemas.jsonld index dc5a70ab00abc..d1117b815a747 100644 --- a/data/drivernet/drivernetbioschemas.jsonld +++ b/data/drivernet/drivernetbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jiarui Ding", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph. A greedy algorithm is used to find the possible driver genes, which may be mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.", "sc:license": "GPL-3.0", "sc:name": "DriverNet", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DriverNet.html", "sc:version": "1.14.0" diff --git a/data/drl4cellmovement/drl4cellmovementbioschemas.jsonld b/data/drl4cellmovement/drl4cellmovementbioschemas.jsonld index 83a274ae74d92..70c6f544eb19d 100644 --- a/data/drl4cellmovement/drl4cellmovementbioschemas.jsonld +++ b/data/drl4cellmovement/drl4cellmovementbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis.", "sc:name": "drl4cellmovement", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/zwang84/drl4cellmovement" } \ No newline at end of file diff --git a/data/droids/droidsbioschemas.jsonld b/data/droids/droidsbioschemas.jsonld index 8ff3c1966c8f1..0a8d034056564 100644 --- a/data/droids/droidsbioschemas.jsonld +++ b/data/droids/droidsbioschemas.jsonld @@ -15,19 +15,19 @@ "biotools:primaryContact": "Gregory A Babbitt", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC5883555", { "@id": "https://doi.org/10.1016/j.bpj.2018.01.020" }, - "pubmed:29539389", - "pmcid:PMC5883555" + "pubmed:29539389" ], "sc:description": "DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a “comparative computational microscope” for observing the biophysical effects of mutations and other chemical changes in proteins.", "sc:featureList": [ { - "@id": "edam:operation_2476" + "@id": "edam:operation_1777" }, { - "@id": "edam:operation_1777" + "@id": "edam:operation_2476" } ], "sc:license": "GPL-3.0", diff --git a/data/dropclust/dropclustbioschemas.jsonld b/data/dropclust/dropclustbioschemas.jsonld index c81a162d66c99..5232afd90cab8 100644 --- a/data/dropclust/dropclustbioschemas.jsonld +++ b/data/dropclust/dropclustbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/dropClust", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", - "Web application" + "Web application", + "Library" ], "sc:description": "Clustering tool for single-cell RNA sequencing data that uses Locality Sensitive Hashing algorithm.", "sc:license": "GPL-3.0", "sc:name": "dropClust", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://debsinha.shinyapps.io/dropClust/" } \ No newline at end of file diff --git a/data/dropletutils/dropletutilsbioschemas.jsonld b/data/dropletutils/dropletutilsbioschemas.jsonld index c04fe83251588..1ab77be6f6008 100644 --- a/data/dropletutils/dropletutilsbioschemas.jsonld +++ b/data/dropletutils/dropletutilsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "DropletUtils", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DropletUtils.html", "sc:version": "1.0.2" diff --git a/data/dropnet/dropnetbioschemas.jsonld b/data/dropnet/dropnetbioschemas.jsonld index 26421abdae88b..fa1b13c65d600 100644 --- a/data/dropnet/dropnetbioschemas.jsonld +++ b/data/dropnet/dropnetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DroPNet", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://dropnet.isima.fr" } \ No newline at end of file diff --git a/data/drsasp/drsaspbioschemas.jsonld b/data/drsasp/drsaspbioschemas.jsonld index 482111aa2753d..59e045efaf3d0 100644 --- a/data/drsasp/drsaspbioschemas.jsonld +++ b/data/drsasp/drsaspbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP)", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.compbio.dundee.ac.uk/drsasp.html" diff --git a/data/drtext/drtextbioschemas.jsonld b/data/drtext/drtextbioschemas.jsonld index cab1541bd00dc..3af4864581b5f 100644 --- a/data/drtext/drtextbioschemas.jsonld +++ b/data/drtext/drtextbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", + "EMBOSS Contributors", "Wellcome Trust", - "EMBOSS Contributors" + "UK BBSRC", + "UK MRC" ], "sc:description": "Get data resource entries complete text.", "sc:funder": [ @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "drtext", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/drug2gene/drug2genebioschemas.jsonld b/data/drug2gene/drug2genebioschemas.jsonld index 6b4a594c4bc4d..62c0d8c5ef14a 100644 --- a/data/drug2gene/drug2genebioschemas.jsonld +++ b/data/drug2gene/drug2genebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Free database unifying popular public resources to provide structured and organized information for identified and reported relations between genes/proteins and drugs/compounds. You can flag, comment and update relations, import new drug-gene relations valuable for a specific project. Gene orthology and similarity info is matched to certain entries assisting the prediction of new unreported drug-gene associations. Available links to the original source of the reported relation.", "sc:name": "Drug2Gene", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.metalife.com/products/metalife_trinity/drug2gene.html" } \ No newline at end of file diff --git a/data/drug_reposer/drug_reposerbioschemas.jsonld b/data/drug_reposer/drug_reposerbioschemas.jsonld index ed6a9f5065067..3a43b273b2614 100644 --- a/data/drug_reposer/drug_reposerbioschemas.jsonld +++ b/data/drug_reposer/drug_reposerbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-4275-4663", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/Drug_ReposER", "@type": "sc:SoftwareApplication", @@ -17,8 +21,8 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6602481", "pubmed:31106379", + "pmcid:PMC6602481", { "@id": "https://doi.org/10.1093/NAR/GKZ391" } @@ -26,10 +30,10 @@ "sc:description": "Web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning.", "sc:featureList": [ { - "@id": "edam:operation_0478" + "@id": "edam:operation_0480" }, { - "@id": "edam:operation_0480" + "@id": "edam:operation_0478" }, { "@id": "edam:operation_0420" @@ -38,19 +42,15 @@ "sc:license": "Unlicense", "sc:name": "Drug ReposER", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://mfrlab.org/drugreposer/" }, { "@id": "https://doi.org/10.1093/NAR/GKZ391", "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0003-4275-4663", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/drugbank/drugbankbioschemas.jsonld b/data/drugbank/drugbankbioschemas.jsonld index 554ebd2c11503..6c535f3df7a95 100644 --- a/data/drugbank/drugbankbioschemas.jsonld +++ b/data/drugbank/drugbankbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 FDA approved small molecule and biotech drugs as well as >3200 experimental drugs. Additionally, >14,000 protein or drug target sequences are linked to these drug entries.", "sc:name": "DrugBank", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://redpoll.pharmacy.ualberta.ca/drugbank/index.html" } \ No newline at end of file diff --git a/data/drugcomb/drugcombbioschemas.jsonld b/data/drugcomb/drugcombbioschemas.jsonld index d4dc4750d5106..be36229273e6a 100644 --- a/data/drugcomb/drugcombbioschemas.jsonld +++ b/data/drugcomb/drugcombbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-7480-7710", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ337", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/DrugComb", "@type": "sc:SoftwareApplication", @@ -24,8 +16,8 @@ "@id": "https://orcid.org/0000-0001-7480-7710" }, "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ { @@ -37,10 +29,10 @@ "sc:description": "> COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/predrbr (DENGLAB.ORG), bio.tools/deepsacon (DENGLAB.ORG), bio.tools/predhs (DENGLAB.ORG) | an integrative cancer drug combination data portal | DrugComb is an open-access, community-driven data portal where the results of drug combination screening studies for a large variety of cancer cell lines are accumulated, standardized and harmonized. An actively expanding array of data visualization and computational tools is provided for the analysis of drug combination data | Please pay attention that the template header format is changed. Analysis function is also updated | response column should be renamed to inhibition as in the template file | Sharing data leads to novel knowledge | Start analyzing your own drug combination data by uploading | File should be a comma separated value(csv)", "sc:featureList": [ { - "@id": "edam:operation_2929" + "@id": "edam:operation_3894" }, { - "@id": "edam:operation_3894" + "@id": "edam:operation_2929" }, { "@id": "edam:operation_3431" @@ -49,11 +41,19 @@ "sc:license": "Unlicense", "sc:name": "DrugComb", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://drugcomb.fimm.fi" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ337", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0001-7480-7710", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/drugebility_blast_search/drugebility_blast_searchbioschemas.jsonld b/data/drugebility_blast_search/drugebility_blast_searchbioschemas.jsonld index 69798cf22b657..c1daf677d223f 100644 --- a/data/drugebility_blast_search/drugebility_blast_searchbioschemas.jsonld +++ b/data/drugebility_blast_search/drugebility_blast_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "BLAST search against structural domains stored in DrugEBIlity database.", "sc:name": "DrugEBIlity BLAST Search", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "https://www.ebi.ac.uk/chembl/drugebility/blast", diff --git a/data/drugevar/drugevarbioschemas.jsonld b/data/drugevar/drugevarbioschemas.jsonld index ebcc6844229ac..a575449da3e20 100644 --- a/data/drugevar/drugevarbioschemas.jsonld +++ b/data/drugevar/drugevarbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A database triangulating between drugs, genes and pharmacogenomics biomarkers in regulatory agencies-approved drugs", "sc:name": "DruGeVar", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.genomicmedicinealliance.org/working-groups/pharmacogenomics/80-genomic-medicine-alliance/137-drugevar-database" diff --git a/data/drugr/drugrbioschemas.jsonld b/data/drugr/drugrbioschemas.jsonld index 248dde5329114..72a52a7bfec9c 100644 --- a/data/drugr/drugrbioschemas.jsonld +++ b/data/drugr/drugrbioschemas.jsonld @@ -11,22 +11,22 @@ "@id": "https://bio.tools/DrugR", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yosef Masoudi-Sobhanzadeh", - "Yadollah Omidi", "Ali Masoudi-Nejad", - "Massoud Amanlou" + "Massoud Amanlou", + "Yadollah Omidi", + "Yosef Masoudi-Sobhanzadeh" ], "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": "pubmed:31096089", "sc:description": "Database for drug repurposing, combination therapy, and replacement therapy.", "sc:license": "MIT", "sc:name": "DrugR+", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.drugr.ir" diff --git a/data/drugscoreppi/drugscoreppibioschemas.jsonld b/data/drugscoreppi/drugscoreppibioschemas.jsonld index 6463c931b6fa4..bba9039b9b5aa 100644 --- a/data/drugscoreppi/drugscoreppibioschemas.jsonld +++ b/data/drugscoreppi/drugscoreppibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "DrugScorePPI web server performs alanine scanning within a given protein-protein complex in silico. Useful for guiding biological experiments and in the development of protein-protein interaction modulators.", "sc:name": "DrugScorePPI", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://cpclab.uni-duesseldorf.de/dsppi" } \ No newline at end of file diff --git a/data/drugvsdisease/bioconda_drugvsdisease.yaml b/data/drugvsdisease/bioconda_drugvsdisease.yaml index b974d9a7d20be..3c28bbe1b2691 100644 --- a/data/drugvsdisease/bioconda_drugvsdisease.yaml +++ b/data/drugvsdisease/bioconda_drugvsdisease.yaml @@ -9,7 +9,6 @@ description: This package generates ranked lists of differential gene expression home: https://bioconductor.org/packages/3.10/bioc/html/DrugVsDisease.html identifiers: - biotools:drugvsdisease -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-drugvsdisease diff --git a/data/drugvsdisease/drugvsdiseasebioschemas.jsonld b/data/drugvsdisease/drugvsdiseasebioschemas.jsonld index 08151e23a16c3..eb841521af362 100644 --- a/data/drugvsdisease/drugvsdiseasebioschemas.jsonld +++ b/data/drugvsdisease/drugvsdiseasebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "DrugVsDisease", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DrugVsDisease.html", "sc:version": "2.14.0" diff --git a/data/drvm/drvmbioschemas.jsonld b/data/drvm/drvmbioschemas.jsonld index 3a0f262a5e39f..d24fb405ddd3f 100644 --- a/data/drvm/drvmbioschemas.jsonld +++ b/data/drvm/drvmbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/GIGASCIENCE/GIX003", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/drvm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yu-Chieh Liao", - "Hsin-Hung Lin" + "Hsin-Hung Lin", + "Yu-Chieh Liao" ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5466706", - "pubmed:28369462", { "@id": "https://doi.org/10.1093/GIGASCIENCE/GIX003" - } + }, + "pubmed:28369462", + "pmcid:PMC5466706" ], "sc:description": "Efficient genome assembly of known eukaryotic viruses from metagenomes.", "sc:featureList": { @@ -31,10 +35,6 @@ "sc:license": "GPL-3.0", "sc:name": "drVM", "sc:url": "https://sourceforge.net/projects/sb2nhri/files/drVM/" - }, - { - "@id": "https://doi.org/10.1093/GIGASCIENCE/GIX003", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dsap/dsapbioschemas.jsonld b/data/dsap/dsapbioschemas.jsonld index 49b9b3240feff..dc722d9531989 100644 --- a/data/dsap/dsapbioschemas.jsonld +++ b/data/dsap/dsapbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology.", "sc:name": "DSAP", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://dsap.cgu.edu.tw" diff --git a/data/dscheck/dscheckbioschemas.jsonld b/data/dscheck/dscheckbioschemas.jsonld index 53986af2a7a23..9d69258b7672f 100644 --- a/data/dscheck/dscheckbioschemas.jsonld +++ b/data/dscheck/dscheckbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "dsCheck", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://dscheck.rnai.jp/" } \ No newline at end of file diff --git a/data/dsea/dseabioschemas.jsonld b/data/dsea/dseabioschemas.jsonld index c5989da4b9605..bb98766b7b035 100644 --- a/data/dsea/dseabioschemas.jsonld +++ b/data/dsea/dseabioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/DSEA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Francesco Napolitano", + "Diego di Bernardo", "Diego Carrella", - "Diego di Bernardo" + "Francesco Napolitano" ], "sc:additionalType": "Web application", "sc:description": "Drug-Set Enrichment Analysis (DSEA) - computational method based on drug-induced gene expression profiles, which is able to identify the molecular pathways that are targeted by most of the drugs in the set.", "sc:license": "Other", "sc:name": "DSEA", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://dsea.tigem.it/" } \ No newline at end of file diff --git a/data/dsgseq/dsgseqbioschemas.jsonld b/data/dsgseq/dsgseqbioschemas.jsonld index 5213ef82e0406..ff74bca2eee93 100644 --- a/data/dsgseq/dsgseqbioschemas.jsonld +++ b/data/dsgseq/dsgseqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "This program aims to identify differentially spliced genes from two groups of RNA-seq samples.", "sc:name": "DSGseq", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioinfo.au.tsinghua.edu.cn/software/DSGseq" diff --git a/data/dshift/dshiftbioschemas.jsonld b/data/dshift/dshiftbioschemas.jsonld index 182b7e07b843e..11332387cd8ea 100644 --- a/data/dshift/dshiftbioschemas.jsonld +++ b/data/dshift/dshiftbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "DSHIFT", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.chem.cuhk.edu.hk/DSHIFT/" } \ No newline at end of file diff --git a/data/dsimer/dsimerbioschemas.jsonld b/data/dsimer/dsimerbioschemas.jsonld index 189df7f7f3cde..47e899be5572d 100644 --- a/data/dsimer/dsimerbioschemas.jsonld +++ b/data/dsimer/dsimerbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Peng Ni", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "R package which provides computation of nine methods for measuring disease-disease similarity, including a standard cosine similarity measure and eight function-based methods. The disease similarity matrix obtained from these nine methods can be visualized through heatmap and network. Biological data widely used in disease-disease associations study are also provided.", "sc:license": "GPL-2.0", "sc:name": "dSimer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/dSimer.html", "sc:version": "1.0.0" diff --git a/data/dsk/dskbioschemas.jsonld b/data/dsk/dskbioschemas.jsonld index 780c0cde0cf1c..24a8c33e21cf2 100644 --- a/data/dsk/dskbioschemas.jsonld +++ b/data/dsk/dskbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/dsk", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Guillaume Rizk", "Rayan Chikhi", + "Guillaume Rizk", "Dominique Lavenier" ], "sc:additionalType": "Command-line tool", diff --git a/data/dsm/dsmbioschemas.jsonld b/data/dsm/dsmbioschemas.jsonld index 2f5fed3e884f0..cc6d7a4480350 100644 --- a/data/dsm/dsmbioschemas.jsonld +++ b/data/dsm/dsmbioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:24845653", + "pmcid:PMC4230234", { "@id": "https://doi.org/10.1093/bioinformatics/btu340" - }, - "pmcid:PMC4230234", - "pubmed:24845653" + } ], "sc:description": "Software of content-based exploration and retrieval method for whole metagenome sequencing samples.", "sc:featureList": { diff --git a/data/dsrc/dsrcbioschemas.jsonld b/data/dsrc/dsrcbioschemas.jsonld index e21aa3545ce4d..f45244c9c244d 100644 --- a/data/dsrc/dsrcbioschemas.jsonld +++ b/data/dsrc/dsrcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Compression algorithm for genomic data in FASTQ format", "sc:name": "DSRC", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sun.aei.polsl.pl/dsrc" } \ No newline at end of file diff --git a/data/dss/dssbioschemas.jsonld b/data/dss/dssbioschemas.jsonld index fb9637913841e..fdc2fe75c3f5a 100644 --- a/data/dss/dssbioschemas.jsonld +++ b/data/dss/dssbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "DSS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DSS.html", diff --git a/data/dssp/dsspbioschemas.jsonld b/data/dssp/dsspbioschemas.jsonld index 5fe46fc1cd121..1adcc697b9a17 100644 --- a/data/dssp/dsspbioschemas.jsonld +++ b/data/dssp/dsspbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).", "sc:name": "DSSP secondary structure database", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "Radboud University Medical Center", diff --git a/data/dsspcont/dsspcontbioschemas.jsonld b/data/dsspcont/dsspcontbioschemas.jsonld index 61276a477a50e..0a33558e25f73 100644 --- a/data/dsspcont/dsspcontbioschemas.jsonld +++ b/data/dsspcont/dsspcontbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Other", "sc:name": "DSSPcont", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.cbs.dtu.dk/services/DSSPcont/" } \ No newline at end of file diff --git a/data/dssr/dssrbioschemas.jsonld b/data/dssr/dssrbioschemas.jsonld index 542ee812c1bf7..46841de5556a5 100644 --- a/data/dssr/dssrbioschemas.jsonld +++ b/data/dssr/dssrbioschemas.jsonld @@ -35,9 +35,9 @@ "sc:license": "Other", "sc:name": "DSSR", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://x3dna.org/", "sc:version": "1.8.0" diff --git a/data/dstarm/dstarmbioschemas.jsonld b/data/dstarm/dstarmbioschemas.jsonld index 9183f61de646c..ba61d1f4661e7 100644 --- a/data/dstarm/dstarmbioschemas.jsonld +++ b/data/dstarm/dstarmbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "DstarM", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://cran.r-project.org/package=DstarM" diff --git a/data/dstruct/dstructbioschemas.jsonld b/data/dstruct/dstructbioschemas.jsonld index 80d3b5c8d4522..afd2a4bb2020f 100644 --- a/data/dstruct/dstructbioschemas.jsonld +++ b/data/dstruct/dstructbioschemas.jsonld @@ -18,8 +18,8 @@ ], "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6385470", "pubmed:30791935", + "pmcid:PMC6385470", { "@id": "https://doi.org/10.1186/s13059-019-1641-3" } @@ -39,9 +39,9 @@ "sc:license": "BSD-2-Clause", "sc:name": "dStruct", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/AviranLab/dStruct" }, diff --git a/data/dsuite/dsuitebioschemas.jsonld b/data/dsuite/dsuitebioschemas.jsonld index 270c2d1b31422..d3d37913322dd 100644 --- a/data/dsuite/dsuitebioschemas.jsonld +++ b/data/dsuite/dsuitebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Unlicense", "sc:name": "Dsuite", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/millanek/Dsuite" } \ No newline at end of file diff --git a/data/dta/dtabioschemas.jsonld b/data/dta/dtabioschemas.jsonld index 720bdf3acb6c3..84d5737a68516 100644 --- a/data/dta/dtabioschemas.jsonld +++ b/data/dta/dtabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "DTA", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DTA.html", "sc:version": "2.20.0" diff --git a/data/dualks/dualksbioschemas.jsonld b/data/dualks/dualksbioschemas.jsonld index faee560957698..bc3863bf66835 100644 --- a/data/dualks/dualksbioschemas.jsonld +++ b/data/dualks/dualksbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/dualks", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Eric J. Kort", - "Yarong Yang" + "Yarong Yang", + "Eric J. Kort" ], "sc:additionalType": [ "Library", @@ -22,9 +22,9 @@ "sc:license": "GPL-2.0", "sc:name": "dualKS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/dualKS.html", "sc:version": "1.34.0" diff --git a/data/ductape/ductapebioschemas.jsonld b/data/ductape/ductapebioschemas.jsonld index aa7db67b02da1..86233687ccde4 100644 --- a/data/ductape/ductapebioschemas.jsonld +++ b/data/ductape/ductapebioschemas.jsonld @@ -20,8 +20,8 @@ "Linux" ], "sc:provider": [ - "ELIXIR-ITA-FIRENZE", - "University of Florence" + "University of Florence", + "ELIXIR-ITA-FIRENZE" ], "sc:url": "http://combogenomics.github.io/DuctApe/", "sc:version": "0.17.4" diff --git a/data/dupchecker/dupcheckerbioschemas.jsonld b/data/dupchecker/dupcheckerbioschemas.jsonld index 8aad94d0db0f6..9538a93467194 100644 --- a/data/dupchecker/dupcheckerbioschemas.jsonld +++ b/data/dupchecker/dupcheckerbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-15-323", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dupchecker", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4261523", "pubmed:25267467", { "@id": "https://doi.org/10.1186/1471-2105-15-323" - } + }, + "pmcid:PMC4261523" ], "sc:description": "Meta-analysis has become a popular approach for high-throughput genomic data analysis because it can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often-encountered problem. Not removing duplicates would make study results questionable. We developed a BioConductor package that efficiently identifies duplicated samples by generating MD5 fingerprints for raw data.", "sc:featureList": { @@ -35,12 +31,16 @@ "sc:license": "GPL-2.0", "sc:name": "DupChecker", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DupChecker.html", "sc:version": "1.12.0" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-15-323", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dupgen_finder/dupgen_finderbioschemas.jsonld b/data/dupgen_finder/dupgen_finderbioschemas.jsonld index 4b4daf78a292d..ea362e1355a3f 100644 --- a/data/dupgen_finder/dupgen_finderbioschemas.jsonld +++ b/data/dupgen_finder/dupgen_finderbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Xin Qiao", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:30791939", + "pmcid:PMC6383267", { "@id": "https://doi.org/10.1186/s13059-019-1650-2" }, - "pmcid:PMC6383267" + "pubmed:30791939" ], "sc:description": "Tool for identification of different modes of duplicated gene pairs.", "sc:featureList": { diff --git a/data/dupradar/dupradarbioschemas.jsonld b/data/dupradar/dupradarbioschemas.jsonld index 1e8940dda9497..1cea48cabe23a 100644 --- a/data/dupradar/dupradarbioschemas.jsonld +++ b/data/dupradar/dupradarbioschemas.jsonld @@ -10,11 +10,11 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0002-3877-4170", + "@id": "http://orcid.org/0000-0002-6904-2319", "@type": "schema:Person" }, { - "@id": "http://orcid.org/0000-0002-6904-2319", + "@id": "http://orcid.org/0000-0002-3877-4170", "@type": "schema:Person" }, { @@ -29,15 +29,15 @@ } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:27769170", - "pmcid:PMC5073875", { "@id": "https://doi.org/10.1186/s12859-016-1276-2" - } + }, + "pmcid:PMC5073875", + "pubmed:27769170" ], "sc:description": "Duplication rate quality control for RNA-Seq datasets.", "sc:featureList": { @@ -46,9 +46,9 @@ "sc:license": "GPL-3.0", "sc:name": "dupRadar", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/dupRadar.html" }, diff --git a/data/dvass/dvassbioschemas.jsonld b/data/dvass/dvassbioschemas.jsonld index 304b751836698..c5cfcce279f36 100644 --- a/data/dvass/dvassbioschemas.jsonld +++ b/data/dvass/dvassbioschemas.jsonld @@ -25,30 +25,30 @@ }, "sc:additionalType": "Script", "sc:citation": [ + "pubmed:31106330", { "@id": "https://doi.org/10.1093/NAR/GKZ427" }, - "pmcid:PMC6582333", - "pubmed:31106330" + "pmcid:PMC6582333" ], "sc:description": "Algorithm based on the distance variation allowed by secondary structure (DVASS), which ranks restraints according to their importance to RNA tertiary structure prediction.", "sc:featureList": [ { - "@id": "edam:operation_0502" + "@id": "edam:operation_0278" }, { "@id": "edam:operation_2441" }, { - "@id": "edam:operation_0278" + "@id": "edam:operation_0502" } ], "sc:license": "Unlicense", "sc:name": "DVASS", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://bitbucket.org/dokhlab/dvass" } diff --git a/data/dyebias/dyebiasbioschemas.jsonld b/data/dyebias/dyebiasbioschemas.jsonld index 1d6266361b0f1..89f8854c1d85f 100644 --- a/data/dyebias/dyebiasbioschemas.jsonld +++ b/data/dyebias/dyebiasbioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/msb.2009.21", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/dyebias", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Philip Lijnzaad", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pubmed:19401678", @@ -36,11 +32,15 @@ "sc:name": "dyebias", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/dyebias.html", "sc:version": "1.34.0" + }, + { + "@id": "https://doi.org/10.1038/msb.2009.21", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/dynamicproteomics_db/dynamicproteomics_dbbioschemas.jsonld b/data/dynamicproteomics_db/dynamicproteomics_dbbioschemas.jsonld index 0e26d8d8dbcbd..085d5550d6fec 100644 --- a/data/dynamicproteomics_db/dynamicproteomics_dbbioschemas.jsonld +++ b/data/dynamicproteomics_db/dynamicproteomics_dbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Dynamic Proteomics database contains information on the position and amounts of endogenous proteins in individual living human cells. This is based on the Library of Annotated Reporter Cell-clones (LARC). The Dynamic Proteomics interface facilitates searches for genes of interest, downloads of protein fluorescent movies and alignments of dynamics following drug addition.", "sc:name": "DynamicProteomics DB", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.weizmann.ac.il/mcb/UriAlon/DynamProt/" } \ No newline at end of file diff --git a/data/dynamine/dynaminebioschemas.jsonld b/data/dynamine/dynaminebioschemas.jsonld index 8f6717fc21903..a6c1077f19294 100644 --- a/data/dynamine/dynaminebioschemas.jsonld +++ b/data/dynamine/dynaminebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Wim Vranken", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:description": "Protein backbone dynamics prediction from sequence.", "sc:name": "DynaMine", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "vub.ac.be", "sc:url": "http://dynamine.ibsquare.be/", diff --git a/data/dynamut/dynamutbioschemas.jsonld b/data/dynamut/dynamutbioschemas.jsonld index 86c6aadf6e7e2..59eada3459e3d 100644 --- a/data/dynamut/dynamutbioschemas.jsonld +++ b/data/dynamut/dynamutbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Implements two distinct, well established normal mode approaches, which can be used to analyze and visualize protein dynamics by sampling conformations and assess the impact of mutations on protein dynamics and stability resulting from vibrational entropy changes. It integrates our graph-based signatures along with normal mode dynamics to generate a consensus prediction of the impact of a mutation on protein stability.", "sc:name": "DynaMut", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://biosig.unimelb.edu.au/dynamut/" diff --git a/data/dynapho/dynaphobioschemas.jsonld b/data/dynapho/dynaphobioschemas.jsonld index bc38a82279806..be0f439b239ba 100644 --- a/data/dynapho/dynaphobioschemas.jsonld +++ b/data/dynapho/dynaphobioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Inferring the dynamics of time-series phosphoproteomics.", "sc:name": "DynaPho", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://dynapho.jhlab.tw/" diff --git a/data/dynasti/dynastibioschemas.jsonld b/data/dynasti/dynastibioschemas.jsonld index e39e96eafbeff..4ca5bf2f88381 100644 --- a/data/dynasti/dynastibioschemas.jsonld +++ b/data/dynasti/dynastibioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-3669-6313", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/DynaStI", "@type": "sc:SoftwareApplication", @@ -18,10 +22,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC6572260", - "pubmed:31052310", { "@id": "https://doi.org/10.3390/METABO9050085" - } + }, + "pubmed:31052310" ], "sc:description": "Dynamic Retention Time Database for Steroidomics.", "sc:featureList": [ @@ -35,8 +39,8 @@ "sc:license": "Unlicense", "sc:name": "DynaStI", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://dynasti.vital-it.ch" @@ -44,10 +48,6 @@ { "@id": "https://doi.org/10.3390/METABO9050085", "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0003-3669-6313", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/dyndoc/bioconda_dyndoc.yaml b/data/dyndoc/bioconda_dyndoc.yaml index ce48f29f4825e..d7879bc01857e 100644 --- a/data/dyndoc/bioconda_dyndoc.yaml +++ b/data/dyndoc/bioconda_dyndoc.yaml @@ -4,7 +4,6 @@ description: A set of functions to create and interact with dynamic documents an home: https://bioconductor.org/packages/3.10/bioc/html/DynDoc.html identifiers: - biotools:dyndoc -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-dyndoc summary: Dynamic document tools diff --git a/data/dyndoc/dyndocbioschemas.jsonld b/data/dyndoc/dyndocbioschemas.jsonld index 5484623f62a40..7805587e16b90 100644 --- a/data/dyndoc/dyndocbioschemas.jsonld +++ b/data/dyndoc/dyndocbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "DynDoc", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/DynDoc.html", "sc:version": "1.52.0" diff --git a/data/e-lea3d/e-lea3dbioschemas.jsonld b/data/e-lea3d/e-lea3dbioschemas.jsonld index 8d6f0092d4d75..7d1b700e0521f 100644 --- a/data/e-lea3d/e-lea3dbioschemas.jsonld +++ b/data/e-lea3d/e-lea3dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "e-LEA3D web server performs computer aided drug design from molecular fragments. Several design tools are included.", "sc:name": "e-LEA3D", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioinfo.ipmc.cnrs.fr/lea.html" } \ No newline at end of file diff --git a/data/e-rna/e-rnabioschemas.jsonld b/data/e-rna/e-rnabioschemas.jsonld index f4f7efc05d849..39a3932b75489 100644 --- a/data/e-rna/e-rnabioschemas.jsonld +++ b/data/e-rna/e-rnabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Collection of web servers for comparative RNA structure prediction and visualisation.", "sc:name": "e-RNA", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.e-rna.org" } \ No newline at end of file diff --git a/data/e-rnai/e-rnaibioschemas.jsonld b/data/e-rnai/e-rnaibioschemas.jsonld index e8dcb8c937c51..481d2d86d71e8 100644 --- a/data/e-rnai/e-rnaibioschemas.jsonld +++ b/data/e-rnai/e-rnaibioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "E-RNAi", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://e-rnai.dkfz.de/" } \ No newline at end of file diff --git a/data/e-talen/e-talenbioschemas.jsonld b/data/e-talen/e-talenbioschemas.jsonld index ffb6bcd69f18b..25d27ab9e2025 100644 --- a/data/e-talen/e-talenbioschemas.jsonld +++ b/data/e-talen/e-talenbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKT789", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/e-talen", "@type": "sc:SoftwareApplication", @@ -27,15 +31,11 @@ }, "sc:name": "E-TALEN", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.e-talen.org/E-TALEN/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKT789", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/e1ds/e1dsbioschemas.jsonld b/data/e1ds/e1dsbioschemas.jsonld index ee3dc2f749f00..4ac374c128586 100644 --- a/data/e1ds/e1dsbioschemas.jsonld +++ b/data/e1ds/e1dsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.", "sc:name": "E1DS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://e1ds.csbb.ntu.edu.tw/" diff --git a/data/e2g/e2gbioschemas.jsonld b/data/e2g/e2gbioschemas.jsonld index 5c569e20eae5d..678cc4cc2e050 100644 --- a/data/e2g/e2gbioschemas.jsonld +++ b/data/e2g/e2gbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/e2g", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jan Krüger", - "Alexander Sczyrba" + "Alexander Sczyrba", + "Jan Krüger" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:15215398", @@ -20,8 +20,8 @@ "sc:name": "E2G", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bibiserv.techfak.uni-bielefeld.de/e2g/" } \ No newline at end of file diff --git a/data/eager/eagerbioschemas.jsonld b/data/eager/eagerbioschemas.jsonld index 2896221875c32..e53f8ef853f83 100644 --- a/data/eager/eagerbioschemas.jsonld +++ b/data/eager/eagerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "EAGER", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/apeltzer/EAGER-GUI" diff --git a/data/eagle_gxe/eagle_gxebioschemas.jsonld b/data/eagle_gxe/eagle_gxebioschemas.jsonld index 70d8c35d817e5..15d5f3a573664 100644 --- a/data/eagle_gxe/eagle_gxebioschemas.jsonld +++ b/data/eagle_gxe/eagle_gxebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An R package for detecting Gene-by-Environment (GxE) interaction effects on the transcriptome using Allele Specific Expression (ASE) quantified from RNA-seq", "sc:name": "EAGLE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/davidaknowles/eagle" } \ No newline at end of file diff --git a/data/eagleview/eagleviewbioschemas.jsonld b/data/eagleview/eagleviewbioschemas.jsonld index b946ac7fc1c07..97004344731f6 100644 --- a/data/eagleview/eagleviewbioschemas.jsonld +++ b/data/eagleview/eagleviewbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Information-rich genome assembler viewer with data integration capability.", "sc:name": "EagleView genome viewer", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/index.cfm" } \ No newline at end of file diff --git a/data/easyfrap-web/easyfrap-webbioschemas.jsonld b/data/easyfrap-web/easyfrap-webbioschemas.jsonld index f30c42ad698eb..3510190dd7e04 100644 --- a/data/easyfrap-web/easyfrap-webbioschemas.jsonld +++ b/data/easyfrap-web/easyfrap-webbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gky508", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/easyFRAP-web", "@type": "sc:SoftwareApplication", @@ -17,11 +21,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6030846", + "pubmed:29901776", { "@id": "https://doi.org/10.1093/nar/gky508" }, - "pubmed:29901776" + "pmcid:PMC6030846" ], "sc:description": "EasyFRAP-web is a web-based application which enables fast and interactive qualitative and quantitative analysis of Fluorecence Recovery After Photobleaching (FRAP) data. EasyFRAP-web allows large data-sets to be rapidly evaluated and normalized fluorescence recovery curves to be generated and exported. It also performs curve fitting and provides quantitative parameters (mobile fraction and recovery half time) necessary for comparison across data-sets.", "sc:featureList": [ @@ -29,24 +33,20 @@ "@id": "edam:operation_2409" }, { - "@id": "edam:operation_2945" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_2945" } ], "sc:license": "Unlicense", "sc:name": "easyFRAP-web", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://easyfrap.vmnet.upatras.gr/" - }, - { - "@id": "https://doi.org/10.1093/nar/gky508", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/easyfrap/easyfrapbioschemas.jsonld b/data/easyfrap/easyfrapbioschemas.jsonld index 32a9f46d5092d..c7ddd2d512b3d 100644 --- a/data/easyfrap/easyfrapbioschemas.jsonld +++ b/data/easyfrap/easyfrapbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-1.0", "sc:name": "easyFRAP", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://ccl.med.upatras.gr/easyfrap.html" } \ No newline at end of file diff --git a/data/easygene/easygenebioschemas.jsonld b/data/easygene/easygenebioschemas.jsonld index b0e76aa1dff97..a3c9905b8794f 100644 --- a/data/easygene/easygenebioschemas.jsonld +++ b/data/easygene/easygenebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Fully automated gene prediction for prokaryotes. It produces a list of predicted genes for a chosen prokaryotic genome.", "sc:name": "EasyGene", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "binf.ku.dk", "sc:url": "http://servers.binf.ku.dk/cgi-bin/easygene/search", diff --git a/data/easyqc/easyqcbioschemas.jsonld b/data/easyqc/easyqcbioschemas.jsonld index 33dcaaff1250f..1660c0de0a685 100644 --- a/data/easyqc/easyqcbioschemas.jsonld +++ b/data/easyqc/easyqcbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "An R-package that provides advanced funcionality to perform file-level QC of single genome-wide association (GWA) data-sets, to conduct quality control across several GWA data-sets (meta-level QC) and to simplify data-handling of large-scale GWA data-sets.", "sc:name": "EasyQC", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.uni-regensburg.de/medizin/epidemiologie-praeventivmedizin/genetische-epidemiologie/software/index.html", "sc:version": "9.2" diff --git a/data/easyqpcr/easyqpcrbioschemas.jsonld b/data/easyqpcr/easyqpcrbioschemas.jsonld index 9a188acd8a9a7..1d0e37ddf17e7 100644 --- a/data/easyqpcr/easyqpcrbioschemas.jsonld +++ b/data/easyqpcr/easyqpcrbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Le Pape Sylvain", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package is based on the qBase algorithms published by Hellemans et al. in 2007. The package allows you to import easily qPCR data files as described in the vignette. You can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes chosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors.", "sc:license": "GPL-2.0", "sc:name": "EasyqpcR", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EasyqpcR.html", "sc:version": "1.16.0" diff --git a/data/easyrnaseq/easyrnaseqbioschemas.jsonld b/data/easyrnaseq/easyrnaseqbioschemas.jsonld index 9a357023e30fb..87126f8010471 100644 --- a/data/easyrnaseq/easyrnaseqbioschemas.jsonld +++ b/data/easyrnaseq/easyrnaseqbioschemas.jsonld @@ -14,15 +14,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nicolas Delhomme", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pubmed:22847932", "pmcid:PMC3463124", { "@id": "https://doi.org/10.1093/bioinformatics/bts477" - }, - "pubmed:22847932" + } ], "sc:description": "Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.", "sc:featureList": { @@ -31,9 +31,9 @@ "sc:license": "Artistic-2.0", "sc:name": "easyRNASeq", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/easyRNASeq.html", "sc:version": "2.10.0" diff --git a/data/eat-rice/eat-ricebioschemas.jsonld b/data/eat-rice/eat-ricebioschemas.jsonld index d9c29311e059f..53c6159b3fc47 100644 --- a/data/eat-rice/eat-ricebioschemas.jsonld +++ b/data/eat-rice/eat-ricebioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-5525-4011", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006942", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/EAT-Rice", "@type": "sc:SoftwareApplication", @@ -18,10 +26,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC6505892", - "pubmed:31067213", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006942" - } + }, + "pubmed:31067213" ], "sc:description": "Predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches.", "sc:featureList": [ @@ -35,19 +43,11 @@ "sc:license": "Unlicense", "sc:name": "EAT-Rice", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://predictor.nchu.edu.tw/EAT-Rice" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006942", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0002-5525-4011", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/eb-eye/eb-eyebioschemas.jsonld b/data/eb-eye/eb-eyebioschemas.jsonld index e7fddf5617149..2bf056d0830d5 100644 --- a/data/eb-eye/eb-eyebioschemas.jsonld +++ b/data/eb-eye/eb-eyebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Search globally across all EMBL-EBI databases.", "sc:name": "EB-eye", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/eb-eye_rest#clients", "sc:version": "1" diff --git a/data/ebarrays/ebarraysbioschemas.jsonld b/data/ebarrays/ebarraysbioschemas.jsonld index 15e6f74507946..14bc9bb046d26 100644 --- a/data/ebarrays/ebarraysbioschemas.jsonld +++ b/data/ebarrays/ebarraysbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ming Yuan", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This software provides tools for the analysis of replicated/unreplicated microarray data.", "sc:license": "GPL-2.0", "sc:name": "EBarrays", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EBarrays.html", "sc:version": "2.38.0" diff --git a/data/ebas/ebasbioschemas.jsonld b/data/ebas/ebasbioschemas.jsonld index 7e39b0b2d3969..db1c946aa6f89 100644 --- a/data/ebas/ebasbioschemas.jsonld +++ b/data/ebas/ebasbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Analyze groups of proteins or entire proteomes for the presence of eMOTIFs in batch fashion.", "sc:name": "eBAS", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://motif.stanford.edu/distributions/emotif/", "sc:version": "3.6" diff --git a/data/ebcoexpress/ebcoexpressbioschemas.jsonld b/data/ebcoexpress/ebcoexpressbioschemas.jsonld index 29d7ffb9333d0..016db831dff4f 100644 --- a/data/ebcoexpress/ebcoexpressbioschemas.jsonld +++ b/data/ebcoexpress/ebcoexpressbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "John A. Dawson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "An Empirical Bayesian Approach to Differential Co-Expression Analysis at the Gene-Pair Level.", "sc:license": "GPL-2.0", "sc:name": "EBcoexpress", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EBcoexpress.html", diff --git a/data/ebi_metagenomics/ebi_metagenomicsbioschemas.jsonld b/data/ebi_metagenomics/ebi_metagenomicsbioschemas.jsonld index e0a553e92acc2..305fdcdf03d4a 100644 --- a/data/ebi_metagenomics/ebi_metagenomicsbioschemas.jsonld +++ b/data/ebi_metagenomics/ebi_metagenomicsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Web resource targeted at metagenomic researchers.", "sc:name": "MGnify (was EBI Metagenomics)", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "EMBL-EBI Databases", diff --git a/data/ebi_tools/ebi_toolsbioschemas.jsonld b/data/ebi_tools/ebi_toolsbioschemas.jsonld index 376d803887771..97a6550d04111 100644 --- a/data/ebi_tools/ebi_toolsbioschemas.jsonld +++ b/data/ebi_tools/ebi_toolsbioschemas.jsonld @@ -9,18 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkm291", - "@type": "sc:CreativeWork" - }, { "@id": "https://doi.org/10.1093/nar/gki491", "@type": "sc:CreativeWork" }, - { - "@id": "https://doi.org/10.1093/nar/gkp302", - "@type": "sc:CreativeWork" - }, { "@id": "https://doi.org/10.1093/nar/gkt376", "@type": "sc:CreativeWork" @@ -34,45 +26,53 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "EMBL - European Bioinformatics Institute", "sc:additionalType": [ - "Web service", "Web application", - "Web API" + "Web API", + "Web service" ], "sc:citation": [ - { - "@id": "https://doi.org/10.1093/nar/gkm291" - }, + "pubmed:17576686", + "pubmed:15215339", { "@id": "https://doi.org/10.1093/nar/gkp302" }, - "pubmed:23671338", - "pubmed:15980463", - "pmcid:PMC1933145", + "pmcid:PMC1160251", + "pmcid:PMC2703973", "pubmed:19435877", - "pubmed:17576686", + "pmcid:PMC1933145", { "@id": "https://doi.org/10.1093/nar/gkh405" }, - "pubmed:15215339", - "pmcid:PMC1160251", - "pmcid:PMC3692137", + "pubmed:23671338", + "pmcid:PMC441543", + { + "@id": "https://doi.org/10.1093/nar/gkm291" + }, { "@id": "https://doi.org/10.1093/nar/gkt376" }, - "pmcid:PMC441543", + "pmcid:PMC3692137", + "pubmed:15980463", { "@id": "https://doi.org/10.1093/nar/gki491" - }, - "pmcid:PMC2703973" + } ], "sc:description": "EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.", "sc:name": "EBI Tools", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkm291", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://doi.org/10.1093/nar/gkp302", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ebic/ebicbioschemas.jsonld b/data/ebic/ebicbioschemas.jsonld index 57557780220be..66be69ea32e92 100644 --- a/data/ebic/ebicbioschemas.jsonld +++ b/data/ebic/ebicbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/EBIC", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Patryk Orzechowski", - "Jason H. Moore" + "Jason H. Moore", + "Patryk Orzechowski" ], "sc:additionalType": "Command-line tool", "sc:description": "Evolutionary-based BIClustering (EBIC), a next-generation biclustering algorithm for mining genetic data.", "sc:license": "MIT", "sc:name": "EBIC", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/EpistasisLab/ebic" } \ No newline at end of file diff --git a/data/ebimage/ebimagebioschemas.jsonld b/data/ebimage/ebimagebioschemas.jsonld index adc44b22e2b02..37e1ea1b36413 100644 --- a/data/ebimage/ebimagebioschemas.jsonld +++ b/data/ebimage/ebimagebioschemas.jsonld @@ -18,20 +18,20 @@ }, "sc:additionalType": "Command-line tool", "sc:author": [ + "Gregoire Pau", + "Mike Smith", { "@id": "http://orcid.org/0000-0002-0474-2218" }, - "Mike Smith", - "Gregoire Pau", - "Oleg Sklyar", - "Andrzej Oleś" + "Andrzej Oleś", + "Oleg Sklyar" ], "sc:citation": [ "pubmed:20338898", - "pmcid:PMC2844988", { "@id": "https://doi.org/10.1093/bioinformatics/btq046" - } + }, + "pmcid:PMC2844988" ], "sc:description": "R package which provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, It offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.", "sc:featureList": { @@ -40,8 +40,8 @@ "sc:license": "LGPL-2.1", "sc:name": "EBImage", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ diff --git a/data/ebola_genome_portal/ebola_genome_portalbioschemas.jsonld b/data/ebola_genome_portal/ebola_genome_portalbioschemas.jsonld index b54728de8dc18..6f1882bf0418c 100644 --- a/data/ebola_genome_portal/ebola_genome_portalbioschemas.jsonld +++ b/data/ebola_genome_portal/ebola_genome_portalbioschemas.jsonld @@ -14,26 +14,26 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:25685613", + "pmcid:PMC4318873", { "@id": "https://doi.org/10.1371/currents.outbreaks.386ab0964ab4d6c8cb550bfb6071d822" - }, - "pubmed:25685613", - "pmcid:PMC4318873" + } ], "sc:description": "The 2014 Ebola epidemic in West Africa has stirred international response and renewed efforts to develop effective preventative and treatment options. In response to a request for help from vaccine researchers, the UCSC Ebola Genome Browser was built with viral sequences from previous outbreaks as well as the 2014 outbreak. This site also provides related tools and information that can be used to further the understanding of Ebola.", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_0564" }, { - "@id": "edam:operation_0564" + "@id": "edam:operation_0337" } ], "sc:name": "UCSC Ebola Genome Portal", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "rki.de", "sc:url": "https://genome.ucsc.edu/ebolaPortal/" diff --git a/data/ebolaid/ebolaidbioschemas.jsonld b/data/ebolaid/ebolaidbioschemas.jsonld index 1753b21c20a4a..c417949170c51 100644 --- a/data/ebolaid/ebolaidbioschemas.jsonld +++ b/data/ebolaid/ebolaidbioschemas.jsonld @@ -25,11 +25,11 @@ }, "sc:additionalType": "Database portal", "sc:citation": [ + "pmcid:PMC4956216", { "@id": "https://doi.org/10.1371/journal.pntd.0004757" }, - "pubmed:27441375", - "pmcid:PMC4956216" + "pubmed:27441375" ], "sc:description": "Provides a complete, quality checked and regularly updated list of oligonucleotides for the Ebola virus. The database describes the genetic diversity across the Ebola genome to facilitate the design of accurate diagnostic methods and therapeutic approaches.\nThe database provides different measures of sequence conservation for each target region obtained from multiple sequence alignments, allowing the selection of the most conserved oligonucleotides.", "sc:featureList": { @@ -37,9 +37,9 @@ }, "sc:name": "EbolaID", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://ebolaid.portugene.com" } diff --git a/data/ebprot/ebprotbioschemas.jsonld b/data/ebprot/ebprotbioschemas.jsonld index 64211449a2a9a..8fc11a2b43ad0 100644 --- a/data/ebprot/ebprotbioschemas.jsonld +++ b/data/ebprot/ebprotbioschemas.jsonld @@ -11,10 +11,10 @@ "@id": "https://bio.tools/ebprot", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Christine Vogel", - "Hiromi W.L. Koh", + "Hyungwon Choi", "Yunbin Zhang", - "Hyungwon Choi" + "Hiromi W.L. Koh", + "Christine Vogel" ], "sc:additionalType": "Plug-in", "sc:citation": "pubmed:30411623", diff --git a/data/ebsea/bioconda_ebsea.yaml b/data/ebsea/bioconda_ebsea.yaml index 6ba4dcb2420fe..abce180096559 100644 --- a/data/ebsea/bioconda_ebsea.yaml +++ b/data/ebsea/bioconda_ebsea.yaml @@ -4,7 +4,6 @@ description: Calculates differential expression of genes based on exon counts of home: https://bioconductor.org/packages/3.10/bioc/html/EBSEA.html identifiers: - biotools:ebsea -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-ebsea diff --git a/data/ebsea/ebseabioschemas.jsonld b/data/ebsea/ebseabioschemas.jsonld index 8529c9cf424b2..c27b5ca0ea6b9 100644 --- a/data/ebsea/ebseabioschemas.jsonld +++ b/data/ebsea/ebseabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "EBSEA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EBSEA.html", diff --git a/data/ebseq/ebseqbioschemas.jsonld b/data/ebseq/ebseqbioschemas.jsonld index 018f2aab925a5..adc95b3d1935a 100644 --- a/data/ebseq/ebseqbioschemas.jsonld +++ b/data/ebseq/ebseqbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ning Leng", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Differential Expression analysis at both gene and isoform level using RNA-seq data.", "sc:license": "Artistic-2.0", diff --git a/data/ebseqhmm/ebseqhmmbioschemas.jsonld b/data/ebseqhmm/ebseqhmmbioschemas.jsonld index 6c30ba505e021..c59ba7ea61f6d 100644 --- a/data/ebseqhmm/ebseqhmmbioschemas.jsonld +++ b/data/ebseqhmm/ebseqhmmbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ning Leng", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package implements an auto-regressive hidden Markov model for statistical analysis in ordered RNA-seq experiments (e.g. time course or spatial course data). It provides functions to identify genes and isoforms that have non-constant expression profile over the time points/positions, and cluster them into expression paths.", "sc:license": "Artistic-2.0", "sc:name": "EBSeqHMM", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EBSeqHMM.html", "sc:version": "1.8.0" diff --git a/data/ecccl/eccclbioschemas.jsonld b/data/ecccl/eccclbioschemas.jsonld index 26468a69a6758..09a8550700adf 100644 --- a/data/ecccl/eccclbioschemas.jsonld +++ b/data/ecccl/eccclbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1783-9", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ecccl", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mona Riemenschneider", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5561639", { "@id": "https://doi.org/10.1186/s12859-017-1783-9" }, - "pubmed:28818036" + "pubmed:28818036", + "pmcid:PMC5561639" ], "sc:description": "Parallelized GPU implementation of Ensemble Classifier Chains.", "sc:featureList": { @@ -36,6 +32,10 @@ "Mac" ], "sc:url": "http://heiderlab.de/?page_id=684" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1783-9", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/eccetera/ecceterabioschemas.jsonld b/data/eccetera/ecceterabioschemas.jsonld index c80db8a3ac0b4..e9f5934f3c925 100644 --- a/data/eccetera/ecceterabioschemas.jsonld +++ b/data/eccetera/ecceterabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses.", "sc:name": "ecceTERA", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera" } \ No newline at end of file diff --git a/data/echo/echobioschemas.jsonld b/data/echo/echobioschemas.jsonld index 519252fc997a4..08656999afd7f 100644 --- a/data/echo/echobioschemas.jsonld +++ b/data/echo/echobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/echo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wei-Chun Kao", - "Andrew H. Chan" + "Andrew H. Chan", + "Wei-Chun Kao" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:21482625", @@ -20,8 +20,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "ECHO", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://uc-echo.sourceforge.net/" diff --git a/data/echobase/echobasebioschemas.jsonld b/data/echobase/echobasebioschemas.jsonld index 3d97aa4beb14d..afc022a274845 100644 --- a/data/echobase/echobasebioschemas.jsonld +++ b/data/echobase/echobasebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.", "sc:name": "EchoBASE", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "University of York", "sc:url": "http://www.york.ac.uk/res/thomas/" diff --git a/data/eclair/eclairbioschemas.jsonld b/data/eclair/eclairbioschemas.jsonld index 557a9f507e70f..d93160beedd30 100644 --- a/data/eclair/eclairbioschemas.jsonld +++ b/data/eclair/eclairbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "ECLAIR", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/GGiecold/ECLAIR" } \ No newline at end of file diff --git a/data/ecolitk/ecolitkbioschemas.jsonld b/data/ecolitk/ecolitkbioschemas.jsonld index a1432c39ee462..ecbedcc585dfc 100644 --- a/data/ecolitk/ecolitkbioschemas.jsonld +++ b/data/ecolitk/ecolitkbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laurent Gautier", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.", "sc:license": "GPL-2.0", "sc:name": "ecolitk", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ecolitk.html", diff --git a/data/ecoprestmet/ecoprestmetbioschemas.jsonld b/data/ecoprestmet/ecoprestmetbioschemas.jsonld index 51540eaabda81..a3faaa6c2e6c4 100644 --- a/data/ecoprestmet/ecoprestmetbioschemas.jsonld +++ b/data/ecoprestmet/ecoprestmetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "CC-BY-NC-4.0", "sc:name": "EcoPrestMet", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://zampierigroup.shinyapps.io/EcoPrestMet" diff --git a/data/ecr_browser/ecr_browserbioschemas.jsonld b/data/ecr_browser/ecr_browserbioschemas.jsonld index 3c1e92277e2ea..20f81bb6b8d9c 100644 --- a/data/ecr_browser/ecr_browserbioschemas.jsonld +++ b/data/ecr_browser/ecr_browserbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.", "sc:name": "ECR Browser", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ecrbrowser.dcode.org/" } \ No newline at end of file diff --git a/data/ecrbpome/ecrbpomebioschemas.jsonld b/data/ecrbpome/ecrbpomebioschemas.jsonld index 94ce4836825df..f29823fd35029 100644 --- a/data/ecrbpome/ecrbpomebioschemas.jsonld +++ b/data/ecrbpome/ecrbpomebioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-6642-2367", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/S12864-019-5755-5", "@type": "sc:CreativeWork" }, + { + "@id": "https://orcid.org/0000-0002-6642-2367", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/EcRBPome", "@type": "sc:SoftwareApplication", @@ -24,34 +24,34 @@ "@id": "https://orcid.org/0000-0002-6642-2367" }, "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ + "pmcid:PMC6530084", "pubmed:31117939", { "@id": "https://doi.org/10.1186/S12864-019-5755-5" - }, - "pmcid:PMC6530084" + } ], "sc:description": "Comprehensive database of Escherichia coli RNA-binding proteins (RBPs). This database documents RBPs identified by genome-wide survey of all known complete E. coli proteomes. EcRBPome also presents a cross-strain comparative account of these RBPs, as well as the constituent RNA-binding domains (RBDs).", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3901" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_3901" } ], "sc:license": "Unlicense", "sc:name": "EcRBPome", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://caps.ncbs.res.in/ecrbpome" } diff --git a/data/edal/edalbioschemas.jsonld b/data/edal/edalbioschemas.jsonld index 9e879a90427f1..c06deda2ca556 100644 --- a/data/edal/edalbioschemas.jsonld +++ b/data/edal/edalbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/edal", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", "Web API", + "Desktop application", "Command-line tool" ], "sc:description": "e!DAL is a lightweight software framework for publishing and sharing research data. Its main features are version tracking, metadata management, information retrieval, journal and founding agency proven registration of persistent identifiers (DOI), an embedded HTTP(S) server for public data access, access as a network file system, and a scalable storage backend.", "sc:license": "CC-BY-4.0", "sc:name": "eDAL - electronic data archive library", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://edal.ipk-gatersleben.de/", diff --git a/data/edam-browser/edam-browserbioschemas.jsonld b/data/edam-browser/edam-browserbioschemas.jsonld index e2e6bd43641db..f554cdf913e1d 100644 --- a/data/edam-browser/edam-browserbioschemas.jsonld +++ b/data/edam-browser/edam-browserbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "MIT", "sc:name": "EDAM-Browser", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/IFB-ElixirFr/edam-browser", "sc:version": "1.0" diff --git a/data/edamdef/edamdefbioschemas.jsonld b/data/edamdef/edamdefbioschemas.jsonld index e28ed725699de..c86308ade69f3 100644 --- a/data/edamdef/edamdefbioschemas.jsonld +++ b/data/edamdef/edamdefbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK BBSRC", "EMBOSS Contributors", - "UK MRC" + "UK MRC", + "UK BBSRC", + "Wellcome Trust" ], "sc:description": "Find EDAM ontology terms by definition.", "sc:funder": [ - "Wellcome Trust", + "UK BBSRC", "UK MRC", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "edamdef", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/edamhasinput/edamhasinputbioschemas.jsonld b/data/edamhasinput/edamhasinputbioschemas.jsonld index b92dcccfce875..52fbbe64f3c84 100644 --- a/data/edamhasinput/edamhasinputbioschemas.jsonld +++ b/data/edamhasinput/edamhasinputbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK BBSRC", "EMBOSS Contributors", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:description": "Find EDAM ontology terms by has_input relation.", "sc:funder": [ - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "edamhasinput", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/edamhasinput.html", "sc:version": "r6" diff --git a/data/edamhasoutput/edamhasoutputbioschemas.jsonld b/data/edamhasoutput/edamhasoutputbioschemas.jsonld index 2b5c4788c88d4..97dd384220893 100644 --- a/data/edamhasoutput/edamhasoutputbioschemas.jsonld +++ b/data/edamhasoutput/edamhasoutputbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK MRC", "UK BBSRC", "EMBOSS Contributors", - "UK MRC", "Wellcome Trust" ], "sc:description": "Find EDAM ontology terms by has_output relation.", "sc:funder": [ "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "edamhasoutput", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": [ diff --git a/data/edamisformat/edamisformatbioschemas.jsonld b/data/edamisformat/edamisformatbioschemas.jsonld index 07301b32f2210..3d1fd73c94259 100644 --- a/data/edamisformat/edamisformatbioschemas.jsonld +++ b/data/edamisformat/edamisformatbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK BBSRC", "EMBOSS Contributors", "UK MRC", - "UK BBSRC", "Wellcome Trust" ], "sc:description": "Find EDAM ontology terms by is_format_of relation.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "edamisformat", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/edamisid/edamisidbioschemas.jsonld b/data/edamisid/edamisidbioschemas.jsonld index d254cf58f4d6e..99983b9f5a4ba 100644 --- a/data/edamisid/edamisidbioschemas.jsonld +++ b/data/edamisid/edamisidbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "EMBOSS Contributors", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "UK MRC", + "EMBOSS Contributors" ], "sc:description": "Find EDAM ontology terms by is_identifier_of relation.", "sc:funder": [ - "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "edamisid", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ diff --git a/data/edamname/edamnamebioschemas.jsonld b/data/edamname/edamnamebioschemas.jsonld index ac0b8693964ba..de4871d2132e7 100644 --- a/data/edamname/edamnamebioschemas.jsonld +++ b/data/edamname/edamnamebioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "Wellcome Trust", + "UK BBSRC", "EMBOSS Contributors", - "UK BBSRC" + "UK MRC", + "Wellcome Trust" ], "sc:description": "Find EDAM ontology terms by name.", "sc:funder": [ - "Wellcome Trust", "UK MRC", + "Wellcome Trust", "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "edamname", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/edamname.html", "sc:version": "r6" diff --git a/data/edaseq/edaseqbioschemas.jsonld b/data/edaseq/edaseqbioschemas.jsonld index 6454d930081f8..b50e55ac27057 100644 --- a/data/edaseq/edaseqbioschemas.jsonld +++ b/data/edaseq/edaseqbioschemas.jsonld @@ -22,27 +22,27 @@ "Command-line tool" ], "sc:citation": [ + "pmcid:PMC4067528", + "pubmed:24929920", { "@id": "https://doi.org/10.1186/1471-2105-15-188" - }, - "pmcid:PMC4067528", - "pubmed:24929920" + } ], "sc:description": "Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).", "sc:featureList": [ { - "@id": "edam:operation_0564" + "@id": "edam:operation_3680" }, { - "@id": "edam:operation_3680" + "@id": "edam:operation_0564" } ], "sc:license": "Artistic-2.0", "sc:name": "EDASeq", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EDASeq.html", "sc:version": "2.8.0" diff --git a/data/edda/eddabioschemas.jsonld b/data/edda/eddabioschemas.jsonld index 9257b84a238bc..5b0ee8ce76ce1 100644 --- a/data/edda/eddabioschemas.jsonld +++ b/data/edda/eddabioschemas.jsonld @@ -22,9 +22,9 @@ "sc:license": "GPL-2.0", "sc:name": "EDDA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EDDA.html", "sc:version": "1.12.0" diff --git a/data/edgar/edgarbioschemas.jsonld b/data/edgar/edgarbioschemas.jsonld index 47f1a1376ba08..286a5e31bc6bf 100644 --- a/data/edgar/edgarbioschemas.jsonld +++ b/data/edgar/edgarbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/edgar", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Giulia Babbi", - "ELIXIR-ITA-BOLOGNA" + "ELIXIR-ITA-BOLOGNA", + "Giulia Babbi" ], "sc:additionalType": [ "Database portal", @@ -23,8 +23,8 @@ "sc:name": "eDGAR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://edgar.biocomp.unibo.it" } \ No newline at end of file diff --git a/data/edgar_genomics/edgar_genomicsbioschemas.jsonld b/data/edgar_genomics/edgar_genomicsbioschemas.jsonld index 6c8d62685d288..a6399b1c13a50 100644 --- a/data/edgar_genomics/edgar_genomicsbioschemas.jsonld +++ b/data/edgar_genomics/edgar_genomicsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-6455-3622", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1093/nar/gkw255", "@type": "sc:CreativeWork" @@ -28,11 +24,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:27098043", - "pmcid:PMC4987874", { "@id": "https://doi.org/10.1093/nar/gkw255" - } + }, + "pmcid:PMC4987874", + "pubmed:27098043" ], "sc:description": "The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. To support these studies EDGAR - \"Efficient Database framework for comparative Genome Analyses using BLAST score Ratios\" - was developed.", "sc:featureList": { @@ -43,6 +39,10 @@ "sc:provider": "bigi", "sc:url": "http://edgar.computational.bio", "sc:version": "2.0" + }, + { + "@id": "http://orcid.org/0000-0001-6455-3622", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/edge/edgebioschemas.jsonld b/data/edge/edgebioschemas.jsonld index 7b765fdc73e9f..153431d3320b2 100644 --- a/data/edge/edgebioschemas.jsonld +++ b/data/edge/edgebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/edge", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Andrew J. Bass", - "John D. Storey" + "John D. Storey", + "Andrew J. Bass" ], "sc:additionalType": [ "Library", @@ -23,8 +23,8 @@ "sc:name": "edge", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/edge.html", "sc:version": "2.6.0" diff --git a/data/edger/edgerbioschemas.jsonld b/data/edger/edgerbioschemas.jsonld index 9ece9030e983a..e19649c1113d3 100644 --- a/data/edger/edgerbioschemas.jsonld +++ b/data/edger/edgerbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gks042", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/edger", "@type": "sc:SoftwareApplication", @@ -17,19 +21,19 @@ "@id": "http://orcid.org/0000-0002-2218-6833" }, "Aaron Lun", - "Mark Robinson", + "Yunshun Chen", "Gordon Smyth", - "Yunshun Chen" + "Mark Robinson" ], "edam:has_input": { "@id": "edam:data_2044" }, "edam:has_output": [ { - "@id": "edam:data_2884" + "@id": "edam:data_1669" }, { - "@id": "edam:data_1669" + "@id": "edam:data_2884" } ], "sc:additionalType": [ @@ -48,11 +52,11 @@ } ], "sc:citation": [ + "pubmed:22287627", + "pmcid:PMC3378882", { "@id": "https://doi.org/10.1093/nar/gks042" - }, - "pubmed:22287627", - "pmcid:PMC3378882" + } ], "sc:description": "Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.", "sc:featureList": { @@ -71,10 +75,6 @@ { "@id": "http://orcid.org/0000-0002-2218-6833", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/nar/gks042", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/edia/ediabioschemas.jsonld b/data/edia/ediabioschemas.jsonld index 6f617ccf14cc6..41f7be1184203 100644 --- a/data/edia/ediabioschemas.jsonld +++ b/data/edia/ediabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Easily interpretable electron density score for individual atoms. It quantifies the electron density support of each single atom by computing a weighted sum over an oversampled electron density grid in the proximity of the atom. Atomic EDIA values can also be combined with the help of the power mean to compute EDIA_m, an electron density score for small molecules, fragments, or residues.", "sc:name": "EDIA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "University of Hamburg - Center for Bioinformatics", "sc:url": "http://proteinsplus.zbh.uni-hamburg.de/#edia" diff --git a/data/edialign/edialignbioschemas.jsonld b/data/edialign/edialignbioschemas.jsonld index 95c4bbc774395..4786dbf0d3f62 100644 --- a/data/edialign/edialignbioschemas.jsonld +++ b/data/edialign/edialignbioschemas.jsonld @@ -19,16 +19,16 @@ ], "sc:description": "Local multiple alignment of sequences.", "sc:funder": [ - "UK MRC", "Wellcome Trust", + "UK MRC", "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "edialign", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/edisa/edisabioschemas.jsonld b/data/edisa/edisabioschemas.jsonld index 7cade29305545..89b1129592eaf 100644 --- a/data/edisa/edisabioschemas.jsonld +++ b/data/edisa/edisabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Extended Dimension Iterative Signature Algorithm is a novel probabilistic clustering approach for 3D gene-condition-time datasets. Based on mathematical definitions of gene expression modules,Its samples initial modules from the dataset which are then refined by removing genes and conditions until they comply with the module definition. A subsequent extension step ensures gene and condition maximality.", "sc:name": "EDISA", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ra.cs.uni-tuebingen.de/software/EDISA/welcome_e.html", "sc:version": "1.0" diff --git a/data/eds/edsbioschemas.jsonld b/data/eds/edsbioschemas.jsonld index 497d95678782b..42b712423e59d 100644 --- a/data/eds/edsbioschemas.jsonld +++ b/data/eds/edsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. In addition to electron density maps and tools to view these maps, statistics and plots are provided for assessing the goodness-of-fit between the deposited models (structures) and the experimental data represented by the electron density calculated using the models and their associated structure factor amplitudes.", "sc:name": "Electron density server at Uppsala university", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "Uppsala University", "sc:url": "http://eds.bmc.uu.se/eds/" diff --git a/data/eduliss/edulissbioschemas.jsonld b/data/eduliss/edulissbioschemas.jsonld index d94f8b724df3d..94a284cb6585c 100644 --- a/data/eduliss/edulissbioschemas.jsonld +++ b/data/eduliss/edulissbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Database stores structural, physicochemical and pharmacophoric properties of small molecules. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for unique compound recognition is demonstrated by making use of small subgroups of the descriptors.", "sc:name": "EDULISS", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://eduliss.bch.ed.ac.uk/" diff --git a/data/eegc/eegcbioschemas.jsonld b/data/eegc/eegcbioschemas.jsonld index 086569ca6497b..5d562d3b4c847 100644 --- a/data/eegc/eegcbioschemas.jsonld +++ b/data/eegc/eegcbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xiaoyuan Zhou", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package evaluates cellular engineering processes for direct differentiation of stem cells or conversion (transdifferentiation) of somatic cells to primary cells based on high throughput gene expression data screened either by DNA microarray or RNA sequencing. It performs DE analysis for each pair-wise sample comparison to identify and evaluate the transcriptional differences.", "sc:license": "GPL-2.0", "sc:name": "eegc", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/eegc.html", diff --git a/data/eegmir/eegmirbioschemas.jsonld b/data/eegmir/eegmirbioschemas.jsonld index d1f0a882e242a..ec743e05e4969 100644 --- a/data/eegmir/eegmirbioschemas.jsonld +++ b/data/eegmir/eegmirbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "EEGMIR", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://uazu.net/eegmir/" } \ No newline at end of file diff --git a/data/eegnet/eegnetbioschemas.jsonld b/data/eegnet/eegnetbioschemas.jsonld index 5bc6e503ca7ed..1cca5488ab901 100644 --- a/data/eegnet/eegnetbioschemas.jsonld +++ b/data/eegnet/eegnetbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Mahmoud Hassan", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC4574940", + "pubmed:26379232", { "@id": "https://doi.org/10.1371/journal.pone.0138297" - }, - "pmcid:PMC4574940", - "pubmed:26379232" + } ], "sc:description": "EEGNET is software designed to enclose the different steps from EEG signal preprocessing to brain network visualization.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "CECILL-1.0", "sc:name": "EEGNET", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://sites.google.com/site/eegnetworks/home" } diff --git a/data/eem_solver/eem_solverbioschemas.jsonld b/data/eem_solver/eem_solverbioschemas.jsonld index 6d6ac617679a0..a8144d4c57b3c 100644 --- a/data/eem_solver/eem_solverbioschemas.jsonld +++ b/data/eem_solver/eem_solverbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Calculates partial atomic charges for small organic molecules, drug-like molecules. The tool is deprecated, we recommend the use of AtomicChargeCalculator.", "sc:name": "EEM Solver", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "ELIXIR-CZ", "sc:url": "http://ncbr.muni.cz/~svobodova/eem_abeem", diff --git a/data/ef-seek/ef-seekbioschemas.jsonld b/data/ef-seek/ef-seekbioschemas.jsonld index 775291d5893e0..238106075e410 100644 --- a/data/ef-seek/ef-seekbioschemas.jsonld +++ b/data/ef-seek/ef-seekbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.", "sc:name": "eF-seek", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://ef-site.hgc.jp/eF-seek/index.jsp" } \ No newline at end of file diff --git a/data/efetch_pmc/efetch_pmcbioschemas.jsonld b/data/efetch_pmc/efetch_pmcbioschemas.jsonld index 6f42ae760c9db..fce68437f361a 100644 --- a/data/efetch_pmc/efetch_pmcbioschemas.jsonld +++ b/data/efetch_pmc/efetch_pmcbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.", "sc:name": "eFetch Pmc", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/books/NBK25501/", diff --git a/data/efetch_sequence/efetch_sequencebioschemas.jsonld b/data/efetch_sequence/efetch_sequencebioschemas.jsonld index 1fc13f93f5dfa..619a35bb419be 100644 --- a/data/efetch_sequence/efetch_sequencebioschemas.jsonld +++ b/data/efetch_sequence/efetch_sequencebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Retrieves sequences in requested format from a list of one or more unique identifiers.", "sc:name": "eFetch Sequence", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetch_help.html", "sc:version": "1" diff --git a/data/efetch_snp/efetch_snpbioschemas.jsonld b/data/efetch_snp/efetch_snpbioschemas.jsonld index 3f214965371e8..ad191016d43f6 100644 --- a/data/efetch_snp/efetch_snpbioschemas.jsonld +++ b/data/efetch_snp/efetch_snpbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Get SNPs information given SNP ID list.", "sc:name": "eFetch Snp", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html", "sc:version": "1" diff --git a/data/effectiveccbd/effectiveccbdbioschemas.jsonld b/data/effectiveccbd/effectiveccbdbioschemas.jsonld index af6a799345db8..767a29d2e7905 100644 --- a/data/effectiveccbd/effectiveccbdbioschemas.jsonld +++ b/data/effectiveccbd/effectiveccbdbioschemas.jsonld @@ -41,9 +41,9 @@ "sc:isAccessibleForFree": true, "sc:name": "EffectiveCCBD", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "AT-CUBE", "sc:softwareHelp": { diff --git a/data/effectivedb/effectivedbbioschemas.jsonld b/data/effectivedb/effectivedbbioschemas.jsonld index 733710190dcd8..62427abed2019 100644 --- a/data/effectivedb/effectivedbbioschemas.jsonld +++ b/data/effectivedb/effectivedbbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkq1154", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/effectivedb", "@type": "sc:SoftwareApplication", @@ -24,10 +28,10 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0080" + "@id": "edam:topic_3174" }, { - "@id": "edam:topic_3174" + "@id": "edam:topic_0080" }, { "@id": "edam:topic_3510" @@ -37,27 +41,27 @@ } ], "sc:citation": [ + "pmcid:PMC3013723", + "pubmed:21071416", { "@id": "https://doi.org/10.1093/nar/gkq1154" - }, - "pmcid:PMC3013723", - "pubmed:21071416" + } ], "sc:description": "Prediction of intact bacterial protein secretion systems and putative secreted proteins.", "sc:featureList": [ { - "@id": "edam:operation_3461" + "@id": "edam:operation_3092" }, { - "@id": "edam:operation_3092" + "@id": "edam:operation_3461" } ], "sc:isAccessibleForFree": true, "sc:name": "EffectiveDB", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ "CUBE - Computational Systems Biology", @@ -67,10 +71,6 @@ "@id": "http://www.effectivedb.org/" }, "sc:url": "http://www.effectivedb.org/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkq1154", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/effectiveeld/effectiveeldbioschemas.jsonld b/data/effectiveeld/effectiveeldbioschemas.jsonld index 04e0d0b8baccc..55b18cf3bc6f9 100644 --- a/data/effectiveeld/effectiveeldbioschemas.jsonld +++ b/data/effectiveeld/effectiveeldbioschemas.jsonld @@ -26,8 +26,8 @@ { "@id": "https://doi.org/10.1093/nar/gkq1154" }, - "pmcid:PMC3013723", - "pubmed:21071416" + "pubmed:21071416", + "pmcid:PMC3013723" ], "sc:description": "Prediction of putative secreted proteins based on eukaryotic-like domains (ELD).", "sc:featureList": { @@ -41,8 +41,8 @@ "Mac" ], "sc:provider": [ - "AT-CUBE", - "CUBE - Computational Systems Biology" + "CUBE - Computational Systems Biology", + "AT-CUBE" ], "sc:softwareHelp": { "@id": "http://www.effectivedb.org/method/effectiveeld" diff --git a/data/effectives346/effectives346bioschemas.jsonld b/data/effectives346/effectives346bioschemas.jsonld index cab15ba543856..1e5c0976d1462 100644 --- a/data/effectives346/effectives346bioschemas.jsonld +++ b/data/effectives346/effectives346bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkq1154", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/effectives346", "@type": "sc:SoftwareApplication", @@ -17,10 +21,10 @@ }, "edam:has_output": [ { - "@id": "edam:data_0896" + "@id": "edam:data_0920" }, { - "@id": "edam:data_0920" + "@id": "edam:data_0896" } ], "sc:additionalType": [ @@ -29,17 +33,17 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3174" + "@id": "edam:topic_0797" }, { - "@id": "edam:topic_0797" + "@id": "edam:topic_3174" } ], "sc:citation": [ - "pubmed:21071416", { "@id": "https://doi.org/10.1093/nar/gkq1154" }, + "pubmed:21071416", "pmcid:PMC3013723" ], "sc:description": "Prediction of intact secretion systems III, IV and VI in bacterial genomes by using a Support Vector Machine (SVM) approach.", @@ -49,22 +53,18 @@ "sc:isAccessibleForFree": true, "sc:name": "EffectiveS346", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "AT-CUBE", - "CUBE - Computational Systems Biology" + "CUBE - Computational Systems Biology", + "AT-CUBE" ], "sc:softwareHelp": { "@id": "http://www.effectivedb.org/method/effectives346" }, "sc:url": "http://www.effectivedb.org/method/effectives346" - }, - { - "@id": "https://doi.org/10.1093/nar/gkq1154", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/effectivet3/effectivet3bioschemas.jsonld b/data/effectivet3/effectivet3bioschemas.jsonld index 605434d20c3f5..d40c6dd68274f 100644 --- a/data/effectivet3/effectivet3bioschemas.jsonld +++ b/data/effectivet3/effectivet3bioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-7496-7578", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1371/journal.ppat.1000376", "@type": "sc:CreativeWork" @@ -34,8 +30,8 @@ "@id": "edam:topic_0080" }, "sc:citation": [ - "pmcid:PMC2669295", "pubmed:19390696", + "pmcid:PMC2669295", { "@id": "https://doi.org/10.1371/journal.ppat.1000376" } @@ -50,9 +46,9 @@ "sc:isAccessibleForFree": true, "sc:name": "EffectiveT3", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "AT-CUBE", "sc:softwareHelp": { @@ -60,6 +56,10 @@ }, "sc:url": "http://www.effectivedb.org/method/effectivet3", "sc:version": "2.0.1" + }, + { + "@id": "http://orcid.org/0000-0002-7496-7578", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/efs/efsbioschemas.jsonld b/data/efs/efsbioschemas.jsonld index f0e868ef222f0..cabc5b6650d12 100644 --- a/data/efs/efsbioschemas.jsonld +++ b/data/efs/efsbioschemas.jsonld @@ -19,19 +19,19 @@ "biotools:primaryContact": "Dominik Heider", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5488355", - "pubmed:28674556", { "@id": "https://doi.org/10.1186/s13040-017-0142-8" - } + }, + "pubmed:28674556", + "pmcid:PMC5488355" ], "sc:description": "An ensemble feature selection tool implemented as R-package and web-application.", "sc:featureList": [ { - "@id": "edam:operation_2990" + "@id": "edam:operation_3465" }, { - "@id": "edam:operation_3465" + "@id": "edam:operation_2990" } ], "sc:name": "EFS", diff --git a/data/ega/egabioschemas.jsonld b/data/ega/egabioschemas.jsonld index 2c56177405859..65b2411c427b4 100644 --- a/data/ega/egabioschemas.jsonld +++ b/data/ega/egabioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "European genome-phenome Archive (EGA) - service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.", "sc:name": "EGA", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "EMBL-EBI Databases", "sc:url": "https://ega-archive.org/" diff --git a/data/egad/egadbioschemas.jsonld b/data/egad/egadbioschemas.jsonld index 9ab57ad38ac5a..e49cb9684dd26 100644 --- a/data/egad/egadbioschemas.jsonld +++ b/data/egad/egadbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sara Ballouz", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.", "sc:license": "GPL-2.0", "sc:name": "EGAD", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EGAD.html", diff --git a/data/egassembler/egassemblerbioschemas.jsonld b/data/egassembler/egassemblerbioschemas.jsonld index 9695b730c1ec7..5d68486e29a87 100644 --- a/data/egassembler/egassemblerbioschemas.jsonld +++ b/data/egassembler/egassemblerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.", "sc:name": "EGassembler", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://egassembler.hgc.jp" } \ No newline at end of file diff --git a/data/eggnog-mapper/eggnog-mapperbioschemas.jsonld b/data/eggnog-mapper/eggnog-mapperbioschemas.jsonld index 14deebfd33ec2..4647f7cf5d53b 100644 --- a/data/eggnog-mapper/eggnog-mapperbioschemas.jsonld +++ b/data/eggnog-mapper/eggnog-mapperbioschemas.jsonld @@ -19,13 +19,13 @@ "sc:license": "GPL-3.0", "sc:name": "EggNOG-mapper", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ - "HD-HuB", - "European Molecular Biology Laboratory (EMBL)" + "European Molecular Biology Laboratory (EMBL)", + "HD-HuB" ], "sc:url": "http://beta-eggnogdb.embl.de/#/app/emapper", "sc:version": "1" diff --git a/data/eggnog/eggnogbioschemas.jsonld b/data/eggnog/eggnogbioschemas.jsonld index 3fdbeddce22ec..39bf89eb9935c 100644 --- a/data/eggnog/eggnogbioschemas.jsonld +++ b/data/eggnog/eggnogbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://orcid.org/0000-0003-1429-7485", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1093/nar/gkv1248", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/eggnog", "@type": "sc:SoftwareApplication", @@ -25,12 +21,12 @@ }, "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC4702882", - "pubmed:26582926", "pubmed:17942413", { "@id": "https://doi.org/10.1093/nar/gkv1248" - } + }, + "pubmed:26582926", + "pmcid:PMC4702882" ], "sc:description": "Database of nested orthologous gene groups (NOGs) infered using unsupervised clustering applied to >2,000 complete genomes followed by comprehensive characterization and analysis of the resulting gene families. It provides orthologous group assignments at >100 different taxonomic levels as well as multiple sequence alignments, maximum-likelihood trees and broad functional annotations for each group accessible via a web interface or through bulk download.", "sc:license": "GPL-3.0", @@ -45,6 +41,10 @@ "HD-HuB" ], "sc:url": "http://eggnogdb.embl.de/#/app/home" + }, + { + "@id": "https://doi.org/10.1093/nar/gkv1248", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/egmrg/egmrgbioschemas.jsonld b/data/egmrg/egmrgbioschemas.jsonld index 9529bacfb429a..4c7d38a804614 100644 --- a/data/egmrg/egmrgbioschemas.jsonld +++ b/data/egmrg/egmrgbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Encyclopedia of microbiota regulated genes.", "sc:name": "EGMRG", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "bils.se", "sc:url": "http://microbiota.wall.gu.se/" diff --git a/data/ego_viii/ego_viiibioschemas.jsonld b/data/ego_viii/ego_viiibioschemas.jsonld index 4e795b38bf1e3..84d8f6e1a8bcf 100644 --- a/data/ego_viii/ego_viiibioschemas.jsonld +++ b/data/ego_viii/ego_viiibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX and inhomogeneous clusters of UNIX workstations under PVM or MPI.", "sc:name": "EGO VIII", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.mpibpc.mpg.de/273454/04-EGO_VIII" } \ No newline at end of file diff --git a/data/egsea/egseabioschemas.jsonld b/data/egsea/egseabioschemas.jsonld index 1d8ec25963cc0..c67a10480ca20 100644 --- a/data/egsea/egseabioschemas.jsonld +++ b/data/egsea/egseabioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1093/bioinformatics/btw623", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0002-2411-1325", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/egsea", "@type": "sc:SoftwareApplication", @@ -37,11 +33,11 @@ "@id": "edam:topic_2259" }, "sc:citation": [ - "pubmed:27694195", { "@id": "https://doi.org/10.1093/bioinformatics/btw623" }, - "pmcid:PMC5408797" + "pmcid:PMC5408797", + "pubmed:27694195" ], "sc:description": "This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.", "sc:featureList": { @@ -49,12 +45,16 @@ }, "sc:name": "EGSEA", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EGSEA.html", "sc:version": "1.2.0" + }, + { + "@id": "http://orcid.org/0000-0002-2411-1325", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/ehecregnet/ehecregnetbioschemas.jsonld b/data/ehecregnet/ehecregnetbioschemas.jsonld index d5312f7e37fbe..1b2badb02ddbb 100644 --- a/data/ehecregnet/ehecregnetbioschemas.jsonld +++ b/data/ehecregnet/ehecregnetbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-0282-0462", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/ehecregnet", "@type": "sc:SoftwareApplication", @@ -20,16 +24,12 @@ "sc:description": "Database and analysis platform for pathogenic E. coli transcriptional gene regulatory networks. The database contains the known regulatory network of E. coli K-12 extracted from RegulonDB. In addition, it provides inter-species transferred gene regulatory interactions for 16 pathogenic E. coli strains.", "sc:name": "EhecRegNet", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "bmb.sdu.dk", "sc:url": "https://ehecregnet.compbio.sdu.dk/v2/index.html" - }, - { - "@id": "http://orcid.org/0000-0002-0282-0462", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/einverted/einvertedbioschemas.jsonld b/data/einverted/einvertedbioschemas.jsonld index 51a565dbbc361..d90a6ead097ef 100644 --- a/data/einverted/einvertedbioschemas.jsonld +++ b/data/einverted/einvertedbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "Wellcome Trust", + "EMBOSS Contributors", "UK MRC", "UK BBSRC" ], "sc:description": "Find inverted repeats in nucleotide sequences.", "sc:funder": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "einverted", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/eir/eirbioschemas.jsonld b/data/eir/eirbioschemas.jsonld index a724152b0484a..85da67e2df17e 100644 --- a/data/eir/eirbioschemas.jsonld +++ b/data/eir/eirbioschemas.jsonld @@ -19,13 +19,13 @@ "biotools:primaryContact": "Thomas Girke", "edam:has_input": [ { - "@id": "edam:data_0990" + "@id": "edam:data_1086" }, { "@id": "edam:data_1463" }, { - "@id": "edam:data_1086" + "@id": "edam:data_0990" } ], "edam:has_output": [ @@ -37,23 +37,23 @@ } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0154" + "@id": "edam:topic_0081" }, { - "@id": "edam:topic_0081" + "@id": "edam:topic_0154" } ], "sc:citation": [ - "pmcid:PMC2844998", - "pubmed:20179075", { "@id": "https://doi.org/10.1093/bioinformatics/btq067" - } + }, + "pubmed:20179075", + "pmcid:PMC2844998" ], "sc:description": "This package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.", "sc:featureList": { @@ -62,9 +62,9 @@ "sc:license": "Artistic-2.0", "sc:name": "eiR", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/eiR.html", "sc:version": "1.14.1" diff --git a/data/eisa/eisabioschemas.jsonld b/data/eisa/eisabioschemas.jsonld index 3e4381e3c40fc..7a93030b7526e 100644 --- a/data/eisa/eisabioschemas.jsonld +++ b/data/eisa/eisabioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Gabor Csardi", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:15513996", "sc:description": "The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. The ISA is capable of finding overlapping modules and it is resilient to noise. This package provides a convenient interface to the ISA, using standard BioConductor data structures; and also contains various visualization tools that can be used with other biclustering algorithms.", "sc:license": "GPL-2.0", "sc:name": "eisa", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/eisa.html", "sc:version": "1.26.0" diff --git a/data/el-maven/el-mavenbioschemas.jsonld b/data/el-maven/el-mavenbioschemas.jsonld index 4dcc8e6cd9b62..7ded18abfc3a9 100644 --- a/data/el-maven/el-mavenbioschemas.jsonld +++ b/data/el-maven/el-mavenbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "El-MAVEN", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.ncbi.nlm.nih.gov/pubmed/?term=31119671" } \ No newline at end of file diff --git a/data/el_pssm-rt/el_pssm-rtbioschemas.jsonld b/data/el_pssm-rt/el_pssm-rtbioschemas.jsonld index 2b7c2b0e7c0c0..c1345b56a1d9a 100644 --- a/data/el_pssm-rt/el_pssm-rtbioschemas.jsonld +++ b/data/el_pssm-rt/el_pssm-rtbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation.", "sc:name": "EL_PSSM-RT", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://hlt.hitsz.edu.cn:8080/PSSM-RT_SVM/" diff --git a/data/eland/elandbioschemas.jsonld b/data/eland/elandbioschemas.jsonld index b16eeda456103..80e4405be4f7b 100644 --- a/data/eland/elandbioschemas.jsonld +++ b/data/eland/elandbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Illumina's algorithm for whole genome or reads alignments to a reference genome.", "sc:name": "ELAND", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.illumina.com/" } \ No newline at end of file diff --git a/data/elastodb/elastodbbioschemas.jsonld b/data/elastodb/elastodbbioschemas.jsonld index 1fc7f5717743b..c4eb42bb15c9d 100644 --- a/data/elastodb/elastodbbioschemas.jsonld +++ b/data/elastodb/elastodbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Repository for well-characterized elastin sequences to facilitate its study. The database has since expanded to include other non-elastin sequences that share elastic properties.", "sc:name": "ElastoDB", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.compsysbio.org/elastin/" } \ No newline at end of file diff --git a/data/elbow/elbowbioschemas.jsonld b/data/elbow/elbowbioschemas.jsonld index 56fcae3d92198..c0e985e8b631c 100644 --- a/data/elbow/elbowbioschemas.jsonld +++ b/data/elbow/elbowbioschemas.jsonld @@ -15,15 +15,15 @@ "Graham Alvare" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "FC test that uses cluster analysis and pattern recognition to set cut off limits that are derived directly from intrareplicate variance. It provides the same consistency as fold testing in cross platform analysis and has lower FP and FN rates than standard fold testing. It provides a null value based on initial condition replicates and gives error bounds for results to allow better evaluation of significance.", "sc:name": "ELBOW", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ELBOW.html", "sc:version": "1.10.0" diff --git a/data/elemcor/elemcorbioschemas.jsonld b/data/elemcor/elemcorbioschemas.jsonld index aded7439761bc..99046c294b3e6 100644 --- a/data/elemcor/elemcorbioschemas.jsonld +++ b/data/elemcor/elemcorbioschemas.jsonld @@ -26,22 +26,22 @@ ], "sc:description": "Software tool to correct LC-MS data in isotope labeling experiments.", "sc:featureList": [ - { - "@id": "edam:operation_3632" - }, { "@id": "edam:operation_3638" }, { "@id": "edam:operation_3629" + }, + { + "@id": "edam:operation_3632" } ], "sc:license": "MIT", "sc:name": "ElemCor", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/4dsoftware/elemcor" }, diff --git a/data/elixir_elearning_portal/elixir_elearning_portalbioschemas.jsonld b/data/elixir_elearning_portal/elixir_elearning_portalbioschemas.jsonld index 67597164f52dd..9a81d3324678a 100644 --- a/data/elixir_elearning_portal/elixir_elearning_portalbioschemas.jsonld +++ b/data/elixir_elearning_portal/elixir_elearning_portalbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "ELIXIR eLearning Portal", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "University of Ljubljana, Faculty of Medicine", "sc:url": "https://elixir.mf.uni-lj.si", diff --git a/data/elm/elmbioschemas.jsonld b/data/elm/elmbioschemas.jsonld index c243a1aea32cb..27741be6c6404 100644 --- a/data/elm/elmbioschemas.jsonld +++ b/data/elm/elmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.", "sc:name": "Eukaryotic linear motif resource (ELM)", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://elm.eu.org/" } \ No newline at end of file diff --git a/data/elmer/elmerbioschemas.jsonld b/data/elmer/elmerbioschemas.jsonld index 044d43add680b..d48f9644abe05 100644 --- a/data/elmer/elmerbioschemas.jsonld +++ b/data/elmer/elmerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "ELMER", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ELMER.html", "sc:version": "1.4.0" diff --git a/data/elminstancemapper/elminstancemapperbioschemas.jsonld b/data/elminstancemapper/elminstancemapperbioschemas.jsonld index 06e648cdf8374..1a75da2735ac7 100644 --- a/data/elminstancemapper/elminstancemapperbioschemas.jsonld +++ b/data/elminstancemapper/elminstancemapperbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Map ELM predictions of a query sequence to known annotated ELM instances.", "sc:name": "ELMInstanceMapper", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://api.bioinfo.no/wsdl/ELMInstanceMapper.wsdl", "sc:version": "1" diff --git a/data/elmmatcher/elmmatcherbioschemas.jsonld b/data/elmmatcher/elmmatcherbioschemas.jsonld index 8174c1019d057..1b47e726126fb 100644 --- a/data/elmmatcher/elmmatcherbioschemas.jsonld +++ b/data/elmmatcher/elmmatcherbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Mapping of ELM (Eucaryotic Linear Motifs) motifs to a query sequence.", "sc:name": "ELMMatcher", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://api.bioinfo.no/wsdl/ELMMatcher.wsdl", "sc:version": "1" diff --git a/data/elmmo/elmmobioschemas.jsonld b/data/elmmo/elmmobioschemas.jsonld index 0c820e5c4d1e8..b41f5cfcf0777 100644 --- a/data/elmmo/elmmobioschemas.jsonld +++ b/data/elmmo/elmmobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mihaela Zavolan", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:description": "A website to browse miRNA target predictions from the ElMMo algorithm", "sc:name": "ElMMo", diff --git a/data/elnemo/elnemobioschemas.jsonld b/data/elnemo/elnemobioschemas.jsonld index c2e538f344bea..06a5fadf83777 100644 --- a/data/elnemo/elnemobioschemas.jsonld +++ b/data/elnemo/elnemobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "ElNemo", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.sciences.univ-nantes.fr/elnemo/" } \ No newline at end of file diff --git a/data/elochoice/elochoicebioschemas.jsonld b/data/elochoice/elochoicebioschemas.jsonld index b2112587f3c1b..2f2359e530172 100644 --- a/data/elochoice/elochoicebioschemas.jsonld +++ b/data/elochoice/elochoicebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "EloChoice", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/EloChoice/index.html" } \ No newline at end of file diff --git a/data/elviz/elvizbioschemas.jsonld b/data/elviz/elvizbioschemas.jsonld index e1a3a4b54e77c..306da9a77a7c4 100644 --- a/data/elviz/elvizbioschemas.jsonld +++ b/data/elviz/elvizbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-015-0566-4", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/elviz", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact form (Comments / Questions)", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4432942", - "pubmed:25928663", { "@id": "https://doi.org/10.1186/S12859-015-0566-4" - } + }, + "pubmed:25928663", + "pmcid:PMC4432942" ], "sc:description": "Exploration of metagenome assemblies with an interactive visualization tool", "sc:featureList": { @@ -28,14 +32,10 @@ "sc:name": "Elviz", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://genome.jgi.doe.gov/viz/" - }, - { - "@id": "https://doi.org/10.1186/S12859-015-0566-4", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/emage/emagebioschemas.jsonld b/data/emage/emagebioschemas.jsonld index dc642c4e5cc9b..df120b47b5b37 100644 --- a/data/emage/emagebioschemas.jsonld +++ b/data/emage/emagebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages, allowing data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, data can be queried using text-based methods. Data coverage has been increased by sourcing from a greater selection of journals.", "sc:name": "EMAGE", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.emouseatlas.org/emage/" } \ No newline at end of file diff --git a/data/emap/emapbioschemas.jsonld b/data/emap/emapbioschemas.jsonld index 5a963ecab26a3..ae5a7f968a276 100644 --- a/data/emap/emapbioschemas.jsonld +++ b/data/emap/emapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Edinburgh Mouse Atlas EMAP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "Edinburgh University", "sc:url": "http://www.emouseatlas.org/emap/home.html" diff --git a/data/emase/emasebioschemas.jsonld b/data/emase/emasebioschemas.jsonld index 819786811dc3a..31555edc28ace 100644 --- a/data/emase/emasebioschemas.jsonld +++ b/data/emase/emasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "EMASE", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/churchill-lab/emase" } \ No newline at end of file diff --git a/data/ematchsite/ematchsitebioschemas.jsonld b/data/ematchsite/ematchsitebioschemas.jsonld index fd762073fefc0..a217101a3159c 100644 --- a/data/ematchsite/ematchsitebioschemas.jsonld +++ b/data/ematchsite/ematchsitebioschemas.jsonld @@ -22,8 +22,8 @@ "Web application" ], "sc:citation": [ - "pubmed:25232727", "pmcid:PMC4168975", + "pubmed:25232727", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003829" } diff --git a/data/embedsom/embedsombioschemas.jsonld b/data/embedsom/embedsombioschemas.jsonld index 81f78dfd8685d..cf8904cd4cae4 100644 --- a/data/embedsom/embedsombioschemas.jsonld +++ b/data/embedsom/embedsombioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "EmbedSOM", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioinfo.uochb.cas.cz/embedsom/", "sc:version": "2.1" diff --git a/data/embl2checklists/embl2checklistsbioschemas.jsonld b/data/embl2checklists/embl2checklistsbioschemas.jsonld index 7196bd9989d5d..3a4b1a6638385 100644 --- a/data/embl2checklists/embl2checklistsbioschemas.jsonld +++ b/data/embl2checklists/embl2checklistsbioschemas.jsonld @@ -23,10 +23,10 @@ ], "sc:citation": [ "pmcid:PMC6328100", - "pubmed:30629718", { "@id": "https://doi.org/10.1371/journal.pone.0210347" - } + }, + "pubmed:30629718" ], "sc:description": "Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA. Converts EMBL- or GenBank-formatted flat files to submission-ready checklists for submission to ENA via the interactive Webin submission system.", "sc:featureList": [ @@ -43,9 +43,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "EMBL2checklists", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/michaelgruenstaeudl/EMBL2checklists" } diff --git a/data/emblmygff3/emblmygff3bioschemas.jsonld b/data/emblmygff3/emblmygff3bioschemas.jsonld index a1b8f4f9fed5c..65c5a85483c64 100644 --- a/data/emblmygff3/emblmygff3bioschemas.jsonld +++ b/data/emblmygff3/emblmygff3bioschemas.jsonld @@ -16,13 +16,13 @@ "sc:license": "GPL-3.0", "sc:name": "EMBLmyGFF3", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/NBISweden/EMBLmyGFF3", "sc:version": [ - "1.2.8", "1.2.6", + "1.2.8", "1.3" ] } \ No newline at end of file diff --git a/data/emboss/embossbioschemas.jsonld b/data/emboss/embossbioschemas.jsonld index 7f2bec3d6c401..2d6df9303c404 100644 --- a/data/emboss/embossbioschemas.jsonld +++ b/data/emboss/embossbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Peter Rice", "sc:additionalType": [ - "Suite", - "Web application" + "Web application", + "Suite" ], "sc:citation": "pubmed:10827456", "sc:description": "Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.", "sc:name": "EMBOSS", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://emboss.bioinformatics.nl/" } \ No newline at end of file diff --git a/data/embossdata/embossdatabioschemas.jsonld b/data/embossdata/embossdatabioschemas.jsonld index 93c33b06a9eef..a304d35ceff48 100644 --- a/data/embossdata/embossdatabioschemas.jsonld +++ b/data/embossdata/embossdatabioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "Wellcome Trust", + "EMBOSS Contributors", "UK MRC", - "EMBOSS Contributors" + "UK BBSRC", + "Wellcome Trust" ], "sc:description": "Find and retrieve EMBOSS db data files.", "sc:funder": [ + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "embossdata", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/embossdata.html", "sc:version": "r6" diff --git a/data/embossupdate/embossupdatebioschemas.jsonld b/data/embossupdate/embossupdatebioschemas.jsonld index 814ce68d23952..1709ac940210e 100644 --- a/data/embossupdate/embossupdatebioschemas.jsonld +++ b/data/embossupdate/embossupdatebioschemas.jsonld @@ -13,9 +13,9 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", + "UK BBSRC", "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK MRC" ], "sc:description": "Check for more recent updates to EMBOSS.", "sc:funder": [ @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "embossupdate", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/embossversion/embossversionbioschemas.jsonld b/data/embossversion/embossversionbioschemas.jsonld index 3f0b1c9a2e389..17f3860ec7387 100644 --- a/data/embossversion/embossversionbioschemas.jsonld +++ b/data/embossversion/embossversionbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "Wellcome Trust", + "EMBOSS Contributors", "UK BBSRC", - "EMBOSS Contributors" + "Wellcome Trust", + "UK MRC" ], "sc:description": "Report the current EMBOSS db version number.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", + "UK BBSRC", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "embossversion", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/embossversion.html", "sc:version": "r6" diff --git a/data/emdb/emdbbioschemas.jsonld b/data/emdb/emdbbioschemas.jsonld index 0c866ac56c1a8..442520fb05d3c 100644 --- a/data/emdb/emdbbioschemas.jsonld +++ b/data/emdb/emdbbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "EMDB", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.ebi.ac.uk/pdbe/emdb/" } \ No newline at end of file diff --git a/data/emdomics/emdomicsbioschemas.jsonld b/data/emdomics/emdomicsbioschemas.jsonld index 11e00f36936e4..9f61836d44a1f 100644 --- a/data/emdomics/emdomicsbioschemas.jsonld +++ b/data/emdomics/emdomicsbioschemas.jsonld @@ -15,16 +15,16 @@ "Daniel Schmolze" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Algorithm used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Traditional methods use significance tests based on summary statistics of the distributions. This approach lacks power to identify differences between groups with high levels of intra-group heterogeneity. The algorithm transforms one distribution into another, providing the overall difference in shape between two distributions.", "sc:license": "MIT", "sc:name": "EMDomics", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EMDomics.html", "sc:version": "2.4.0" diff --git a/data/emhp/emhpbioschemas.jsonld b/data/emhp/emhpbioschemas.jsonld index 295547f15140e..2a9b28a768081 100644 --- a/data/emhp/emhpbioschemas.jsonld +++ b/data/emhp/emhpbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Accurate automated hole masking algorithm for single-particle cryo-EM image processing.", "sc:name": "EMHP", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://bitbucket.org/chazbot/emhp" } \ No newline at end of file diff --git a/data/emma/emmabioschemas.jsonld b/data/emma/emmabioschemas.jsonld index f35dd6db94274..91b5db11730b9 100644 --- a/data/emma/emmabioschemas.jsonld +++ b/data/emma/emmabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK BBSRC", "Wellcome Trust", - "UK MRC" + "UK MRC", + "EMBOSS Contributors" ], "sc:description": "Multiple sequence alignment (ClustalW wrapper).", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "emma", @@ -31,8 +31,8 @@ "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/emma.html", "sc:version": "r6" diff --git a/data/emma2/emma2bioschemas.jsonld b/data/emma2/emma2bioschemas.jsonld index b4a95ca1c4f3c..bdb097bd3b0b6 100644 --- a/data/emma2/emma2bioschemas.jsonld +++ b/data/emma2/emma2bioschemas.jsonld @@ -15,13 +15,13 @@ "sc:license": "LGPL-2.1", "sc:name": "EMMA2", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ - "Bielefeld University", "bigi", + "Bielefeld University", "CeBiTec" ], "sc:url": "http://emma.cebitec.uni-bielefeld.de", diff --git a/data/emma2_ws/emma2_wsbioschemas.jsonld b/data/emma2_ws/emma2_wsbioschemas.jsonld index 2d3691994a27b..1d86a983f814a 100644 --- a/data/emma2_ws/emma2_wsbioschemas.jsonld +++ b/data/emma2_ws/emma2_wsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A MAGE-compliant system for the collaborative analysis and integration of microarray data.", "sc:name": "EMMA2 WS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://wiki.cebitec.uni-bielefeld.de/brf-software/index.php/UsingTheWSInterface", "sc:version": "1" diff --git a/data/emmax/emmaxbioschemas.jsonld b/data/emmax/emmaxbioschemas.jsonld index 7c8236a3bb4fb..3a305c07bb574 100644 --- a/data/emmax/emmaxbioschemas.jsonld +++ b/data/emmax/emmaxbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/ng.548", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/emmax", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:20208533", + "pmcid:PMC3092069", { "@id": "https://doi.org/10.1038/ng.548" - }, - "pmcid:PMC3092069" + } ], "sc:description": "Efficient Mixed-Model Association eXpedited is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the efficiency obtained by the EMMA algorithm, EMMAX takes advantage of the fact that each locus explains only a small fraction of complex traits allowing the avoidance of repetitive variance component estimation procedures.", "sc:featureList": { @@ -32,6 +28,10 @@ "sc:name": "EMMAX", "sc:operatingSystem": "Linux", "sc:url": "http://genetics.cs.ucla.edu/emmax/" + }, + { + "@id": "https://doi.org/10.1038/ng.548", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/emowse/emowsebioschemas.jsonld b/data/emowse/emowsebioschemas.jsonld index 97bafc4efcf4c..edb08c44066a6 100644 --- a/data/emowse/emowsebioschemas.jsonld +++ b/data/emowse/emowsebioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "Wellcome Trust", + "EMBOSS Contributors", "UK MRC", - "EMBOSS Contributors" + "UK BBSRC", + "Wellcome Trust" ], "sc:description": "Search protein sequences by digest fragment molecular weight.", "sc:funder": [ - "Wellcome Trust", "UK MRC", + "Wellcome Trust", "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "emowse", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/emowse.html", "sc:version": "r6" diff --git a/data/empiricalbrownsmethod/empiricalbrownsmethodbioschemas.jsonld b/data/empiricalbrownsmethod/empiricalbrownsmethodbioschemas.jsonld index 82b062ba35289..ecfbdf2a9add5 100644 --- a/data/empiricalbrownsmethod/empiricalbrownsmethodbioschemas.jsonld +++ b/data/empiricalbrownsmethod/empiricalbrownsmethodbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David Gibbs", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.", "sc:license": "MIT", "sc:name": "EmpiricalBrownsMethod", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EmpiricalBrownsMethod.html", diff --git a/data/empprior/emppriorbioschemas.jsonld b/data/empprior/emppriorbioschemas.jsonld index c0bd7884647ef..7c69f31e5d8a6 100644 --- a/data/empprior/emppriorbioschemas.jsonld +++ b/data/empprior/emppriorbioschemas.jsonld @@ -9,30 +9,22 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-1447-8633", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1132-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/empprior", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "John J. Andersen", { "@id": "http://orcid.org/0000-0002-1447-8633" - }, - "John J. Andersen" + } ], "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:27342194", - "pmcid:PMC4919878", { "@id": "https://doi.org/10.1186/s12859-016-1132-4" - } + }, + "pubmed:27342194", + "pmcid:PMC4919878" ], "sc:description": "EmpPrior facilitates the collection and incorporation of relevant, outside information when setting branch-length priors for phylogenetics.", "sc:featureList": { @@ -47,6 +39,14 @@ ], "sc:url": "https://github.com/jembrown/EmpPrior", "sc:version": "0.21" + }, + { + "@id": "https://doi.org/10.1186/s12859-016-1132-4", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-1447-8633", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/empusa/empusabioschemas.jsonld b/data/empusa/empusabioschemas.jsonld index b1b6a55f22ee6..d8c6acc0fff6e 100644 --- a/data/empusa/empusabioschemas.jsonld +++ b/data/empusa/empusabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-9395-5559", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/empusa", "@type": "sc:SoftwareApplication", @@ -23,8 +27,8 @@ "sc:license": "MIT", "sc:name": "Empusa", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://empusa.org", "sc:version": "1" @@ -32,10 +36,6 @@ { "@id": "https://orcid.org/0000-0001-8172-8981", "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0001-9395-5559", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/emvclass/emvclassbioschemas.jsonld b/data/emvclass/emvclassbioschemas.jsonld index d9cc97bd755af..398d5d18057f4 100644 --- a/data/emvclass/emvclassbioschemas.jsonld +++ b/data/emvclass/emvclassbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/emvclass", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": "pubmed:23757202", "sc:description": "Emory Genetics Laboratory's (EGL) Variant Classification Catalog contains variants of the gene of interest that has been seen and analysed by EGL Genetics.", "sc:name": "EmVClass", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://www.egl-eurofins.com/emvclass/emvclass.php" } \ No newline at end of file diff --git a/data/ena/enabioschemas.jsonld b/data/ena/enabioschemas.jsonld index 7b83b0f5de564..4ae65a4c31a73 100644 --- a/data/ena/enabioschemas.jsonld +++ b/data/ena/enabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "A globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data.", "sc:name": "European Nucleotide Archive (ENA)", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ebi.ac.uk/ena" diff --git a/data/encodexplorer/bioconda_encodexplorer.yaml b/data/encodexplorer/bioconda_encodexplorer.yaml index a5af9acf85e81..1b6b58d0356a9 100644 --- a/data/encodexplorer/bioconda_encodexplorer.yaml +++ b/data/encodexplorer/bioconda_encodexplorer.yaml @@ -5,7 +5,6 @@ description: This package allows user to quickly access ENCODE project files met home: https://bioconductor.org/packages/3.10/bioc/html/ENCODExplorer.html identifiers: - biotools:encodexplorer -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-encodexplorer summary: A compilation of ENCODE metadata diff --git a/data/encodexplorer/encodexplorerbioschemas.jsonld b/data/encodexplorer/encodexplorerbioschemas.jsonld index c6e84e272ae43..68168cb7cb758 100644 --- a/data/encodexplorer/encodexplorerbioschemas.jsonld +++ b/data/encodexplorer/encodexplorerbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Charles Joly Beauparlant", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.", "sc:license": "Artistic-2.0", diff --git a/data/encyclopedia/encyclopediabioschemas.jsonld b/data/encyclopedia/encyclopediabioschemas.jsonld index 598dcdd7fa8a2..f84178d0d4880 100644 --- a/data/encyclopedia/encyclopediabioschemas.jsonld +++ b/data/encyclopedia/encyclopediabioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "EncyclopeDIA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://bitbucket.org/searleb/encyclopedia/", "sc:version": "0.8.1" diff --git a/data/endeavour/endeavourbioschemas.jsonld b/data/endeavour/endeavourbioschemas.jsonld index 99659c516e3a9..796f2ca4c559b 100644 --- a/data/endeavour/endeavourbioschemas.jsonld +++ b/data/endeavour/endeavourbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.", "sc:name": "ENDEAVOUR", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://endeavour.esat.kuleuven.be/" diff --git a/data/enetxplorer/enetxplorerbioschemas.jsonld b/data/enetxplorer/enetxplorerbioschemas.jsonld index ffa2e3c2588ee..200ea45a81585 100644 --- a/data/enetxplorer/enetxplorerbioschemas.jsonld +++ b/data/enetxplorer/enetxplorerbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2778-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/eNetXplorer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Julian Candia", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:30991955", - "pmcid:PMC6469092", { "@id": "https://doi.org/10.1186/s12859-019-2778-5" - } + }, + "pmcid:PMC6469092", + "pubmed:30991955" ], "sc:description": "R package for the quantitative exploration of elastic net families for generalized linear models.", "sc:featureList": [ @@ -37,12 +33,16 @@ "sc:license": "GPL-3.0", "sc:name": "eNetXplorer", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/package=eNetXplorer", "sc:version": "1.0.2" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2778-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/enhancerdb/enhancerdbbioschemas.jsonld b/data/enhancerdb/enhancerdbbioschemas.jsonld index 5c9f7fbb236be..00cf92b42d9bb 100644 --- a/data/enhancerdb/enhancerdbbioschemas.jsonld +++ b/data/enhancerdb/enhancerdbbioschemas.jsonld @@ -9,32 +9,36 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/database/bay141", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/EnhancerDB", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Z. Guo", "sc:additionalType": [ - "Database portal", "Web API", + "Database portal", "Web application" ], "sc:citation": [ - "pmcid:PMC6344666", "pubmed:30689845", { "@id": "https://doi.org/10.1093/database/bay141" - } + }, + "pmcid:PMC6344666" ], "sc:description": "Database to discover the regulate relationships in the context of enhancers.", "sc:featureList": [ { - "@id": "edam:operation_3792" + "@id": "edam:operation_3232" }, { "@id": "edam:operation_0441" }, { - "@id": "edam:operation_3232" + "@id": "edam:operation_3792" } ], "sc:name": "EnhancerDB", @@ -44,10 +48,6 @@ "Windows" ], "sc:url": "http://lcbb.swjtu.edu.cn/EnhancerDB/" - }, - { - "@id": "https://doi.org/10.1093/database/bay141", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/enigma/enigmabioschemas.jsonld b/data/enigma/enigmabioschemas.jsonld index b55c9173d72c5..1574103c7efcc 100644 --- a/data/enigma/enigmabioschemas.jsonld +++ b/data/enigma/enigmabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering.", "sc:name": "Enigma", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "PSB", "sc:url": "http://bioinformatics.psb.ugent.be/ENIGMA/", diff --git a/data/enimpute/enimputebioschemas.jsonld b/data/enimpute/enimputebioschemas.jsonld index 4c4e1fdb6f43c..7ee6472e03a01 100644 --- a/data/enimpute/enimputebioschemas.jsonld +++ b/data/enimpute/enimputebioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "EnImpute", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/Zhangxf-ccnu/EnImpute" } \ No newline at end of file diff --git a/data/enly/enlybioschemas.jsonld b/data/enly/enlybioschemas.jsonld index 1f407e6cafe6a..eb3de6f2ba572 100644 --- a/data/enly/enlybioschemas.jsonld +++ b/data/enly/enlybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Simple tool based on the iterative mapping of sequence reads at contig edges, capable to extend the genomic contigs deriving from high-throughput sequencing, especially those deriving by Newbler-like assemblies. Testing it on a set of de novo draft genomes led to the closure of up to 20% of the gaps originally present. It is cross-platform and most of the steps of its pipeline are parallelizable, making easy and fast to improve a draft genome resulting from a de novo assembly.", "sc:name": "Enly", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-FIRENZE", "sc:url": "http://enly.sourceforge.net/", diff --git a/data/enmix/enmixbioschemas.jsonld b/data/enmix/enmixbioschemas.jsonld index 5b2ddd8c90f3b..ea247042af2b1 100644 --- a/data/enmix/enmixbioschemas.jsonld +++ b/data/enmix/enmixbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12864-016-3426-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/enmix", "@type": "sc:SoftwareApplication", @@ -24,13 +20,13 @@ }, "edam:has_output": [ { - "@id": "edam:data_3117" + "@id": "edam:data_2884" }, { "@id": "edam:data_2048" }, { - "@id": "edam:data_2884" + "@id": "edam:data_3117" } ], "sc:additionalType": [ @@ -39,21 +35,21 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3572" + "@id": "edam:topic_3518" }, { "@id": "edam:topic_3295" }, { - "@id": "edam:topic_3518" + "@id": "edam:topic_3572" } ], "sc:citation": [ - "pubmed:28049437", - "pmcid:PMC5209853", { "@id": "https://doi.org/10.1186/s12864-016-3426-3" - } + }, + "pmcid:PMC5209853", + "pubmed:28049437" ], "sc:description": "This package provides an efficient data pre-processing tool designed to reduce background noise and improve signal for DNA methylation estimation from Illumina Methylation BeadChip array measurements. It is a model based background correction method that can significantly improve accuracy and reproducibility of methylation measures.", "sc:featureList": [ @@ -68,12 +64,16 @@ "sc:name": "ENmix", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ENmix.html", "sc:version": "1.10.0" }, + { + "@id": "https://doi.org/10.1186/s12864-016-3426-3", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0002-9034-8902", "@type": "schema:Person" diff --git a/data/enrichedheatmap/enrichedheatmapbioschemas.jsonld b/data/enrichedheatmap/enrichedheatmapbioschemas.jsonld index b502b44d3a13d..f8f71fea051c6 100644 --- a/data/enrichedheatmap/enrichedheatmapbioschemas.jsonld +++ b/data/enrichedheatmap/enrichedheatmapbioschemas.jsonld @@ -18,38 +18,38 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Zuguang Gu", "edam:has_input": [ - { - "@id": "edam:data_1017" - }, { "@id": "edam:data_2603" }, { "@id": "edam:data_1276" + }, + { + "@id": "edam:data_1017" } ], "edam:has_output": { "@id": "edam:data_1636" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3511" + "@id": "edam:topic_0092" }, { - "@id": "edam:topic_0092" + "@id": "edam:topic_3511" } ], "sc:author": "Zuguang Gu", "sc:citation": [ "pubmed:29618320", + "pmcid:PMC5885322", { "@id": "https://doi.org/10.1186/s12864-018-4625-x" - }, - "pmcid:PMC5885322" + } ], "sc:description": "Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement Enriched heatmap by ComplexHeatmap package.", "sc:featureList": { @@ -59,8 +59,8 @@ "sc:name": "EnrichedHeatmap", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EnrichedHeatmap.html", "sc:version": "1.12.0" diff --git a/data/enrichment/enrichmentbioschemas.jsonld b/data/enrichment/enrichmentbioschemas.jsonld index d1fe4d81f52d3..01514212b0f21 100644 --- a/data/enrichment/enrichmentbioschemas.jsonld +++ b/data/enrichment/enrichmentbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A Python library providing two methods to perform enrichment analysis, such as gene set enrichment analysis in bioinformatics.", "sc:name": "enrichment", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/ajmazurie/xstats.enrichment", "sc:version": "1.0b" diff --git a/data/enrichmentbrowser/enrichmentbrowserbioschemas.jsonld b/data/enrichmentbrowser/enrichmentbrowserbioschemas.jsonld index b54de247ef332..e2acd10cd72f5 100644 --- a/data/enrichmentbrowser/enrichmentbrowserbioschemas.jsonld +++ b/data/enrichmentbrowser/enrichmentbrowserbioschemas.jsonld @@ -23,8 +23,8 @@ "Library" ], "sc:citation": [ - "pubmed:28448473", "pmcid:PMC5454835", + "pubmed:28448473", { "@id": "https://doi.org/10.3390/ijms18050922" } @@ -48,13 +48,13 @@ "sc:url": "http://bioconductor.org/packages/release/bioc/html/EnrichmentBrowser.html", "sc:version": "2.4.5" }, - { - "@id": "http://orcid.org/0000-0002-0429-3846", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.3390/ijms18050922", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-0429-3846", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/enrichmentmap/enrichmentmapbioschemas.jsonld b/data/enrichmentmap/enrichmentmapbioschemas.jsonld index 247f84e2f54a0..8fc7a346270c9 100644 --- a/data/enrichmentmap/enrichmentmapbioschemas.jsonld +++ b/data/enrichmentmap/enrichmentmapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A Cytoscape plugin for functional enrichment visualization. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the \"\"enrichment map\"\"). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. It also enables the comparison of two different enrichment results in the same map.", "sc:name": "Enrichment Map Cytoscape Plugin", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://baderlab.org/Software/EnrichmentMap" } \ No newline at end of file diff --git a/data/enrichnet/enrichnetbioschemas.jsonld b/data/enrichnet/enrichnetbioschemas.jsonld index 5a9df2bb5f128..cbc589eba4b1f 100644 --- a/data/enrichnet/enrichnetbioschemas.jsonld +++ b/data/enrichnet/enrichnetbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-3977-7469", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/bioinformatics/bts389", "@type": "sc:CreativeWork" @@ -21,33 +25,33 @@ }, "edam:has_input": [ { - "@id": "edam:data_1033" + "@id": "edam:data_3021" }, { - "@id": "edam:data_3021" + "@id": "edam:data_1033" } ], "edam:has_output": { "@id": "edam:data_2600" }, "sc:additionalType": [ - "Web API", - "Web application" + "Web application", + "Web API" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0121" + "@id": "edam:topic_3308" }, { - "@id": "edam:topic_3308" + "@id": "edam:topic_0121" } ], "sc:citation": [ { "@id": "https://doi.org/10.1093/bioinformatics/bts389" }, - "pmcid:PMC3436816", - "pubmed:22962466" + "pubmed:22962466", + "pmcid:PMC3436816" ], "sc:description": "Network-based enrichment analysis", "sc:featureList": { @@ -69,10 +73,6 @@ }, "sc:url": "http://www.enrichnet.org/", "sc:version": "1.1" - }, - { - "@id": "http://orcid.org/0000-0003-3977-7469", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/enrichplot/enrichplotbioschemas.jsonld b/data/enrichplot/enrichplotbioschemas.jsonld index 4f5b08a2f69c4..c47bd1acfcc84 100644 --- a/data/enrichplot/enrichplotbioschemas.jsonld +++ b/data/enrichplot/enrichplotbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "enrichplot", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/enrichplot.html", diff --git a/data/enrichr/enrichrbioschemas.jsonld b/data/enrichr/enrichrbioschemas.jsonld index b8463f3384f4e..55f7864a9733d 100644 --- a/data/enrichr/enrichrbioschemas.jsonld +++ b/data/enrichr/enrichrbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Integrative web-based and mobile gene-list enrichment analysis tool that includes over 30 gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library Data Driven Documents (D3).", "sc:name": "Enrichr", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://amp.pharm.mssm.edu/Enrichr/" } \ No newline at end of file diff --git a/data/ensembl/ensemblbioschemas.jsonld b/data/ensembl/ensemblbioschemas.jsonld index b5924073b9526..224f0de82bd75 100644 --- a/data/ensembl/ensemblbioschemas.jsonld +++ b/data/ensembl/ensemblbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "Ensembl", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "EMBL-EBI Databases", "sc:url": "http://www.ensembl.org/" diff --git a/data/ensembl_api/ensembl_apibioschemas.jsonld b/data/ensembl_api/ensembl_apibioschemas.jsonld index 6f0436ab4625c..efd615c717918 100644 --- a/data/ensembl_api/ensembl_apibioschemas.jsonld +++ b/data/ensembl_api/ensembl_apibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Test: convert json OpenAPI to json Biotools", "sc:name": "Ensembl APl", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://bigcat-um.github.io/EnsemblOpenAPI/" diff --git a/data/ensembl_compara/ensembl_comparabioschemas.jsonld b/data/ensembl_compara/ensembl_comparabioschemas.jsonld index 14516ace2f1ce..bc603aaddf591 100644 --- a/data/ensembl_compara/ensembl_comparabioschemas.jsonld +++ b/data/ensembl_compara/ensembl_comparabioschemas.jsonld @@ -11,21 +11,21 @@ "@id": "https://bio.tools/Ensembl_Compara", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web service", + "Web API", "Database portal", - "Web API" + "Web service" ], "sc:description": "Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.", "sc:license": "Unlicense", "sc:name": "Ensembl Compara", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ensembl.org/info/genome/compara/index.html", "sc:version": [ - "e81", - "e56" + "e56", + "e81" ] } \ No newline at end of file diff --git a/data/ensembl_drosophila_genome_browser/ensembl_drosophila_genome_browserbioschemas.jsonld b/data/ensembl_drosophila_genome_browser/ensembl_drosophila_genome_browserbioschemas.jsonld index 173d080a7e6e9..8c101b06da756 100644 --- a/data/ensembl_drosophila_genome_browser/ensembl_drosophila_genome_browserbioschemas.jsonld +++ b/data/ensembl_drosophila_genome_browser/ensembl_drosophila_genome_browserbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).", "sc:name": "Ensembl Drosophila Genome Browser", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ensembl.org/Drosophila_melanogaster/" } \ No newline at end of file diff --git a/data/ensembl_fugu_genome_browser/ensembl_fugu_genome_browserbioschemas.jsonld b/data/ensembl_fugu_genome_browser/ensembl_fugu_genome_browserbioschemas.jsonld index fdac3adbcae77..17e167c9b325b 100644 --- a/data/ensembl_fugu_genome_browser/ensembl_fugu_genome_browserbioschemas.jsonld +++ b/data/ensembl_fugu_genome_browser/ensembl_fugu_genome_browserbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Ensembl Fugu Genome Browser", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ensembl.org/Takifugu_rubripes/Info/Index" } \ No newline at end of file diff --git a/data/ensembl_genomes/ensembl_genomesbioschemas.jsonld b/data/ensembl_genomes/ensembl_genomesbioschemas.jsonld index b11f81e16f058..b62b2c7ad2062 100644 --- a/data/ensembl_genomes/ensembl_genomesbioschemas.jsonld +++ b/data/ensembl_genomes/ensembl_genomesbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Ensembl Genomes", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI Databases", "sc:url": "http://www.ensemblgenomes.org/" diff --git a/data/ensembl_genomes_bacteria_blast/ensembl_genomes_bacteria_blastbioschemas.jsonld b/data/ensembl_genomes_bacteria_blast/ensembl_genomes_bacteria_blastbioschemas.jsonld index ff9ba8b9c1feb..c491860030609 100644 --- a/data/ensembl_genomes_bacteria_blast/ensembl_genomes_bacteria_blastbioschemas.jsonld +++ b/data/ensembl_genomes_bacteria_blast/ensembl_genomes_bacteria_blastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Searches Ensembl Bacteria sequences using WU-BLAST.", "sc:name": "Ensembl Genomes Bacteria Blast", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://bacteria.ensembl.org/Multi/blastview", diff --git a/data/ensembl_genomes_bacteria_id_history_converter/ensembl_genomes_bacteria_id_history_converterbioschemas.jsonld b/data/ensembl_genomes_bacteria_id_history_converter/ensembl_genomes_bacteria_id_history_converterbioschemas.jsonld index 3b29d3def795c..50fdd26cadfd7 100644 --- a/data/ensembl_genomes_bacteria_id_history_converter/ensembl_genomes_bacteria_id_history_converterbioschemas.jsonld +++ b/data/ensembl_genomes_bacteria_id_history_converter/ensembl_genomes_bacteria_id_history_converterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Convert a set of Ensembl IDs from a previous release into their current equivalents.", "sc:name": "Ensembl Genomes Bacteria ID history converter", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://bacteria.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_bacteria_sequence_search/ensembl_genomes_bacteria_sequence_searchbioschemas.jsonld b/data/ensembl_genomes_bacteria_sequence_search/ensembl_genomes_bacteria_sequence_searchbioschemas.jsonld index 375adb6365d1c..de32018567848 100644 --- a/data/ensembl_genomes_bacteria_sequence_search/ensembl_genomes_bacteria_sequence_searchbioschemas.jsonld +++ b/data/ensembl_genomes_bacteria_sequence_search/ensembl_genomes_bacteria_sequence_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Searches Ensembl Bacteria sequences using Exonerate.", "sc:name": "Ensembl Genomes Bacteria sequence search", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://bacteria.ensembl.org/Multi/enasearch", diff --git a/data/ensembl_genomes_fungi_assembly_converter/ensembl_genomes_fungi_assembly_converterbioschemas.jsonld b/data/ensembl_genomes_fungi_assembly_converter/ensembl_genomes_fungi_assembly_converterbioschemas.jsonld index 7a7f19b6e4d12..1b82712d8f96f 100644 --- a/data/ensembl_genomes_fungi_assembly_converter/ensembl_genomes_fungi_assembly_converterbioschemas.jsonld +++ b/data/ensembl_genomes_fungi_assembly_converter/ensembl_genomes_fungi_assembly_converterbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Ensembl Genomes Fungi assembly converter", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://fungi.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_fungi_blast/ensembl_genomes_fungi_blastbioschemas.jsonld b/data/ensembl_genomes_fungi_blast/ensembl_genomes_fungi_blastbioschemas.jsonld index 22cb78ad76322..7682455a933b3 100644 --- a/data/ensembl_genomes_fungi_blast/ensembl_genomes_fungi_blastbioschemas.jsonld +++ b/data/ensembl_genomes_fungi_blast/ensembl_genomes_fungi_blastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Searches Ensembl Fungi sequences using Exonerate.", "sc:name": "Ensembl Genomes Fungi Blast", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://fungi.ensembl.org/Multi/blastview", diff --git a/data/ensembl_genomes_fungi_data_slicer/ensembl_genomes_fungi_data_slicerbioschemas.jsonld b/data/ensembl_genomes_fungi_data_slicer/ensembl_genomes_fungi_data_slicerbioschemas.jsonld index bde03ff3019f4..23fed094e5f8e 100644 --- a/data/ensembl_genomes_fungi_data_slicer/ensembl_genomes_fungi_data_slicerbioschemas.jsonld +++ b/data/ensembl_genomes_fungi_data_slicer/ensembl_genomes_fungi_data_slicerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Get a subset of data from a BAM | VCF file.", "sc:name": "Ensembl Genomes Fungi data slicer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://fungi.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_fungi_id_history_converter/ensembl_genomes_fungi_id_history_converterbioschemas.jsonld b/data/ensembl_genomes_fungi_id_history_converter/ensembl_genomes_fungi_id_history_converterbioschemas.jsonld index c7ffb2684e50b..144243c697bfa 100644 --- a/data/ensembl_genomes_fungi_id_history_converter/ensembl_genomes_fungi_id_history_converterbioschemas.jsonld +++ b/data/ensembl_genomes_fungi_id_history_converter/ensembl_genomes_fungi_id_history_converterbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Ensembl Genomes Fungi ID history converter", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://fungi.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_fungi_sequence_search/ensembl_genomes_fungi_sequence_searchbioschemas.jsonld b/data/ensembl_genomes_fungi_sequence_search/ensembl_genomes_fungi_sequence_searchbioschemas.jsonld index 1784fd9d634bb..21deb714b08ff 100644 --- a/data/ensembl_genomes_fungi_sequence_search/ensembl_genomes_fungi_sequence_searchbioschemas.jsonld +++ b/data/ensembl_genomes_fungi_sequence_search/ensembl_genomes_fungi_sequence_searchbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Ensembl Genomes Fungi sequence search", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://fungi.ensembl.org/Multi/enasearch", diff --git a/data/ensembl_genomes_metazoa_data_slicer/ensembl_genomes_metazoa_data_slicerbioschemas.jsonld b/data/ensembl_genomes_metazoa_data_slicer/ensembl_genomes_metazoa_data_slicerbioschemas.jsonld index 8d9dfd6fe2240..182eea6f86ada 100644 --- a/data/ensembl_genomes_metazoa_data_slicer/ensembl_genomes_metazoa_data_slicerbioschemas.jsonld +++ b/data/ensembl_genomes_metazoa_data_slicer/ensembl_genomes_metazoa_data_slicerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Get a subset of data from a BAM | VCF file.", "sc:name": "Ensembl Genomes Metazoa data slicer", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://metazoa.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_metazoa_id_history_converter/ensembl_genomes_metazoa_id_history_converterbioschemas.jsonld b/data/ensembl_genomes_metazoa_id_history_converter/ensembl_genomes_metazoa_id_history_converterbioschemas.jsonld index dd1d7fa1073b6..9c6a29c51b114 100644 --- a/data/ensembl_genomes_metazoa_id_history_converter/ensembl_genomes_metazoa_id_history_converterbioschemas.jsonld +++ b/data/ensembl_genomes_metazoa_id_history_converter/ensembl_genomes_metazoa_id_history_converterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Convert a set of Ensembl IDs from a previous release into their current equivalents.", "sc:name": "Ensembl Genomes Metazoa ID history converter", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://metazoa.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_metazoa_sequence_search/ensembl_genomes_metazoa_sequence_searchbioschemas.jsonld b/data/ensembl_genomes_metazoa_sequence_search/ensembl_genomes_metazoa_sequence_searchbioschemas.jsonld index 0fe5c64008469..684d7596b2d58 100644 --- a/data/ensembl_genomes_metazoa_sequence_search/ensembl_genomes_metazoa_sequence_searchbioschemas.jsonld +++ b/data/ensembl_genomes_metazoa_sequence_search/ensembl_genomes_metazoa_sequence_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Searches Ensembl Metazoa sequences using Exonerate.", "sc:name": "Ensembl Genomes Metazoa sequence search", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://metazoa.ensembl.org/Multi/enasearch", diff --git a/data/ensembl_genomes_plants_blast/ensembl_genomes_plants_blastbioschemas.jsonld b/data/ensembl_genomes_plants_blast/ensembl_genomes_plants_blastbioschemas.jsonld index 89ae6974727f2..79ec7fb3d212b 100644 --- a/data/ensembl_genomes_plants_blast/ensembl_genomes_plants_blastbioschemas.jsonld +++ b/data/ensembl_genomes_plants_blast/ensembl_genomes_plants_blastbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Ensembl Genomes Plants Blast", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://plants.ensembl.org/Multi/blastview", diff --git a/data/ensembl_genomes_plants_data_slicer/ensembl_genomes_plants_data_slicerbioschemas.jsonld b/data/ensembl_genomes_plants_data_slicer/ensembl_genomes_plants_data_slicerbioschemas.jsonld index a0a070132d1d2..8f2af7644c488 100644 --- a/data/ensembl_genomes_plants_data_slicer/ensembl_genomes_plants_data_slicerbioschemas.jsonld +++ b/data/ensembl_genomes_plants_data_slicer/ensembl_genomes_plants_data_slicerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Get a subset of data from a BAM | VCF file.", "sc:name": "Ensembl Genomes Plants data slicer", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://plants.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_plants_id_history_converter/ensembl_genomes_plants_id_history_converterbioschemas.jsonld b/data/ensembl_genomes_plants_id_history_converter/ensembl_genomes_plants_id_history_converterbioschemas.jsonld index 0b01e8036f6e0..0e7d8c4c53259 100644 --- a/data/ensembl_genomes_plants_id_history_converter/ensembl_genomes_plants_id_history_converterbioschemas.jsonld +++ b/data/ensembl_genomes_plants_id_history_converter/ensembl_genomes_plants_id_history_converterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Convert a set of Ensembl IDs from a previous release into their current equivalents.", "sc:name": "Ensembl Genomes Plants ID history converter", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "EMBL-EBI", diff --git a/data/ensembl_genomes_plants_sequence_search/ensembl_genomes_plants_sequence_searchbioschemas.jsonld b/data/ensembl_genomes_plants_sequence_search/ensembl_genomes_plants_sequence_searchbioschemas.jsonld index 255a63ace5b07..b6bbef088a016 100644 --- a/data/ensembl_genomes_plants_sequence_search/ensembl_genomes_plants_sequence_searchbioschemas.jsonld +++ b/data/ensembl_genomes_plants_sequence_search/ensembl_genomes_plants_sequence_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Search Ensembl Plants sequences with Exonerate.", "sc:name": "Ensembl Genomes Plants sequence search", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://plants.ensembl.org/Multi/enasearch", diff --git a/data/ensembl_genomes_protists_assembly_converter/ensembl_genomes_protists_assembly_converterbioschemas.jsonld b/data/ensembl_genomes_protists_assembly_converter/ensembl_genomes_protists_assembly_converterbioschemas.jsonld index 1249aa3433cbd..6e98df83cc7f5 100644 --- a/data/ensembl_genomes_protists_assembly_converter/ensembl_genomes_protists_assembly_converterbioschemas.jsonld +++ b/data/ensembl_genomes_protists_assembly_converter/ensembl_genomes_protists_assembly_converterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Map your data to the current assembly.", "sc:name": "Ensembl Genomes Protists assembly converter", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://protists.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_protists_blast/ensembl_genomes_protists_blastbioschemas.jsonld b/data/ensembl_genomes_protists_blast/ensembl_genomes_protists_blastbioschemas.jsonld index 1fccf476114b7..7c7773f35c278 100644 --- a/data/ensembl_genomes_protists_blast/ensembl_genomes_protists_blastbioschemas.jsonld +++ b/data/ensembl_genomes_protists_blast/ensembl_genomes_protists_blastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Searches Ensembl Protists sequences using WU-BLAST.", "sc:name": "Ensembl Genomes Protists Blast", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://protists.ensembl.org/Multi/blastview", diff --git a/data/ensembl_genomes_protists_data_slicer/ensembl_genomes_protists_data_slicerbioschemas.jsonld b/data/ensembl_genomes_protists_data_slicer/ensembl_genomes_protists_data_slicerbioschemas.jsonld index 77bedeb528564..7df41ba36024e 100644 --- a/data/ensembl_genomes_protists_data_slicer/ensembl_genomes_protists_data_slicerbioschemas.jsonld +++ b/data/ensembl_genomes_protists_data_slicer/ensembl_genomes_protists_data_slicerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Get a subset of data from a BAM | VCF file.", "sc:name": "Ensembl Genomes Protists data slicer", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://protists.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_protists_id_history_converter/ensembl_genomes_protists_id_history_converterbioschemas.jsonld b/data/ensembl_genomes_protists_id_history_converter/ensembl_genomes_protists_id_history_converterbioschemas.jsonld index 15731700b750e..4926aa90cbd1a 100644 --- a/data/ensembl_genomes_protists_id_history_converter/ensembl_genomes_protists_id_history_converterbioschemas.jsonld +++ b/data/ensembl_genomes_protists_id_history_converter/ensembl_genomes_protists_id_history_converterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Convert a set of Ensembl IDs from a previous release into their current equivalents.", "sc:name": "Ensembl Genomes Protists ID history converter", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://protists.ensembl.org/tools.html", diff --git a/data/ensembl_genomes_protists_sequence_search/ensembl_genomes_protists_sequence_searchbioschemas.jsonld b/data/ensembl_genomes_protists_sequence_search/ensembl_genomes_protists_sequence_searchbioschemas.jsonld index 1711dd638ccbb..25c5eeffcea65 100644 --- a/data/ensembl_genomes_protists_sequence_search/ensembl_genomes_protists_sequence_searchbioschemas.jsonld +++ b/data/ensembl_genomes_protists_sequence_search/ensembl_genomes_protists_sequence_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Searches Ensembl Protists sequences using Exonerate.", "sc:name": "Ensembl Genomes Protists sequence search", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://protists.ensembl.org/Multi/enasearch", diff --git a/data/ensembl_rat_genome_browser/ensembl_rat_genome_browserbioschemas.jsonld b/data/ensembl_rat_genome_browser/ensembl_rat_genome_browserbioschemas.jsonld index 9805823d20bf9..ef67b2015b4fd 100644 --- a/data/ensembl_rat_genome_browser/ensembl_rat_genome_browserbioschemas.jsonld +++ b/data/ensembl_rat_genome_browser/ensembl_rat_genome_browserbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).", "sc:name": "Ensembl Rat Genome Browser", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ensembl.org/Rattus_norvegicus/" diff --git a/data/ensembl_sequence_search_blast/ensembl_sequence_search_blastbioschemas.jsonld b/data/ensembl_sequence_search_blast/ensembl_sequence_search_blastbioschemas.jsonld index e9b91258bb544..d02821138bca0 100644 --- a/data/ensembl_sequence_search_blast/ensembl_sequence_search_blastbioschemas.jsonld +++ b/data/ensembl_sequence_search_blast/ensembl_sequence_search_blastbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Ensembl Sequence Search BLAST", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ensembl.org/Multi/blastview", diff --git a/data/ensembl_variant_effect_predictor/ensembl_variant_effect_predictorbioschemas.jsonld b/data/ensembl_variant_effect_predictor/ensembl_variant_effect_predictorbioschemas.jsonld index b16925d405dfe..011a7e2803dcc 100644 --- a/data/ensembl_variant_effect_predictor/ensembl_variant_effect_predictorbioschemas.jsonld +++ b/data/ensembl_variant_effect_predictor/ensembl_variant_effect_predictorbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "William McLarenEmail author,", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.", "sc:license": "Apache-2.0", "sc:name": "Ensembl Variant Effect Predictor", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ensembl.org/info/docs/tools/vep/index.html" } \ No newline at end of file diff --git a/data/ensembl_zebrafish_genome_browser/ensembl_zebrafish_genome_browserbioschemas.jsonld b/data/ensembl_zebrafish_genome_browser/ensembl_zebrafish_genome_browserbioschemas.jsonld index f03f184e7b4ee..9e7e531ce5710 100644 --- a/data/ensembl_zebrafish_genome_browser/ensembl_zebrafish_genome_browserbioschemas.jsonld +++ b/data/ensembl_zebrafish_genome_browser/ensembl_zebrafish_genome_browserbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This ensembl website features the zebrafish whole genome shotgun assembly sequence.", "sc:name": "Ensembl Zebrafish Genome Browser", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ensembl.org/Danio_rerio/" } \ No newline at end of file diff --git a/data/ensembldb/bioconda_ensembldb.yaml b/data/ensembldb/bioconda_ensembldb.yaml index fd2c000b42d69..94a5722a2d83f 100644 --- a/data/ensembldb/bioconda_ensembldb.yaml +++ b/data/ensembldb/bioconda_ensembldb.yaml @@ -12,7 +12,6 @@ description: The package provides functions to create and use transcript centric home: https://bioconductor.org/packages/3.10/bioc/html/ensembldb.html identifiers: - biotools:ensembldb -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-ensembldb diff --git a/data/ensembldb/ensembldbbioschemas.jsonld b/data/ensembldb/ensembldbbioschemas.jsonld index 2ccb6dbb2484e..e45f1bd5694fe 100644 --- a/data/ensembldb/ensembldbbioschemas.jsonld +++ b/data/ensembldb/ensembldbbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Johannes Rainer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the package provides also a filter framework allowing to retrieve annotations for specific entries.", "sc:license": "GPL-3.0", "sc:name": "ensembldb", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ensembldb.html", "sc:version": "1.6.2" diff --git a/data/ensemble_nmf/ensemble_nmfbioschemas.jsonld b/data/ensemble_nmf/ensemble_nmfbioschemas.jsonld index fc0b51dd5e60b..f72e9ddfa369c 100644 --- a/data/ensemble_nmf/ensemble_nmfbioschemas.jsonld +++ b/data/ensemble_nmf/ensemble_nmfbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Ensemble NMF (Non-negative Matrix Factorization ) is a software for clustering and visualising protein interaction networks.", "sc:name": "Ensemble NMF", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://mlg.ucd.ie/nmf", "sc:version": "0.91" diff --git a/data/ensembler/ensemblerbioschemas.jsonld b/data/ensembler/ensemblerbioschemas.jsonld index f2575edbce792..0c79a8bfb224c 100644 --- a/data/ensembler/ensemblerbioschemas.jsonld +++ b/data/ensembler/ensemblerbioschemas.jsonld @@ -13,17 +13,17 @@ "@id": "https://bio.tools/ensembler", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Patrick B. Grinaway", "John D. Chodera", - "Daniel L. Parton" + "Daniel L. Parton", + "Patrick B. Grinaway" ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27337644", + "pmcid:PMC4918922", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1004728" - }, - "pubmed:27337644", - "pmcid:PMC4918922" + } ], "sc:description": "Enabling High-Throughput Molecular Simulations at the Superfamily Scale.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:license": "GPL-2.0", "sc:name": "Ensembler", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/choderalab/ensembler" }, diff --git a/data/ensemblvep/ensemblvepbioschemas.jsonld b/data/ensemblvep/ensemblvepbioschemas.jsonld index 2d116d68a84a1..afedbfacc302f 100644 --- a/data/ensemblvep/ensemblvepbioschemas.jsonld +++ b/data/ensemblvep/ensemblvepbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "BioConductor wrapper for Ensembl VEP", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ensemblVEP.html", "sc:version": "1.14.0" diff --git a/data/enterix/enterixbioschemas.jsonld b/data/enterix/enterixbioschemas.jsonld index 8646a97af0004..64bac78269d51 100644 --- a/data/enterix/enterixbioschemas.jsonld +++ b/data/enterix/enterixbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.", "sc:name": "EnteriX", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://enterix.cbcb.umd.edu/" } \ No newline at end of file diff --git a/data/enterotyping/enterotypingbioschemas.jsonld b/data/enterotyping/enterotypingbioschemas.jsonld index 599d69235ce74..57e58f8a5018f 100644 --- a/data/enterotyping/enterotypingbioschemas.jsonld +++ b/data/enterotyping/enterotypingbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/nature09944", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-1429-7485", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/enterotyping", "@type": "sc:SoftwareApplication", @@ -26,11 +34,11 @@ "@id": "edam:topic_3174" }, "sc:citation": [ + "pmcid:PMC3728647", + "pubmed:21508958", { "@id": "https://doi.org/10.1038/nature09944" - }, - "pmcid:PMC3728647", - "pubmed:21508958" + } ], "sc:description": "Enterotypes are densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified (Arumugam, Raes et al. Nature 2011). Computational methods to detect and characterise enterotypes in any dataset, either to reproduce previous reports or determine enterotypes in new studies, are provided and explained.", "sc:featureList": { @@ -53,14 +61,6 @@ }, "sc:url": "http://enterotype.embl.de", "sc:version": "1.0" - }, - { - "@id": "http://orcid.org/0000-0003-1429-7485", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1038/nature09944", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/entret/entretbioschemas.jsonld b/data/entret/entretbioschemas.jsonld index 96a50abe38bec..25fe4aa6e6efe 100644 --- a/data/entret/entretbioschemas.jsonld +++ b/data/entret/entretbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "Wellcome Trust", "EMBOSS Contributors", "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:description": "Retrieve sequence entries from flatfile databases and files.", "sc:funder": [ - "Wellcome Trust", + "UK BBSRC", "UK MRC", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "entret", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/entret.html", "sc:version": "r6" diff --git a/data/entrez/entrezbioschemas.jsonld b/data/entrez/entrezbioschemas.jsonld index d12125dd4b77d..abac20ef99f39 100644 --- a/data/entrez/entrezbioschemas.jsonld +++ b/data/entrez/entrezbioschemas.jsonld @@ -9,27 +9,26 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkg057", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/entrez", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Entrez contact form", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ + "pmcid:PMC165504", + "pubmed:12519940", { "@id": "https://doi.org/10.1093/nar/gkg057" - }, - "pmcid:PMC165504", - "pubmed:12519940" + } ], "sc:description": "NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.", "sc:featureList": [ + { + "@id": "edam:operation_3431" + }, { "@id": "edam:operation_2403" }, @@ -44,9 +43,6 @@ }, { "@id": "edam:operation_2429" - }, - { - "@id": "edam:operation_3431" } ], "sc:name": "Entrez", @@ -56,6 +52,10 @@ "Mac" ], "sc:url": "https://www.ncbi.nlm.nih.gov/Entrez/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkg057", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/entrez_gene/entrez_genebioschemas.jsonld b/data/entrez_gene/entrez_genebioschemas.jsonld index 9448ca8eee517..446563ae1f3ad 100644 --- a/data/entrez_gene/entrez_genebioschemas.jsonld +++ b/data/entrez_gene/entrez_genebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "NCBI’s database for gene-specific information. It maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis.", "sc:name": "Entrez Gene", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.ncbi.nlm.nih.gov/gene" } \ No newline at end of file diff --git a/data/entrez_protein_clusters/entrez_protein_clustersbioschemas.jsonld b/data/entrez_protein_clusters/entrez_protein_clustersbioschemas.jsonld index 402b0562a62ae..3dbe966d3fa45 100644 --- a/data/entrez_protein_clusters/entrez_protein_clustersbioschemas.jsonld +++ b/data/entrez_protein_clusters/entrez_protein_clustersbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A collection of related protein sequences (clusters) consists of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses.", "sc:name": "Entrez Protein Clusters", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "NCBI", "sc:url": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters" diff --git a/data/entrezpy/entrezpybioschemas.jsonld b/data/entrezpy/entrezpybioschemas.jsonld index 70670fd7fd94b..6eec74da25a6f 100644 --- a/data/entrezpy/entrezpybioschemas.jsonld +++ b/data/entrezpy/entrezpybioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Entrezpy", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://pypi.org/project/entrezpy/" } \ No newline at end of file diff --git a/data/entropyexplorer/entropyexplorerbioschemas.jsonld b/data/entropyexplorer/entropyexplorerbioschemas.jsonld index c251e96bfaae7..9c600dc0d80ff 100644 --- a/data/entropyexplorer/entropyexplorerbioschemas.jsonld +++ b/data/entropyexplorer/entropyexplorerbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13104-015-1786-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/entropyexplorer", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC4696313", + "pubmed:26714840", { "@id": "https://doi.org/10.1186/s13104-015-1786-4" - }, - "pubmed:26714840" + } ], "sc:description": "Rows of two matrices are compared for Shannon entropy, coefficient of variation, and expression. P-values can be requested for all metrics.", "sc:featureList": { @@ -32,12 +28,16 @@ "sc:license": "GPL-3.0", "sc:name": "EntropyExplorer", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/EntropyExplorer/index.html", "sc:version": "1.1" + }, + { + "@id": "https://doi.org/10.1186/s13104-015-1786-4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/envipat/envipatbioschemas.jsonld b/data/envipat/envipatbioschemas.jsonld index a19972dd983a9..40d7027db7351 100644 --- a/data/envipat/envipatbioschemas.jsonld +++ b/data/envipat/envipatbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/envipat", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", + "Web application", "Library", - "Web application" + "Command-line tool" ], "sc:description": "Batch fine structure, profile and centroid calculation with resolution settings provided.", "sc:license": "GPL-2.0", "sc:name": "enviPat", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.envipat.eawag.ch/" diff --git a/data/envisionquery/envisionquerybioschemas.jsonld b/data/envisionquery/envisionquerybioschemas.jsonld index 7a3771e43dccb..07ce822da9287 100644 --- a/data/envisionquery/envisionquerybioschemas.jsonld +++ b/data/envisionquery/envisionquerybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/envisionquery", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alex Lisovich", - "Roger Day" + "Roger Day", + "Alex Lisovich" ], "sc:additionalType": [ "Command-line tool", @@ -22,8 +22,8 @@ "sc:license": "GPL-2.0", "sc:name": "ENVISIONQuery", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ENVISIONQuery.html", diff --git a/data/enzyme/enzymebioschemas.jsonld b/data/enzyme/enzymebioschemas.jsonld index 27c436c6ce4d5..5eb4347a95c69 100644 --- a/data/enzyme/enzymebioschemas.jsonld +++ b/data/enzyme/enzymebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.", "sc:name": "ENZYME - Enzyme nomenclature database", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://enzyme.expasy.org" diff --git a/data/enzyme_portal/enzyme_portalbioschemas.jsonld b/data/enzyme_portal/enzyme_portalbioschemas.jsonld index 36fa643f00176..c9c09ffd52855 100644 --- a/data/enzyme_portal/enzyme_portalbioschemas.jsonld +++ b/data/enzyme_portal/enzyme_portalbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Web service which integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds.", "sc:name": "Enzyme Portal", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "EMBL-EBI Databases", "sc:url": "http://www.ebi.ac.uk/enzymeportal/" diff --git a/data/enzymeportal_protein_sequence_search/enzymeportal_protein_sequence_searchbioschemas.jsonld b/data/enzymeportal_protein_sequence_search/enzymeportal_protein_sequence_searchbioschemas.jsonld index 666c158e04ce9..955fbf3b7afda 100644 --- a/data/enzymeportal_protein_sequence_search/enzymeportal_protein_sequence_searchbioschemas.jsonld +++ b/data/enzymeportal_protein_sequence_search/enzymeportal_protein_sequence_searchbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Enzyme Portal - Protein sequence search", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/enzymeportal/advanceSearch", diff --git a/data/eosc_pipeline-reproducibility/eosc_pipeline-reproducibilitybioschemas.jsonld b/data/eosc_pipeline-reproducibility/eosc_pipeline-reproducibilitybioschemas.jsonld index 64ccde0ad4d42..1fced0052f943 100644 --- a/data/eosc_pipeline-reproducibility/eosc_pipeline-reproducibilitybioschemas.jsonld +++ b/data/eosc_pipeline-reproducibility/eosc_pipeline-reproducibilitybioschemas.jsonld @@ -15,9 +15,9 @@ "Paolo Di Tommaso" ], "sc:additionalType": [ - "Command-line tool", + "Script", "Workflow", - "Script" + "Command-line tool" ], "sc:description": "The described pipeline is aimed to replicate data stored at EGA generated by the GoNL consortium", "sc:license": "Apache-1.0", diff --git a/data/ep3/ep3bioschemas.jsonld b/data/ep3/ep3bioschemas.jsonld index 266bb4cec424a..06d3f40d8eba3 100644 --- a/data/ep3/ep3bioschemas.jsonld +++ b/data/ep3/ep3bioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Identification of the core region of a eukaryotic gene promoter.", "sc:name": "EP3", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/EP3", diff --git a/data/epa-ng/epa-ngbioschemas.jsonld b/data/epa-ng/epa-ngbioschemas.jsonld index c3cbdd7ab018e..da3fd692f6f8a 100644 --- a/data/epa-ng/epa-ngbioschemas.jsonld +++ b/data/epa-ng/epa-ngbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/sysbio/syy054", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/EPA-ng", "@type": "sc:SoftwareApplication", @@ -20,21 +16,21 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:30165689", + "pmcid:PMC6368480", { "@id": "https://doi.org/10.1093/sysbio/syy054" - }, - "pmcid:PMC6368480" + } ], "sc:description": "Complete reimplementation of the evolutionary placement algorithm (EPA) that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER.", "sc:featureList": [ { - "@id": "edam:operation_0362" + "@id": "edam:operation_0310" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_0362" }, { - "@id": "edam:operation_0310" + "@id": "edam:operation_2495" } ], "sc:license": "AGPL-3.0", @@ -44,6 +40,10 @@ "Linux" ], "sc:url": "https://github.com/Pbdas/epa-ng" + }, + { + "@id": "https://doi.org/10.1093/sysbio/syy054", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/epd/epdbioschemas.jsonld b/data/epd/epdbioschemas.jsonld index adf80be6aed6b..300af51d79697 100644 --- a/data/epd/epdbioschemas.jsonld +++ b/data/epd/epdbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "EPD", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://epd.vital-it.ch/" diff --git a/data/epestfind/epestfindbioschemas.jsonld b/data/epestfind/epestfindbioschemas.jsonld index 753b746dc25bf..ec940c226a63f 100644 --- a/data/epestfind/epestfindbioschemas.jsonld +++ b/data/epestfind/epestfindbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", + "UK MRC", "Wellcome Trust", - "EMBOSS Contributors", - "UK MRC" + "EMBOSS Contributors" ], "sc:description": "Find PEST motifs as potential proteolytic cleavage sites.", "sc:funder": [ "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "epestfind", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/epga/epgabioschemas.jsonld b/data/epga/epgabioschemas.jsonld index f90a224231b6a..4ba8b4d1caca5 100644 --- a/data/epga/epgabioschemas.jsonld +++ b/data/epga/epgabioschemas.jsonld @@ -17,12 +17,12 @@ "@id": "https://bio.tools/epga", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "George Potamias", - "George Patrinos" + "George Patrinos", + "George Potamias" ], "sc:additionalType": [ - "Web service", "Web application", + "Web service", "Web API" ], "sc:citation": [ @@ -35,18 +35,18 @@ "sc:description": "Electronic Pharmacogenomics Assistant (ePGA) - browsing pharmacogenomics knowledge on gene-drug-phenotype associations and matching individual genotype-profiles with gene haplotypes and infering the corresponding diplotype and phenotype profiles.", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_2409" }, { - "@id": "edam:operation_2409" + "@id": "edam:operation_0337" } ], "sc:license": "Other", "sc:name": "ePGA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.epga.gr" } diff --git a/data/epi-peptide_designer/epi-peptide_designerbioschemas.jsonld b/data/epi-peptide_designer/epi-peptide_designerbioschemas.jsonld index 0b3083afed238..90d4c39a7b69f 100644 --- a/data/epi-peptide_designer/epi-peptide_designerbioschemas.jsonld +++ b/data/epi-peptide_designer/epi-peptide_designerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "EPI-peptide designer", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.biocomp.icb.ufmg.br/biocomp/software-and-databases/epi-peptide-designer/" } \ No newline at end of file diff --git a/data/epialign/epialignbioschemas.jsonld b/data/epialign/epialignbioschemas.jsonld index 242c9b92419f3..4f8b7d150a223 100644 --- a/data/epialign/epialignbioschemas.jsonld +++ b/data/epialign/epialignbioschemas.jsonld @@ -17,33 +17,33 @@ "@id": "https://bio.tools/EpiAlign", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Haowen Zhang", { "@id": "https://orcid.org/0000-0002-9288-5648" - } + }, + "Haowen Zhang" ], "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC6648345", "pubmed:31045217", { "@id": "https://doi.org/10.1093/NAR/GKZ287" - } + }, + "pmcid:PMC6648345" ], "sc:description": "Alignment-based bioinformatic tool for comparing chromatin state sequences.", "sc:featureList": [ { - "@id": "edam:operation_3891" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_3891" } ], "sc:name": "EpiAlign", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/zzz3639/EpiAlign" }, diff --git a/data/epialignment/epialignmentbioschemas.jsonld b/data/epialignment/epialignmentbioschemas.jsonld index fa8151b0df167..5f88ca627f65b 100644 --- a/data/epialignment/epialignmentbioschemas.jsonld +++ b/data/epialignment/epialignmentbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKZ426", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/EpiAlignment", "@type": "sc:SoftwareApplication", @@ -20,20 +16,24 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC6602515", - "pubmed:31114924", { "@id": "https://doi.org/10.1093/NAR/GKZ426" - } + }, + "pubmed:31114924" ], "sc:description": "Alignment of genomic regions with both sequence and epigenomic information.", "sc:license": "Apache-2.0", "sc:name": "EpiAlignment", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://epialign.ucsd.edu/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ426", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/epianno/epiannobioschemas.jsonld b/data/epianno/epiannobioschemas.jsonld index 2dd2885804dae..2084f8535ee69 100644 --- a/data/epianno/epiannobioschemas.jsonld +++ b/data/epianno/epiannobioschemas.jsonld @@ -9,25 +9,29 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0148321", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/epianno", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hsuan-Yu Chen", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:26859295", + "pmcid:PMC4747527", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0148321" - }, - "pmcid:PMC4747527", - "pubmed:26859295" + } ], "sc:description": "ePIgenomics ANNOtation tool.", "sc:featureList": [ { - "@id": "edam:operation_3225" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_3197" + "@id": "edam:operation_3225" } ], "sc:name": "ePIANNO", @@ -37,10 +41,6 @@ "Windows" ], "sc:url": "http://epianno.stat.sinica.edu.tw/index.html" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0148321", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/epiannotator/epiannotatorbioschemas.jsonld b/data/epiannotator/epiannotatorbioschemas.jsonld index 80967d8c8a4f6..d929210e3d31b 100644 --- a/data/epiannotator/epiannotatorbioschemas.jsonld +++ b/data/epiannotator/epiannotatorbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": [ - "Web application", - "Library" + "Library", + "Web application" ], "sc:description": "Enrichment analyses on epigenomic data in a fast and user-friendly way.", "sc:license": "GPL-3.0", "sc:name": "EpiAnnotator", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://computational-epigenomics.com/en/epiannotator" } \ No newline at end of file diff --git a/data/epic-tabsat/epic-tabsatbioschemas.jsonld b/data/epic-tabsat/epic-tabsatbioschemas.jsonld index ca823efe49438..18a88d192b404 100644 --- a/data/epic-tabsat/epic-tabsatbioschemas.jsonld +++ b/data/epic-tabsat/epic-tabsatbioschemas.jsonld @@ -9,51 +9,51 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-2953-7982", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ398", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/EPIC-TABSAT", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Stephan Pabinger", { "@id": "https://orcid.org/0000-0002-2953-7982" - }, - "Stephan Pabinger" + } ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31106358", - "pmcid:PMC6602470", { "@id": "https://doi.org/10.1093/NAR/GKZ398" - } + }, + "pubmed:31106358", + "pmcid:PMC6602470" ], "sc:description": "Analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies.", "sc:featureList": [ { - "@id": "edam:operation_3207" + "@id": "edam:operation_3186" }, { "@id": "edam:operation_3206" }, { - "@id": "edam:operation_3186" + "@id": "edam:operation_3207" } ], "sc:license": "Unlicense", "sc:name": "EPIC-TABSAT", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://tabsat.ait.ac.at/" + }, + { + "@id": "https://orcid.org/0000-0002-2953-7982", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ398", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/epicompare/epicomparebioschemas.jsonld b/data/epicompare/epicomparebioschemas.jsonld index 511dedbab5651..1c3aa2d8ed642 100644 --- a/data/epicompare/epicomparebioschemas.jsonld +++ b/data/epicompare/epicomparebioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yu He", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Tool to define and explore genomic regions with tissue or cell type-specific epigenomic features.", "sc:license": "Unlicense", diff --git a/data/epidish/epidishbioschemas.jsonld b/data/epidish/epidishbioschemas.jsonld index dc8eafbdfd05b..b08977917b7c4 100644 --- a/data/epidish/epidishbioschemas.jsonld +++ b/data/epidish/epidishbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "EpiDISH", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EpiDISH.html", "sc:version": "1.2.0" diff --git a/data/epig-seq/epig-seqbioschemas.jsonld b/data/epig-seq/epig-seqbioschemas.jsonld index b8a25f16eea6f..cd676bf4e71cd 100644 --- a/data/epig-seq/epig-seqbioschemas.jsonld +++ b/data/epig-seq/epig-seqbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Pierre R. Bushel", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:27004791", + "pmcid:PMC4804494", { "@id": "https://doi.org/10.1186/S12864-016-2584-7" - }, - "pmcid:PMC4804494", - "pubmed:27004791" + } ], "sc:description": "Extracting patterns and identifying co-expressed genes from RNA-Seq data.", "sc:featureList": { diff --git a/data/epigenomix/epigenomixbioschemas.jsonld b/data/epigenomix/epigenomixbioschemas.jsonld index f5cc5b31baf80..188dfe062604e 100644 --- a/data/epigenomix/epigenomixbioschemas.jsonld +++ b/data/epigenomix/epigenomixbioschemas.jsonld @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "epigenomix", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/epigenomix.html", "sc:version": "1.14.0" diff --git a/data/epigraph/epigraphbioschemas.jsonld b/data/epigraph/epigraphbioschemas.jsonld index 0560497b058c6..bd9b1d242e2dc 100644 --- a/data/epigraph/epigraphbioschemas.jsonld +++ b/data/epigraph/epigraphbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Enables biologists to analyze genome and epigenome datasets with powerful statistical and machine learning methods. In a typical workflow, the user uploads a set of genomic regions of interest, and its searches a large database of (epi-) genomic attributes for significant overlap and correlation with the regions in the input dataset. Furthermore, it can predict the status of genomic regions that were not included in the input dataset.", "sc:name": "EpiGRAPH", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://epigraph.mpi-inf.mpg.de/WebGRAPH/" } \ No newline at end of file diff --git a/data/epilog/epilogbioschemas.jsonld b/data/epilog/epilogbioschemas.jsonld index 587ae7eeb7081..c69de1e34a026 100644 --- a/data/epilog/epilogbioschemas.jsonld +++ b/data/epilog/epilogbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "EpiLog", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://epilog-tool.org/" } \ No newline at end of file diff --git a/data/epimethex/epimethexbioschemas.jsonld b/data/epimethex/epimethexbioschemas.jsonld index eb4e989be5595..f6866b648e9d5 100644 --- a/data/epimethex/epimethexbioschemas.jsonld +++ b/data/epimethex/epimethexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "EpiMethEx", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/giupardeb/EpiMethEx" diff --git a/data/epimir/epimirbioschemas.jsonld b/data/epimir/epimirbioschemas.jsonld index 79746e1dc7aeb..bfb83c7b285f1 100644 --- a/data/epimir/epimirbioschemas.jsonld +++ b/data/epimir/epimirbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Database portal", "sc:citation": [ + "pmcid:PMC4037167", + "pubmed:24682734", { "@id": "https://doi.org/10.1093/DATABASE/BAU023" - }, - "pubmed:24682734", - "pmcid:PMC4037167" + } ], "sc:description": "A database of curated mutual regulation between miRNAs and epigenetic modifications.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "EpimiR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://210.46.85.180:8080/EpimiR/" } diff --git a/data/epimodel/epimodelbioschemas.jsonld b/data/epimodel/epimodelbioschemas.jsonld index 25166144ee749..191258cf5e0dc 100644 --- a/data/epimodel/epimodelbioschemas.jsonld +++ b/data/epimodel/epimodelbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.18637/jss.v084.i08", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/epimodel", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Samuel Jenness", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:29731699", - "pmcid:PMC5931789", { "@id": "https://doi.org/10.18637/jss.v084.i08" - } + }, + "pmcid:PMC5931789", + "pubmed:29731699" ], "sc:description": "Mathematical Modeling of Infectious Disease.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "GPL-3.0", "sc:name": "EpiModel", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.epimodel.org/" + }, + { + "@id": "https://doi.org/10.18637/jss.v084.i08", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/epinem/epinembioschemas.jsonld b/data/epinem/epinembioschemas.jsonld index a8e5d4982f2fa..75abd00b9ae53 100644 --- a/data/epinem/epinembioschemas.jsonld +++ b/data/epinem/epinembioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "epiNEM", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/epiNEM.html", "sc:version": "1.4.0" diff --git a/data/epiprofilelite/epiprofilelitebioschemas.jsonld b/data/epiprofilelite/epiprofilelitebioschemas.jsonld index 5f7b4009f37a3..fc9a2cb9afd55 100644 --- a/data/epiprofilelite/epiprofilelitebioschemas.jsonld +++ b/data/epiprofilelite/epiprofilelitebioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://orcid.org/0000-0001-9073-6641", - "@type": "schema:Person" + "@id": "https://doi.org/10.1101/GR.247353.118", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/EpiProfileLite", @@ -21,22 +21,22 @@ }, "sc:additionalType": "Script", "sc:citation": [ - "pubmed:31123082", "pmcid:PMC6581051", { "@id": "https://doi.org/10.1101/GR.247353.118" - } + }, + "pubmed:31123082" ], "sc:description": "Analysis of histone post-translational modifications by direct infusion mass spectrometry\n.", "sc:featureList": [ - { - "@id": "edam:operation_2929" - }, { "@id": "edam:operation_3645" }, { "@id": "edam:operation_0417" + }, + { + "@id": "edam:operation_2929" } ], "sc:license": "GPL-3.0", @@ -45,8 +45,8 @@ "sc:url": "https://github.com/zfyuan/EpiProfileLite" }, { - "@id": "https://doi.org/10.1101/GR.247353.118", - "@type": "sc:CreativeWork" + "@id": "https://orcid.org/0000-0001-9073-6641", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/episcanpy/episcanpybioschemas.jsonld b/data/episcanpy/episcanpybioschemas.jsonld index 0404433ed3263..62ac134bf97c8 100644 --- a/data/episcanpy/episcanpybioschemas.jsonld +++ b/data/episcanpy/episcanpybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/epiScanpy", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Fabian J. Theis", - "Maria Colomé-Tatché" + "Maria Colomé-Tatché", + "Fabian J. Theis" ], "sc:additionalType": "Library", "sc:description": "Epigenomics Single Cell Analysis in Python.", diff --git a/data/epitad/epitadbioschemas.jsonld b/data/epitad/epitadbioschemas.jsonld index fee4d1cdb6ccd..528f1fdf7d0ca 100644 --- a/data/epitad/epitadbioschemas.jsonld +++ b/data/epitad/epitadbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "epiTAD", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://apps.gerkelab.com/epiTAD/" } \ No newline at end of file diff --git a/data/epivizr/epivizrbioschemas.jsonld b/data/epivizr/epivizrbioschemas.jsonld index 3925f5cca29bc..e0fc8f070198c 100644 --- a/data/epivizr/epivizrbioschemas.jsonld +++ b/data/epivizr/epivizrbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "epivizr", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/epivizr.html", "sc:version": "2.4.0" diff --git a/data/epivizrchart/epivizrchartbioschemas.jsonld b/data/epivizrchart/epivizrchartbioschemas.jsonld index 4678aae11a670..6828c36e2236d 100644 --- a/data/epivizrchart/epivizrchartbioschemas.jsonld +++ b/data/epivizrchart/epivizrchartbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "epivizrChart", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/epivizrChart.html", "sc:version": "1.2.0" diff --git a/data/epivizrdata/bioconda_epivizrdata.yaml b/data/epivizrdata/bioconda_epivizrdata.yaml index 525770b0b0daf..673af036d0c32 100644 --- a/data/epivizrdata/bioconda_epivizrdata.yaml +++ b/data/epivizrdata/bioconda_epivizrdata.yaml @@ -3,7 +3,6 @@ description: Serve data from Bioconductor Objects through a WebSocket connection home: https://bioconductor.org/packages/3.10/bioc/html/epivizrData.html identifiers: - biotools:epivizrdata -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-epivizrdata diff --git a/data/epivizrdata/epivizrdatabioschemas.jsonld b/data/epivizrdata/epivizrdatabioschemas.jsonld index fd1b259d907f5..67ccce78f4dd6 100644 --- a/data/epivizrdata/epivizrdatabioschemas.jsonld +++ b/data/epivizrdata/epivizrdatabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "epivizrData", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/epivizrData.html", "sc:version": "1.2.0" diff --git a/data/epivizrserver/bioconda_epivizrserver.yaml b/data/epivizrserver/bioconda_epivizrserver.yaml index b07b194e2d81d..e2aeb7484a6f8 100644 --- a/data/epivizrserver/bioconda_epivizrserver.yaml +++ b/data/epivizrserver/bioconda_epivizrserver.yaml @@ -4,7 +4,6 @@ description: This package provides objects to manage WebSocket connections to ep home: https://bioconductor.org/packages/3.10/bioc/html/epivizrServer.html identifiers: - biotools:epivizrserver -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-epivizrserver diff --git a/data/epivizrserver/epivizrserverbioschemas.jsonld b/data/epivizrserver/epivizrserverbioschemas.jsonld index bdb6d4376da5a..cc5bb922a506d 100644 --- a/data/epivizrserver/epivizrserverbioschemas.jsonld +++ b/data/epivizrserver/epivizrserverbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hector Corrada Bravo", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.", "sc:license": "MIT", diff --git a/data/epivizrstandalone/bioconda_epivizrstandalone.yaml b/data/epivizrstandalone/bioconda_epivizrstandalone.yaml index 36b3d7631ccff..3f7912d43bc28 100644 --- a/data/epivizrstandalone/bioconda_epivizrstandalone.yaml +++ b/data/epivizrstandalone/bioconda_epivizrstandalone.yaml @@ -6,7 +6,6 @@ description: This package imports the epiviz visualization JavaScript app for ge home: https://bioconductor.org/packages/3.10/bioc/html/epivizrStandalone.html identifiers: - biotools:epivizrstandalone -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-epivizrstandalone diff --git a/data/epivizrstandalone/epivizrstandalonebioschemas.jsonld b/data/epivizrstandalone/epivizrstandalonebioschemas.jsonld index 580be8be11b88..ef69802028190 100644 --- a/data/epivizrstandalone/epivizrstandalonebioschemas.jsonld +++ b/data/epivizrstandalone/epivizrstandalonebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "MIT", "sc:name": "epivizrStandalone", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/epivizrStandalone.html", "sc:version": "1.2.0" diff --git a/data/eplant/eplantbioschemas.jsonld b/data/eplant/eplantbioschemas.jsonld index 7548ab9d116e9..7c687126e4720 100644 --- a/data/eplant/eplantbioschemas.jsonld +++ b/data/eplant/eplantbioschemas.jsonld @@ -15,36 +15,36 @@ "biotools:primaryContact": "Jamie Waese", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:21249219", + "pmcid:PMC3018417", { "@id": "https://doi.org/10.1371/journal.pone.0015237" }, - "pmcid:PMC3018417" + "pubmed:21249219" ], "sc:description": "Visualize the natural connections between DNA sequences, natural variation (polymorphisms), molecular structures, protein-protein interactions, and gene expression patterns by combining several data visualization tools with a zoomable user interface.", "sc:featureList": [ { - "@id": "edam:operation_0474" + "@id": "edam:operation_0477" }, { - "@id": "edam:operation_0477" + "@id": "edam:operation_0276" }, { - "@id": "edam:operation_3439" + "@id": "edam:operation_0474" }, { "@id": "edam:operation_0484" }, { - "@id": "edam:operation_0276" + "@id": "edam:operation_3439" } ], "sc:license": "CC-BY-2.5", "sc:name": "ePlant", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bar.utoronto.ca/eplant/" }, diff --git a/data/epmv/epmvbioschemas.jsonld b/data/epmv/epmvbioschemas.jsonld index 708f17a61f089..b07b537fb0d4d 100644 --- a/data/epmv/epmvbioschemas.jsonld +++ b/data/epmv/epmvbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (blender,maya and cinema4D) to provide simultaneous access the capabilities of all of the systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease.", "sc:name": "ePMV", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://epmv.scripps.edu/" } \ No newline at end of file diff --git a/data/eponine/eponinebioschemas.jsonld b/data/eponine/eponinebioschemas.jsonld index e218e1f2de66c..5a0e7bb5ef128 100644 --- a/data/eponine/eponinebioschemas.jsonld +++ b/data/eponine/eponinebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.", "sc:name": "Eponine", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.sanger.ac.uk/resources/software/eponine/" } \ No newline at end of file diff --git a/data/epossum/epossumbioschemas.jsonld b/data/epossum/epossumbioschemas.jsonld index cc312269ee47c..3b8dd0cca3be4 100644 --- a/data/epossum/epossumbioschemas.jsonld +++ b/data/epossum/epossumbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "ePOSSUM analyses the effect of DNA variants on transcription factor binding sites", "sc:name": "ePOSSUM", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://www.mutationdistiller.org/ePOSSUM2/index.html", diff --git a/data/eprimer3/eprimer3bioschemas.jsonld b/data/eprimer3/eprimer3bioschemas.jsonld index fb26c09431241..3d4d8718d9c1a 100644 --- a/data/eprimer3/eprimer3bioschemas.jsonld +++ b/data/eprimer3/eprimer3bioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "UK MRC", "Wellcome Trust", - "EMBOSS Contributors" + "UK BBSRC", + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Pick PCR primers and hybridization oligos.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "eprimer3", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/eprimer3.html", "sc:version": "r6" diff --git a/data/eprimer32/eprimer32bioschemas.jsonld b/data/eprimer32/eprimer32bioschemas.jsonld index ed0eadbae6f32..eae571b88c53e 100644 --- a/data/eprimer32/eprimer32bioschemas.jsonld +++ b/data/eprimer32/eprimer32bioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "Wellcome Trust", "EMBOSS Contributors", - "UK MRC" + "UK BBSRC", + "UK MRC", + "Wellcome Trust" ], "sc:description": "Pick PCR primers and hybridization oligos.", "sc:funder": [ - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "eprimer32", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/eprimer32.html", "sc:version": "r6" diff --git a/data/epsilon/epsilonbioschemas.jsonld b/data/epsilon/epsilonbioschemas.jsonld index bb0c4f2cb5348..fff132c8cc8c6 100644 --- a/data/epsilon/epsilonbioschemas.jsonld +++ b/data/epsilon/epsilonbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "EQTL prioritization using similarity measures derived from local interaction networks.", "sc:name": "EPSILON", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "ugent.be", diff --git a/data/eqtlbma/eqtlbmabioschemas.jsonld b/data/eqtlbma/eqtlbmabioschemas.jsonld index 766aa19859e62..f6e81a06f28e0 100644 --- a/data/eqtlbma/eqtlbmabioschemas.jsonld +++ b/data/eqtlbma/eqtlbmabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "eQtlBma", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/timflutre/eqtlbma/wiki" } \ No newline at end of file diff --git a/data/eqtnminer/eqtnminerbioschemas.jsonld b/data/eqtnminer/eqtnminerbioschemas.jsonld index 1ab94fb46fd1d..aa3786c89c822 100644 --- a/data/eqtnminer/eqtnminerbioschemas.jsonld +++ b/data/eqtnminer/eqtnminerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "eQTNMiner (expression quantitative trait nucleotide Miner) is a computational package to carry out high-resolution mapping of quantitative trait loci (QTL) for high-dimensional genomic features like gene expression, epigenetic modifications, etc… and much more.", "sc:name": "eQTNMiner", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://eqtnminer.sourceforge.net/", "sc:version": "2.0.0" diff --git a/data/equicktandem/equicktandembioschemas.jsonld b/data/equicktandem/equicktandembioschemas.jsonld index 373f501629e52..4275c19df8120 100644 --- a/data/equicktandem/equicktandembioschemas.jsonld +++ b/data/equicktandem/equicktandembioschemas.jsonld @@ -13,21 +13,21 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", + "UK MRC", "EMBOSS Contributors", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:description": "Find tandem repeats in nucleotide sequences.", "sc:funder": [ "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "equicktandem", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": [ diff --git a/data/equilibrator/equilibratorbioschemas.jsonld b/data/equilibrator/equilibratorbioschemas.jsonld index 2550b59320d93..9a946b4673d64 100644 --- a/data/equilibrator/equilibratorbioschemas.jsonld +++ b/data/equilibrator/equilibratorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Biochemical thermodynamics calculator. eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface.", "sc:name": "eQuilibrator", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://equilibrator.weizmann.ac.il/" diff --git a/data/erccdashboard/erccdashboardbioschemas.jsonld b/data/erccdashboard/erccdashboardbioschemas.jsonld index e2e8a3a1d5a1e..17e7635184e49 100644 --- a/data/erccdashboard/erccdashboardbioschemas.jsonld +++ b/data/erccdashboard/erccdashboardbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sarah Munro", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:25254650", "sc:description": "Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures.", diff --git a/data/erdf_analyser/erdf_analyserbioschemas.jsonld b/data/erdf_analyser/erdf_analyserbioschemas.jsonld index f4ee0d471c3ca..13b76e70f7e79 100644 --- a/data/erdf_analyser/erdf_analyserbioschemas.jsonld +++ b/data/erdf_analyser/erdf_analyserbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Janaki Shanmugam", "sc:additionalType": [ - "Plug-in", - "Desktop application" + "Desktop application", + "Plug-in" ], "sc:description": "eRDF Analyser is an interactive MATLAB GUI for reduced density function (RDF) or pair distribution function (PDF) analysis of amorphous and polycrystalline materials to study their local structure.", "sc:license": "GPL-3.0", diff --git a/data/erds/erdsbioschemas.jsonld b/data/erds/erdsbioschemas.jsonld index 83465c70420b2..59927218c3010 100644 --- a/data/erds/erdsbioschemas.jsonld +++ b/data/erds/erdsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/erds", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mingfu Zhu", - "David B.Goldstein" + "David B.Goldstein", + "Mingfu Zhu" ], "sc:additionalType": "Command-line tool", "sc:description": "ERDS is a free, open-source software, designed for detection of copy number variants (CNVs) on human genomes from next generation sequence data. It uses paired Hidden Markov models (PHMM) based on the expected distribution of read depth of short reads and the presence of heterozygous sites. ERDS is NOT good for whole exome data.", diff --git a/data/erebus/erebusbioschemas.jsonld b/data/erebus/erebusbioschemas.jsonld index 1401308c8bf37..ba56297f3ba26 100644 --- a/data/erebus/erebusbioschemas.jsonld +++ b/data/erebus/erebusbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Erebus", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://troll.med.unc.edu/erebus/login.php" } \ No newline at end of file diff --git a/data/erga/ergabioschemas.jsonld b/data/erga/ergabioschemas.jsonld index fda6c1dd36a6a..2cd93851f20f5 100644 --- a/data/erga/ergabioschemas.jsonld +++ b/data/erga/ergabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "eRGA", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.csc.kth.se/~vezzi/software/" } \ No newline at end of file diff --git a/data/erma/ermabioschemas.jsonld b/data/erma/ermabioschemas.jsonld index 33adfd1cdfeb3..f0d2fc89eeb8a 100644 --- a/data/erma/ermabioschemas.jsonld +++ b/data/erma/ermabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "erma", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/erma.html", "sc:version": "0.12.0" diff --git a/data/erminej/erminejbioschemas.jsonld b/data/erminej/erminejbioschemas.jsonld index 4e45204674263..7caf293eb8832 100644 --- a/data/erminej/erminejbioschemas.jsonld +++ b/data/erminej/erminejbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allows users to assess whether microarray data or other gene lists are enriched for a particular pathway or gene class.", "sc:name": "ErmineJ", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://chibi.ubc.ca/ermineJ" } \ No newline at end of file diff --git a/data/erne/ernebioschemas.jsonld b/data/erne/ernebioschemas.jsonld index 4223aba8bc8ad..9c7356abb4451 100644 --- a/data/erne/ernebioschemas.jsonld +++ b/data/erne/ernebioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Cristian Del Fabbro", - "Giuseppe Pigola", - "Francesco Vezzi" + "Francesco Vezzi", + "Giuseppe Pigola" ], "sc:additionalType": "Suite", "sc:citation": "pubmed:24376861", @@ -21,9 +21,9 @@ "sc:license": "GPL-3.0", "sc:name": "ERNE", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://erne.sourceforge.net" } \ No newline at end of file diff --git a/data/eros-dock/eros-dockbioschemas.jsonld b/data/eros-dock/eros-dockbioschemas.jsonld index cd2b441d801f1..20b7670bd244f 100644 --- a/data/eros-dock/eros-dockbioschemas.jsonld +++ b/data/eros-dock/eros-dockbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "EROS-DOCK", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://erosdock.loria.fr" diff --git a/data/esap_plus/esap_plusbioschemas.jsonld b/data/esap_plus/esap_plusbioschemas.jsonld index f720efc6282a9..81325b19eac1f 100644 --- a/data/esap_plus/esap_plusbioschemas.jsonld +++ b/data/esap_plus/esap_plusbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Contact form", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:28155670", "pmcid:PMC5260030", { "@id": "https://doi.org/10.1186/S12864-016-3328-4" - }, - "pubmed:28155670" + } ], "sc:description": "A web-based server for EST-SSR marker development.", "sc:featureList": { @@ -33,8 +33,8 @@ "sc:name": "ESAP plus", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://gbp.kku.ac.th/esap_plus/" } diff --git a/data/esatac/esatacbioschemas.jsonld b/data/esatac/esatacbioschemas.jsonld index dc10dd8d4510f..149edb8db605b 100644 --- a/data/esatac/esatacbioschemas.jsonld +++ b/data/esatac/esatacbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/esatac", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wei Zhang", - "Zheng Wei" + "Zheng Wei", + "Wei Zhang" ], "sc:additionalType": "Library", "sc:description": "framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report.", "sc:license": "GPL-3.0", "sc:name": "esATAC", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://www.bioconductor.org/packages/release/bioc/html/esATAC.html", diff --git a/data/escape_excel/escape_excelbioschemas.jsonld b/data/escape_excel/escape_excelbioschemas.jsonld index 2b490c310460e..15d00c9094d98 100644 --- a/data/escape_excel/escape_excelbioschemas.jsonld +++ b/data/escape_excel/escape_excelbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Open-source tool which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel.", "sc:name": "Escape Excel", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/pstew/escape_excel" } \ No newline at end of file diff --git a/data/escdb/escdbbioschemas.jsonld b/data/escdb/escdbbioschemas.jsonld index 8b42e707e3855..9bc4e56aaf255 100644 --- a/data/escdb/escdbbioschemas.jsonld +++ b/data/escdb/escdbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Freeware", "sc:name": "ESCDb", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "ELIXIR-EE", diff --git a/data/esefinder/esefinderbioschemas.jsonld b/data/esefinder/esefinderbioschemas.jsonld index 07cb1c27aa693..30bcdb2870315 100644 --- a/data/esefinder/esefinderbioschemas.jsonld +++ b/data/esefinder/esefinderbioschemas.jsonld @@ -31,17 +31,17 @@ "@id": "edam:operation_0446" }, { - "@id": "edam:operation_0232" + "@id": "edam:operation_2499" }, { - "@id": "edam:operation_2499" + "@id": "edam:operation_0232" } ], "sc:license": "Unlicense", "sc:name": "ESEfinder", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://rulai.cshl.edu/tools/ESE/", diff --git a/data/esetvis/bioconda_esetvis.yaml b/data/esetvis/bioconda_esetvis.yaml index 81262efcbb8f1..d8946c67d867d 100644 --- a/data/esetvis/bioconda_esetvis.yaml +++ b/data/esetvis/bioconda_esetvis.yaml @@ -6,7 +6,6 @@ description: Utility functions for visualization of expressionSet (or Summarized home: https://bioconductor.org/packages/3.10/bioc/html/esetVis.html identifiers: - biotools:esetvis -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-esetvis diff --git a/data/esetvis/esetvisbioschemas.jsonld b/data/esetvis/esetvisbioschemas.jsonld index d7914cf1f3ac9..2aa96b81a4306 100644 --- a/data/esetvis/esetvisbioschemas.jsonld +++ b/data/esetvis/esetvisbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laure Cougnaud", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Utility functions for visualization of expressionSet (or SummarizedExperiment) BioConductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available.", "sc:license": "GPL-3.0", "sc:name": "esetVis", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/esetVis.html", "sc:version": "1.0.1" diff --git a/data/esimsa2d/esimsa2dbioschemas.jsonld b/data/esimsa2d/esimsa2dbioschemas.jsonld index cc45b255eea73..33200763cb91c 100644 --- a/data/esimsa2d/esimsa2dbioschemas.jsonld +++ b/data/esimsa2d/esimsa2dbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "esimsa2D", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ms-utils.org/esimsa2D.html" } \ No newline at end of file diff --git a/data/esiprot/esiprotbioschemas.jsonld b/data/esiprot/esiprotbioschemas.jsonld index 846b48e49fa0a..ddeb778b410c1 100644 --- a/data/esiprot/esiprotbioschemas.jsonld +++ b/data/esiprot/esiprotbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/esiprot", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Desktop application" + "Desktop application", + "Web application" ], "sc:citation": "pubmed:20049890", "sc:description": "Charge state determination and molecular weight calculation for low resolution electrospray ionization data.", diff --git a/data/eslpred/eslpredbioschemas.jsonld b/data/eslpred/eslpredbioschemas.jsonld index 5c662ab408e2c..ede5000ce49a1 100644 --- a/data/eslpred/eslpredbioschemas.jsonld +++ b/data/eslpred/eslpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.", "sc:name": "ESLpred", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.imtech.res.in/raghava/eslpred/" } \ No newline at end of file diff --git a/data/esp/espbioschemas.jsonld b/data/esp/espbioschemas.jsonld index 9eb4da9c8afa0..71edb778af710 100644 --- a/data/esp/espbioschemas.jsonld +++ b/data/esp/espbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/esp", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": "pubmed:23962721", "sc:description": "NHLBI Exome Sequencing Project (ESP): Exome Variant Server (EVS) for browsing single nucleotide variation data from exome sequencing experiments mainly focused on heart, lung and blood disorders.", "sc:name": "ESP", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://evs.gs.washington.edu/EVS/" } \ No newline at end of file diff --git a/data/est2genome/est2genomebioschemas.jsonld b/data/est2genome/est2genomebioschemas.jsonld index 271c85506347e..27cd963408b1d 100644 --- a/data/est2genome/est2genomebioschemas.jsonld +++ b/data/est2genome/est2genomebioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "EMBOSS Contributors", "UK MRC", - "Wellcome Trust", "UK BBSRC", - "EMBOSS Contributors" + "Wellcome Trust" ], "sc:description": "Align EST sequences to genomic DNA sequence.", "sc:funder": [ @@ -26,8 +26,8 @@ "sc:license": "GPL-3.0", "sc:name": "est2genome", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": [ diff --git a/data/est2genome_ws_husar/est2genome_ws_husarbioschemas.jsonld b/data/est2genome_ws_husar/est2genome_ws_husarbioschemas.jsonld index 96a271041b05e..5ba0b2077e1c3 100644 --- a/data/est2genome_ws_husar/est2genome_ws_husarbioschemas.jsonld +++ b/data/est2genome_ws_husar/est2genome_ws_husarbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Align EST and genomic DNA sequences.", "sc:name": "est2genome WS (husar)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/est2genome.html", "sc:version": "1" diff --git a/data/estscan/estscanbioschemas.jsonld b/data/estscan/estscanbioschemas.jsonld index 12f3eeb0bb541..5527090166cbf 100644 --- a/data/estscan/estscanbioschemas.jsonld +++ b/data/estscan/estscanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "ESTScan can detect coding regions (CDS) in DNA sequences, even if they are of low quality. It also detects/corrects sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. The program may miss a few translated amino acids at termini, but detects coding regions with high selectivity and sensitivity.", "sc:name": "ESTscan", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://myhits.isb-sib.ch/cgi-bin/estscan" diff --git a/data/et_report_maker/et_report_makerbioschemas.jsonld b/data/et_report_maker/et_report_makerbioschemas.jsonld index 04316ca12a349..be79a50ffa28e 100644 --- a/data/et_report_maker/et_report_makerbioschemas.jsonld +++ b/data/et_report_maker/et_report_makerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of functional sites of proteins.", "sc:name": "ET Report Maker", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mammoth.bcm.tmc.edu/report_maker/" } \ No newline at end of file diff --git a/data/etandem/etandembioschemas.jsonld b/data/etandem/etandembioschemas.jsonld index fe05adcfd5b7a..6cbb9506916c2 100644 --- a/data/etandem/etandembioschemas.jsonld +++ b/data/etandem/etandembioschemas.jsonld @@ -13,21 +13,21 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", + "EMBOSS Contributors", "UK MRC", - "Wellcome Trust", - "EMBOSS Contributors" + "Wellcome Trust" ], "sc:description": "Find tandem repeats in a nucleotide sequence.", "sc:funder": [ - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "etandem", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ diff --git a/data/etcal/etcalbioschemas.jsonld b/data/etcal/etcalbioschemas.jsonld index 2424be2bbe3cd..aab5cc392b7d2 100644 --- a/data/etcal/etcalbioschemas.jsonld +++ b/data/etcal/etcalbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "LGPL-2.0", "sc:name": "ETCAL", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/kasprowski/etcal", "sc:version": "0.1" diff --git a/data/etox_allies/etox_alliesbioschemas.jsonld b/data/etox_allies/etox_alliesbioschemas.jsonld index 1a284f56e6b22..cb642d9b0a35b 100644 --- a/data/etox_allies/etox_alliesbioschemas.jsonld +++ b/data/etox_allies/etox_alliesbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "eTOX ALLIES", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/GeerkeLab/eTOX-ALLIES" } \ No newline at end of file diff --git a/data/etriks/etriksbioschemas.jsonld b/data/etriks/etriksbioschemas.jsonld index dd8df250ce31e..507c3777956de 100644 --- a/data/etriks/etriksbioschemas.jsonld +++ b/data/etriks/etriksbioschemas.jsonld @@ -34,8 +34,8 @@ ], "sc:name": "eTRIKS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://www.etriks.org/" diff --git a/data/eudysbiome/eudysbiomebioschemas.jsonld b/data/eudysbiome/eudysbiomebioschemas.jsonld index dd03e4b052fe6..519e339326826 100644 --- a/data/eudysbiome/eudysbiomebioschemas.jsonld +++ b/data/eudysbiome/eudysbiomebioschemas.jsonld @@ -13,14 +13,14 @@ "biotools:primaryContact": "Xiaoyuan Zhou", "sc:additionalType": "Command-line tool", "sc:author": [ - "Xiaoyuan Zhou", - "Christine Nardini" + "Christine Nardini", + "Xiaoyuan Zhou" ], "sc:description": "Package to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases or as unknown based on their ambiguous genus classification. It measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.", "sc:name": "eudysbiome", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "BioConductor", diff --git a/data/eugene/eugenebioschemas.jsonld b/data/eugene/eugenebioschemas.jsonld index 6451581956aa4..626916c7e71af 100644 --- a/data/eugene/eugenebioschemas.jsonld +++ b/data/eugene/eugenebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Gene prediction software for eukaryotic organisms. It is currently mainly tuned for plant and fungal genomes.", "sc:name": "EuGene", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "PSB", diff --git a/data/eugene_hom/eugene_hombioschemas.jsonld b/data/eugene_hom/eugene_hombioschemas.jsonld index 9debf3c4c5c0a..9a44ba4d4b546 100644 --- a/data/eugene_hom/eugene_hombioschemas.jsonld +++ b/data/eugene_hom/eugene_hombioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.", "sc:name": "EUGENE HOM", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl" } \ No newline at end of file diff --git a/data/eugenes/eugenesbioschemas.jsonld b/data/eugenes/eugenesbioschemas.jsonld index 8e2e95b795941..4064bb600578a 100644 --- a/data/eugenes/eugenesbioschemas.jsonld +++ b/data/eugenes/eugenesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information.", "sc:name": "euGenes", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://iubio.bio.indiana.edu:8089/" } \ No newline at end of file diff --git a/data/euhcvdb/euhcvdbbioschemas.jsonld b/data/euhcvdb/euhcvdbbioschemas.jsonld index e980e7136c033..1ef89605d465f 100644 --- a/data/euhcvdb/euhcvdbbioschemas.jsonld +++ b/data/euhcvdb/euhcvdbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "European Hepatitis C virus database.", "sc:name": "European Hepatitis C virus database (euHCVdb)", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://euhcvdb.ibcp.fr/euHCVdb/" } \ No newline at end of file diff --git a/data/eupathdb/eupathdbbioschemas.jsonld b/data/eupathdb/eupathdbbioschemas.jsonld index fe44bc606a480..8492a39e81c02 100644 --- a/data/eupathdb/eupathdbbioschemas.jsonld +++ b/data/eupathdb/eupathdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The database portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", "sc:name": "Eukaryotic Pathongen Database Resources (EuPathDB)", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://EuPathDB.org" } \ No newline at end of file diff --git a/data/eurisco/euriscobioschemas.jsonld b/data/eurisco/euriscobioschemas.jsonld index 42931256b6f5a..ec684f262438d 100644 --- a/data/eurisco/euriscobioschemas.jsonld +++ b/data/eurisco/euriscobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkw755", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0003-4031-9131", "@type": "schema:Person" @@ -31,11 +35,11 @@ }, "sc:author": "Stephan Weise", "sc:citation": [ + "pubmed:27580718", + "pmcid:PMC5210606", { "@id": "https://doi.org/10.1093/nar/gkw755" - }, - "pmcid:PMC5210606", - "pubmed:27580718" + } ], "sc:description": "Search catalogue providing information about ex situ plant collections maintained in Europe. It is based on a European network of ex situ National Inventories (NIs). Currently, it comprises information about 1.9 million germplasm accessions from almost 400 holding institutions from 43 countries. It contains both passport data and phenotypic data.", "sc:featureList": { @@ -49,10 +53,6 @@ ], "sc:url": "http://eurisco.ecpgr.org", "sc:version": "1.4.3" - }, - { - "@id": "https://doi.org/10.1093/nar/gkw755", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/eurocarbdb/eurocarbdbbioschemas.jsonld b/data/eurocarbdb/eurocarbdbbioschemas.jsonld index 25a7f437685e3..a96f6d4e21ecd 100644 --- a/data/eurocarbdb/eurocarbdbbioschemas.jsonld +++ b/data/eurocarbdb/eurocarbdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "EuroCarbDB", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://code.google.com/archive/p/eurocarb/" } \ No newline at end of file diff --git a/data/euroformix/euroformixbioschemas.jsonld b/data/euroformix/euroformixbioschemas.jsonld index b5004605337e8..7c467f93c9199 100644 --- a/data/euroformix/euroformixbioschemas.jsonld +++ b/data/euroformix/euroformixbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "EuroForMix", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.euroformix.com/", "sc:version": "2.1.0" diff --git a/data/europe_pmc/europe_pmcbioschemas.jsonld b/data/europe_pmc/europe_pmcbioschemas.jsonld index 7c6118579a45a..383642287d1c1 100644 --- a/data/europe_pmc/europe_pmcbioschemas.jsonld +++ b/data/europe_pmc/europe_pmcbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Archive of life sciences journal literature.", "sc:name": "Europe PMC", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "EMBL-EBI Databases", "sc:url": "http://europepmc.org/" diff --git a/data/europe_pmc_orcid_tool/europe_pmc_orcid_toolbioschemas.jsonld b/data/europe_pmc_orcid_tool/europe_pmc_orcid_toolbioschemas.jsonld index 0d40632f07b65..e56589febe80a 100644 --- a/data/europe_pmc_orcid_tool/europe_pmc_orcid_toolbioschemas.jsonld +++ b/data/europe_pmc_orcid_tool/europe_pmc_orcid_toolbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Europe PMC ORCID Tool", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://europepmc.org/orcid/import", diff --git a/data/europe_pmc_plus_grant_linking/europe_pmc_plus_grant_linkingbioschemas.jsonld b/data/europe_pmc_plus_grant_linking/europe_pmc_plus_grant_linkingbioschemas.jsonld index c8249fc29369b..fcc2bdc153dee 100644 --- a/data/europe_pmc_plus_grant_linking/europe_pmc_plus_grant_linkingbioschemas.jsonld +++ b/data/europe_pmc_plus_grant_linking/europe_pmc_plus_grant_linkingbioschemas.jsonld @@ -15,13 +15,13 @@ "sc:description": "Link grants to their articles.", "sc:name": "Europe PMC plus Grant Linking", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ - "NCBI", "EMBL-EBI", + "NCBI", "Mimas" ], "sc:url": "http://plus.europepmc.org/emss/login/uls.cgi?rss=wt&url=/plus/menu.html", diff --git a/data/europe_pmc_plus_manuscript_submission_system/europe_pmc_plus_manuscript_submission_systembioschemas.jsonld b/data/europe_pmc_plus_manuscript_submission_system/europe_pmc_plus_manuscript_submission_systembioschemas.jsonld index e06162da85324..a3ccddb82fc13 100644 --- a/data/europe_pmc_plus_manuscript_submission_system/europe_pmc_plus_manuscript_submission_systembioschemas.jsonld +++ b/data/europe_pmc_plus_manuscript_submission_system/europe_pmc_plus_manuscript_submission_systembioschemas.jsonld @@ -21,8 +21,8 @@ ], "sc:provider": [ "EMBL-EBI", - "Mimas", - "NCBI" + "NCBI", + "Mimas" ], "sc:url": "http://plus.europepmc.org/emss/login/uls.cgi?rss=wt&url=/plus/menu.html", "sc:version": "1" diff --git a/data/europepmc/europepmcbioschemas.jsonld b/data/europepmc/europepmcbioschemas.jsonld index d0c124e047323..4d7792f1e1402 100644 --- a/data/europepmc/europepmcbioschemas.jsonld +++ b/data/europepmc/europepmcbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This web service gives programmatic access to all of the publications and related information in Europe PubMed Central (Europe PMC).", "sc:name": "EuropePMC", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://europepmc.org", "sc:version": "1" diff --git a/data/europhenome/europhenomebioschemas.jsonld b/data/europhenome/europhenomebioschemas.jsonld index 79ece3235fbba..de0c207aa9575 100644 --- a/data/europhenome/europhenomebioschemas.jsonld +++ b/data/europhenome/europhenomebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or the predicted phenotype.", "sc:name": "EuroPhenome", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.europhenome.org/" } \ No newline at end of file diff --git a/data/eva/evabioschemas.jsonld b/data/eva/evabioschemas.jsonld index 2fbe3592d76bb..c5212c881a291 100644 --- a/data/eva/evabioschemas.jsonld +++ b/data/eva/evabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The European Variation Archive (EVA) accepts submission of, and provides access to, all types of genetic variants from any species, observed in germline or somatic sources, ranging from SNVs to large structural variants. All of our data is open access via direct query through web and/or programmatic interfaces.", "sc:name": "European Variation Archive (EVA)", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ebi.ac.uk", "sc:url": "https://www.ebi.ac.uk/eva/" diff --git a/data/eva_inbred/eva_inbredbioschemas.jsonld b/data/eva_inbred/eva_inbredbioschemas.jsonld index c008a92a4ab56..8a0199c695acb 100644 --- a/data/eva_inbred/eva_inbredbioschemas.jsonld +++ b/data/eva_inbred/eva_inbredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "EVA", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://www.nordgen.org/en/farm-animals/resources/ocs/" } \ No newline at end of file diff --git a/data/evacon/evaconbioschemas.jsonld b/data/evacon/evaconbioschemas.jsonld index 1251995ce0c53..fd0d1658517a0 100644 --- a/data/evacon/evaconbioschemas.jsonld +++ b/data/evacon/evaconbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "EVAcon", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.pdg.cnb.uam.es/eva/con/index.html" } \ No newline at end of file diff --git a/data/evag/evagbioschemas.jsonld b/data/evag/evagbioschemas.jsonld index 02b0644a6956d..826669229eb15 100644 --- a/data/evag/evagbioschemas.jsonld +++ b/data/evag/evagbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Non-profit organisation dedicated to the characterisation, conservation, production, distribution and characterisation of biological materials in the field of virology.", "sc:name": "European Virus Archive", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "rki.de", "sc:url": "http://www.european-virus-archive.com/" diff --git a/data/eventpointer/eventpointerbioschemas.jsonld b/data/eventpointer/eventpointerbioschemas.jsonld index 374b89f41718b..35dfa67f47bff 100644 --- a/data/eventpointer/eventpointerbioschemas.jsonld +++ b/data/eventpointer/eventpointerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "EventPointer", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/EventPointer.html", "sc:version": "1.4.0" diff --git a/data/evex/evexbioschemas.jsonld b/data/evex/evexbioschemas.jsonld index c12b901586898..c4267f50d207c 100644 --- a/data/evex/evexbioschemas.jsonld +++ b/data/evex/evexbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A text mining resource built on top of PubMed abstracts and PubMed Central full texts.", "sc:name": "EVEX", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "PSB", "sc:url": "http://evexdb.org", diff --git a/data/evidence_finder/evidence_finderbioschemas.jsonld b/data/evidence_finder/evidence_finderbioschemas.jsonld index 9dbd616fe46e7..e44f36e4c4f58 100644 --- a/data/evidence_finder/evidence_finderbioschemas.jsonld +++ b/data/evidence_finder/evidence_finderbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Search tool under development in the UKPMC project. It locates sentences that present evidence in the text of research papers. Sentences from 1.5M papers in the UPMC corpus are indexed based on linguistic analysis and NER. Initial search results take the form of questions representing the most frequent types of relevant evidence in the index. On selecting a question, the user may review details of the documents containing the evidence, including the indexed sentences.", "sc:name": "Evidence Finder", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.nactem.ac.uk/UKPMCWS/EvidenceFinder.html" } \ No newline at end of file diff --git a/data/evinet/evinetbioschemas.jsonld b/data/evinet/evinetbioschemas.jsonld index 5b9d2e386fc94..e54c368d86c05 100644 --- a/data/evinet/evinetbioschemas.jsonld +++ b/data/evinet/evinetbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Network enrichment analysis with flexible definition of gene sets.", "sc:name": "EviNet", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.evinet.org", "sc:version": "1.0" diff --git a/data/evlncrna-pred/evlncrna-predbioschemas.jsonld b/data/evlncrna-pred/evlncrna-predbioschemas.jsonld index eec60f78211f8..d416b1c3d0845 100644 --- a/data/evlncrna-pred/evlncrna-predbioschemas.jsonld +++ b/data/evlncrna-pred/evlncrna-predbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Unlicense", "sc:name": "EVlncRNA-pred", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://biophy.dzu.edu.cn/lncrnapred/index.html" } \ No newline at end of file diff --git a/data/evmutation/evmutationbioschemas.jsonld b/data/evmutation/evmutationbioschemas.jsonld index 41aa5ce08db2c..bd1de7da63098 100644 --- a/data/evmutation/evmutationbioschemas.jsonld +++ b/data/evmutation/evmutationbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Debbie Marks", "sc:additionalType": [ - "Command-line tool", - "Database portal" + "Database portal", + "Command-line tool" ], "sc:description": "A statistical method for predicting the effects of mutations.", "sc:name": "EVmutation", diff --git a/data/evodesign/evodesignbioschemas.jsonld b/data/evodesign/evodesignbioschemas.jsonld index 223f064551d87..37a159dcec783 100644 --- a/data/evodesign/evodesignbioschemas.jsonld +++ b/data/evodesign/evodesignbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "EvoDesign web server is an evolutionary profile based approach to de novo protein design. Starting from a scaffold of target protein structure, EvoDesign first identifies protein families which have similar fold from the PDB library by TM-align.", "sc:name": "EvoDesign", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://zhanglab.ccmb.med.umich.edu/EvoDesign" } \ No newline at end of file diff --git a/data/evoker/evokerbioschemas.jsonld b/data/evoker/evokerbioschemas.jsonld index 532fdf475e839..f09603c8a3fd9 100644 --- a/data/evoker/evokerbioschemas.jsonld +++ b/data/evoker/evokerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Graphical tool for visualizing genotype intensity data in order to assess genotype calls as part of quality control procedures for genome-wide association studies.", "sc:name": "Evoker", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.sanger.ac.uk/science/tools/evoker", "sc:version": "2.2" diff --git a/data/evolqg/evolqgbioschemas.jsonld b/data/evolqg/evolqgbioschemas.jsonld index 8e81aa04ce7f4..85a2780d75cbd 100644 --- a/data/evolqg/evolqgbioschemas.jsonld +++ b/data/evolqg/evolqgbioschemas.jsonld @@ -9,42 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.7082.3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/evolqg", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Diogo Melo", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5022708", { "@id": "https://doi.org/10.12688/F1000RESEARCH.7082.3" }, + "pmcid:PMC5022708", "pubmed:27785352" ], "sc:description": "Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.", "sc:featureList": [ - { - "@id": "edam:operation_3799" - }, { "@id": "edam:operation_2937" }, { "@id": "edam:operation_0289" + }, + { + "@id": "edam:operation_3799" } ], "sc:license": "MIT", "sc:name": "EvolQG", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/evolqg/" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.7082.3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/evolview/evolviewbioschemas.jsonld b/data/evolview/evolviewbioschemas.jsonld index 54b036a3d7704..59aa8f8df8b8f 100644 --- a/data/evolview/evolviewbioschemas.jsonld +++ b/data/evolview/evolviewbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for displaying, managing and customizing phylogenetic trees.", "sc:name": "EvolView", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.evolgenius.info/evolview.html", "sc:version": "2" diff --git a/data/evoppi/evoppibioschemas.jsonld b/data/evoppi/evoppibioschemas.jsonld index e96c674b5375e..01eed6e8223be 100644 --- a/data/evoppi/evoppibioschemas.jsonld +++ b/data/evoppi/evoppibioschemas.jsonld @@ -9,26 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-8749-2703", - "@type": "schema:Person" - }, { "@id": "https://orcid.org/0000-0002-3943-8013", "@type": "schema:Person" }, - { - "@id": "https://orcid.org/0000-0002-6476-7206", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0001-7032-5220", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0002-7139-2107", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/EvoPPI", "@type": "sc:SoftwareApplication", @@ -40,22 +24,38 @@ { "@id": "https://orcid.org/0000-0002-6476-7206" }, - "Noé Vázquez", { "@id": "https://orcid.org/0000-0001-8749-2703" - } + }, + "Noé Vázquez" ], "sc:contributor": [ { - "@id": "https://orcid.org/0000-0002-3943-8013" + "@id": "https://orcid.org/0000-0001-7032-5220" }, { - "@id": "https://orcid.org/0000-0001-7032-5220" + "@id": "https://orcid.org/0000-0002-3943-8013" } ], "sc:description": "EvoPPI allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for the same and distinct species.", "sc:name": "EvoPPI", "sc:url": "http://evoppi.i3s.up.pt/" + }, + { + "@id": "https://orcid.org/0000-0001-8749-2703", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0002-7139-2107", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0002-6476-7206", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0001-7032-5220", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/evoprinter/evoprinterbioschemas.jsonld b/data/evoprinter/evoprinterbioschemas.jsonld index 417526c17fc29..321e7743006c2 100644 --- a/data/evoprinter/evoprinterbioschemas.jsonld +++ b/data/evoprinter/evoprinterbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Comparative genomics tool for discovering conserved DNA sequences that are shared among three or more orthologous DNAs.", "sc:name": "EvoPrinter", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://evoprinter.ninds.nih.gov/evoprintprogramHD/evphd.html" } \ No newline at end of file diff --git a/data/evorha/evorhabioschemas.jsonld b/data/evorha/evorhabioschemas.jsonld index 306ccef04913c..884af4178c643 100644 --- a/data/evorha/evorhabioschemas.jsonld +++ b/data/evorha/evorhabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Evolutionary reconstruction of haplotypes.", "sc:name": "EVORhA", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/kmarchal/EVORhA/", diff --git a/data/ewas/ewasbioschemas.jsonld b/data/ewas/ewasbioschemas.jsonld index ab877029b5fab..3dbe485883ea9 100644 --- a/data/ewas/ewasbioschemas.jsonld +++ b/data/ewas/ewasbioschemas.jsonld @@ -11,13 +11,13 @@ "@id": "https://bio.tools/EWAS", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yongshuai Jiang", "Fanwu Kong", - "Liangde Xu" + "Liangde Xu", + "Yongshuai Jiang" ], "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Epigenome-wide association study software.", "sc:license": "Unlicense", diff --git a/data/exac/exacbioschemas.jsonld b/data/exac/exacbioschemas.jsonld index e51e494b9e76a..69bb38b3bd289 100644 --- a/data/exac/exacbioschemas.jsonld +++ b/data/exac/exacbioschemas.jsonld @@ -25,33 +25,33 @@ "Web application" ], "sc:citation": [ + "pubmed:27899611", + "pmcid:PMC5210650", { "@id": "https://doi.org/10.1093/nar/gkw971" - }, - "pubmed:27899611", - "pmcid:PMC5210650" + } ], "sc:description": "Exome aggregation consortium (ExAC) - browser framework to display large population datasets of genetic variation. The browser aggregates exome sequencing data from a wide variety of large-scale sequencing projects, and to make summary data available for the wider scientific community.", "sc:featureList": [ { - "@id": "edam:operation_3436" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_2403" + "@id": "edam:operation_2421" }, { - "@id": "edam:operation_2421" + "@id": "edam:operation_2403" }, { - "@id": "edam:operation_3197" + "@id": "edam:operation_3436" } ], "sc:license": "ODbL-1.0", "sc:name": "ExAC", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://exac.broadinstitute.org" } diff --git a/data/exalign/exalignbioschemas.jsonld b/data/exalign/exalignbioschemas.jsonld index b6fd2f121d62e..d2e116fcfc5ca 100644 --- a/data/exalign/exalignbioschemas.jsonld +++ b/data/exalign/exalignbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/exalign", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Federico Zambelli", - "Giulio Pavesi" + "Giulio Pavesi", + "Federico Zambelli" ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Compare and search the exon-intron structure of existing gene annotations.", "sc:license": "GPL-3.0", "sc:name": "Exalign", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-MILANO", "sc:url": "http://www.beaconlab.it/exalign", diff --git a/data/examine/examinebioschemas.jsonld b/data/examine/examinebioschemas.jsonld index 3ad0e04eebfc7..71780f332ec24 100644 --- a/data/examine/examinebioschemas.jsonld +++ b/data/examine/examinebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "eXamine", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/ls-cwi/eXamine" } \ No newline at end of file diff --git a/data/excape-db/excape-dbbioschemas.jsonld b/data/excape-db/excape-dbbioschemas.jsonld index be94f44d65165..18274241ca310 100644 --- a/data/excape-db/excape-dbbioschemas.jsonld +++ b/data/excape-db/excape-dbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Integrated large scale dataset facilitating Big Data analysis in chemogenomics.", "sc:name": "ExCAPE-DB", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://solr.ideaconsult.net/search/excape/" diff --git a/data/excemplify/excemplifybioschemas.jsonld b/data/excemplify/excemplifybioschemas.jsonld index b7f2dc29382f4..7b89979b28b5c 100644 --- a/data/excemplify/excemplifybioschemas.jsonld +++ b/data/excemplify/excemplifybioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Web-based application that was developed to support the exchange and long-time storage of experimental data, especially spreadsheets in general and immunoblot-related experiments in particular. It is able to parse these data from the initial experimental setup stage and to automatically generate the following spreadsheet stages in the experimental workflow.", "sc:name": "Excemplify", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "HITS", "sc:url": "http://sabiork.h-its.org/excemplify/", diff --git a/data/exibd/exibdbioschemas.jsonld b/data/exibd/exibdbioschemas.jsonld index e209edbb67e6f..dea0ada54479b 100644 --- a/data/exibd/exibdbioschemas.jsonld +++ b/data/exibd/exibdbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/j.ajhg.2016.09.011", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/exibd", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27745837", "pmcid:PMC5097937", { "@id": "https://doi.org/10.1016/j.ajhg.2016.09.011" - } + }, + "pubmed:27745837" ], "sc:description": "Software package for detecting Identity-by-descent (IBD) segments in exome sequencing data.", "sc:featureList": [ @@ -37,6 +33,10 @@ "sc:name": "ExIBD", "sc:operatingSystem": "Linux", "sc:url": "http://akeylab.princeton.edu/downloads.html" + }, + { + "@id": "https://doi.org/10.1016/j.ajhg.2016.09.011", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/eximir/eximirbioschemas.jsonld b/data/eximir/eximirbioschemas.jsonld index f4e7102afa9eb..4c4aaf7893e8d 100644 --- a/data/eximir/eximirbioschemas.jsonld +++ b/data/eximir/eximirbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sylvain Gubian", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.", "sc:license": "GPL-2.0", diff --git a/data/exms/exmsbioschemas.jsonld b/data/exms/exmsbioschemas.jsonld index 5135d773f79c6..08b3067aca02b 100644 --- a/data/exms/exmsbioschemas.jsonld +++ b/data/exms/exmsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "MATLAB program for analyzing H/D-exchange data.", "sc:name": "ExMS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://hx2.med.upenn.edu/download.html" } \ No newline at end of file diff --git a/data/exocarta/exocartabioschemas.jsonld b/data/exocarta/exocartabioschemas.jsonld index 71e61fb0194c3..31411ad9ac5f5 100644 --- a/data/exocarta/exocartabioschemas.jsonld +++ b/data/exocarta/exocartabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Manually curated database of exosomal proteins, RNA, and lipids. Catalogs information from both published and unpublished exosomal studies. Currently contains info on 11,261 protein entries, 2375 mRNA entries, and 764 miRNA entries obtained from 134 exosomal studies.", "sc:name": "ExoCarta", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.exocarta.org/" } \ No newline at end of file diff --git a/data/exolocator/exolocatorbioschemas.jsonld b/data/exolocator/exolocatorbioschemas.jsonld index e0d1f3ddcca7b..e37ae250bec2f 100644 --- a/data/exolocator/exolocatorbioschemas.jsonld +++ b/data/exolocator/exolocatorbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "ExoLocator is a database of protein coding exons from completed vertebrate genomes in Ensembl. Exons are organized into alignments of ortologous and paralogous sequences, and when an exon appears to be missing form a species, we look for it using our own hardware accelerated version of Smith-Waterman algorithm.", "sc:name": "ExoLocator", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://exolocator.bii.a-star.edu.sg/" diff --git a/data/exomecnv/exomecnvbioschemas.jsonld b/data/exomecnv/exomecnvbioschemas.jsonld index 68cea829d297f..d63254400088f 100644 --- a/data/exomecnv/exomecnvbioschemas.jsonld +++ b/data/exomecnv/exomecnvbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ExomeCNV", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/src/contrib/Archive/ExomeCNV/" } \ No newline at end of file diff --git a/data/exomecopy/exomecopybioschemas.jsonld b/data/exomecopy/exomecopybioschemas.jsonld index 6908b22bc610d..3c025da88ee29 100644 --- a/data/exomecopy/exomecopybioschemas.jsonld +++ b/data/exomecopy/exomecopybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Love", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.", "sc:license": "GPL-2.0", "sc:name": "exomeCopy", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/exomeCopy.html", "sc:version": "1.20.0" diff --git a/data/exomedepth/exomedepthbioschemas.jsonld b/data/exomedepth/exomedepthbioschemas.jsonld index dc3317b520150..4f87af4afabdb 100644 --- a/data/exomedepth/exomedepthbioschemas.jsonld +++ b/data/exomedepth/exomedepthbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/bts526", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/exomedepth", "@type": "sc:SoftwareApplication", @@ -20,35 +16,39 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:22942019", + "pmcid:PMC3476336", { "@id": "https://doi.org/10.1093/bioinformatics/bts526" - }, - "pmcid:PMC3476336" + } ], "sc:description": "Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.", "sc:featureList": [ { "@id": "edam:operation_3196" }, - { - "@id": "edam:operation_3233" - }, { "@id": "edam:operation_2403" }, { "@id": "edam:operation_3227" + }, + { + "@id": "edam:operation_3233" } ], "sc:license": "GPL-3.0", "sc:name": "ExomeDepth", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/ExomeDepth/index.html", "sc:version": "1.1.10" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/bts526", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/exomepeak/exomepeakbioschemas.jsonld b/data/exomepeak/exomepeakbioschemas.jsonld index 11177b6e3f14b..138dc42010d89 100644 --- a/data/exomepeak/exomepeakbioschemas.jsonld +++ b/data/exomepeak/exomepeakbioschemas.jsonld @@ -13,20 +13,20 @@ "@id": "https://bio.tools/exomepeak", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Jia Meng", "Lian Liu", - "Lin Zhang", - "Jia Meng" + "Lin Zhang" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pubmed:24979058", + "pmcid:PMC4194139", { "@id": "https://doi.org/10.1016/j.ymeth.2014.06.008" - }, - "pubmed:24979058", - "pmcid:PMC4194139" + } ], "sc:description": "The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built based on the MATLAB package (Meng, Jia, et al. \"Exome-based analysis for RNA epigenome sequencing data.\" Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome.", "sc:featureList": { @@ -35,8 +35,8 @@ "sc:license": "GPL-2.0", "sc:name": "exomePeak", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/exomePeak.html", diff --git a/data/exomiser/exomiserbioschemas.jsonld b/data/exomiser/exomiserbioschemas.jsonld index b57385c93df20..9617aafc6f158 100644 --- a/data/exomiser/exomiserbioschemas.jsonld +++ b/data/exomiser/exomiserbioschemas.jsonld @@ -17,38 +17,38 @@ "@id": "https://bio.tools/exomiser", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr Jules Jacobsen", - "Dr Damian Smedley" + "Dr Damian Smedley", + "Dr Jules Jacobsen" ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:26562621", { "@id": "https://doi.org/10.1038/nprot.2015.124" }, - "pubmed:26562621", "pmcid:PMC5467691" ], "sc:description": "A program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. Starting from a VCF file and a set of phenotypes encoded using the Human Phenotype Ontology (HPO) it will annotate, filter and prioritise likely causative variants depending on the user-defined criteria.", "sc:featureList": [ { - "@id": "edam:operation_2403" + "@id": "edam:operation_3695" }, { "@id": "edam:operation_3226" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_2403" }, { - "@id": "edam:operation_3695" + "@id": "edam:operation_3436" } ], "sc:license": "GPL-3.0", "sc:name": "Exomiser", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.sanger.ac.uk/science/tools/exomiser" } diff --git a/data/exon_array_analyzer/exon_array_analyzerbioschemas.jsonld b/data/exon_array_analyzer/exon_array_analyzerbioschemas.jsonld index d3aba79bf1d6b..d1163ab71089e 100644 --- a/data/exon_array_analyzer/exon_array_analyzerbioschemas.jsonld +++ b/data/exon_array_analyzer/exon_array_analyzerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Exon Array Analyzer (EAA) allow to process CEL files from Affymetrix, Inc. GeneChip® Exon 1.0 ST Arrays. Various processign steps and visualizations are implemented to identify alternative splicing events. Three simple steps have to be performed to submit a set of CEL files. After the processing is completed the results can be viewed in the browser.", "sc:name": "Exon Array Analyzer", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://eaa.mpi-bn.mpg.de" } \ No newline at end of file diff --git a/data/expa/expabioschemas.jsonld b/data/expa/expabioschemas.jsonld index 92a239547f86a..173da87a76c7f 100644 --- a/data/expa/expabioschemas.jsonld +++ b/data/expa/expabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "ExPa (extreme pathways analysis) , a generating set for all possible steady state flux maps in a biochemical reaction network, can be computed from the stoichiometric matrix, an incidence-like matrix reflecting the network topology. ExPa compute these pathways.", "sc:name": "ExPA", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://gcrg.ucsd.edu/Downloads/ExtremePathwayAnalysis", "sc:version": "50216" diff --git a/data/expander/expanderbioschemas.jsonld b/data/expander/expanderbioschemas.jsonld index 60247540f8182..e42979f9f51b5 100644 --- a/data/expander/expanderbioschemas.jsonld +++ b/data/expander/expanderbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "EXPANDER", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://acgt.cs.tau.ac.il/expander/" } \ No newline at end of file diff --git a/data/exparna-p/exparna-pbioschemas.jsonld b/data/exparna-p/exparna-pbioschemas.jsonld index 17fb11e020dc0..91fcd02a177c6 100644 --- a/data/exparna-p/exparna-pbioschemas.jsonld +++ b/data/exparna-p/exparna-pbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-8231-3323", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/exparna-p", "@type": "sc:SoftwareApplication", @@ -73,10 +77,6 @@ { "@id": "https://doi.org/10.1186/s12859-014-0404-0", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-8231-3323", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/exparna/exparnabioschemas.jsonld b/data/exparna/exparnabioschemas.jsonld index a72984567b9b9..3746602a2c2c7 100644 --- a/data/exparna/exparnabioschemas.jsonld +++ b/data/exparna/exparnabioschemas.jsonld @@ -9,15 +9,27 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btp065", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-9497-7538", + "@type": "schema:Person" + }, + { + "@id": "http://orcid.org/0000-0001-8231-3323", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/exparna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "http://orcid.org/0000-0001-8231-3323" + "@id": "http://orcid.org/0000-0002-9497-7538" }, { - "@id": "http://orcid.org/0000-0002-9497-7538" + "@id": "http://orcid.org/0000-0001-8231-3323" } ], "edam:has_input": { @@ -35,10 +47,10 @@ "Steffen Heyne" ], "sc:citation": [ - "pubmed:19189979", { "@id": "https://doi.org/10.1093/bioinformatics/btp065" }, + "pubmed:19189979", "pmcid:PMC2722993" ], "sc:description": "Structure motif based alignment generation.", @@ -57,18 +69,6 @@ }, "sc:url": "http://www.bioinf.uni-freiburg.de/Software/#ExpaRNA-download", "sc:version": "1.0.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btp065", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-9497-7538", - "@type": "schema:Person" - }, - { - "@id": "http://orcid.org/0000-0001-8231-3323", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/expasy/expasybioschemas.jsonld b/data/expasy/expasybioschemas.jsonld index dd768585d9582..86cf1ea9c16a5 100644 --- a/data/expasy/expasybioschemas.jsonld +++ b/data/expasy/expasybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ExPASy is the bioinformatics resource portal for access to programs and databases for the analysis of proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.", "sc:name": "ExPASy", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.expasy.org/" } \ No newline at end of file diff --git a/data/expedition/expeditionbioschemas.jsonld b/data/expedition/expeditionbioschemas.jsonld index 544de532ee0d6..c8e6e4e62816d 100644 --- a/data/expedition/expeditionbioschemas.jsonld +++ b/data/expedition/expeditionbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Expedition", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/YeoLab/Expedition" } \ No newline at end of file diff --git a/data/experimenthub/experimenthubbioschemas.jsonld b/data/experimenthub/experimenthubbioschemas.jsonld index 9ec2dc5858236..18e956e221f41 100644 --- a/data/experimenthub/experimenthubbioschemas.jsonld +++ b/data/experimenthub/experimenthubbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "ExperimentHub", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ExperimentHub.html", "sc:version": "1.0.0" diff --git a/data/experimenthubdata/experimenthubdatabioschemas.jsonld b/data/experimenthubdata/experimenthubdatabioschemas.jsonld index 77123a0d3224c..c415d93826a05 100644 --- a/data/experimenthubdata/experimenthubdatabioschemas.jsonld +++ b/data/experimenthubdata/experimenthubdatabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "ExperimentHubData", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ExperimentHubData.html", "sc:version": "1.0.0" diff --git a/data/explora/explorabioschemas.jsonld b/data/explora/explorabioschemas.jsonld index 0938bd67d80b3..717c7233389d0 100644 --- a/data/explora/explorabioschemas.jsonld +++ b/data/explora/explorabioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-2169-4588", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/nar/gkw298", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/explora", "@type": "sc:SoftwareApplication", @@ -53,6 +45,14 @@ "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/explora-web/", "sc:version": "1" + }, + { + "@id": "http://orcid.org/0000-0002-2169-4588", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gkw298", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/explorase/explorasebioschemas.jsonld b/data/explorase/explorasebioschemas.jsonld index 3a812e2250ae6..cea69c2961947 100644 --- a/data/explorase/explorasebioschemas.jsonld +++ b/data/explorase/explorasebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "explorase", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/explorase.html", "sc:version": "1.38.0" diff --git a/data/export_sbw/export_sbwbioschemas.jsonld b/data/export_sbw/export_sbwbioschemas.jsonld index 02de61411b25a..5c556c4fd7745 100644 --- a/data/export_sbw/export_sbwbioschemas.jsonld +++ b/data/export_sbw/export_sbwbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Export history data for SynBioWatch projet files and user.", "sc:name": "export_sbw", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/export_sbw/export_sbw/1.0", "sc:version": "1.0" diff --git a/data/express/expressbioschemas.jsonld b/data/express/expressbioschemas.jsonld index 742ad3fb0b46c..9b3d1aab78b34 100644 --- a/data/express/expressbioschemas.jsonld +++ b/data/express/expressbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Apache-2.0", "sc:name": "eXpress", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://pachterlab.github.io/eXpress/index.html", "sc:version": "1.5.1" diff --git a/data/expression_atlas/expression_atlasbioschemas.jsonld b/data/expression_atlas/expression_atlasbioschemas.jsonld index 69e3c09b416f9..a07547f449133 100644 --- a/data/expression_atlas/expression_atlasbioschemas.jsonld +++ b/data/expression_atlas/expression_atlasbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Open science resource that gives users a powerful way to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others.", "sc:name": "Expression Atlas", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI Databases", "sc:url": "https://www.ebi.ac.uk/gxa/" diff --git a/data/expressionatlas/expressionatlasbioschemas.jsonld b/data/expressionatlas/expressionatlasbioschemas.jsonld index 3ff48eba436b0..70688983da6a7 100644 --- a/data/expressionatlas/expressionatlasbioschemas.jsonld +++ b/data/expressionatlas/expressionatlasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "ExpressionAtlas", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ExpressionAtlas.html", diff --git a/data/expressionview/expressionviewbioschemas.jsonld b/data/expressionview/expressionviewbioschemas.jsonld index 56d21d371628f..696c3e6d9c696 100644 --- a/data/expressionview/expressionviewbioschemas.jsonld +++ b/data/expressionview/expressionviewbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "ExpressionView", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www2.unil.ch/cbg/index.php?title=ExpressionView", "sc:version": "1.26.0" diff --git a/data/expresso/expressobioschemas.jsonld b/data/expresso/expressobioschemas.jsonld index 7a37ff76fe1c9..e225dc6df63d8 100644 --- a/data/expresso/expressobioschemas.jsonld +++ b/data/expresso/expressobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/expresso", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Delasa Aghamirzaie", - "Karthik Raja Velmurugan" + "Karthik Raja Velmurugan", + "Delasa Aghamirzaie" ], "sc:additionalType": "Web application", "sc:description": "identify and explore the binding of transcription factors to their target genes in plants using available ChIP-Seq data.", diff --git a/data/expressyourself/expressyourselfbioschemas.jsonld b/data/expressyourself/expressyourselfbioschemas.jsonld index a3eeb570cbe02..2ca7c1a7db0cb 100644 --- a/data/expressyourself/expressyourselfbioschemas.jsonld +++ b/data/expressyourself/expressyourselfbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.", "sc:name": "ExpressYourself", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://array.mbb.yale.edu/analysis/" diff --git a/data/expvip/expvipbioschemas.jsonld b/data/expvip/expvipbioschemas.jsonld index 6b2f136d98a66..8d52bf14c455f 100644 --- a/data/expvip/expvipbioschemas.jsonld +++ b/data/expvip/expvipbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Cristobal Uauy", "sc:additionalType": "Database portal", "sc:citation": [ + "pmcid:PMC4825114", "pubmed:26869702", { "@id": "https://doi.org/10.1104/PP.15.01667" - }, - "pmcid:PMC4825114" + } ], "sc:description": "Customizable RNA-seq Data Analysis and Visualization Platform.", "sc:featureList": [ diff --git a/data/extract/extractbioschemas.jsonld b/data/extract/extractbioschemas.jsonld index e28b26624f817..e15bc64ded9ca 100644 --- a/data/extract/extractbioschemas.jsonld +++ b/data/extract/extractbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/database/baw005", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/extract", "@type": "sc:SoftwareApplication", @@ -24,19 +20,19 @@ "@id": "edam:data_3779" }, "sc:additionalType": [ - "Web application", "Web API", - "Web service" + "Web service", + "Web application" ], "sc:applicationSubCategory": { "@id": "edam:topic_0218" }, "sc:citation": [ - "pubmed:26896844", + "pmcid:PMC4761108", { "@id": "https://doi.org/10.1093/database/baw005" }, - "pmcid:PMC4761108" + "pubmed:26896844" ], "sc:description": "EXTRACT identifies genes/proteins, chemical compounds, organisms, environments, tissues, diseases, phenotypes and Gene Ontology terms mentioned in a given piece of text and maps them to their corresponding ontology/taxonomy entries.", "sc:featureList": { @@ -52,6 +48,10 @@ ], "sc:url": "https://extract.jensenlab.org/", "sc:version": "2.0" + }, + { + "@id": "https://doi.org/10.1093/database/baw005", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/extract_archive_merge/extract_archive_mergebioschemas.jsonld b/data/extract_archive_merge/extract_archive_mergebioschemas.jsonld index 2b061f607444c..dd2b11e08339f 100644 --- a/data/extract_archive_merge/extract_archive_mergebioschemas.jsonld +++ b/data/extract_archive_merge/extract_archive_mergebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool for decompressing an archive file (zip, gz, tar.gz, fastq.gz, fastq.bz2 or tar.bz2) and merging all files into only one.", "sc:name": "extract_archive_merge", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=extract_archive_merge", "sc:version": "1.0.0" diff --git a/data/extractalign/extractalignbioschemas.jsonld b/data/extractalign/extractalignbioschemas.jsonld index 16525d2bb9abd..8c478452ce8da 100644 --- a/data/extractalign/extractalignbioschemas.jsonld +++ b/data/extractalign/extractalignbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "UK BBSRC", - "Wellcome Trust", - "EMBOSS Contributors" + "UK MRC", + "EMBOSS Contributors", + "Wellcome Trust" ], "sc:description": "Extract regions from a sequence alignment.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "extractalign", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/extractcentralregions/extractcentralregionsbioschemas.jsonld b/data/extractcentralregions/extractcentralregionsbioschemas.jsonld index 88b11eb0b6032..e0fe2874ecaca 100644 --- a/data/extractcentralregions/extractcentralregionsbioschemas.jsonld +++ b/data/extractcentralregions/extractcentralregionsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Extract central regions of ChIP-seq peaks.", "sc:name": "extractcentralregions", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/extractcentralregions/extractCentralRegions/1.0", "sc:version": "1.0" diff --git a/data/extractfeat/extractfeatbioschemas.jsonld b/data/extractfeat/extractfeatbioschemas.jsonld index 568010570b7ce..413715d54c962 100644 --- a/data/extractfeat/extractfeatbioschemas.jsonld +++ b/data/extractfeat/extractfeatbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:contributor": [ "UK BBSRC", "Wellcome Trust", - "EMBOSS Contributors", - "UK MRC" + "UK MRC", + "EMBOSS Contributors" ], "sc:description": "Extract some features from sequence(s).", "sc:funder": [ @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "extractfeat", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/extractfeat.html", "sc:version": "r6" diff --git a/data/extractseq/extractseqbioschemas.jsonld b/data/extractseq/extractseqbioschemas.jsonld index c4269d2d939e8..f06cb8388caa4 100644 --- a/data/extractseq/extractseqbioschemas.jsonld +++ b/data/extractseq/extractseqbioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK MRC", - "UK BBSRC", + "EMBOSS Contributors", "Wellcome Trust", - "EMBOSS Contributors" + "UK BBSRC" ], "sc:description": "Extract regions from a sequence.", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "extractseq", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/extractseq.html", "sc:version": "r6" diff --git a/data/faapred/faapredbioschemas.jsonld b/data/faapred/faapredbioschemas.jsonld index 2dc299be52728..b3dfedf855746 100644 --- a/data/faapred/faapredbioschemas.jsonld +++ b/data/faapred/faapredbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "FaaPred is a SVM-based prediction method for fungal adhesins and adhesin-like proteins", "sc:name": "FaaPred", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioinfo.icgeb.res.in/faap/" } \ No newline at end of file diff --git a/data/faas/faasbioschemas.jsonld b/data/faas/faasbioschemas.jsonld index efdf1b0e12d9b..af9a29b33986c 100644 --- a/data/faas/faasbioschemas.jsonld +++ b/data/faas/faasbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.2-68.V1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/faas", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC3752736", { "@id": "https://doi.org/10.12688/F1000RESEARCH.2-68.V1" }, - "pubmed:24358855" + "pubmed:24358855", + "pmcid:PMC3752736" ], "sc:description": "Focal Adhesion Analysis Server. Implements a set of computer vision algorithms designed to automatically process time-lapse images of fluorescently labeled focal adhesion proteins in motile cells.", "sc:featureList": { @@ -26,10 +30,6 @@ }, "sc:name": "FAAS", "sc:url": "http://faas.bme.unc.edu" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.2-68.V1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fabia/fabiabioschemas.jsonld b/data/fabia/fabiabioschemas.jsonld index 63813c6ee37e8..74cf2796aafa6 100644 --- a/data/fabia/fabiabioschemas.jsonld +++ b/data/fabia/fabiabioschemas.jsonld @@ -24,15 +24,15 @@ "@id": "http://orcid.org/0000-0001-7449-2528" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC2881408", - "pubmed:20418340", { "@id": "https://doi.org/10.1093/bioinformatics/btq227" - } + }, + "pubmed:20418340" ], "sc:description": "Model-based technique for biclustering where the biclusters are found by factor analysis. It is a multiplicative model that extracts linear dependencies between samples and feature patterns capturing realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. Finally, it ranks biclusters according to their information content and separates spurious biclusters from true biclusters.", "sc:featureList": [ @@ -46,9 +46,9 @@ "sc:license": "GPL-2.0", "sc:name": "fabia", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/fabia.html", "sc:version": "2.20.0" diff --git a/data/fabox/faboxbioschemas.jsonld b/data/fabox/faboxbioschemas.jsonld index c78300150a197..c12b56005ec7e 100644 --- a/data/fabox/faboxbioschemas.jsonld +++ b/data/fabox/faboxbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An online fasta sequence toolbox.", "sc:name": "FASTA online toolbox", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "birc.au.dk", "sc:url": "http://users-birc.au.dk/palle/php/fabox/", diff --git a/data/facets/facetsbioschemas.jsonld b/data/facets/facetsbioschemas.jsonld index 9439ecb3523d4..0385da6c03bc4 100644 --- a/data/facets/facetsbioschemas.jsonld +++ b/data/facets/facetsbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Venkatraman E. Seshan", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27270079", "pmcid:PMC5027494", { "@id": "https://doi.org/10.1093/nar/gkw520" - } + }, + "pubmed:27270079" ], "sc:description": "FACETS is an ASCN tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:license": "Other", "sc:name": "FACETS", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sites.google.com/site/mskfacets/" }, diff --git a/data/facopy/facopybioschemas.jsonld b/data/facopy/facopybioschemas.jsonld index 68184f642354e..2422fe7911fd2 100644 --- a/data/facopy/facopybioschemas.jsonld +++ b/data/facopy/facopybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David Mosen-Ansorena", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Package for fine-tuned cancer CNA association modeling. Association is measured directly at the genomic features of interest and, in the case of genes, downstream gene-set enrichment analysis can be performed thanks to novel internal processing of the data. The software opens a way to systematically scrutinize the differences in CNA distribution across tumoral phenotypes, such as those that relate to tumor type, location and progression.", "sc:license": "CC-BY-NC-4.0", "sc:name": "facopy", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/facopy.html", "sc:version": "1.8.0" diff --git a/data/facta_plus/facta_plusbioschemas.jsonld b/data/facta_plus/facta_plusbioschemas.jsonld index 6dea6a8a89660..8cda1d124dbae 100644 --- a/data/facta_plus/facta_plusbioschemas.jsonld +++ b/data/facta_plus/facta_plusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed, with additional features to help users to discover and visualize indirect associations between important biomedical concepts such as genes, diseases and chemical compounds.", "sc:name": "FACTA plus", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://refine1-nactem.mc.man.ac.uk/facta/" } \ No newline at end of file diff --git a/data/factdesign/factdesignbioschemas.jsonld b/data/factdesign/factdesignbioschemas.jsonld index daf9e614a33eb..9741c3e7ba1d8 100644 --- a/data/factdesign/factdesignbioschemas.jsonld +++ b/data/factdesign/factdesignbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Denise Scholtens", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.", "sc:license": "GPL-3.0", diff --git a/data/fairdatapoint/fairdatapointbioschemas.jsonld b/data/fairdatapoint/fairdatapointbioschemas.jsonld index 47a8638e46e70..c7a2825064735 100644 --- a/data/fairdatapoint/fairdatapointbioschemas.jsonld +++ b/data/fairdatapoint/fairdatapointbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-1164-1351", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0002-1215-167X", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/FAIRDataPoint", "@type": "sc:SoftwareApplication", @@ -39,8 +31,8 @@ "Kees burger" ], "sc:contributor": [ - "Kees burger", "Mark Thompson", + "Kees burger", { "@id": "https://orcid.org/0000-0002-1215-167X" } @@ -54,6 +46,14 @@ "Windows" ], "sc:url": "https://github.com/FAIRDataTeam/FAIRDataPoint" + }, + { + "@id": "https://orcid.org/0000-0002-1164-1351", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0002-1215-167X", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/falc-loop/falc-loopbioschemas.jsonld b/data/falc-loop/falc-loopbioschemas.jsonld index 2c1de4fdda606..fc1324b3120a6 100644 --- a/data/falc-loop/falc-loopbioschemas.jsonld +++ b/data/falc-loop/falc-loopbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/falc-loop", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:21576220", "sc:description": "Web server allows for protein loop modeling by employing the fragment assembly and analytical loop closure (FALC) loop modeling method.", diff --git a/data/falcon/falconbioschemas.jsonld b/data/falcon/falconbioschemas.jsonld index ed1374fd4e19f..9962eeaa64a0c 100644 --- a/data/falcon/falconbioschemas.jsonld +++ b/data/falcon/falconbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Experimental PacBio diploid assembler.", "sc:name": "Falcon", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/pratas/falcon" } \ No newline at end of file diff --git a/data/famagg/famaggbioschemas.jsonld b/data/famagg/famaggbioschemas.jsonld index 575283eea6b4a..db462bef9b09d 100644 --- a/data/famagg/famaggbioschemas.jsonld +++ b/data/famagg/famaggbioschemas.jsonld @@ -16,15 +16,15 @@ "@id": "http://orcid.org/0000-0002-6977-7147" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ { "@id": "https://doi.org/10.1093/bioinformatics/btw019" }, - "pubmed:26803158", - "pmcid:PMC4866523" + "pmcid:PMC4866523", + "pubmed:26803158" ], "sc:description": "Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.", "sc:featureList": { @@ -33,9 +33,9 @@ "sc:license": "MIT", "sc:name": "FamAgg", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/FamAgg.html", "sc:version": "1.2.1" diff --git a/data/fame/famebioschemas.jsonld b/data/fame/famebioschemas.jsonld index cd0487cefc532..6a7b47acdfaf1 100644 --- a/data/fame/famebioschemas.jsonld +++ b/data/fame/famebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-2-Clause", "sc:name": "FAME", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://f-a-m-e.fame-vu.surf-hosted.nl/ajax/page1.php" } \ No newline at end of file diff --git a/data/famflm/famflmbioschemas.jsonld b/data/famflm/famflmbioschemas.jsonld index 9dcf7f2a33bfb..548eff81c09a0 100644 --- a/data/famflm/famflmbioschemas.jsonld +++ b/data/famflm/famflmbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/famflm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Gulnara Svishcheva", - "Nadezhda Belonogova" + "Nadezhda Belonogova", + "Gulnara Svishcheva" ], "sc:additionalType": "Command-line tool", "sc:description": "A region-based association test for familial data under functional linear models", diff --git a/data/famplex/famplexbioschemas.jsonld b/data/famplex/famplexbioschemas.jsonld index e1e3f8ab89d37..47dfdd120ce44 100644 --- a/data/famplex/famplexbioschemas.jsonld +++ b/data/famplex/famplexbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC0-1.0", "sc:name": "FamPlex", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/sorgerlab/famplex" } \ No newline at end of file diff --git a/data/fangorn_forest/fangorn_forestbioschemas.jsonld b/data/fangorn_forest/fangorn_forestbioschemas.jsonld index 2b67dd81ebecb..3b33544dd84d3 100644 --- a/data/fangorn_forest/fangorn_forestbioschemas.jsonld +++ b/data/fangorn_forest/fangorn_forestbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/fangorn_forest", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Fabio R. Cerqueira", - "Elizabeth P. B. Fontes" + "Elizabeth P. B. Fontes", + "Fabio R. Cerqueira" ], "sc:additionalType": "Database portal", "sc:description": "Machine learning approach to classify genes and genera in the family Geminiviridae.", "sc:name": "Fangorn Forest (F2)", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.geminivirus.org:8080/geminivirusdw/discoveryGeminivirus.jsp" } \ No newline at end of file diff --git a/data/fanmod/fanmodbioschemas.jsonld b/data/fanmod/fanmodbioschemas.jsonld index bda48b66dbf8e..da6e740895c19 100644 --- a/data/fanmod/fanmodbioschemas.jsonld +++ b/data/fanmod/fanmodbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Fast Network Motif Detection is for fast network motif detection; it relies on recently developed algorithms to improve the efficiency of network motif detection by some orders of magnitude over existing tools. This facilitates the detection of larger motifs in bigger networks than previously possible. Its additional benefits are the ability to analyze colored networks, a graphical user interface and the ability to export results to a variety of machine- and human-readable file formats.", "sc:name": "FANMOD", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://theinf1.informatik.uni-jena.de/~wernicke/motifs/index.html", "sc:version": "20061223" diff --git a/data/fantom_funannotmouse/fantom_funannotmousebioschemas.jsonld b/data/fantom_funannotmouse/fantom_funannotmousebioschemas.jsonld index b0ac371486015..39de792523dd7 100644 --- a/data/fantom_funannotmouse/fantom_funannotmousebioschemas.jsonld +++ b/data/fantom_funannotmouse/fantom_funannotmousebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/fantom_funannotmouse", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "for inquiry to the FANTOM Administrative Office", - "questions or comments on Annotation or FANTOM system" + "questions or comments on Annotation or FANTOM system", + "for inquiry to the FANTOM Administrative Office" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:15383211", diff --git a/data/fardeep/fardeepbioschemas.jsonld b/data/fardeep/fardeepbioschemas.jsonld index 5fa33d1e9fb5e..68a4a9dba38a0 100644 --- a/data/fardeep/fardeepbioschemas.jsonld +++ b/data/fardeep/fardeepbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-1049-2219", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0002-9868-9824", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/FARDEEP", "@type": "sc:SoftwareApplication", @@ -22,11 +30,11 @@ ], "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6522071", - "pubmed:31059559", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006976" - } + }, + "pubmed:31059559", + "pmcid:PMC6522071" ], "sc:description": "Fast And Robust DEconvolution of Expression Profiles (FARDEEP) - machine learning tool for enumerating immune cell subsets from whole tumor tissue samples.", "sc:featureList": [ @@ -49,14 +57,6 @@ ], "sc:url": "https://github.com/YuningHao/FARDEEP.git" }, - { - "@id": "https://orcid.org/0000-0002-1049-2219", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0002-9868-9824", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006976", "@type": "sc:CreativeWork" diff --git a/data/farms/farmsbioschemas.jsonld b/data/farms/farmsbioschemas.jsonld index cf6f264ac7e9f..39eeea8c39a7b 100644 --- a/data/farms/farmsbioschemas.jsonld +++ b/data/farms/farmsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-4191-2156", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/farms", "@type": "sc:SoftwareApplication", @@ -24,16 +28,12 @@ "sc:license": "GPL-2.0", "sc:name": "farms", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/farms.html", "sc:version": "1.26.0" - }, - { - "@id": "http://orcid.org/0000-0003-4191-2156", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/fast-lmm/fast-lmmbioschemas.jsonld b/data/fast-lmm/fast-lmmbioschemas.jsonld index ef534f59e3b7c..742a96f87fe5b 100644 --- a/data/fast-lmm/fast-lmmbioschemas.jsonld +++ b/data/fast-lmm/fast-lmmbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Factored Spectrally Transformed Linear Mixed Models is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets.", "sc:name": "FaST-LMM", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.microsoft.com/en-us/research/project/fastlmm/" } \ No newline at end of file diff --git a/data/fasta/fastabioschemas.jsonld b/data/fasta/fastabioschemas.jsonld index 3f6845945b319..5d57a93825c25 100644 --- a/data/fasta/fastabioschemas.jsonld +++ b/data/fasta/fastabioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "FASTA", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://fasta.bioch.virginia.edu/" } \ No newline at end of file diff --git a/data/fasta_api_ebi/fasta_api_ebibioschemas.jsonld b/data/fasta_api_ebi/fasta_api_ebibioschemas.jsonld index 1ffcd3f9583ae..5b44f27b0b81c 100644 --- a/data/fasta_api_ebi/fasta_api_ebibioschemas.jsonld +++ b/data/fasta_api_ebi/fasta_api_ebibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "FASTA stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison.", "sc:name": "FASTA API (EBI)", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/sss/fasta_rest", diff --git a/data/fasta_canonical_sequences/fasta_canonical_sequencesbioschemas.jsonld b/data/fasta_canonical_sequences/fasta_canonical_sequencesbioschemas.jsonld index 68a090e8350b6..8dd810482daf9 100644 --- a/data/fasta_canonical_sequences/fasta_canonical_sequencesbioschemas.jsonld +++ b/data/fasta_canonical_sequences/fasta_canonical_sequencesbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "FASTA Canonical Sequences deletes comments from FASTA files. It can also change sequences by deleting specified characters or whitespace, introduce newlines for readibility, or change sequence case.", "sc:name": "FASTA Canonical Sequences", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/software/program.html?uid=15", diff --git a/data/fasta_ebi/fasta_ebibioschemas.jsonld b/data/fasta_ebi/fasta_ebibioschemas.jsonld index 585d7f290eb6f..5270f41733393 100644 --- a/data/fasta_ebi/fasta_ebibioschemas.jsonld +++ b/data/fasta_ebi/fasta_ebibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Sequence similarity searching against protein databases. FASTX and FASTY translate a DNA query. Optimal searches with SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query, local database).", "sc:name": "FASTA (EBI)", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ "University of Virginia", diff --git a/data/fastaextract/fastaextractbioschemas.jsonld b/data/fastaextract/fastaextractbioschemas.jsonld index 358ba2c162d56..7bcc24d3a3a71 100644 --- a/data/fastaextract/fastaextractbioschemas.jsonld +++ b/data/fastaextract/fastaextractbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Extract/Exclude one or more sequence(s) from a multifasta file using a dataset of identifiers.", "sc:name": "fastaextract", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/C3BI-pasteur-fr/fastaextract", "sc:version": "0.99" diff --git a/data/fastafrombed/fastafrombedbioschemas.jsonld b/data/fastafrombed/fastafrombedbioschemas.jsonld index ac9aaac978852..18602c4c8af35 100644 --- a/data/fastafrombed/fastafrombedbioschemas.jsonld +++ b/data/fastafrombed/fastafrombedbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Create fasta files with DNA sequences given a BED file.", "sc:name": "fastafrombed", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/arq5x/bedtools2", "sc:version": "1.0" diff --git a/data/fastbaps/fastbapsbioschemas.jsonld b/data/fastbaps/fastbapsbioschemas.jsonld index 85a52e9ed64f0..d9325cff85653 100644 --- a/data/fastbaps/fastbapsbioschemas.jsonld +++ b/data/fastbaps/fastbapsbioschemas.jsonld @@ -46,9 +46,9 @@ "sc:license": "MIT", "sc:name": "fastbaps", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/gtonkinhill/fastbaps" } diff --git a/data/fastcontact/fastcontactbioschemas.jsonld b/data/fastcontact/fastcontactbioschemas.jsonld index 0934e7470a659..086bf05f5bc3b 100644 --- a/data/fastcontact/fastcontactbioschemas.jsonld +++ b/data/fastcontact/fastcontactbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "FastContact is a free energy scoring tool for protein-protein complex structures.", "sc:name": "FastContact", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://structure.pitt.edu/servers/fastcontact/" diff --git a/data/fasteprr/fasteprrbioschemas.jsonld b/data/fasteprr/fasteprrbioschemas.jsonld index 0a24e90fd112e..da60aab906936 100644 --- a/data/fasteprr/fasteprrbioschemas.jsonld +++ b/data/fasteprr/fasteprrbioschemas.jsonld @@ -9,15 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1534/g3.116.028233", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/fasteprr", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4889653", { "@id": "https://doi.org/10.1534/g3.116.028233" }, - "pmcid:PMC4889653", "pubmed:27172192" ], "sc:description": "An extremely fast open-source software package to estimate population recombination rate based on intraspecific DNA polymorphism data.", @@ -27,15 +31,11 @@ "sc:license": "Other", "sc:name": "FastEPRR", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.picb.ac.cn/evolgen/softwares/FastEPRR.html", "sc:version": "1.0" - }, - { - "@id": "https://doi.org/10.1534/g3.116.028233", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/faster/fasterbioschemas.jsonld b/data/faster/fasterbioschemas.jsonld index 38b1620f19ade..b4458c7e3daee 100644 --- a/data/faster/fasterbioschemas.jsonld +++ b/data/faster/fasterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "fastER", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://bsse.ethz.ch/csd/software/faster.html" } \ No newline at end of file diff --git a/data/fastgenogam/fastgenogambioschemas.jsonld b/data/fastgenogam/fastgenogambioschemas.jsonld index 7ffe8de11bfe9..40c1ac541fd8d 100644 --- a/data/fastgenogam/fastgenogambioschemas.jsonld +++ b/data/fastgenogam/fastgenogambioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "fastGenoGAM", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/gstricker/fastGenoGAM", "sc:version": "2.0" diff --git a/data/fasthmm/fasthmmbioschemas.jsonld b/data/fasthmm/fasthmmbioschemas.jsonld index 9c9de6e58c64d..7ddb843b1f213 100644 --- a/data/fasthmm/fasthmmbioschemas.jsonld +++ b/data/fasthmm/fasthmmbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "FastHMM and FastBLAST are fast heuristics to replace HMM search, InterProScan, and all-versus-all BLAST. FastHMM uses PSI-BLAST to quickly select likely members of the family and then uses HMMer to confirm those hits. FastBLAST relies on alignments of proteins to known families from FastHMM and from rpsblast against COG. FastBLAST uses these alignments to avoid most of the work of all-versus-all BLAST. FastBLAST further reduces the work by clustering similar sequences.", "sc:name": "FastHMM", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://microbesonline.org/fasthmm/" diff --git a/data/fastjt/fastjtbioschemas.jsonld b/data/fastjt/fastjtbioschemas.jsonld index 60e4174cf6594..e61a808b99269 100644 --- a/data/fastjt/fastjtbioschemas.jsonld +++ b/data/fastjt/fastjtbioschemas.jsonld @@ -14,17 +14,17 @@ "sc:additionalType": "Library", "sc:author": [ "Kouros Owzar", + "Ivo Shterev", "Jiaxing Lin", - "Alexander Sibley", - "Ivo Shterev" + "Alexander Sibley" ], "sc:citation": "pubmed:31195980", "sc:description": "R package for robust and efficient feature selection for machine learning and genome-wide association studies.", "sc:license": "GPL-3.0", "sc:name": "fastJT", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://cran.r-project.org/package=fastJT", diff --git a/data/fastliquidassociation/fastliquidassociationbioschemas.jsonld b/data/fastliquidassociation/fastliquidassociationbioschemas.jsonld index 9990198779c57..0789e3250d377 100644 --- a/data/fastliquidassociation/fastliquidassociationbioschemas.jsonld +++ b/data/fastliquidassociation/fastliquidassociationbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "fastLiquidAssociation", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/fastLiquidAssociation.html", "sc:version": "1.10.0" diff --git a/data/fastm_api_ebi/fastm_api_ebibioschemas.jsonld b/data/fastm_api_ebi/fastm_api_ebibioschemas.jsonld index c3f5946cbb3de..0795ddff15eb0 100644 --- a/data/fastm_api_ebi/fastm_api_ebibioschemas.jsonld +++ b/data/fastm_api_ebi/fastm_api_ebibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "FASTM API (EBI)", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/sss/fastm_rest", "sc:version": "1" diff --git a/data/fastm_ebi/fastm_ebibioschemas.jsonld b/data/fastm_ebi/fastm_ebibioschemas.jsonld index 8897222ef843a..326fb06786688 100644 --- a/data/fastm_ebi/fastm_ebibioschemas.jsonld +++ b/data/fastm_ebi/fastm_ebibioschemas.jsonld @@ -19,13 +19,13 @@ "sc:description": "Sequence similarity search with peptide fragment searches using the FASTF, FASTM or FASTS programs from the FASTA suite.", "sc:name": "FASTM (EBI)", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ - "EMBL-EBI", - "University of Virginia" + "University of Virginia", + "EMBL-EBI" ], "sc:url": "http://www.ebi.ac.uk/Tools/sss/fastm/", "sc:version": "1" diff --git a/data/fastmap/fastmapbioschemas.jsonld b/data/fastmap/fastmapbioschemas.jsonld index d48fcd8759d37..9caaae87e9413 100644 --- a/data/fastmap/fastmapbioschemas.jsonld +++ b/data/fastmap/fastmapbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It is used for fast and efficient eQTL mapping in homozygous inbred populations with binary allele calls. It exploits the discrete nature and structure of the measured single nucleotide polymorphisms. SNPs are organized into a Hamming distance-based tree. Its tree can be used to perform both single marker mapping and haplotype association mapping over an m-SNP window. These performance enhancements also permit permutation-based significance testing.", "sc:name": "FastMap", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://comptox.unc.edu/fastmap.php", "sc:version": "2.0" diff --git a/data/fastme/fastmebioschemas.jsonld b/data/fastme/fastmebioschemas.jsonld index 855d404877f72..255a96dc9ca03 100644 --- a/data/fastme/fastmebioschemas.jsonld +++ b/data/fastme/fastmebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "FastME", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "LIRMM", "sc:url": "http://www.atgc-montpellier.fr/fastme/", diff --git a/data/fasto/fastobioschemas.jsonld b/data/fasto/fastobioschemas.jsonld index d32078a64e9b7..d3330ef18da9a 100644 --- a/data/fasto/fastobioschemas.jsonld +++ b/data/fasto/fastobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-9559-4352", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/FASTO", "@type": "sc:SoftwareApplication", @@ -20,19 +24,19 @@ { "@id": "https://doi.org/10.1186/S12911-019-0806-Z" }, - "pubmed:31077222", - "pmcid:PMC6511155" + "pmcid:PMC6511155", + "pubmed:31077222" ], "sc:description": "FHIR And SSN based Type 1 diabetes Ontology (FASTO) is an OWL 2 ontology for real time management of insulin for diabetes patients especially type 1 diabetics.", "sc:featureList": [ - { - "@id": "edam:operation_3559" - }, { "@id": "edam:operation_3501" }, { "@id": "edam:operation_3352" + }, + { + "@id": "edam:operation_3559" } ], "sc:license": "Unlicense", @@ -44,10 +48,6 @@ ], "sc:url": "https://bioportal.bioontology.org/ontologies/FASTO" }, - { - "@id": "https://orcid.org/0000-0002-9559-4352", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/S12911-019-0806-Z", "@type": "sc:CreativeWork" diff --git a/data/fastproject/fastprojectbioschemas.jsonld b/data/fastproject/fastprojectbioschemas.jsonld index 61b46b72a8dc6..a04ff4737f6e4 100644 --- a/data/fastproject/fastprojectbioschemas.jsonld +++ b/data/fastproject/fastprojectbioschemas.jsonld @@ -28,9 +28,9 @@ "sc:license": "Other", "sc:name": "FastProject", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/YosefLab/FastProject" }, diff --git a/data/fastprongs/fastprongsbioschemas.jsonld b/data/fastprongs/fastprongsbioschemas.jsonld index 2199947d05348..521e46e46eb41 100644 --- a/data/fastprongs/fastprongsbioschemas.jsonld +++ b/data/fastprongs/fastprongsbioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2936-9", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/FastProNGS", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "G. Zhang", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:31208325", - "pmcid:PMC6580563", { "@id": "https://doi.org/10.1186/s12859-019-2936-9" - } + }, + "pubmed:31208325", + "pmcid:PMC6580563" ], "sc:description": "Fast preprocessing of next-generation sequencing reads.", "sc:featureList": [ - { - "@id": "edam:operation_3237" - }, { "@id": "edam:operation_3192" }, { "@id": "edam:operation_3219" + }, + { + "@id": "edam:operation_3237" } ], "sc:license": "GPL-3.0", "sc:name": "FastProNGS", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/Megagenomics/FastProNGS" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2936-9", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fastqc/fastqcbioschemas.jsonld b/data/fastqc/fastqcbioschemas.jsonld index 5577ab4ddde5b..92a2cf6a8ae96 100644 --- a/data/fastqc/fastqcbioschemas.jsonld +++ b/data/fastqc/fastqcbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Simon Andrews", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.", "sc:license": "GPL-3.0", diff --git a/data/fastqc_toolshed/fastqc_toolshedbioschemas.jsonld b/data/fastqc_toolshed/fastqc_toolshedbioschemas.jsonld index 30d1666445821..e352789d29450 100644 --- a/data/fastqc_toolshed/fastqc_toolshedbioschemas.jsonld +++ b/data/fastqc_toolshed/fastqc_toolshedbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "fastqc_toolshed", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/", "sc:version": "0.1" diff --git a/data/fastqpuri/fastqpuribioschemas.jsonld b/data/fastqpuri/fastqpuribioschemas.jsonld index b3360eb038986..a8a6cce521747 100644 --- a/data/fastqpuri/fastqpuribioschemas.jsonld +++ b/data/fastqpuri/fastqpuribioschemas.jsonld @@ -15,27 +15,27 @@ "biotools:primaryContact": "Julia Engelmann", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:31053060", - "pmcid:PMC6500068", { "@id": "https://doi.org/10.1186/s12859-019-2799-0" - } + }, + "pmcid:PMC6500068", + "pubmed:31053060" ], "sc:contributor": [ - "Paula Pérez Rubio", "Julia Engelmann", + "Paula Pérez Rubio", "Claudio Lottaz" ], "sc:description": "High-performance preprocessing tool for RNA-seq data.", "sc:featureList": [ { - "@id": "edam:operation_3180" + "@id": "edam:operation_3800" }, { - "@id": "edam:operation_3219" + "@id": "edam:operation_3180" }, { - "@id": "edam:operation_3800" + "@id": "edam:operation_3219" } ], "sc:license": "GPL-3.0", diff --git a/data/fastqvalidator/fastqvalidatorbioschemas.jsonld b/data/fastqvalidator/fastqvalidatorbioschemas.jsonld index 27e1378897390..227fe6a57d570 100644 --- a/data/fastqvalidator/fastqvalidatorbioschemas.jsonld +++ b/data/fastqvalidator/fastqvalidatorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Checking that FastQ files are follows standards.", "sc:name": "FastQValidator", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genome.sph.umich.edu/wiki/FastQValidator" } \ No newline at end of file diff --git a/data/fastqz/fastqzbioschemas.jsonld b/data/fastqz/fastqzbioschemas.jsonld index 5cb92dd4e75e5..f6ee902d6e696 100644 --- a/data/fastqz/fastqzbioschemas.jsonld +++ b/data/fastqz/fastqzbioschemas.jsonld @@ -29,9 +29,9 @@ }, "sc:name": "Fastqz", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://mattmahoney.net/dc/fastqz/", "sc:version": "1.5" diff --git a/data/fastr3d/fastr3dbioschemas.jsonld b/data/fastr3d/fastr3dbioschemas.jsonld index 09516accd23d7..e415f4cb5ce9e 100644 --- a/data/fastr3d/fastr3dbioschemas.jsonld +++ b/data/fastr3d/fastr3dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "FASTR3D is a web based search tool that allows users to search the PDB database for structurally similar RNAs from input queries of PDB coordinates for an RNA molecule, an RNA secondary structure or RNA primary sequence.", "sc:name": "FASTR3D", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://genome.cs.nthu.edu.tw/FASTR3D/" } \ No newline at end of file diff --git a/data/fastscop/fastscopbioschemas.jsonld b/data/fastscop/fastscopbioschemas.jsonld index 9f3c076ccbb30..14961db4e02bc 100644 --- a/data/fastscop/fastscopbioschemas.jsonld +++ b/data/fastscop/fastscopbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.", "sc:name": "fastSCOP", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://gemdock.life.nctu.edu.tw/fastSCOP/" } \ No newline at end of file diff --git a/data/fastseg/fastsegbioschemas.jsonld b/data/fastseg/fastsegbioschemas.jsonld index d03a1297639ec..5acc47edfddf8 100644 --- a/data/fastseg/fastsegbioschemas.jsonld +++ b/data/fastseg/fastsegbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gks003", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/fastseg", "@type": "sc:SoftwareApplication", @@ -16,15 +20,15 @@ "@id": "http://orcid.org/0000-0003-2861-5552" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC3351174", "pubmed:22302147", { "@id": "https://doi.org/10.1093/nar/gks003" - }, - "pmcid:PMC3351174" + } ], "sc:description": "Implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. It can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector.", "sc:featureList": { @@ -33,9 +37,9 @@ "sc:license": "GPL-2.0", "sc:name": "fastseg", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/fastseg.html", "sc:version": "1.20.0" @@ -43,10 +47,6 @@ { "@id": "http://orcid.org/0000-0003-2861-5552", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/nar/gks003", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fastskat/fastskatbioschemas.jsonld b/data/fastskat/fastskatbioschemas.jsonld index 0a97615b1cb8b..1266fab6df68d 100644 --- a/data/fastskat/fastskatbioschemas.jsonld +++ b/data/fastskat/fastskatbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "FastSKAT", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/tslumley/bigQF" diff --git a/data/fasttree/fasttreebioschemas.jsonld b/data/fasttree/fasttreebioschemas.jsonld index 9f29bc2163365..97d9f19e86d0f 100644 --- a/data/fasttree/fasttreebioschemas.jsonld +++ b/data/fasttree/fasttreebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.", "sc:name": "FastTree", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.microbesonline.org/fasttree/" } \ No newline at end of file diff --git a/data/fastx-toolkit/fastx-toolkitbioschemas.jsonld b/data/fastx-toolkit/fastx-toolkitbioschemas.jsonld index 2a020ea696d7c..9b6dfb6dd8818 100644 --- a/data/fastx-toolkit/fastx-toolkitbioschemas.jsonld +++ b/data/fastx-toolkit/fastx-toolkitbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "AGPL-3.0", "sc:name": "FASTX-Toolkit", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://hannonlab.cshl.edu/fastx_toolkit/" } \ No newline at end of file diff --git a/data/fastxreader/fastxreaderbioschemas.jsonld b/data/fastxreader/fastxreaderbioschemas.jsonld index 99cf26a96b6bf..5f8207232b2d1 100644 --- a/data/fastxreader/fastxreaderbioschemas.jsonld +++ b/data/fastxreader/fastxreaderbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "FASTX::Reader", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://metacpan.org/pod/FASTX::Reader", "sc:version": "0.6" diff --git a/data/fatcat/fatcatbioschemas.jsonld b/data/fatcat/fatcatbioschemas.jsonld index 8e2254038f91e..25cdfed11089d 100644 --- a/data/fatcat/fatcatbioschemas.jsonld +++ b/data/fatcat/fatcatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "FATCAT provides the means to compare two PDB-format protein structures, or to search for structures similar to a given PDB structure. The user can supply a PDB ID or upload a structure file. The FATCAT web server employs the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT) algorithm.", "sc:name": "FATCAT", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://fatcat.burnham.org/" diff --git a/data/fathmm-indel/fathmm-indelbioschemas.jsonld b/data/fathmm-indel/fathmm-indelbioschemas.jsonld index 1d2e039adce01..8687a9396582f 100644 --- a/data/fathmm-indel/fathmm-indelbioschemas.jsonld +++ b/data/fathmm-indel/fathmm-indelbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Predict the functional class, pathogenic or neutral, of small indels throughout the whole non-coding genome.", "sc:name": "FATHMM-indel", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://indels.biocompute.org.uk/" diff --git a/data/fatslim/fatslimbioschemas.jsonld b/data/fatslim/fatslimbioschemas.jsonld index a91c72be1f9ef..245b3b773b5f7 100644 --- a/data/fatslim/fatslimbioschemas.jsonld +++ b/data/fatslim/fatslimbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "FATSLiM", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://fatslim.github.io/" } \ No newline at end of file diff --git a/data/fccac/fccacbioschemas.jsonld b/data/fccac/fccacbioschemas.jsonld index e65e1a46243b3..a1fb85cca4037 100644 --- a/data/fccac/fccacbioschemas.jsonld +++ b/data/fccac/fccacbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btw724", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/fccac", "@type": "sc:SoftwareApplication", @@ -16,8 +20,8 @@ "@id": "http://orcid.org/0000-0003-1959-8199" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pmcid:PMC5408813", @@ -33,17 +37,13 @@ "sc:license": "Artistic-2.0", "sc:name": "fCCAC", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/fCCAC.html", "sc:version": "1.0.0" }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btw724", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-1959-8199", "@type": "schema:Person" diff --git a/data/fci/fcibioschemas.jsonld b/data/fci/fcibioschemas.jsonld index 6e108e1b47a45..b4a2684700645 100644 --- a/data/fci/fcibioschemas.jsonld +++ b/data/fci/fcibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "fCI", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/fCI.html", "sc:version": "1.4.0" diff --git a/data/fdetect/fdetectbioschemas.jsonld b/data/fdetect/fdetectbioschemas.jsonld index 1489cbb4e3a77..72bbf905f9d1b 100644 --- a/data/fdetect/fdetectbioschemas.jsonld +++ b/data/fdetect/fdetectbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Fast predictor of propensity for protein production, purification, and crystallization.", "sc:name": "fDETECT", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://biomine.cs.vcu.edu/servers/fDETECT/" } \ No newline at end of file diff --git a/data/fdrame/fdramebioschemas.jsonld b/data/fdrame/fdramebioschemas.jsonld index 2a5d73aa150eb..d5d2f04e3c2ec 100644 --- a/data/fdrame/fdramebioschemas.jsonld +++ b/data/fdrame/fdramebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "fdrame", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/fdrame.html", "sc:version": "1.46.0" diff --git a/data/featcopy/featcopybioschemas.jsonld b/data/featcopy/featcopybioschemas.jsonld index 2cdd55558e570..9b802c57ca152 100644 --- a/data/featcopy/featcopybioschemas.jsonld +++ b/data/featcopy/featcopybioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK BBSRC", + "EMBOSS Contributors", "UK MRC", "Wellcome Trust" ], "sc:description": "Read and write a feature table.", "sc:funder": [ "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "featcopy", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/featcopy.html", "sc:version": "r6" diff --git a/data/feather/featherbioschemas.jsonld b/data/feather/featherbioschemas.jsonld index d9d4f19a2fc08..d6b3616adcea1 100644 --- a/data/feather/featherbioschemas.jsonld +++ b/data/feather/featherbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "FEATHER", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/perkinslab/AppFEATHER/tree/V1.4", "sc:version": "1.4" diff --git a/data/featmerge/featmergebioschemas.jsonld b/data/featmerge/featmergebioschemas.jsonld index 1b6c5d3be976b..bc6f91f7da6db 100644 --- a/data/featmerge/featmergebioschemas.jsonld +++ b/data/featmerge/featmergebioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", "Wellcome Trust", - "EMBOSS Contributors" + "UK MRC", + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "An Emboss tool that merges two overlapping feature tables into one single table.", "sc:funder": [ diff --git a/data/featreport/featreportbioschemas.jsonld b/data/featreport/featreportbioschemas.jsonld index e53451121d068..221af20cc700a 100644 --- a/data/featreport/featreportbioschemas.jsonld +++ b/data/featreport/featreportbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", - "EMBOSS Contributors", "Wellcome Trust", - "UK MRC" + "UK MRC", + "EMBOSS Contributors" ], "sc:description": "Read and write a feature table.", "sc:funder": [ - "UK MRC", "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "featreport", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/feattext/feattextbioschemas.jsonld b/data/feattext/feattextbioschemas.jsonld index 2b1442104db66..edfe37e37c2b0 100644 --- a/data/feattext/feattextbioschemas.jsonld +++ b/data/feattext/feattextbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK MRC", "UK BBSRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "Wellcome Trust", + "UK MRC" ], "sc:description": "Return a feature table original text.", "sc:funder": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "feattext", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/featurecounts/featurecountsbioschemas.jsonld b/data/featurecounts/featurecountsbioschemas.jsonld index bee06c35e25ec..c6878275a5310 100644 --- a/data/featurecounts/featurecountsbioschemas.jsonld +++ b/data/featurecounts/featurecountsbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/featurecounts", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Yang Liao", "Wei Shi", - "Gordon K Smyth", - "Yang Liao" + "Gordon K Smyth" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:24227677", diff --git a/data/featureextract/featureextractbioschemas.jsonld b/data/featureextract/featureextractbioschemas.jsonld index aa3ff3e198edb..aec8f5c55c8f2 100644 --- a/data/featureextract/featureextractbioschemas.jsonld +++ b/data/featureextract/featureextractbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Other", "sc:name": "FeatureExtract", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.cbs.dtu.dk/services/FeatureExtract/" } \ No newline at end of file diff --git a/data/featuremap3d/featuremap3dbioschemas.jsonld b/data/featuremap3d/featuremap3dbioschemas.jsonld index b35e5ea9ad5d8..0db159d4c4781 100644 --- a/data/featuremap3d/featuremap3dbioschemas.jsonld +++ b/data/featuremap3d/featuremap3dbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "Other", "sc:name": "FeatureMap3D", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.cbs.dtu.dk/services/FeatureMap3D/" } \ No newline at end of file diff --git a/data/featureselect/featureselectbioschemas.jsonld b/data/featureselect/featureselectbioschemas.jsonld index eed7f54861402..e2772f333f3fd 100644 --- a/data/featureselect/featureselectbioschemas.jsonld +++ b/data/featureselect/featureselectbioschemas.jsonld @@ -15,26 +15,26 @@ "biotools:primaryContact": "LBBSoft", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC6446290", + "pubmed:30943889", { "@id": "https://doi.org/10.1186/s12859-019-2754-0" - }, - "pubmed:30943889", - "pmcid:PMC6446290" + } ], "sc:description": "Software for feature selection based on machine learning approaches.", "sc:featureList": [ { - "@id": "edam:operation_3659" + "@id": "edam:operation_3435" }, { - "@id": "edam:operation_3435" + "@id": "edam:operation_3659" } ], "sc:name": "FeatureSelect", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/LBBSoft/FeatureSelect" }, diff --git a/data/fedro/fedrobioschemas.jsonld b/data/fedro/fedrobioschemas.jsonld index 4201867c5d113..6a1a9f632059c 100644 --- a/data/fedro/fedrobioschemas.jsonld +++ b/data/fedro/fedrobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2696-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/FEDRO", "@type": "sc:SoftwareApplication", @@ -20,18 +16,18 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pubmed:30999847", - "pmcid:PMC6471690", { "@id": "https://doi.org/10.1186/s12859-019-2696-6" - } + }, + "pmcid:PMC6471690" ], "sc:description": "Software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing.", "sc:featureList": [ { - "@id": "edam:operation_0436" + "@id": "edam:operation_3557" }, { - "@id": "edam:operation_3557" + "@id": "edam:operation_0436" }, { "@id": "edam:operation_3096" @@ -39,11 +35,15 @@ ], "sc:name": "FEDRO", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://math.unipa.it/rombo/FEDRO" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2696-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/feedr/feedrbioschemas.jsonld b/data/feedr/feedrbioschemas.jsonld index 5b6c0411c2936..fd8d4bfc9adf1 100644 --- a/data/feedr/feedrbioschemas.jsonld +++ b/data/feedr/feedrbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "feedr", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/animalnexus/feedr", "sc:version": "0.10.0" diff --git a/data/feelnc/feelncbioschemas.jsonld b/data/feelnc/feelncbioschemas.jsonld index 2aea0573089a7..0c49932fc37f4 100644 --- a/data/feelnc/feelncbioschemas.jsonld +++ b/data/feelnc/feelncbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkw1306", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/feelnc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Thomas Derrien", "Valentin Wucher", + "Thomas Derrien", "Fabrice Legeai" ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5416892", { "@id": "https://doi.org/10.1093/nar/gkw1306" }, + "pmcid:PMC5416892", "pubmed:28053114" ], "sc:description": "A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.", @@ -32,15 +36,11 @@ "sc:license": "GPL-3.0", "sc:name": "FEELnc", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/tderrien/FEELnc", "sc:version": "0.1.1" - }, - { - "@id": "https://doi.org/10.1093/nar/gkw1306", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fells/fellsbioschemas.jsonld b/data/fells/fellsbioschemas.jsonld index e369d0f55dfbc..bb6ccf67558e6 100644 --- a/data/fells/fellsbioschemas.jsonld +++ b/data/fells/fellsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-4525-7793", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/fells", "@type": "sc:SoftwareApplication", @@ -20,21 +16,25 @@ "@id": "http://orcid.org/0000-0003-4525-7793" }, "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:citation": "pubmed:28186245", "sc:description": "This tool features secondary structure, disorder, aggragation, sequence complexity predictions along with amino acid propensity from sequence.", "sc:license": "CC-BY-NC-ND-4.0", "sc:name": "FELLS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", "sc:url": "http://protein.bio.unipd.it/fells/", "sc:version": "1.1" + }, + { + "@id": "http://orcid.org/0000-0003-4525-7793", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/fem/fembioschemas.jsonld b/data/fem/fembioschemas.jsonld index eea788b9461a8..b1aaf636d364e 100644 --- a/data/fem/fembioschemas.jsonld +++ b/data/fem/fembioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Zhen Yang", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:24794928", "sc:description": "This package performs a systems-level integrative analysis of DNA methylation and gene expression data. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed.", "sc:license": "GPL-2.0", "sc:name": "FEM", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/FEM.html", diff --git a/data/fetal_xcmr/fetal_xcmrbioschemas.jsonld b/data/fetal_xcmr/fetal_xcmrbioschemas.jsonld index be59b384a8e06..0974eff0d6b97 100644 --- a/data/fetal_xcmr/fetal_xcmrbioschemas.jsonld +++ b/data/fetal_xcmr/fetal_xcmrbioschemas.jsonld @@ -18,19 +18,19 @@ ], "sc:additionalType": "Script", "sc:citation": [ + "pmcid:PMC6532268", "pubmed:31118056", { "@id": "https://doi.org/10.1186/S12968-019-0539-2" - }, - "pmcid:PMC6532268" + } ], "sc:description": "Numerical phantom for fetal cardiovascular magnetic resonance imaging.", "sc:license": "Unlicense", "sc:name": "Fetal XCMR", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/cwroy/Fetal-XCMR/" }, diff --git a/data/fetchprodom/fetchprodombioschemas.jsonld b/data/fetchprodom/fetchprodombioschemas.jsonld index cf5eddf97c341..41a59b25444ca 100644 --- a/data/fetchprodom/fetchprodombioschemas.jsonld +++ b/data/fetchprodom/fetchprodombioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/26.1.323", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/fetchprodom", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web service", "sc:citation": [ + "pmcid:PMC539988", "pubmed:15608179", { "@id": "https://doi.org/10.1093/nar/26.1.323" - }, - "pmcid:PMC539988" + } ], "sc:description": "Retrieve information from ProDom, a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.", "sc:featureList": { @@ -30,12 +26,16 @@ }, "sc:name": "FetchProDom WS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://prodom.prabi.fr/prodom/current/documentation/fetchProDom.html", "sc:version": "1" + }, + { + "@id": "https://doi.org/10.1093/nar/26.1.323", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ffas/ffasbioschemas.jsonld b/data/ffas/ffasbioschemas.jsonld index 5bdd97a61c37c..fbe1f0c457df3 100644 --- a/data/ffas/ffasbioschemas.jsonld +++ b/data/ffas/ffasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.", "sc:name": "FFAS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://ffas.godziklab.org" diff --git a/data/ffbskat/ffbskatbioschemas.jsonld b/data/ffbskat/ffbskatbioschemas.jsonld index 58b6bc0a55cdf..9541989b4d30a 100644 --- a/data/ffbskat/ffbskatbioschemas.jsonld +++ b/data/ffbskat/ffbskatbioschemas.jsonld @@ -31,8 +31,8 @@ "sc:license": "GPL-3.0", "sc:name": "FFBSKAT", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://mga.bionet.nsc.ru/soft/FFBSKAT/" diff --git a/data/ffged/ffgedbioschemas.jsonld b/data/ffged/ffgedbioschemas.jsonld index e79a7f9b8914d..f48ea69cbf814 100644 --- a/data/ffged/ffgedbioschemas.jsonld +++ b/data/ffged/ffgedbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "User-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. The web server functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.", "sc:name": "FFGED", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioinfo.townsend.yale.edu/" } \ No newline at end of file diff --git a/data/ffpe/ffpebioschemas.jsonld b/data/ffpe/ffpebioschemas.jsonld index b4a15eb69a050..951346e9e176a 100644 --- a/data/ffpe/ffpebioschemas.jsonld +++ b/data/ffpe/ffpebioschemas.jsonld @@ -24,12 +24,12 @@ "@id": "http://orcid.org/0000-0003-2725-0694" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:23136189", "pmcid:PMC3500412", + "pubmed:23136189", { "@id": "https://doi.org/10.1158/1078-0432.CCR-12-1915" } diff --git a/data/fgap/fgapbioschemas.jsonld b/data/fgap/fgapbioschemas.jsonld index 8f098d8d99421..8276a1a1cdeb1 100644 --- a/data/fgap/fgapbioschemas.jsonld +++ b/data/fgap/fgapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "An automated gap closing tool.", "sc:name": "FGAP", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "zedat.fu-berlin.de", "sc:url": "http://sourceforge.net/projects/fgap/", diff --git a/data/fgdb/fgdbbioschemas.jsonld b/data/fgdb/fgdbbioschemas.jsonld index 07b1da71f95fb..621836ec5a31b 100644 --- a/data/fgdb/fgdbbioschemas.jsonld +++ b/data/fgdb/fgdbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "FGDB", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mips.gsf.de/genre/proj/FGDB/" } \ No newline at end of file diff --git a/data/fgdp/fgdpbioschemas.jsonld b/data/fgdp/fgdpbioschemas.jsonld index 5c2f8652e6917..b2046643576db 100644 --- a/data/fgdp/fgdpbioschemas.jsonld +++ b/data/fgdp/fgdpbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The FGDP (functional genomics data pipeline) is a Java-based, Microarray or Genechip data analysis system. The FGDP provides an integrated, extendable analysis environment permitting multiple, simultaneous analyses to be automatically performed, and provides a web server and interface for presenting results", "sc:name": "FGDP", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinformatics.fccc.edu/software/OpenSource/FGDP/FGDP.shtml" } \ No newline at end of file diff --git a/data/fgmp/fgmpbioschemas.jsonld b/data/fgmp/fgmpbioschemas.jsonld index 02bc431c2bd88..b63d1ebd8865c 100644 --- a/data/fgmp/fgmpbioschemas.jsonld +++ b/data/fgmp/fgmpbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:license": "MIT", "sc:name": "FGMP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://github.com/stajichlab/FGMP", "sc:version": "1.0.0" diff --git a/data/fgnet/fgnetbioschemas.jsonld b/data/fgnet/fgnetbioschemas.jsonld index d34422b0b9110..07e0374ebd7da 100644 --- a/data/fgnet/fgnetbioschemas.jsonld +++ b/data/fgnet/fgnetbioschemas.jsonld @@ -30,18 +30,18 @@ "@id": "edam:data_2048" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": { "@id": "edam:topic_0602" }, "sc:citation": [ + "pubmed:25600944", { "@id": "https://doi.org/10.1093/bioinformatics/btu864" }, - "pmcid:PMC4426835", - "pubmed:25600944" + "pmcid:PMC4426835" ], "sc:description": "Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO.", "sc:featureList": { diff --git a/data/fgsea/fgseabioschemas.jsonld b/data/fgsea/fgseabioschemas.jsonld index 74d8006bfeeda..c9c0e165c1b0b 100644 --- a/data/fgsea/fgseabioschemas.jsonld +++ b/data/fgsea/fgseabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alexey Sergushichev", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.", "sc:license": "MIT", "sc:name": "fgsea", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/fgsea.html", "sc:version": "1.0.2" diff --git a/data/fhitings/fhitingsbioschemas.jsonld b/data/fhitings/fhitingsbioschemas.jsonld index c9d32dec6c0ad..500462f2338e6 100644 --- a/data/fhitings/fhitingsbioschemas.jsonld +++ b/data/fhitings/fhitingsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "\"FHiTINGS is designed for use in rapidly identifying, classifying, and parsing internal transcribed spacer (ITS) DNA sequences after a BLASTn search. This software is useful for fungal ecology studies using next generation sequencing (NGS).\"", "sc:name": "FHiTINGS", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://sourceforge.net/projects/fhitings/" } \ No newline at end of file diff --git a/data/fidea/fideabioschemas.jsonld b/data/fidea/fideabioschemas.jsonld index 2ea635a98ea49..7dbe951f9ea5e 100644 --- a/data/fidea/fideabioschemas.jsonld +++ b/data/fidea/fideabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web server designed to facilitate the functional interpretation of differential expression analysis. It is aimed at allowing experimentalists to \"play with\" their RNA-Seq data in an easy and at the same time exhaustive fashion within a single tool.", "sc:name": "FIDEA", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-ITA-SAPIENZA", "sc:url": "http://www.biocomputing.it/fidea", diff --git a/data/fidlib/fidlibbioschemas.jsonld b/data/fidlib/fidlibbioschemas.jsonld index dfdebc8a71e86..84befcbdbee93 100644 --- a/data/fidlib/fidlibbioschemas.jsonld +++ b/data/fidlib/fidlibbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "LGPL-3.0", "sc:name": "fidlib", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://uazu.net/fidlib/" diff --git a/data/fido-snp/fido-snpbioschemas.jsonld b/data/fido-snp/fido-snpbioschemas.jsonld index 9b1399e3d11b1..efba4c2d00183 100644 --- a/data/fido-snp/fido-snpbioschemas.jsonld +++ b/data/fido-snp/fido-snpbioschemas.jsonld @@ -21,29 +21,29 @@ "@id": "https://bio.tools/Fido-SNP", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Piero Fariselli", { "@id": "https://orcid.org/0000-0002-2323-0963" - }, - "Piero Fariselli" + } ], "sc:additionalType": [ "Web service", "Web application" ], "sc:citation": [ + "pubmed:31114899", + "pmcid:PMC6602425", { "@id": "https://doi.org/10.1093/NAR/GKZ420" - }, - "pmcid:PMC6602425", - "pubmed:31114899" + } ], "sc:description": "Webserver for scoring the impact of single nucleotide variants in the dog genome.", "sc:featureList": [ { - "@id": "edam:operation_0484" + "@id": "edam:operation_0331" }, { - "@id": "edam:operation_0331" + "@id": "edam:operation_0484" }, { "@id": "edam:operation_3227" @@ -52,8 +52,8 @@ "sc:license": "CC-BY-NC-SA-4.0", "sc:name": "Fido-SNP", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://fidosnp.bca.unipd.it/" diff --git a/data/fidpd/fidpdbioschemas.jsonld b/data/fidpd/fidpdbioschemas.jsonld index 94b621ac73b85..e2c65da7e4027 100644 --- a/data/fidpd/fidpdbioschemas.jsonld +++ b/data/fidpd/fidpdbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "fiDPD", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://202.119.249.49" } \ No newline at end of file diff --git a/data/figaro/figarobioschemas.jsonld b/data/figaro/figarobioschemas.jsonld index 011f82736d42e..b5d1ffc0916bc 100644 --- a/data/figaro/figarobioschemas.jsonld +++ b/data/figaro/figarobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/figaro", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mihai Pop", - "James A. Yorke" + "James A. Yorke", + "Mihai Pop" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:18202027", diff --git a/data/figtree/figtreebioschemas.jsonld b/data/figtree/figtreebioschemas.jsonld index 6c09fe10fcde7..715d3e14457d0 100644 --- a/data/figtree/figtreebioschemas.jsonld +++ b/data/figtree/figtreebioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/figtree", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "This tool is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.", "sc:name": "FigTree", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://tree.bio.ed.ac.uk/software/figtree/" } \ No newline at end of file diff --git a/data/filter/filterbioschemas.jsonld b/data/filter/filterbioschemas.jsonld index f66d8297a497f..d36c4c2fb14b6 100644 --- a/data/filter/filterbioschemas.jsonld +++ b/data/filter/filterbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/filter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Tamas Dalmay", - "Vincent Moulton" + "Vincent Moulton", + "Tamas Dalmay" ], "sc:additionalType": "Desktop application", "sc:description": "Produce a filtered version of an sRNA dataset, controlled by several user-defined criteria, including sequence length, abundance, complexity, transfer and ribosomal RNA removal.", @@ -20,8 +20,8 @@ "sc:name": "Filter", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://srna-workbench.cmp.uea.ac.uk/filter-2/" } \ No newline at end of file diff --git a/data/filtercontrol/filtercontrolbioschemas.jsonld b/data/filtercontrol/filtercontrolbioschemas.jsonld index cec19402c12f7..aea6772df1ea8 100644 --- a/data/filtercontrol/filtercontrolbioschemas.jsonld +++ b/data/filtercontrol/filtercontrolbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Filter out peaks present both in ChIP and Control dataset.", "sc:name": "filtercontrol", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/filtercontrolpeaks/filterControl/1.0", "sc:version": "1.0" diff --git a/data/fimtrack/fimtrackbioschemas.jsonld b/data/fimtrack/fimtrackbioschemas.jsonld index 8674efb6cc670..16160bce406c6 100644 --- a/data/fimtrack/fimtrackbioschemas.jsonld +++ b/data/fimtrack/fimtrackbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "FIMTrack", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.uni-muenster.de/PRIA/en/FIM/index.html" } \ No newline at end of file diff --git a/data/fimtyper/fimtyperbioschemas.jsonld b/data/fimtyper/fimtyperbioschemas.jsonld index ffce948c5a864..75d4359d0e41f 100644 --- a/data/fimtyper/fimtyperbioschemas.jsonld +++ b/data/fimtyper/fimtyperbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Louise Roer", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:28592545", + "pmcid:PMC5527432", { "@id": "https://doi.org/10.1128/JCM.00737-17" - }, - "pubmed:28592545", - "pmcid:PMC5527432" + } ], "sc:description": "Escherichia coli Subtyping Based on fimH Alleles.", "sc:featureList": { diff --git a/data/findbase/findbasebioschemas.jsonld b/data/findbase/findbasebioschemas.jsonld index ee7af64c11129..4fdf1fbf06b72 100644 --- a/data/findbase/findbasebioschemas.jsonld +++ b/data/findbase/findbasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population.", "sc:name": "FINDbase", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.findbase.org" } \ No newline at end of file diff --git a/data/findgeo/findgeobioschemas.jsonld b/data/findgeo/findgeobioschemas.jsonld index 7f425ba10ce17..5c7276e208377 100644 --- a/data/findgeo/findgeobioschemas.jsonld +++ b/data/findgeo/findgeobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Determine metal coordination geometry.", "sc:name": "FindGeo", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "CERM", diff --git a/data/findkm/findkmbioschemas.jsonld b/data/findkm/findkmbioschemas.jsonld index c1d32b38869c7..d43ba3b2b751c 100644 --- a/data/findkm/findkmbioschemas.jsonld +++ b/data/findkm/findkmbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK MRC", "EMBOSS Contributors", - "UK BBSRC" + "UK BBSRC", + "UK MRC", + "Wellcome Trust" ], "sc:description": "Calculate and plot enzyme reaction data.", "sc:funder": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "findkm", diff --git a/data/findmyfriends/bioconda_findmyfriends.yaml b/data/findmyfriends/bioconda_findmyfriends.yaml index b418f7be0de61..c9a987aba56ff 100644 --- a/data/findmyfriends/bioconda_findmyfriends.yaml +++ b/data/findmyfriends/bioconda_findmyfriends.yaml @@ -8,7 +8,6 @@ description: A framework for doing microbial comparative genomics in R. The main home: https://bioconductor.org/packages/3.10/bioc/html/FindMyFriends.html identifiers: - biotools:findmyfriends -- doi:10.1038/nmeth.3252 license: GPL (>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-findmyfriends diff --git a/data/findmyfriends/findmyfriendsbioschemas.jsonld b/data/findmyfriends/findmyfriendsbioschemas.jsonld index f7d0c210a776b..b339c020c17d0 100644 --- a/data/findmyfriends/findmyfriendsbioschemas.jsonld +++ b/data/findmyfriends/findmyfriendsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas Lin Pedersen", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. It provides many novel approaches to doing pangenomic analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible.", "sc:license": "GPL-2.0", "sc:name": "FindMyFriends", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/FindMyFriends.html", "sc:version": "1.4.0" diff --git a/data/findpeaks/findpeaksbioschemas.jsonld b/data/findpeaks/findpeaksbioschemas.jsonld index d1276d6a61458..fbaef45a3712e 100644 --- a/data/findpeaks/findpeaksbioschemas.jsonld +++ b/data/findpeaks/findpeaksbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "FindPeaks 4.0 (Vancouver Short Read Package)", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://vancouvershortr.sourceforge.net/" diff --git a/data/findpept/findpeptbioschemas.jsonld b/data/findpept/findpeptbioschemas.jsonld index 262e6196f01cc..83d5182766157 100644 --- a/data/findpept/findpeptbioschemas.jsonld +++ b/data/findpept/findpeptbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage.", "sc:name": "FindPept", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://web.expasy.org/findpept/" } \ No newline at end of file diff --git a/data/findpromoter/findpromoterbioschemas.jsonld b/data/findpromoter/findpromoterbioschemas.jsonld index 54b30079a204e..9fdd75a5c45f7 100644 --- a/data/findpromoter/findpromoterbioschemas.jsonld +++ b/data/findpromoter/findpromoterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "findpromoter", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/promoteur_tools/findpromoter/1.0", "sc:version": "1.0" diff --git a/data/findzebra/findzebrabioschemas.jsonld b/data/findzebra/findzebrabioschemas.jsonld index 952b34d97d5f0..b812669abf98a 100644 --- a/data/findzebra/findzebrabioschemas.jsonld +++ b/data/findzebra/findzebrabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A search engine for rare diseases.", "sc:name": "FindZebra", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.findzebra.com/raredisease" } \ No newline at end of file diff --git a/data/finestr/finestrbioschemas.jsonld b/data/finestr/finestrbioschemas.jsonld index acb589d4511d5..a8cf79af02e79 100644 --- a/data/finestr/finestrbioschemas.jsonld +++ b/data/finestr/finestrbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "FineStr (pronounced as (fi-nes’tru), from Latin fenestra—window, and from fine structure]) server allows users to upload genomic sequences in FASTA format and to perform a single-base-resolution nucleosome mapping on them.", "sc:name": "FineStr", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.cs.bgu.ac.il/~nucleom/", diff --git a/data/fingerprintscan/fingerprintscanbioschemas.jsonld b/data/fingerprintscan/fingerprintscanbioschemas.jsonld index 6c0ea52b0e2d6..8fcfb44ba6da4 100644 --- a/data/fingerprintscan/fingerprintscanbioschemas.jsonld +++ b/data/fingerprintscan/fingerprintscanbioschemas.jsonld @@ -20,12 +20,12 @@ "sc:name": "FingerPRINTScan", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "University of Manchester", - "EMBL-EBI" + "EMBL-EBI", + "University of Manchester" ], "sc:url": "http://www.ebi.ac.uk/Tools/pfa/fingerprintscan/", "sc:version": "1" diff --git a/data/fire-pro/fire-probioschemas.jsonld b/data/fire-pro/fire-probioschemas.jsonld index 4af31c9a91e5b..e3d960e97535c 100644 --- a/data/fire-pro/fire-probioschemas.jsonld +++ b/data/fire-pro/fire-probioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Motif discovery and characterization program for proteins based on mutual information", "sc:name": "FIRE-pro", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://tavazoielab.c2b2.columbia.edu/FIRE-pro/", "sc:version": "1.1" diff --git a/data/firedb/firedbbioschemas.jsonld b/data/firedb/firedbbioschemas.jsonld index bf25ce2fbd65b..e29df2e41f35f 100644 --- a/data/firedb/firedbbioschemas.jsonld +++ b/data/firedb/firedbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A curated inventory of catalytic and biologically relevant small ligand-binding residues.", "sc:name": "FireDB", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://firedb.bioinfo.cnio.es/", "sc:version": "1" diff --git a/data/firedb_ws/firedb_wsbioschemas.jsonld b/data/firedb_ws/firedb_wsbioschemas.jsonld index 6d140a6aca5dc..c6b4c16ef4575 100644 --- a/data/firedb_ws/firedb_wsbioschemas.jsonld +++ b/data/firedb_ws/firedb_wsbioschemas.jsonld @@ -18,8 +18,8 @@ "Linux" ], "sc:provider": [ - "cnio.es", - "CNIO" + "CNIO", + "cnio.es" ], "sc:url": "http://firedb.bioinfo.cnio.es/rest/FireDB_rest.pl", "sc:version": "1" diff --git a/data/firedock/firedockbioschemas.jsonld b/data/firedock/firedockbioschemas.jsonld index e5bdaac9fb030..54f144c419969 100644 --- a/data/firedock/firedockbioschemas.jsonld +++ b/data/firedock/firedockbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The FireDock web server performs high-throughput flexible refinement and scoring of protein-protein docking solutions. Side chain conformations and rigid body orientations are optimized, and outputs viewed in three-dimensional space.", "sc:name": "FireDock", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/FireDock/" } \ No newline at end of file diff --git a/data/fireprot/fireprotbioschemas.jsonld b/data/fireprot/fireprotbioschemas.jsonld index 77f48f84d3b49..a9a6f8b371657 100644 --- a/data/fireprot/fireprotbioschemas.jsonld +++ b/data/fireprot/fireprotbioschemas.jsonld @@ -12,25 +12,25 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:author": [ - "Jan Stourac", - "Milos Musil" + "Milos Musil", + "Jan Stourac" ], "sc:contributor": [ - "Jaroslav Zendulka", "Tomas Martinek", - "Jan Brezovsky", - "David Bednar", "Jaroslav Bendl", + "David Bednar", + "Jan Brezovsky", "Jiri Damborsky", - "Zbynek Prokop" + "Zbynek Prokop", + "Jaroslav Zendulka" ], "sc:description": "FireProt is a web server for an automated design of thermostable mutants. The design of thermostable mutants is based on the integration of structural and evolutionary information obtained from several bioinformatics databases and computational tools.", "sc:license": "Proprietary", "sc:name": "FireProt", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://loschmidt.chemi.muni.cz/fireprot/", "sc:version": "1.1" diff --git a/data/firestar/firestarbioschemas.jsonld b/data/firestar/firestarbioschemas.jsonld index 964e799142a90..baa8e3f732a15 100644 --- a/data/firestar/firestarbioschemas.jsonld +++ b/data/firestar/firestarbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "firestar", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "CNIO", diff --git a/data/first_person_bioimage/first_person_bioimagebioschemas.jsonld b/data/first_person_bioimage/first_person_bioimagebioschemas.jsonld index 669ecf8f3ebb2..e452b8d7fea1e 100644 --- a/data/first_person_bioimage/first_person_bioimagebioschemas.jsonld +++ b/data/first_person_bioimage/first_person_bioimagebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "CC-BY-NC-SA-4.0", "sc:name": "First Person Bioimage", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://fpb.ceb.cam.ac.uk/" } \ No newline at end of file diff --git a/data/firstef/firstefbioschemas.jsonld b/data/firstef/firstefbioschemas.jsonld index 965d997c3091e..00c6be64992fd 100644 --- a/data/firstef/firstefbioschemas.jsonld +++ b/data/firstef/firstefbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "First Exon Finder (FirstEF) is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree.", "sc:name": "FirstEF", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://rulai.cshl.org/tools/FirstEF/" } \ No newline at end of file diff --git a/data/firth_tools/firth_toolsbioschemas.jsonld b/data/firth_tools/firth_toolsbioschemas.jsonld index d373e2b983384..8e41174dbecc6 100644 --- a/data/firth_tools/firth_toolsbioschemas.jsonld +++ b/data/firth_tools/firth_toolsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR.", "sc:name": "Firth Software Tools", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://guinevere.otago.ac.nz/stats.html" diff --git a/data/fish_amyloid/fish_amyloidbioschemas.jsonld b/data/fish_amyloid/fish_amyloidbioschemas.jsonld index 350620db1466b..af67f6f391fbb 100644 --- a/data/fish_amyloid/fish_amyloidbioschemas.jsonld +++ b/data/fish_amyloid/fish_amyloidbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-15-54", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/fish_amyloid", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:24564523", { "@id": "https://doi.org/10.1186/1471-2105-15-54" }, - "pmcid:PMC3941796" + "pmcid:PMC3941796", + "pubmed:24564523" ], "sc:description": "FISH Amyloid is a new method for finding amyloidogenic segments in proteins based on site specific co-occurrence of aminoacids.", "sc:featureList": { @@ -31,10 +35,6 @@ "Linux" ], "sc:url": "http://comprec-lin.iiar.pwr.edu.pl/fishInput/" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-15-54", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fish_finder/fish_finderbioschemas.jsonld b/data/fish_finder/fish_finderbioschemas.jsonld index 455113ca6e856..5adf9ac7295cd 100644 --- a/data/fish_finder/fish_finderbioschemas.jsonld +++ b/data/fish_finder/fish_finderbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus.FISH Finder is a graphical software tool to automatically analyze FISH images that vary significantly.", "sc:name": "FISH Finder", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://code.google.com/p/fishfinder/", diff --git a/data/fish_oracle/fish_oraclebioschemas.jsonld b/data/fish_oracle/fish_oraclebioschemas.jsonld index 78646523ad9de..9c3fa20ec8e02 100644 --- a/data/fish_oracle/fish_oraclebioschemas.jsonld +++ b/data/fish_oracle/fish_oraclebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Visualizes data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. It comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and  zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats.", "sc:name": "FISH Oracle", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.zbh.uni-hamburg.de/forschung/arbeitsgruppe-genominformatik/software/fish-oracle-2.html", "sc:version": "2" diff --git a/data/fishalyser/bioconda_fishalyser.yaml b/data/fishalyser/bioconda_fishalyser.yaml index 3f5bd71e5e24c..1417e37993347 100644 --- a/data/fishalyser/bioconda_fishalyser.yaml +++ b/data/fishalyser/bioconda_fishalyser.yaml @@ -6,7 +6,6 @@ description: FISHalyseR provides functionality to process and analyse digital ce home: https://bioconductor.org/packages/3.10/bioc/html/FISHalyseR.html identifiers: - biotools:fishalyser -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-fishalyser summary: FISHalyseR a package for automated FISH quantification diff --git a/data/fishalyser/fishalyserbioschemas.jsonld b/data/fishalyser/fishalyserbioschemas.jsonld index b8e148be61023..cb4c363500cf0 100644 --- a/data/fishalyser/fishalyserbioschemas.jsonld +++ b/data/fishalyser/fishalyserbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/fishalyser", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Karesh Arunakirinathan", - "Andreas Heindl" + "Andreas Heindl", + "Karesh Arunakirinathan" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This software provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.", "sc:license": "Artistic-2.0", "sc:name": "FISHalyseR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/FISHalyseR.html", "sc:version": "1.8.0" diff --git a/data/fishplot/fishplotbioschemas.jsonld b/data/fishplot/fishplotbioschemas.jsonld index 69b39743711e6..e70b1e6653bad 100644 --- a/data/fishplot/fishplotbioschemas.jsonld +++ b/data/fishplot/fishplotbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-4266-6700", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/s12864-016-3195-z", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/fishplot", "@type": "sc:SoftwareApplication", @@ -31,18 +39,10 @@ "sc:name": "fishplot", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/chrisamiller/fishplot" - }, - { - "@id": "http://orcid.org/0000-0003-4266-6700", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/s12864-016-3195-z", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fishresp/fishrespbioschemas.jsonld b/data/fishresp/fishrespbioschemas.jsonld index 5c6cfb55ec47b..19ec733b8c1e6 100644 --- a/data/fishresp/fishrespbioschemas.jsonld +++ b/data/fishresp/fishrespbioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Sergey Morozov", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6364290", { "@id": "https://doi.org/10.1093/conphys/coz003" }, - "pmcid:PMC6364290", "pubmed:30746152" ], "sc:description": "R package and GUI application for analysis of aquatic respirometry data.", diff --git a/data/fit/fitbioschemas.jsonld b/data/fit/fitbioschemas.jsonld index 22c73d39f152f..1594e706e11d4 100644 --- a/data/fit/fitbioschemas.jsonld +++ b/data/fit/fitbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MPL-2.0", "sc:name": "FIT", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://cran.r-project.org/package=FIT", "sc:version": "0.0.6" diff --git a/data/fitchi/fitchibioschemas.jsonld b/data/fitchi/fitchibioschemas.jsonld index 9fea85a5ced5d..1b25ef200dc7e 100644 --- a/data/fitchi/fitchibioschemas.jsonld +++ b/data/fitchi/fitchibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Python script that produces haplotype genealogy graphs from alignment files in Nexus format, along with summary statistics.", "sc:name": "Fitchi", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.evoinformatics.eu/fitchi.htm" diff --git a/data/fithic/fithicbioschemas.jsonld b/data/fithic/fithicbioschemas.jsonld index bf363e492deae..f0ac2727b1e25 100644 --- a/data/fithic/fithicbioschemas.jsonld +++ b/data/fithic/fithicbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ruyu Tan", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.", "sc:license": "GPL-2.0", diff --git a/data/fitmunk/fitmunkbioschemas.jsonld b/data/fitmunk/fitmunkbioschemas.jsonld index 2ba15f8865824..8334e6717f3ce 100644 --- a/data/fitmunk/fitmunkbioschemas.jsonld +++ b/data/fitmunk/fitmunkbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Framework for fitting conformations on a fixed backbone into electron density.", "sc:name": "Fitmunk", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://witold.med.virginia.edu/fitmunk/server/" } \ No newline at end of file diff --git a/data/fitom/fitombioschemas.jsonld b/data/fitom/fitombioschemas.jsonld index 43f792474a650..3730b6ff3a8af 100644 --- a/data/fitom/fitombioschemas.jsonld +++ b/data/fitom/fitombioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computer program for the detection of binding sites in DNA or RNA sequences. It implements several methods described in the literature to compute an approximation of binding affinity for a particular site based on a collection of binding sequences provided by the user.", "sc:name": "FiToM", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://erilllab.umbc.edu/research/software/fitom/" } \ No newline at end of file diff --git a/data/fittetra/fittetrabioschemas.jsonld b/data/fittetra/fittetrabioschemas.jsonld index 082710048d154..dba3acd57780e 100644 --- a/data/fittetra/fittetrabioschemas.jsonld +++ b/data/fittetra/fittetrabioschemas.jsonld @@ -9,25 +9,29 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2703-y", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/fitTetra", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Roeland E. Voorrips", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6425654", + "pubmed:30894135", { "@id": "https://doi.org/10.1186/s12859-019-2703-y" }, - "pubmed:30894135" + "pmcid:PMC6425654" ], "sc:description": "R package for genotype calling for tetraploids with multiple population and parental data support.", "sc:featureList": [ { - "@id": "edam:operation_0484" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_0484" }, { "@id": "edam:operation_3227" @@ -36,16 +40,12 @@ "sc:license": "GPL-3.0", "sc:name": "fitTetra", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://cran.r-project.org/package=fitPoly", "sc:version": "2.0" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2703-y", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fiview/fiviewbioschemas.jsonld b/data/fiview/fiviewbioschemas.jsonld index 38761a6086c2d..d6b207ad48d7e 100644 --- a/data/fiview/fiviewbioschemas.jsonld +++ b/data/fiview/fiviewbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Fiview", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://uazu.net/fiview/" } \ No newline at end of file diff --git a/data/fixseq/fixseqbioschemas.jsonld b/data/fixseq/fixseqbioschemas.jsonld index 07effd3ebf933..a587e4e0900bb 100644 --- a/data/fixseq/fixseqbioschemas.jsonld +++ b/data/fixseq/fixseqbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pcbi.1003494", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/fixseq", "@type": "sc:SoftwareApplication", @@ -36,10 +32,14 @@ "sc:license": "Not licensed", "sc:name": "FixSEQ", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bitbucket.org/thashim/fixseq" + }, + { + "@id": "https://doi.org/10.1371/journal.pcbi.1003494", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fizzy/fizzybioschemas.jsonld b/data/fizzy/fizzybioschemas.jsonld index e722b41682ae9..2c77acbd50cf0 100644 --- a/data/fizzy/fizzybioschemas.jsonld +++ b/data/fizzy/fizzybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Feature subset selection tool that uses FEAST in the background to run feature selection on biological data formats.", "sc:name": "Fizzy", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/EESI/Fizzy" } \ No newline at end of file diff --git a/data/flad/fladbioschemas.jsonld b/data/flad/fladbioschemas.jsonld index 30f87618a819c..33953fee1af59 100644 --- a/data/flad/fladbioschemas.jsonld +++ b/data/flad/fladbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Forensic loci allele database.", "sc:name": "FLAD", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://forensic.ugent.be/FLAD/" diff --git a/data/flagme/bioconda_flagme.yaml b/data/flagme/bioconda_flagme.yaml index b25328b0fa37d..9ab93ec661d86 100644 --- a/data/flagme/bioconda_flagme.yaml +++ b/data/flagme/bioconda_flagme.yaml @@ -4,7 +4,6 @@ description: Fragment-level analysis of gas chromatography - mass spectrometry m home: https://bioconductor.org/packages/3.10/bioc/html/flagme.html identifiers: - biotools:flagme -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-flagme diff --git a/data/flagme/flagmebioschemas.jsonld b/data/flagme/flagmebioschemas.jsonld index 81c1e4ab126e1..a00acf5fa8260 100644 --- a/data/flagme/flagmebioschemas.jsonld +++ b/data/flagme/flagmebioschemas.jsonld @@ -15,16 +15,16 @@ "Riccardo Romoli" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data.", "sc:license": "GPL-2.0", "sc:name": "flagme", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flagme.html", "sc:version": "1.30.0" diff --git a/data/flea/fleabioschemas.jsonld b/data/flea/fleabioschemas.jsonld index 69b23498e3872..9fd06d5200db7 100644 --- a/data/flea/fleabioschemas.jsonld +++ b/data/flea/fleabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "FLEA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/veg/flea-pipeline" } \ No newline at end of file diff --git a/data/fledfold/fledfoldbioschemas.jsonld b/data/fledfold/fledfoldbioschemas.jsonld index ae96f0ad43f2c..36c9efaafcd0f 100644 --- a/data/fledfold/fledfoldbioschemas.jsonld +++ b/data/fledfold/fledfoldbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Hao Zhang", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:29123460", + "pmcid:PMC5652076", { "@id": "https://doi.org/10.2174/1570178614666170419122621" - }, - "pmcid:PMC5652076", - "pubmed:29123460" + } ], "sc:description": "Combines both thermodynamic and kinetic factors for RNA secondary structure and can predict RNA secondary structures from single primary sequences. Our early work has shown the accuracy of it is higher than the accuracy of traditional methods, especially for RNAs without pseudoknots.", "sc:featureList": { diff --git a/data/flexbar/flexbarbioschemas.jsonld b/data/flexbar/flexbarbioschemas.jsonld index 9a734b133b961..79ecc28a4a584 100644 --- a/data/flexbar/flexbarbioschemas.jsonld +++ b/data/flexbar/flexbarbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Flexbar", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/seqan/flexbar", "sc:version": "3.5.0" diff --git a/data/flexflux/flexfluxbioschemas.jsonld b/data/flexflux/flexfluxbioschemas.jsonld index 57b9d6285eeb7..91d806e482488 100644 --- a/data/flexflux/flexfluxbioschemas.jsonld +++ b/data/flexflux/flexfluxbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12918-015-0238-Z", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/flexflux", "@type": "sc:SoftwareApplication", @@ -22,8 +18,8 @@ { "@id": "https://doi.org/10.1186/S12918-015-0238-Z" }, - "pubmed:26666757", - "pmcid:PMC4678642" + "pmcid:PMC4678642", + "pubmed:26666757" ], "sc:description": "Combining metabolic flux and regulatory network analyses.", "sc:featureList": { @@ -32,10 +28,14 @@ "sc:license": "GPL-1.0", "sc:name": "FlexFlux", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://lipm-bioinfo.toulouse.inra.fr/flexflux/" + }, + { + "@id": "https://doi.org/10.1186/S12918-015-0238-Z", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/flexgsea/flexgseabioschemas.jsonld b/data/flexgsea/flexgseabioschemas.jsonld index 1b101f56e68ba..f409c16172b54 100644 --- a/data/flexgsea/flexgseabioschemas.jsonld +++ b/data/flexgsea/flexgseabioschemas.jsonld @@ -20,11 +20,11 @@ "@id": "https://orcid.org/0000-0001-6514-4767" }, "sc:citation": [ + "pmcid:PMC1239896", + "pubmed:16199517", { "@id": "https://doi.org/10.1073/pnas.0506580102." - }, - "pubmed:16199517", - "pmcid:PMC1239896" + } ], "sc:description": "Flexgsea is a R package to do gene set enrichment analysis. Main advantages:\n - Allows user defined functions. So you can use you favorite package for differential expression.\n - Calculates significance by sample permutation.\n - Parallelization using the foreach package.\n - Can calculate normalized enrichment scores (NES) and significance based on that.\n - Implements the weighted KS-like statistic.", "sc:featureList": { @@ -33,19 +33,19 @@ "sc:license": "Apache-2.0", "sc:name": "flexgsea", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/NKI-CCB/flexgsea-r" }, - { - "@id": "https://orcid.org/0000-0001-6514-4767", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1073/pnas.0506580102.", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0001-6514-4767", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/flexportal/flexportalbioschemas.jsonld b/data/flexportal/flexportalbioschemas.jsonld index 8259b45ce81d5..8a229dc2893fd 100644 --- a/data/flexportal/flexportalbioschemas.jsonld +++ b/data/flexportal/flexportalbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "FlexPortal", "sc:operatingSystem": "Linux", "sc:provider": [ - "irbbarcelona.org", - "IRB-BSC" + "IRB-BSC", + "irbbarcelona.org" ], "sc:url": "http://mmb.irbbarcelona.org/FlexPortal/", "sc:version": "1" diff --git a/data/flexpred/flexpredbioschemas.jsonld b/data/flexpred/flexpredbioschemas.jsonld index b13fdb9787d95..d1bad890c3be2 100644 --- a/data/flexpred/flexpredbioschemas.jsonld +++ b/data/flexpred/flexpredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "FlexPred", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://flexpred.rit.albany.edu/" } \ No newline at end of file diff --git a/data/flexprot/flexprotbioschemas.jsonld b/data/flexprot/flexprotbioschemas.jsonld index fdbfaed35ac23..13f27f94ec8a9 100644 --- a/data/flexprot/flexprotbioschemas.jsonld +++ b/data/flexprot/flexprotbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Detect the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected.", "sc:name": "FlexProt", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/FlexProt/" diff --git a/data/flexserv/flexservbioschemas.jsonld b/data/flexserv/flexservbioschemas.jsonld index a8d5b075489c0..1928bc1c31632 100644 --- a/data/flexserv/flexservbioschemas.jsonld +++ b/data/flexserv/flexservbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "FlexServ", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mmb.irbbarcelona.org/FlexServ", "sc:version": "1.0" diff --git a/data/flipflop/flipflopbioschemas.jsonld b/data/flipflop/flipflopbioschemas.jsonld index 051c37a00bc29..d732738964304 100644 --- a/data/flipflop/flipflopbioschemas.jsonld +++ b/data/flipflop/flipflopbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btu317", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/flipflop", "@type": "sc:SoftwareApplication", @@ -24,12 +20,12 @@ "@id": "edam:data_1255" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:24813214", "pmcid:PMC4147886", + "pubmed:24813214", { "@id": "https://doi.org/10.1093/bioinformatics/btu317" } @@ -52,6 +48,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flipflop.html", "sc:version": "1.12.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btu317", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/flippant/flippantbioschemas.jsonld b/data/flippant/flippantbioschemas.jsonld index f983ae6df08fa..c66b5d8271c27 100644 --- a/data/flippant/flippantbioschemas.jsonld +++ b/data/flippant/flippantbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1542-y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/flippant", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Richard J. Cotton", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:28253836", - "pmcid:PMC5335725", { "@id": "https://doi.org/10.1186/s12859-017-1542-y" - } + }, + "pubmed:28253836", + "pmcid:PMC5335725" ], "sc:description": "Automated analysis of dithionite scramblase assays.", "sc:featureList": { @@ -33,10 +29,14 @@ "sc:name": "flippant", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bitbucket.org/graumannlabtools/flippant" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1542-y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/flipper/flipperbioschemas.jsonld b/data/flipper/flipperbioschemas.jsonld index afdad0ae10b5a..1b614fe7148c3 100644 --- a/data/flipper/flipperbioschemas.jsonld +++ b/data/flipper/flipperbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Flipper", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "uma.es", "sc:url": "http://bitlab-es.com/flipper/", diff --git a/data/floremi/floremibioschemas.jsonld b/data/floremi/floremibioschemas.jsonld index a27d92ea2a8b7..9cd941ffa9d29 100644 --- a/data/floremi/floremibioschemas.jsonld +++ b/data/floremi/floremibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Automated analysis for cytometry data.", "sc:name": "FloReMi", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/SofieVG/FloReMi", diff --git a/data/floss/flossbioschemas.jsonld b/data/floss/flossbioschemas.jsonld index 45a4ee8f92988..19feb13309df4 100644 --- a/data/floss/flossbioschemas.jsonld +++ b/data/floss/flossbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "FLOSS", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://faculty.washington.edu/browning/floss/floss.htm", "sc:version": "1.4.1" diff --git a/data/flowai/flowaibioschemas.jsonld b/data/flowai/flowaibioschemas.jsonld index 16c8eb269db6d..c92b9b0795545 100644 --- a/data/flowai/flowaibioschemas.jsonld +++ b/data/flowai/flowaibioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Gianni Monaco", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: 1) flow rate, 2) signal acquisition, 3) dynamic range, the quality control enables the detection and removal of anomalies.", "sc:license": "GPL-3.0", "sc:name": "flowAI", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowAI.html", "sc:version": "1.2.0" diff --git a/data/flowand/flowandbioschemas.jsonld b/data/flowand/flowandbioschemas.jsonld index 462924392d757..73c2cdb6ca92d 100644 --- a/data/flowand/flowandbioschemas.jsonld +++ b/data/flowand/flowandbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "FlowAnd is designed to analyze and integrate largescale, multi-color flow cytometry data. It implements methods for data importing, various transformations, several clustering algorithms for automatic clustering, visualization tools as well as straightforward statistical testing.", "sc:name": "FlowAnd", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://csbi.ltdk.helsinki.fi/flowand/", "sc:version": "1.0" diff --git a/data/flowbeads/bioconda_flowbeads.yaml b/data/flowbeads/bioconda_flowbeads.yaml index 233fb7b27fa8f..3c5b960b91a29 100644 --- a/data/flowbeads/bioconda_flowbeads.yaml +++ b/data/flowbeads/bioconda_flowbeads.yaml @@ -5,7 +5,6 @@ description: This package extends flowCore to provide functionality specific to home: https://bioconductor.org/packages/3.10/bioc/html/flowBeads.html identifiers: - biotools:flowbeads -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-flowbeads summary: 'flowBeads: Analysis of flow bead data' diff --git a/data/flowbeads/flowbeadsbioschemas.jsonld b/data/flowbeads/flowbeadsbioschemas.jsonld index 3071af9438a6c..800f40c8dda87 100644 --- a/data/flowbeads/flowbeadsbioschemas.jsonld +++ b/data/flowbeads/flowbeadsbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "flowBeads", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowBeads.html", "sc:version": "1.12.0" diff --git a/data/flowbin/flowbinbioschemas.jsonld b/data/flowbin/flowbinbioschemas.jsonld index 5557e3fb03e55..eedad8d79bd02 100644 --- a/data/flowbin/flowbinbioschemas.jsonld +++ b/data/flowbin/flowbinbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Kieran O'Neill", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.", "sc:license": "Artistic-2.0", diff --git a/data/flowcal/flowcalbioschemas.jsonld b/data/flowcal/flowcalbioschemas.jsonld index 4afb6226943c4..16e88d1963979 100644 --- a/data/flowcal/flowcalbioschemas.jsonld +++ b/data/flowcal/flowcalbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1021/acssynbio.5b00284", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/flowcal", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jeffrey J. Tabor", "sc:additionalType": "Plug-in", "sc:citation": [ - "pubmed:27110723", "pmcid:PMC5556937", { "@id": "https://doi.org/10.1021/acssynbio.5b00284" - } + }, + "pubmed:27110723" ], "sc:description": "A Python package that can be used to calibrate flow cytometry data as well as automatically gate data, calculate common statistics, and produce publication quality plots.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "MIT", "sc:name": "FlowCal", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/taborlab/FlowCal", "sc:version": "1.2.0" + }, + { + "@id": "https://doi.org/10.1021/acssynbio.5b00284", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/flowcatchr/flowcatchrbioschemas.jsonld b/data/flowcatchr/flowcatchrbioschemas.jsonld index b15641fc143c1..6754b3be5d9a5 100644 --- a/data/flowcatchr/flowcatchrbioschemas.jsonld +++ b/data/flowcatchr/flowcatchrbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "BSD-4-Clause", "sc:name": "flowcatchR", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowcatchR.html", "sc:version": "1.8.0" diff --git a/data/flowchic/flowchicbioschemas.jsonld b/data/flowchic/flowchicbioschemas.jsonld index 863d9d58c1fc4..dcd93f97bc255 100644 --- a/data/flowchic/flowchicbioschemas.jsonld +++ b/data/flowchic/flowchicbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Author: Joachim Schumann", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A package to analyze flow cytometric data of complex microbial communities based on histogram images.", "sc:license": "GPL-2.0", "sc:name": "flowCHIC", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowCHIC.html", "sc:version": "1.8.0" diff --git a/data/flowcl/flowclbioschemas.jsonld b/data/flowcl/flowclbioschemas.jsonld index 8a31174fffd93..6be40b134f5c6 100644 --- a/data/flowcl/flowclbioschemas.jsonld +++ b/data/flowcl/flowclbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Justin Meskas", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Semantic labelling of flow cytometric cell populations.", "sc:license": "Artistic-2.0", diff --git a/data/flowclean/flowcleanbioschemas.jsonld b/data/flowclean/flowcleanbioschemas.jsonld index b7f9efa41cb13..f984b98b898be 100644 --- a/data/flowclean/flowcleanbioschemas.jsonld +++ b/data/flowclean/flowcleanbioschemas.jsonld @@ -14,14 +14,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Kipper Fletez-Brant", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:26990501", { "@id": "https://doi.org/10.1002/cyto.a.22837" }, + "pubmed:26990501", "pmcid:PMC5522377" ], "sc:description": "A quality control tool for flow cytometry data based on compositional data analysis.", @@ -36,8 +36,8 @@ "sc:license": "Artistic-2.0", "sc:name": "flowClean", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowClean.html", diff --git a/data/flowclust/flowclustbioschemas.jsonld b/data/flowclust/flowclustbioschemas.jsonld index 2aec717a1a974..59360a589ebf2 100644 --- a/data/flowclust/flowclustbioschemas.jsonld +++ b/data/flowclust/flowclustbioschemas.jsonld @@ -23,9 +23,9 @@ "sc:license": "Artistic-2.0", "sc:name": "flowClust", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowClust.html", "sc:version": "3.12.1" diff --git a/data/flowcore/flowcorebioschemas.jsonld b/data/flowcore/flowcorebioschemas.jsonld index 122197a93d893..66bf2ac3b8008 100644 --- a/data/flowcore/flowcorebioschemas.jsonld +++ b/data/flowcore/flowcorebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "M.Jiang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Provides S4 data structures and basic functions to deal with flow cytometry data.", "sc:license": "Artistic-2.0", "sc:name": "flowCore", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowCore.html", "sc:version": "1.40.3" diff --git a/data/flowcybar/flowcybarbioschemas.jsonld b/data/flowcybar/flowcybarbioschemas.jsonld index 37f5a61c52100..3aa626bdb23d0 100644 --- a/data/flowcybar/flowcybarbioschemas.jsonld +++ b/data/flowcybar/flowcybarbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "flowCyBar", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowCyBar.html", "sc:version": "1.10.0" diff --git a/data/flowdensity/flowdensitybioschemas.jsonld b/data/flowdensity/flowdensitybioschemas.jsonld index 258dbae4cc9e3..834ee0a7c9777 100644 --- a/data/flowdensity/flowdensitybioschemas.jsonld +++ b/data/flowdensity/flowdensitybioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mehrnoush Malek", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.", "sc:license": "Artistic-2.0", diff --git a/data/flowdiv/flowdivbioschemas.jsonld b/data/flowdiv/flowdivbioschemas.jsonld index 8be62d92e2ee5..6a1ba53786fd6 100644 --- a/data/flowdiv/flowdivbioschemas.jsonld +++ b/data/flowdiv/flowdivbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2787-4", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/flowDiv", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:31138128", - "pmcid:PMC6540361", { "@id": "https://doi.org/10.1186/s12859-019-2787-4" - } + }, + "pmcid:PMC6540361" ], "sc:description": "Pipeline for analyzing flow cytometric diversity.", "sc:featureList": { @@ -28,16 +32,12 @@ "sc:license": "GPL-3.0", "sc:name": "flowDiv", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/package=flowDiv", "sc:version": "2.0" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2787-4", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/flowfit/flowfitbioschemas.jsonld b/data/flowfit/flowfitbioschemas.jsonld index 7dac2b97af26a..21082d6793336 100644 --- a/data/flowfit/flowfitbioschemas.jsonld +++ b/data/flowfit/flowfitbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Davide Rambaldi", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package estimate the proliferation of a cell population in cell-tracking dye studies. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.", "sc:license": "Artistic-2.0", "sc:name": "flowFit", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowFit.html", "sc:version": "1.12.0" diff --git a/data/flowfp/flowfpbioschemas.jsonld b/data/flowfp/flowfpbioschemas.jsonld index c7b701a036649..457e946a4f47d 100644 --- a/data/flowfp/flowfpbioschemas.jsonld +++ b/data/flowfp/flowfpbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Herb Holyst", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.", "sc:license": "Artistic-2.0", "sc:name": "flowFP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowFP.html", "sc:version": "1.32.0" diff --git a/data/flowmap/flowmapbioschemas.jsonld b/data/flowmap/flowmapbioschemas.jsonld index cf9ea41816ebf..d8c2fb7f36ff3 100644 --- a/data/flowmap/flowmapbioschemas.jsonld +++ b/data/flowmap/flowmapbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "flowMap", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowMap.html", "sc:version": "1.12.0" diff --git a/data/flowmatch/bioconda_flowmatch.yaml b/data/flowmatch/bioconda_flowmatch.yaml index 1a5cb6012377f..44e3714ae9f7f 100644 --- a/data/flowmatch/bioconda_flowmatch.yaml +++ b/data/flowmatch/bioconda_flowmatch.yaml @@ -4,7 +4,6 @@ description: Matching cell populations and building meta-clusters and templates home: https://bioconductor.org/packages/3.10/bioc/html/flowMatch.html identifiers: - biotools:flowmatch -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-flowmatch summary: Matching and meta-clustering in flow cytometry diff --git a/data/flowmatch/flowmatchbioschemas.jsonld b/data/flowmatch/flowmatchbioschemas.jsonld index 6facfb7e10db4..b34a1badd251a 100644 --- a/data/flowmatch/flowmatchbioschemas.jsonld +++ b/data/flowmatch/flowmatchbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "flowMatch", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowMatch.html", diff --git a/data/flowmeans/flowmeansbioschemas.jsonld b/data/flowmeans/flowmeansbioschemas.jsonld index 21ee6c5e6b2c9..cad83b91c43b2 100644 --- a/data/flowmeans/flowmeansbioschemas.jsonld +++ b/data/flowmeans/flowmeansbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nima Aghaeepour", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. R 2.11.0 or newer is required.", "sc:license": "Artistic-2.0", "sc:name": "flowMeans", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowMeans.html", "sc:version": "1.34.0" diff --git a/data/flowmerge/flowmergebioschemas.jsonld b/data/flowmerge/flowmergebioschemas.jsonld index f9d247e0111ed..5f34ec1d2bd91 100644 --- a/data/flowmerge/flowmergebioschemas.jsonld +++ b/data/flowmerge/flowmergebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Greg Finak", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Users should have a working copy of flowClust 2.0 installed.", "sc:license": "Artistic-2.0", "sc:name": "flowMerge", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowMerge.html", "sc:version": "2.22.0" diff --git a/data/flowpeaks/flowpeaksbioschemas.jsonld b/data/flowpeaks/flowpeaksbioschemas.jsonld index 28d15ba6a6356..b30e17d988bb0 100644 --- a/data/flowpeaks/flowpeaksbioschemas.jsonld +++ b/data/flowpeaks/flowpeaksbioschemas.jsonld @@ -14,31 +14,31 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yongchao Ge", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ { "@id": "https://doi.org/10.1093/bioinformatics/bts300" }, - "pubmed:22595209", - "pmcid:PMC3400953" + "pmcid:PMC3400953", + "pubmed:22595209" ], "sc:description": "A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.", "sc:featureList": [ { - "@id": "edam:operation_3432" + "@id": "edam:operation_3214" }, { - "@id": "edam:operation_3214" + "@id": "edam:operation_3432" } ], "sc:license": "Artistic-1.0", "sc:name": "flowPeaks", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowPeaks.html", "sc:version": "1.18.0" diff --git a/data/flowploidy/bioconda_flowploidy.yaml b/data/flowploidy/bioconda_flowploidy.yaml index c9a40c1c277db..3cddc5ac4ed29 100644 --- a/data/flowploidy/bioconda_flowploidy.yaml +++ b/data/flowploidy/bioconda_flowploidy.yaml @@ -5,7 +5,6 @@ description: Determine sample ploidy via flow cytometry histogram analysis. Read home: https://bioconductor.org/packages/3.10/bioc/html/flowPloidy.html identifiers: - biotools:flowploidy -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-flowploidy diff --git a/data/flowploidy/flowploidybioschemas.jsonld b/data/flowploidy/flowploidybioschemas.jsonld index ad2adfb518bc9..b7738670551ff 100644 --- a/data/flowploidy/flowploidybioschemas.jsonld +++ b/data/flowploidy/flowploidybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "flowPloidy", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowPloidy.html", "sc:version": "1.0.0" diff --git a/data/flowplots/flowplotsbioschemas.jsonld b/data/flowplots/flowplotsbioschemas.jsonld index a752a0b17409a..9bc363a639490 100644 --- a/data/flowplots/flowplotsbioschemas.jsonld +++ b/data/flowplots/flowplotsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "flowPlots", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowPlots.html", "sc:version": "1.22.0" diff --git a/data/flowq/flowqbioschemas.jsonld b/data/flowq/flowqbioschemas.jsonld index 78728a1fed7e3..da83803d4f37c 100644 --- a/data/flowq/flowqbioschemas.jsonld +++ b/data/flowq/flowqbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mike Jiang", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Provides quality control and quality assessment tools for flow cytometry data.", "sc:license": "Artistic-2.0", "sc:name": "flowQ", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowQ.html", diff --git a/data/flowqb/flowqbbioschemas.jsonld b/data/flowqb/flowqbbioschemas.jsonld index 49bef1b9f9c59..d23abbbbd1296 100644 --- a/data/flowqb/flowqbbioschemas.jsonld +++ b/data/flowqb/flowqbbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "flowQB", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowQB.html", "sc:version": "2.2.0" diff --git a/data/flowrepositoryr/flowrepositoryrbioschemas.jsonld b/data/flowrepositoryr/flowrepositoryrbioschemas.jsonld index 8e398420574ca..9a71eb3316d31 100644 --- a/data/flowrepositoryr/flowrepositoryrbioschemas.jsonld +++ b/data/flowrepositoryr/flowrepositoryrbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Josef Spidlen", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides an interface to search and download data and annotations from FlowRepository (flowrepository.org). It uses the FlowRepository programming interface to communicate with a FlowRepository server.", "sc:license": "Artistic-2.0", "sc:name": "FlowRepositoryR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/FlowRepositoryR.html", "sc:version": "1.6.0" diff --git a/data/flowsom/flowsombioschemas.jsonld b/data/flowsom/flowsombioschemas.jsonld index 4f8b3b3d9816d..d342eb6aa167c 100644 --- a/data/flowsom/flowsombioschemas.jsonld +++ b/data/flowsom/flowsombioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Visualizing millions of cells.", "sc:name": "FlowSOM", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/SofieVG/FlowSOM", diff --git a/data/flowstats/flowstatsbioschemas.jsonld b/data/flowstats/flowstatsbioschemas.jsonld index dc965556a1497..d9ff0af57b712 100644 --- a/data/flowstats/flowstatsbioschemas.jsonld +++ b/data/flowstats/flowstatsbioschemas.jsonld @@ -15,15 +15,15 @@ "Greg Finak" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.", "sc:license": "Artistic-2.0", "sc:name": "flowStats", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowStats.html", diff --git a/data/flowtime/flowtimebioschemas.jsonld b/data/flowtime/flowtimebioschemas.jsonld index 7802d4b4a6103..d7d866f403387 100644 --- a/data/flowtime/flowtimebioschemas.jsonld +++ b/data/flowtime/flowtimebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "flowTime", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowTime.html", "sc:version": "1.4.0" diff --git a/data/flowtrans/flowtransbioschemas.jsonld b/data/flowtrans/flowtransbioschemas.jsonld index 9eb7046d46dcc..07bfde852a897 100644 --- a/data/flowtrans/flowtransbioschemas.jsonld +++ b/data/flowtrans/flowtransbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Greg Finak", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Profile maximum likelihood estimation of parameters for flow cytometry data transformations.", "sc:license": "Artistic-2.0", "sc:name": "flowTrans", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowTrans.html", "sc:version": "1.26.0" diff --git a/data/flowtype/flowtypebioschemas.jsonld b/data/flowtype/flowtypebioschemas.jsonld index bd62428064d84..acc9b1c31f5c7 100644 --- a/data/flowtype/flowtypebioschemas.jsonld +++ b/data/flowtype/flowtypebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nima Aghaeepour", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Phenotyping Flow Cytometry Assays using multidimentional expansion of single dimentional partitions.", "sc:license": "Artistic-2.0", "sc:name": "flowType", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowType.html", "sc:version": "2.12.0" diff --git a/data/flowutils/flowutilsbioschemas.jsonld b/data/flowutils/flowutilsbioschemas.jsonld index 5dca1a1976cdf..71dc6f2aab9d3 100644 --- a/data/flowutils/flowutilsbioschemas.jsonld +++ b/data/flowutils/flowutilsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Josef Spidlen", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Provides utilities for flow cytometry data.", "sc:license": "Artistic-2.0", "sc:name": "flowUtils", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowUtils.html", "sc:version": "1.38.0" diff --git a/data/flowviz/flowvizbioschemas.jsonld b/data/flowviz/flowvizbioschemas.jsonld index 4d03c47949402..58603b59c772d 100644 --- a/data/flowviz/flowvizbioschemas.jsonld +++ b/data/flowviz/flowvizbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "flowViz", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowViz.html", "sc:version": "1.38.0" diff --git a/data/flowvs/flowvsbioschemas.jsonld b/data/flowvs/flowvsbioschemas.jsonld index e208045bcfe82..210e7c3d6e38b 100644 --- a/data/flowvs/flowvsbioschemas.jsonld +++ b/data/flowvs/flowvsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "flowVS", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowVS.html", "sc:version": "1.6.0" diff --git a/data/flowworkspace/flowworkspacebioschemas.jsonld b/data/flowworkspace/flowworkspacebioschemas.jsonld index bfe2909408fd0..6dd1be5d9aff6 100644 --- a/data/flowworkspace/flowworkspacebioschemas.jsonld +++ b/data/flowworkspace/flowworkspacebioschemas.jsonld @@ -15,16 +15,16 @@ "Mike Jiang" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.", "sc:license": "Artistic-2.0", "sc:name": "flowWorkspace", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/flowWorkspace.html", "sc:version": "3.20.2" diff --git a/data/fluevidencesynthesis/fluevidencesynthesisbioschemas.jsonld b/data/fluevidencesynthesis/fluevidencesynthesisbioschemas.jsonld index 01fc66790fa30..b761e61247777 100644 --- a/data/fluevidencesynthesis/fluevidencesynthesisbioschemas.jsonld +++ b/data/fluevidencesynthesis/fluevidencesynthesisbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "fluEvidenceSynthesis", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/MJomaba/flu-evidence-synthesis" } \ No newline at end of file diff --git a/data/fluff/fluffbioschemas.jsonld b/data/fluff/fluffbioschemas.jsonld index 638092aa595e9..d5f92f5768059 100644 --- a/data/fluff/fluffbioschemas.jsonld +++ b/data/fluff/fluffbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.7717/peerj.2209", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-0411-3219", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/fluff", "@type": "sc:SoftwareApplication", @@ -31,14 +39,6 @@ "sc:name": "fluff", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/simonvh/fluff" - }, - { - "@id": "http://orcid.org/0000-0002-0411-3219", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.7717/peerj.2209", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fluorocelltrack/fluorocelltrackbioschemas.jsonld b/data/fluorocelltrack/fluorocelltrackbioschemas.jsonld index 0bed798cadce3..ff543b57507a3 100644 --- a/data/fluorocelltrack/fluorocelltrackbioschemas.jsonld +++ b/data/fluorocelltrack/fluorocelltrackbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-0484-5871", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0215337", "@type": "sc:CreativeWork" @@ -34,20 +30,24 @@ "sc:description": "Algorithm for automated analysis of high-throughput droplet microfluidic data.", "sc:featureList": [ { - "@id": "edam:operation_3799" + "@id": "edam:operation_3443" }, { - "@id": "edam:operation_3443" + "@id": "edam:operation_3799" } ], "sc:license": "Unlicense", "sc:name": "FluoroCellTrack", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/Manibarathi/FluoroCellTrack" + }, + { + "@id": "https://orcid.org/0000-0003-0484-5871", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/fluxmap/fluxmapbioschemas.jsonld b/data/fluxmap/fluxmapbioschemas.jsonld index 6558930f228f4..7b50ab2ebfd5c 100644 --- a/data/fluxmap/fluxmapbioschemas.jsonld +++ b/data/fluxmap/fluxmapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Easy to use tool for the advanced visualization of simulated or measured flux data in biological networks. Flux data import is achieved via a structured template basing on intuitive reaction equations. Flux data is mapped onto any network and visualized using edge thickness. Various visualization options and interaction possibilities enable comparison and visual analysis of complex experimental setups in an interactive way.", "sc:name": "FluxMap", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://immersive-analytics.infotech.monash.edu/vanted/addons/fluxmap/" diff --git a/data/fluxmodecalculator/fluxmodecalculatorbioschemas.jsonld b/data/fluxmodecalculator/fluxmodecalculatorbioschemas.jsonld index 51fbc85587f4a..5960ec4897350 100644 --- a/data/fluxmodecalculator/fluxmodecalculatorbioschemas.jsonld +++ b/data/fluxmodecalculator/fluxmodecalculatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "MATLAB toolbox for computing the elementary flux modes, extreme pathways or minimal generating sets in stoichiometric models", "sc:name": "FluxModeCalculator", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.lumc.nl/org/humane-genetica/medewerkers/jan-bert-van-klinken" } \ No newline at end of file diff --git a/data/fluxpyt/fluxpytbioschemas.jsonld b/data/fluxpyt/fluxpytbioschemas.jsonld index 1a37e83c6c9cf..d425e5710744a 100644 --- a/data/fluxpyt/fluxpytbioschemas.jsonld +++ b/data/fluxpyt/fluxpytbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Shireesh Srivastava", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5933345", "pubmed:29736347", { "@id": "https://doi.org/10.7717/peerj.4716" - } + }, + "pmcid:PMC5933345" ], "sc:description": "Stationary 13C metabolic flux analysis for estimation of intracellular flux distribution.", "sc:featureList": { diff --git a/data/fluxviz/fluxvizbioschemas.jsonld b/data/fluxviz/fluxvizbioschemas.jsonld index b136ede070a1e..a1bdbc8aeb108 100644 --- a/data/fluxviz/fluxvizbioschemas.jsonld +++ b/data/fluxviz/fluxvizbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Open-source Cytoscape plug-in for the visualization of flux distributions in molecular interaction networks.", "sc:name": "FluxViz", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://apps.cytoscape.org/apps/fluxviz" } \ No newline at end of file diff --git a/data/flybase/flybasebioschemas.jsonld b/data/flybase/flybasebioschemas.jsonld index 72c3585eefbff..374ac5eeab7c3 100644 --- a/data/flybase/flybasebioschemas.jsonld +++ b/data/flybase/flybasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database and web portal for genetic and genomic information on fruit fly Drosophila melanogaster and related fly species.", "sc:name": "FlyBase", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://flybase.org/" } \ No newline at end of file diff --git a/data/flyfactorsurvey/flyfactorsurveybioschemas.jsonld b/data/flyfactorsurvey/flyfactorsurveybioschemas.jsonld index 29f5d28d5d812..37f7b2f533dfb 100644 --- a/data/flyfactorsurvey/flyfactorsurveybioschemas.jsonld +++ b/data/flyfactorsurvey/flyfactorsurveybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "A database of DNA binding specificities for Drosophila transcription factors determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information for individual TFs, groups of TFs or for all TFs with characterized binding specificities.", "sc:name": "FlyFactorSurvey", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://pgfe.umassmed.edu/TFDBS/" } \ No newline at end of file diff --git a/data/flymine/flyminebioschemas.jsonld b/data/flymine/flyminebioschemas.jsonld index 71fc2e5b44c74..2b23dfb3653d1 100644 --- a/data/flymine/flyminebioschemas.jsonld +++ b/data/flymine/flyminebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/flymine", "@type": "sc:SoftwareApplication", "sc:additionalType": [ + "Database portal", "Web application", - "Web service", - "Database portal" + "Web service" ], "sc:description": "An integrated database for Drosophila and Anopheles genomics.", "sc:license": "LGPL-2.1", "sc:name": "FlyMine", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://flymine.org/flymine", "sc:version": "48 2019 October" diff --git a/data/flyode/flyodebioschemas.jsonld b/data/flyode/flyodebioschemas.jsonld index 1fff882c23ecb..656f9cac06288 100644 --- a/data/flyode/flyodebioschemas.jsonld +++ b/data/flyode/flyodebioschemas.jsonld @@ -9,6 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-7223-8291", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.12688/f1000research.7556.1", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-6785-3719", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/flyode", "@type": "sc:SoftwareApplication", @@ -23,10 +35,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:26998229", + "pmcid:PMC4786896", { "@id": "https://doi.org/10.12688/f1000research.7556.1" - }, - "pmcid:PMC4786896" + } ], "sc:description": "Systematic assembly of data on Drosophila melanogaster eye development. It consists of data on eye development obtained from the literature, and a web interface for users to interactively display these data as a gene regulatory network.", "sc:featureList": [ @@ -40,18 +52,6 @@ "sc:license": "MIT", "sc:name": "FLyOde", "sc:url": "http://flyode.boun.edu.tr" - }, - { - "@id": "http://orcid.org/0000-0001-6785-3719", - "@type": "schema:Person" - }, - { - "@id": "http://orcid.org/0000-0002-7223-8291", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.12688/f1000research.7556.1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/flyrnai/flyrnaibioschemas.jsonld b/data/flyrnai/flyrnaibioschemas.jsonld index 3053002b24ab0..28143730d7db3 100644 --- a/data/flyrnai/flyrnaibioschemas.jsonld +++ b/data/flyrnai/flyrnaibioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "FlyRNAi", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.flyrnai.org/" } \ No newline at end of file diff --git a/data/flytf/flytfbioschemas.jsonld b/data/flytf/flytfbioschemas.jsonld index 4216d3adc5fe6..260b54d89a4f5 100644 --- a/data/flytf/flytfbioschemas.jsonld +++ b/data/flytf/flytfbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. This database contains information on the manual curation of 1052 FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database.", "sc:name": "FlyTF", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.html" } \ No newline at end of file diff --git a/data/fmm/fmmbioschemas.jsonld b/data/fmm/fmmbioschemas.jsonld index 71c72d02d2b9b..5a98def3d353d 100644 --- a/data/fmm/fmmbioschemas.jsonld +++ b/data/fmm/fmmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.", "sc:name": "FMM", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://FMM.mbc.nctu.edu.tw/" } \ No newline at end of file diff --git a/data/fnbtools/fnbtoolsbioschemas.jsonld b/data/fnbtools/fnbtoolsbioschemas.jsonld index ad6747721f191..d27553296f87d 100644 --- a/data/fnbtools/fnbtoolsbioschemas.jsonld +++ b/data/fnbtools/fnbtoolsbioschemas.jsonld @@ -30,8 +30,8 @@ }, "sc:name": "FNBtools", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/noble-research-institute/fnbtools" }, diff --git a/data/fnv/fnvbioschemas.jsonld b/data/fnv/fnvbioschemas.jsonld index f9fa2ad49ffa1..40bd1852952e4 100644 --- a/data/fnv/fnvbioschemas.jsonld +++ b/data/fnv/fnvbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Visualize small to moderately sized biological networks and pathways. The tool can also be used to embed pathways inside PDF files for the communication of pathways in soft publication materials", "sc:name": "FNV", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://maayanlab.net/FNV/" diff --git a/data/focal/focalbioschemas.jsonld b/data/focal/focalbioschemas.jsonld index 54485a831573c..e3fba4c92d970 100644 --- a/data/focal/focalbioschemas.jsonld +++ b/data/focal/focalbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "FOCAL", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.utm.utoronto.ca/milsteinlab/resources/Software/FOCAL/" } \ No newline at end of file diff --git a/data/focalcall/focalcallbioschemas.jsonld b/data/focalcall/focalcallbioschemas.jsonld index befc8e1f79125..fef49eb15406b 100644 --- a/data/focalcall/focalcallbioschemas.jsonld +++ b/data/focalcall/focalcallbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "focalCall", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/focalCall.html", diff --git a/data/focus-point/focus-pointbioschemas.jsonld b/data/focus-point/focus-pointbioschemas.jsonld index 2aa0793005247..b106a39944c4e 100644 --- a/data/focus-point/focus-pointbioschemas.jsonld +++ b/data/focus-point/focus-pointbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "FoCuS-point", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://dwaithe.github.io/FCS_point_correlator/" } \ No newline at end of file diff --git a/data/focusedmds/focusedmdsbioschemas.jsonld b/data/focusedmds/focusedmdsbioschemas.jsonld index 37a69bd5a24af..e18b258f95f57 100644 --- a/data/focusedmds/focusedmdsbioschemas.jsonld +++ b/data/focusedmds/focusedmdsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "focusedMDS", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/anders-biostat/focusedMDS", "sc:version": "1.3.3" diff --git a/data/fodis/fodisbioschemas.jsonld b/data/fodis/fodisbioschemas.jsonld index 914afffc7c6d2..d8e80a8c1346e 100644 --- a/data/fodis/fodisbioschemas.jsonld +++ b/data/fodis/fodisbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Apache-2.0", "sc:name": "Fodis", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/nicolagalvanetto/Fodis" } \ No newline at end of file diff --git a/data/fog/fogbioschemas.jsonld b/data/fog/fogbioschemas.jsonld index 5083074c7f65a..9cfd028862aff 100644 --- a/data/fog/fogbioschemas.jsonld +++ b/data/fog/fogbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "FOG can help mapping important genomic features to the latest version of the human genome and also to annotate new features. such as miRNAs, microarray primers or probes, Chip-on-Chip data, CpG islands and SNPs to name a few.", "sc:name": "FOG", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.bioinformatics.org/webfog/wiki/", "sc:version": "1.0" diff --git a/data/fold-rate/fold-ratebioschemas.jsonld b/data/fold-rate/fold-ratebioschemas.jsonld index a901e5bd1abf0..811a805082db7 100644 --- a/data/fold-rate/fold-ratebioschemas.jsonld +++ b/data/fold-rate/fold-ratebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Predict the folding rates of proteins from their amino acid sequences.", "sc:name": "FOLD-RATE", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.iitm.ac.in/bioinfo/fold-rate/" } \ No newline at end of file diff --git a/data/foldhandedness/foldhandednessbioschemas.jsonld b/data/foldhandedness/foldhandednessbioschemas.jsonld index b02134957efe6..bf625cc5814a4 100644 --- a/data/foldhandedness/foldhandednessbioschemas.jsonld +++ b/data/foldhandedness/foldhandednessbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "FoldHandedness", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfo.protres.ru/foldhandedness/" } \ No newline at end of file diff --git a/data/foldit_standalone/foldit_standalonebioschemas.jsonld b/data/foldit_standalone/foldit_standalonebioschemas.jsonld index af3ffd86f8008..558a8512529c1 100644 --- a/data/foldit_standalone/foldit_standalonebioschemas.jsonld +++ b/data/foldit_standalone/foldit_standalonebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Foldit Standalone", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://fold.it/dist/external/standalone/quickstart.html" } \ No newline at end of file diff --git a/data/foldnucleus/foldnucleusbioschemas.jsonld b/data/foldnucleus/foldnucleusbioschemas.jsonld index 8a6dfdf34d4d6..267f2b626f8ca 100644 --- a/data/foldnucleus/foldnucleusbioschemas.jsonld +++ b/data/foldnucleus/foldnucleusbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Server  to calculate the folding nucleus for RNA molecules with known 3D structures-including pseudoknots, tRNAs, hairpins, and ribozymes-and for protein molecules with known 3D structures, as long as they are smaller than 200 amino acid residues.", "sc:name": "FoldNucleus", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioinfo.protres.ru/foldnucleus/" diff --git a/data/foldx/foldxbioschemas.jsonld b/data/foldx/foldxbioschemas.jsonld index 0cb297c8009ce..667969942a501 100644 --- a/data/foldx/foldxbioschemas.jsonld +++ b/data/foldx/foldxbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/foldx", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Luis Serrano", "Javier Delgado", - "Webmaster", - "Luis Serrano" + "Webmaster" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:15980494", "sc:description": "FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.", "sc:name": "FoldX", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://foldx.embl.de/" } \ No newline at end of file diff --git a/data/footer/footerbioschemas.jsonld b/data/footer/footerbioschemas.jsonld index 0c87c19b42f8a..60b2761467839 100644 --- a/data/footer/footerbioschemas.jsonld +++ b/data/footer/footerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Footer", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://biodev.hgen.pitt.edu/Footer/" } \ No newline at end of file diff --git a/data/fopa/fopabioschemas.jsonld b/data/fopa/fopabioschemas.jsonld index e0e40209d5b06..5489d2ebd1c03 100644 --- a/data/fopa/fopabioschemas.jsonld +++ b/data/fopa/fopabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "FoPA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/fmansoori/FoPA" } \ No newline at end of file diff --git a/data/forcefield_ncaa/forcefield_ncaabioschemas.jsonld b/data/forcefield_ncaa/forcefield_ncaabioschemas.jsonld index 2749c263c8695..a1c3c150942ab 100644 --- a/data/forcefield_ncaa/forcefield_ncaabioschemas.jsonld +++ b/data/forcefield_ncaa/forcefield_ncaabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Set of self-consistent AMBER forcefield parameters for non-canonical amino acids. It allows you to design and derivatize peptides containing NCAAs for use as drugs.", "sc:name": "Forcefield_NCAA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://selene.princeton.edu/FFNCAA/" } \ No newline at end of file diff --git a/data/forcefield_ptm/forcefield_ptmbioschemas.jsonld b/data/forcefield_ptm/forcefield_ptmbioschemas.jsonld index e0a40153e180c..02f83aef938b0 100644 --- a/data/forcefield_ptm/forcefield_ptmbioschemas.jsonld +++ b/data/forcefield_ptm/forcefield_ptmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Forcefield_PTM", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://selene.princeton.edu/FFPTM/" } \ No newline at end of file diff --git a/data/forecast/forecastbioschemas.jsonld b/data/forecast/forecastbioschemas.jsonld index d0a525c630c7f..10552a2bbf15c 100644 --- a/data/forecast/forecastbioschemas.jsonld +++ b/data/forecast/forecastbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/FORECasT", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Computational predictor of the mutations generated by repair of CRISPR-Cas9-induced double-strand breaks.", "sc:license": "CC-BY-3.0", "sc:name": "FORECasT", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://partslab.sanger.ac.uk/FORECasT" diff --git a/data/foresee/foreseebioschemas.jsonld b/data/foresee/foreseebioschemas.jsonld index caa590e6d07cf..f9268da0006fb 100644 --- a/data/foresee/foreseebioschemas.jsonld +++ b/data/foresee/foreseebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "FORESEE", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://osf.io/rf6qk/" diff --git a/data/forester/foresterbioschemas.jsonld b/data/forester/foresterbioschemas.jsonld index 67d1dd4e06a50..afe591140b8ab 100644 --- a/data/forester/foresterbioschemas.jsonld +++ b/data/forester/foresterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "forester", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sites.google.com/site/cmzmasek/home/software/forester" } \ No newline at end of file diff --git a/data/forge/forgebioschemas.jsonld b/data/forge/forgebioschemas.jsonld index 9b1a8f2767b64..964df59bad53f 100644 --- a/data/forge/forgebioschemas.jsonld +++ b/data/forge/forgebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:description": "Functional element Overlap analysis of the Results of GWAS Experiments . Discover cell specific enrichments of GWAS associated SNPs in regulatory regions and provides tabular and graphical summaries of the enrichments.", "sc:name": "FORGE", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://phase3browser.1000genomes.org/Homo_sapiens/UserData/Forge" } \ No newline at end of file diff --git a/data/forgi/forgibioschemas.jsonld b/data/forgi/forgibioschemas.jsonld index 2e81fa1a282a4..1dbb0a6d9886e 100644 --- a/data/forgi/forgibioschemas.jsonld +++ b/data/forgi/forgibioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.18458.2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/forgi", "@type": "sc:SoftwareApplication", @@ -28,23 +24,27 @@ "sc:description": "Python library to analyze the tertiary structure of RNA secondary structure elements.", "sc:featureList": [ { - "@id": "edam:operation_0570" + "@id": "edam:operation_0278" }, { - "@id": "edam:operation_0502" + "@id": "edam:operation_0570" }, { - "@id": "edam:operation_0278" + "@id": "edam:operation_0502" } ], "sc:license": "GPL-3.0", "sc:name": "forgi", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/ViennaRNA/forgi" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.18458.2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/formatomatic/formatomaticbioschemas.jsonld b/data/formatomatic/formatomaticbioschemas.jsonld index 8987783f73256..277859c38041c 100644 --- a/data/formatomatic/formatomaticbioschemas.jsonld +++ b/data/formatomatic/formatomaticbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool creates infiles for several population genetic analysis programs from csv, genepop or convert* (excel) files. It only handles diploid microsatellite data for now.", "sc:name": "Formatomatic", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://taylor0.biology.ucla.edu/~manoukis/Pub_programs/Formatomatic/" } \ No newline at end of file diff --git a/data/forna/fornabioschemas.jsonld b/data/forna/fornabioschemas.jsonld index b94d071ec017b..10349a763d359 100644 --- a/data/forna/fornabioschemas.jsonld +++ b/data/forna/fornabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btv372", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/forna", "@type": "sc:SoftwareApplication", @@ -23,26 +19,26 @@ "@id": "edam:data_2884" }, "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:applicationSubCategory": [ - { - "@id": "edam:topic_0097" - }, { "@id": "edam:topic_0080" }, { "@id": "edam:topic_0099" + }, + { + "@id": "edam:topic_0097" } ], "sc:citation": [ + "pmcid:PMC4595900", + "pubmed:26099263", { "@id": "https://doi.org/10.1093/bioinformatics/btv372" - }, - "pubmed:26099263", - "pmcid:PMC4595900" + } ], "sc:description": "Web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations.", "sc:featureList": { @@ -50,13 +46,17 @@ }, "sc:name": "Forna", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "bioinf.uni-leipzig.de", "sc:url": "http://rna.tbi.univie.ac.at/forna/", "sc:version": "1.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv372", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/forwsim/forwsimbioschemas.jsonld b/data/forwsim/forwsimbioschemas.jsonld index ca424f2c1b9f7..fb6e396048d50 100644 --- a/data/forwsim/forwsimbioschemas.jsonld +++ b/data/forwsim/forwsimbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Forward-time simulation programs for the standard neutral model.", "sc:name": "ForwSim", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://badri-populationgeneticsimulators.blogspot.com/" } \ No newline at end of file diff --git a/data/founder_sequences/founder_sequencesbioschemas.jsonld b/data/founder_sequences/founder_sequencesbioschemas.jsonld index 67c48583ae37d..df52d291f2883 100644 --- a/data/founder_sequences/founder_sequencesbioschemas.jsonld +++ b/data/founder_sequences/founder_sequencesbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-4454-1493", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/S13015-019-0147-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/founder_sequences", "@type": "sc:SoftwareApplication", @@ -34,16 +26,24 @@ "sc:description": "Given a minimum segment length and m sequences of length n drawn from an alphabet of size σ, create a segmentation in O(mn log σ) time and use various matching strategies to join the segment texts to generate founder sequences.", "sc:featureList": [ { - "@id": "edam:operation_3211" + "@id": "edam:operation_0487" }, { - "@id": "edam:operation_0487" + "@id": "edam:operation_3211" } ], "sc:license": "MIT", "sc:name": "founder sequences", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/tsnorri/founder-sequences" + }, + { + "@id": "https://doi.org/10.1186/S13015-019-0147-6", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0003-4454-1493", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/foundertracker/foundertrackerbioschemas.jsonld b/data/foundertracker/foundertrackerbioschemas.jsonld index 4e8b63993dac2..595c9435d330b 100644 --- a/data/foundertracker/foundertrackerbioschemas.jsonld +++ b/data/foundertracker/foundertrackerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/foundertracker", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:22567117", "sc:description": "Computational method for detecting significantly recurrent identity by descent (IBD) in a set of haplotypes. This tool was designed for the discovery of founder mutations in dense SNP array data from a population sample of tumors.", diff --git a/data/fourcseq/fourcseqbioschemas.jsonld b/data/fourcseq/fourcseqbioschemas.jsonld index 2b936a571a905..b65274734e380 100644 --- a/data/fourcseq/fourcseqbioschemas.jsonld +++ b/data/fourcseq/fourcseqbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btv335", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/fourcseq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Felix A. Klein", "edam:has_input": [ { - "@id": "edam:data_0849" + "@id": "edam:data_1383" }, { - "@id": "edam:data_1383" + "@id": "edam:data_0849" } ], "edam:has_output": [ @@ -44,11 +40,11 @@ "@id": "edam:topic_3168" }, "sc:citation": [ + "pubmed:26034064", + "pmcid:PMC4576695", { "@id": "https://doi.org/10.1093/bioinformatics/btv335" - }, - "pubmed:26034064", - "pmcid:PMC4576695" + } ], "sc:description": "R package dedicated to the analysis of (multiplexed) 4C sequencing data. It provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a python script to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.", "sc:featureList": { @@ -57,12 +53,16 @@ "sc:license": "GPL-3.0", "sc:name": "FourCSeq", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/FourCSeq.html", "sc:version": "1.8.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv335", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/foxs/foxsbioschemas.jsonld b/data/foxs/foxsbioschemas.jsonld index 803d41d3248c4..a37b3668e7ecb 100644 --- a/data/foxs/foxsbioschemas.jsonld +++ b/data/foxs/foxsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "FoXS", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://salilab.org/foxs" } \ No newline at end of file diff --git a/data/fp2vec/fp2vecbioschemas.jsonld b/data/fp2vec/fp2vecbioschemas.jsonld index 8d53c20e5299c..667c56834b145 100644 --- a/data/fp2vec/fp2vecbioschemas.jsonld +++ b/data/fp2vec/fp2vecbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "FP2VEC", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/wsjeon92/FP2VEC" } \ No newline at end of file diff --git a/data/fpb/fpbbioschemas.jsonld b/data/fpb/fpbbioschemas.jsonld index 2085d81f89f4f..4b4e3cdd19a28 100644 --- a/data/fpb/fpbbioschemas.jsonld +++ b/data/fpb/fpbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "FPB is a new data-independent tool suitable for large scale projects as well as mapping of few clones.", "sc:name": "FPB", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://services.appliedgenomics.org/software/fpb/", "sc:version": "1.1" diff --git a/data/fpbase/fpbasebioschemas.jsonld b/data/fpbase/fpbasebioschemas.jsonld index a0d95fce9342d..c9b6e2b57ad0f 100644 --- a/data/fpbase/fpbasebioschemas.jsonld +++ b/data/fpbase/fpbasebioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-3.0", "sc:name": "FPbase", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://www.fpbase.org/", "sc:version": "1.2.0" diff --git a/data/fpbioimage/fpbioimagebioschemas.jsonld b/data/fpbioimage/fpbioimagebioschemas.jsonld index a5e7f960c63fb..e38eddb37ddcf 100644 --- a/data/fpbioimage/fpbioimagebioschemas.jsonld +++ b/data/fpbioimage/fpbioimagebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "CC-BY-SA-4.0", "sc:name": "FPBioimage", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://fpb.ceb.cam.ac.uk/" diff --git a/data/fpc/fpcbioschemas.jsonld b/data/fpc/fpcbioschemas.jsonld index 38f029aeb3a40..3466257b1a8ea 100644 --- a/data/fpc/fpcbioschemas.jsonld +++ b/data/fpc/fpcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "FPC is a tool to assemble contigs from a set of clones and their restriction fragments.", "sc:name": "FPC", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.agcol.arizona.edu/software/fpc/" } \ No newline at end of file diff --git a/data/fpclass/fpclassbioschemas.jsonld b/data/fpclass/fpclassbioschemas.jsonld index f6e5d126c3ca9..91dd5ef3abe79 100644 --- a/data/fpclass/fpclassbioschemas.jsonld +++ b/data/fpclass/fpclassbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "FpClass", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://dcv.uhnres.utoronto.ca/FPCLASS/" } \ No newline at end of file diff --git a/data/fpocket/fpocketbioschemas.jsonld b/data/fpocket/fpocketbioschemas.jsonld index 2dfdce1db6f93..7e5e4fb8a3502 100644 --- a/data/fpocket/fpocketbioschemas.jsonld +++ b/data/fpocket/fpocketbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-1033-9895", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/fpocket", "@type": "sc:SoftwareApplication", @@ -22,10 +26,6 @@ "sc:name": "Fpocket", "sc:url": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::fpocket", "sc:version": "1.0" - }, - { - "@id": "https://orcid.org/0000-0003-1033-9895", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/fpsac/fpsacbioschemas.jsonld b/data/fpsac/fpsacbioschemas.jsonld index 4ceb4c60ede63..1b28db944d93c 100644 --- a/data/fpsac/fpsacbioschemas.jsonld +++ b/data/fpsac/fpsacbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "FPSAC (Fast Phylogentic Scaffolding of Ancient Contigs) is a software for fast phylogenetic scaffolding of ancient contigs. The author apply it on a set of 2134 ancient contigs assembled from the recently sequenced Black Death agent genome.", "sc:name": "FPSAC", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://paleogenomics.irmacs.sfu.ca/FPSAC/index.html", "sc:version": "1.0" diff --git a/data/fqconvert/fqconvertbioschemas.jsonld b/data/fqconvert/fqconvertbioschemas.jsonld index 52e364d8a828d..08a1e5c457b6e 100644 --- a/data/fqconvert/fqconvertbioschemas.jsonld +++ b/data/fqconvert/fqconvertbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Convert quality scoring to Sanger in FASTQ files.", "sc:name": "fqconvert", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "sc:version": "1.0.0" diff --git a/data/fractalsim/fractalsimbioschemas.jsonld b/data/fractalsim/fractalsimbioschemas.jsonld index 3e61fa6a56033..18fea2df0644a 100644 --- a/data/fractalsim/fractalsimbioschemas.jsonld +++ b/data/fractalsim/fractalsimbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Multi-scenario genome-wide medical population genetics simulation framework.", "sc:name": "FractalSIM", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://web.cbio.uct.ac.za/~emile/software.html" } \ No newline at end of file diff --git a/data/fractbias/fractbiasbioschemas.jsonld b/data/fractbias/fractbiasbioschemas.jsonld index 95466aa340c01..fa58902d4aaab 100644 --- a/data/fractbias/fractbiasbioschemas.jsonld +++ b/data/fractbias/fractbiasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "FractBias", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://genomevolution.org/CoGe/SynMap.pl" } \ No newline at end of file diff --git a/data/fragfit/fragfitbioschemas.jsonld b/data/fragfit/fragfitbioschemas.jsonld index 6e9ed4d160506..853d6fee7702c 100644 --- a/data/fragfit/fragfitbioschemas.jsonld +++ b/data/fragfit/fragfitbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Guided modeling of missing segments such as loops or hinge regions into cryo-Electron Microscopy (cryo-EM) density maps [1]. Segments of up to 3-35 residues length can be effectively modeled into maps of different resolution.", "sc:name": "FragFit", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://proteinformatics.charite.de/ngl-tools/fragfit/start.php", "sc:version": "2.52" diff --git a/data/fraghmment/fraghmmentbioschemas.jsonld b/data/fraghmment/fraghmmentbioschemas.jsonld index 0b969db9a3177..19d2645211cad 100644 --- a/data/fraghmment/fraghmmentbioschemas.jsonld +++ b/data/fraghmment/fraghmmentbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Residue-residue contact prediction.", "sc:name": "FragHMMent", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://predictioncenter.org/Services/FragHMMent/descr.html", diff --git a/data/fragmentationanalyzer/fragmentationanalyzerbioschemas.jsonld b/data/fragmentationanalyzer/fragmentationanalyzerbioschemas.jsonld index f0a39536e1a17..d74d3c46b9557 100644 --- a/data/fragmentationanalyzer/fragmentationanalyzerbioschemas.jsonld +++ b/data/fragmentationanalyzer/fragmentationanalyzerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "FragmentationAnalyzer", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://compomics.github.io/projects/fragmentation-analyzer.html" } \ No newline at end of file diff --git a/data/fragmentstore/fragmentstorebioschemas.jsonld b/data/fragmentstore/fragmentstorebioschemas.jsonld index ec9e2cda00687..e898905cb10c9 100644 --- a/data/fragmentstore/fragmentstorebioschemas.jsonld +++ b/data/fragmentstore/fragmentstorebioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/fragmentstore", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Catherine Sargent", "Paul Thaben", - "Robert Preissner", - "Jessica Ahmed" + "Catherine Sargent", + "Jessica Ahmed", + "Robert Preissner" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:20965964", "sc:description": "A resource for the comparison of fragments found in metabolites, drugs or toxic compounds. We generated 35,000 different building blocks (fragments), which are not only relevant to their biosynthesis and degradation but also provide important information regarding side-effects and toxicity. It provides a variety of search options. Various analysis tools have been implemented including the calculation of amino acid preferences of fragments binding sites and classification of fragments.", "sc:name": "FragmentStore", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioinformatics.charite.de/fragment_store" } \ No newline at end of file diff --git a/data/fragrus/fragrusbioschemas.jsonld b/data/fragrus/fragrusbioschemas.jsonld index 0ec7d82abcccd..479bec93c8217 100644 --- a/data/fragrus/fragrusbioschemas.jsonld +++ b/data/fragrus/fragrusbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web application designed to sample alternative protein backbone conformations in loop regions using the geometrical constrains of smotifs.", "sc:name": "Frag r Us", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.bioinsilico.org/FRAGRUS/" diff --git a/data/frama/framabioschemas.jsonld b/data/frama/framabioschemas.jsonld index f0b9c3166556b..59abfcb2fce25 100644 --- a/data/frama/framabioschemas.jsonld +++ b/data/frama/framabioschemas.jsonld @@ -13,13 +13,13 @@ "@id": "https://bio.tools/frama", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Bens M", - "Szafranski K" + "Szafranski K", + "Bens M" ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:26763976", "pmcid:PMC4712544", + "pubmed:26763976", { "@id": "https://doi.org/10.1186/S12864-015-2349-8" } @@ -27,10 +27,10 @@ "sc:description": "A transcriptome assembly and mRNA annotation pipeline, which utilizies external and newly developed software components.", "sc:featureList": [ { - "@id": "edam:operation_0310" + "@id": "edam:operation_0361" }, { - "@id": "edam:operation_0361" + "@id": "edam:operation_0310" } ], "sc:name": "FRAMA", diff --git a/data/framed/framedbioschemas.jsonld b/data/framed/framedbioschemas.jsonld index b2190b9330d7f..fe80ed3dc2edb 100644 --- a/data/framed/framedbioschemas.jsonld +++ b/data/framed/framedbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "FrameD", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://genoweb.toulouse.inra.fr/FrameD/FD" } \ No newline at end of file diff --git a/data/framedp/framedpbioschemas.jsonld b/data/framedp/framedpbioschemas.jsonld index 9085c79b72fa6..60eb8496f16a8 100644 --- a/data/framedp/framedpbioschemas.jsonld +++ b/data/framedp/framedpbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/framedp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ludovic Cottret", - "Sébastien Carrere", "Jérôme Gouzy", - "Erika Sallet" + "Erika Sallet", + "Ludovic Cottret", + "Sébastien Carrere" ], "sc:additionalType": "Web application", "sc:description": "Sensitive peptide detection on noisy matured sequences. A self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.", "sc:name": "FrameDP", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://iant.toulouse.inra.fr/FrameDP" } \ No newline at end of file diff --git a/data/fread/freadbioschemas.jsonld b/data/fread/freadbioschemas.jsonld index 7b5d9bc032bbf..27260eb7a72f0 100644 --- a/data/fread/freadbioschemas.jsonld +++ b/data/fread/freadbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "FREAD is a database search loop structure prediction protocol. Loops are generally located in the protein’s surface and they are known to be notoriously difficult to predict.The basic assumption of FREAD is that local sequence similarity may determine the backbone structure of a local protein structure if it is constrained within anchor structures.", "sc:name": "FREAD", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://opig.stats.ox.ac.uk/webapps/fread/php/index.php", "sc:version": "3.0.1" diff --git a/data/freak/freakbioschemas.jsonld b/data/freak/freakbioschemas.jsonld index caf5d12a74631..671fa8d28f681 100644 --- a/data/freak/freakbioschemas.jsonld +++ b/data/freak/freakbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", + "UK MRC", "UK BBSRC", "Wellcome Trust", - "UK MRC" + "EMBOSS Contributors" ], "sc:description": "Generate residue/base frequency table or plot.", "sc:funder": [ @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "freak", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/freak.html", "sc:version": "r6" diff --git a/data/freclu/freclubioschemas.jsonld b/data/freclu/freclubioschemas.jsonld index ac9d516387d4b..8dc6dda6f885f 100644 --- a/data/freclu/freclubioschemas.jsonld +++ b/data/freclu/freclubioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "a frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure. In this structure, each “child” sequence is considered to be derived from its “parent” sequence with one mutation through sequencing errors. The root node is the most frequently observed sequence that represents all erroneous reads in the entire tree.", "sc:name": "FreClu", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mlab.cb.k.u-tokyo.ac.jp/%7Equwei/DeNovoShortReadClustering/" } \ No newline at end of file diff --git a/data/fred/fredbioschemas.jsonld b/data/fred/fredbioschemas.jsonld index 43eff4426b9fe..413933ec2723c 100644 --- a/data/fred/fredbioschemas.jsonld +++ b/data/fred/fredbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "FRED", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://abi.inf.uni-tuebingen.de/Software/FRED", "sc:version": "1.0" diff --git a/data/freec/freecbioschemas.jsonld b/data/freec/freecbioschemas.jsonld index a3aabb791a56d..df0590f8a5f2d 100644 --- a/data/freec/freecbioschemas.jsonld +++ b/data/freec/freecbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/freec", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Valentina Boeva", - "Carino Gurjao" + "Carino Gurjao", + "Valentina Boeva" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:21081509", "sc:description": "A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.", "sc:name": "FREEC", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://boevalab.com/FREEC/" } \ No newline at end of file diff --git a/data/freect_wfbp/freect_wfbpbioschemas.jsonld b/data/freect_wfbp/freect_wfbpbioschemas.jsonld index 8c95fc295f6e0..108aa82cccf68 100644 --- a/data/freect_wfbp/freect_wfbpbioschemas.jsonld +++ b/data/freect_wfbp/freect_wfbpbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1118/1.4941953", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/freect_wfbp", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4769265", + "pubmed:26936725", { "@id": "https://doi.org/10.1118/1.4941953" - }, - "pmcid:PMC4769265", - "pubmed:26936725" + } ], "sc:description": "FreeCT_wFBP is a software package capable of reconstructing helical scans acquired with arbitrary pitch-values, and sampling techniques such as flying focal spots and a quarter-detector offset.", "sc:featureList": { @@ -28,10 +32,6 @@ "sc:name": "FreeCT_wFBP", "sc:operatingSystem": "Linux", "sc:url": "http://cvib.ucla.edu/freect/" - }, - { - "@id": "https://doi.org/10.1118/1.4941953", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/freesasa/freesasabioschemas.jsonld b/data/freesasa/freesasabioschemas.jsonld index 46fc9158008c5..7cc89d8ee60d0 100644 --- a/data/freesasa/freesasabioschemas.jsonld +++ b/data/freesasa/freesasabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/freesasa", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:author": "Simon Mitternacht", "sc:description": "FreeSASA is an open source library and command line tool to calculate the solvent accessible surface areas of protein molecules. The library is as fast and accurate as existing tools, with the advantage of being open source and available as both a library, a command line tool and it has Python bindings.", @@ -20,8 +20,8 @@ "sc:name": "FreeSASA", "sc:operatingSystem": "Linux", "sc:provider": [ - "UiB", - "University Library, University of Bergen, Bergen, Norway" + "University Library, University of Bergen, Bergen, Norway", + "UiB" ], "sc:url": "http://freesasa.github.io/", "sc:version": "2.0.1" diff --git a/data/fregat/fregatbioschemas.jsonld b/data/fregat/fregatbioschemas.jsonld index 165ee95442880..f4d81835427c1 100644 --- a/data/fregat/fregatbioschemas.jsonld +++ b/data/fregat/fregatbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Fast regional association analysis of quantitative traits for family-based and population studies.", "sc:name": "FREGAT", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/FREGAT/index.html" diff --git a/data/freiburg_rna_tools/freiburg_rna_toolsbioschemas.jsonld b/data/freiburg_rna_tools/freiburg_rna_toolsbioschemas.jsonld index 492db521b9fac..47970c2cf4995 100644 --- a/data/freiburg_rna_tools/freiburg_rna_toolsbioschemas.jsonld +++ b/data/freiburg_rna_tools/freiburg_rna_toolsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact form", "sc:additionalType": [ - "Suite", - "Web application" + "Web application", + "Suite" ], "sc:citation": "pubmed:20444875", "sc:description": "The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.", "sc:name": "Freiburg RNA Tools", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://rna.informatik.uni-freiburg.de" } \ No newline at end of file diff --git a/data/fresco/frescobioschemas.jsonld b/data/fresco/frescobioschemas.jsonld index 15fa5008b9a51..b813e666a952e 100644 --- a/data/fresco/frescobioschemas.jsonld +++ b/data/fresco/frescobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "General open-source framework to compress large amounts of biological sequence data.", "sc:name": "FRESCO", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/resources#fresco" } \ No newline at end of file diff --git a/data/fretbursts/fretburstsbioschemas.jsonld b/data/fretbursts/fretburstsbioschemas.jsonld index 64cb02e09eac8..e8d5008791267 100644 --- a/data/fretbursts/fretburstsbioschemas.jsonld +++ b/data/fretbursts/fretburstsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0160716", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0002-9348-1397", "@type": "schema:Person" @@ -21,11 +25,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27532626", + "pmcid:PMC4988647", { "@id": "https://doi.org/10.1371/journal.pone.0160716" - }, - "pubmed:27532626", - "pmcid:PMC4988647" + } ], "sc:description": "FRETBursts is an open source software for analysis of freely-diffusing single-molecule Förster Resonance Energy Transfer (smFRET) data.", "sc:featureList": { @@ -38,10 +42,6 @@ "Windows" ], "sc:url": "http://tritemio.github.io/FRETBursts/" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0160716", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/frgepistasis/frgepistasisbioschemas.jsonld b/data/frgepistasis/frgepistasisbioschemas.jsonld index 8c305cdfb1a48..60a0fec2cc48a 100644 --- a/data/frgepistasis/frgepistasisbioschemas.jsonld +++ b/data/frgepistasis/frgepistasisbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6043-1756", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1101/gr.161760.113", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/frgepistasis", "@type": "sc:SoftwareApplication", @@ -42,8 +50,8 @@ } ], "sc:citation": [ - "pmcid:PMC4032862", "pubmed:24803592", + "pmcid:PMC4032862", { "@id": "https://doi.org/10.1101/gr.161760.113" } @@ -51,10 +59,10 @@ "sc:description": "A Tool for Epistasis Analysis Based on Functional Regression Model.", "sc:featureList": [ { - "@id": "edam:operation_3197" + "@id": "edam:operation_3659" }, { - "@id": "edam:operation_3659" + "@id": "edam:operation_3197" } ], "sc:license": "GPL-2.0", @@ -66,14 +74,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/FRGEpistasis.html", "sc:version": "1.10.0" - }, - { - "@id": "http://orcid.org/0000-0002-6043-1756", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1101/gr.161760.113", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/frida/fridabioschemas.jsonld b/data/frida/fridabioschemas.jsonld index 27c111327db14..8cb9d2b5b6861 100644 --- a/data/frida/fridabioschemas.jsonld +++ b/data/frida/fridabioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/modpathol.2008.111", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/frida", "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ "pubmed:18567993", - "pmcid:PMC3170853", { "@id": "https://doi.org/10.1038/modpathol.2008.111" - } + }, + "pmcid:PMC3170853" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-5018-8078" @@ -34,8 +30,8 @@ "sc:name": "Frida", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bui3.win.ad.jhu.edu/frida/", "sc:version": "1.1.0" @@ -43,6 +39,10 @@ { "@id": "http://orcid.org/0000-0002-5018-8078", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1038/modpathol.2008.111", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/friend/friendbioschemas.jsonld b/data/friend/friendbioschemas.jsonld index a73c58b42af84..d142688bb1529 100644 --- a/data/friend/friendbioschemas.jsonld +++ b/data/friend/friendbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features.", "sc:name": "Friend", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ilyinlab.org/friend/" } \ No newline at end of file diff --git a/data/frma/frmabioschemas.jsonld b/data/frma/frmabioschemas.jsonld index 29502b3d1dfa0..8c28f2f6760e9 100644 --- a/data/frma/frmabioschemas.jsonld +++ b/data/frma/frmabioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "frma", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/frma.html", "sc:version": "1.26.0" diff --git a/data/frmatools/frmatoolsbioschemas.jsonld b/data/frmatools/frmatoolsbioschemas.jsonld index e5ead52bfab3b..9d3c1d0264366 100644 --- a/data/frmatools/frmatoolsbioschemas.jsonld +++ b/data/frmatools/frmatoolsbioschemas.jsonld @@ -25,18 +25,18 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3047" + "@id": "edam:topic_0203" }, { - "@id": "edam:topic_0203" + "@id": "edam:topic_3047" } ], "sc:citation": [ - "pubmed:21923903", { "@id": "https://doi.org/10.1186/1471-2105-12-369" }, - "pmcid:PMC3180392" + "pmcid:PMC3180392", + "pubmed:21923903" ], "sc:description": "Tools for advanced use of the frma package.", "sc:featureList": { diff --git a/data/frog/frogbioschemas.jsonld b/data/frog/frogbioschemas.jsonld index 0d8add97196d4..0d6dc20f657e6 100644 --- a/data/frog/frogbioschemas.jsonld +++ b/data/frog/frogbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/frog", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "General", "Bug report", - "Administrator" + "Administrator", + "General" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:17485475", diff --git a/data/frog2/frog2bioschemas.jsonld b/data/frog2/frog2bioschemas.jsonld index 8a4f62894c2f3..d692f85caff28 100644 --- a/data/frog2/frog2bioschemas.jsonld +++ b/data/frog2/frog2bioschemas.jsonld @@ -13,11 +13,11 @@ "@id": "https://bio.tools/frog2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Frederic Guyon", "Maria A. Miteva", { "@id": "https://orcid.org/0000-0003-1033-9895" - }, - "Frederic Guyon" + } ], "sc:additionalType": "Web application", "sc:citation": "pubmed:20444874", diff --git a/data/frogs_affiliation_otu/frogs_affiliation_otubioschemas.jsonld b/data/frogs_affiliation_otu/frogs_affiliation_otubioschemas.jsonld index 6faad14f76b89..5bb7d91fdea07 100644 --- a/data/frogs_affiliation_otu/frogs_affiliation_otubioschemas.jsonld +++ b/data/frogs_affiliation_otu/frogs_affiliation_otubioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "frogs_affiliation_otu", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://frogs.toulouse.inra.fr/", "sc:version": "0.7.0" diff --git a/data/frogs_affiliations_stat/frogs_affiliations_statbioschemas.jsonld b/data/frogs_affiliations_stat/frogs_affiliations_statbioschemas.jsonld index 3c4b508717364..ea83545c8028a 100644 --- a/data/frogs_affiliations_stat/frogs_affiliations_statbioschemas.jsonld +++ b/data/frogs_affiliations_stat/frogs_affiliations_statbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Process some metrics on taxonomies.", "sc:name": "frogs_affiliations_stat", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://frogs.toulouse.inra.fr/", "sc:version": "1.1.0" diff --git a/data/frogs_biom_to_stdbiom/frogs_biom_to_stdbiombioschemas.jsonld b/data/frogs_biom_to_stdbiom/frogs_biom_to_stdbiombioschemas.jsonld index 9509814a886f8..d494136239c41 100644 --- a/data/frogs_biom_to_stdbiom/frogs_biom_to_stdbiombioschemas.jsonld +++ b/data/frogs_biom_to_stdbiom/frogs_biom_to_stdbiombioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Converts a FROGS BIOM in fully compatible BIOM.", "sc:name": "frogs_biom_to_stdbiom", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://frogs.toulouse.inra.fr/", diff --git a/data/frogs_biom_to_tsv/frogs_biom_to_tsvbioschemas.jsonld b/data/frogs_biom_to_tsv/frogs_biom_to_tsvbioschemas.jsonld index 28397a69aece0..99dee7268a71b 100644 --- a/data/frogs_biom_to_tsv/frogs_biom_to_tsvbioschemas.jsonld +++ b/data/frogs_biom_to_tsv/frogs_biom_to_tsvbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "frogs_biom_to_tsv", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://frogs.toulouse.inra.fr/", "sc:version": "2.1.0" diff --git a/data/frogs_clustering/frogs_clusteringbioschemas.jsonld b/data/frogs_clustering/frogs_clusteringbioschemas.jsonld index 7a7507261bf4f..f8122d591a156 100644 --- a/data/frogs_clustering/frogs_clusteringbioschemas.jsonld +++ b/data/frogs_clustering/frogs_clusteringbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool uses an iterative growth process and the use of sequence abundance values to delineate OTUs.", "sc:name": "frogs_clustering", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://frogs.toulouse.inra.fr/", "sc:version": "2.3.0" diff --git a/data/frogs_clusters_stat/frogs_clusters_statbioschemas.jsonld b/data/frogs_clusters_stat/frogs_clusters_statbioschemas.jsonld index 857f0365fb6f3..95d45293bc16b 100644 --- a/data/frogs_clusters_stat/frogs_clusters_statbioschemas.jsonld +++ b/data/frogs_clusters_stat/frogs_clusters_statbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Process some metrics on clusters.", "sc:name": "frogs_clusters_stat", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://frogs.toulouse.inra.fr/", "sc:version": "1.4.0" diff --git a/data/frogs_demultiplex/frogs_demultiplexbioschemas.jsonld b/data/frogs_demultiplex/frogs_demultiplexbioschemas.jsonld index 185732d948e09..7c60b127e4f8c 100644 --- a/data/frogs_demultiplex/frogs_demultiplexbioschemas.jsonld +++ b/data/frogs_demultiplex/frogs_demultiplexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "frogs_demultiplex", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://frogs.toulouse.inra.fr/", "sc:version": "1.1.0" diff --git a/data/frogs_normalisation/frogs_normalisationbioschemas.jsonld b/data/frogs_normalisation/frogs_normalisationbioschemas.jsonld index 1188f3d029887..a083f70295a62 100644 --- a/data/frogs_normalisation/frogs_normalisationbioschemas.jsonld +++ b/data/frogs_normalisation/frogs_normalisationbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Keeps in each sample the same number of element by random sampling.", "sc:name": "frogs_normalisation", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://frogs.toulouse.inra.fr/", "sc:version": "1.1.0" diff --git a/data/frogs_preprocess/frogs_preprocessbioschemas.jsonld b/data/frogs_preprocess/frogs_preprocessbioschemas.jsonld index c0346d6b7efad..282b8b33cfe71 100644 --- a/data/frogs_preprocess/frogs_preprocessbioschemas.jsonld +++ b/data/frogs_preprocess/frogs_preprocessbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Denoising and dereplication in metagenomic analysis.", "sc:name": "frogs_preprocess", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://frogs.toulouse.inra.fr/", "sc:version": "1.4.2" diff --git a/data/frogs_remove_chimera/frogs_remove_chimerabioschemas.jsonld b/data/frogs_remove_chimera/frogs_remove_chimerabioschemas.jsonld index 2f5e23049c5a3..299aa806a122d 100644 --- a/data/frogs_remove_chimera/frogs_remove_chimerabioschemas.jsonld +++ b/data/frogs_remove_chimera/frogs_remove_chimerabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Remove PCR chimera in each sample.", "sc:name": "frogs_remove_chimera", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://frogs.toulouse.inra.fr/", "sc:version": "1.3.0" diff --git a/data/fromp/frompbioschemas.jsonld b/data/fromp/frompbioschemas.jsonld index a9794fedab8ec..4cba350dd1ac9 100644 --- a/data/fromp/frompbioschemas.jsonld +++ b/data/fromp/frompbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software for mapping and visualizing enzyme annotations onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways or custom-made pathways and comparing the samples in terms of their Pathway Completeness Scores, their relative Activity Scores or enzyme enrichment odds ratios.", "sc:name": "FROMP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/LaRocheLab/FROMP" } \ No newline at end of file diff --git a/data/frst/frstbioschemas.jsonld b/data/frst/frstbioschemas.jsonld index 71cff8a3bad9c..0077c4df324ae 100644 --- a/data/frst/frstbioschemas.jsonld +++ b/data/frst/frstbioschemas.jsonld @@ -21,9 +21,9 @@ "sc:license": "Other", "sc:name": "FRST", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/frst", diff --git a/data/fstval/fstvalbioschemas.jsonld b/data/fstval/fstvalbioschemas.jsonld index d46db4d78e637..185c820154e55 100644 --- a/data/fstval/fstvalbioschemas.jsonld +++ b/data/fstval/fstvalbioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1746-4811-8-19", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/fstval", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC3439307", "pubmed:22709793", + "pmcid:PMC3439307", { "@id": "https://doi.org/10.1186/1746-4811-8-19" } @@ -27,10 +31,6 @@ "sc:name": "FSTVAL", "sc:operatingSystem": "Linux", "sc:url": "http://bioinfo.mju.ac.kr/fstval/" - }, - { - "@id": "https://doi.org/10.1186/1746-4811-8-19", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/fsuite/fsuitebioschemas.jsonld b/data/fsuite/fsuitebioschemas.jsonld index 07d80ecb3c084..adec0c343f4ee 100644 --- a/data/fsuite/fsuitebioschemas.jsonld +++ b/data/fsuite/fsuitebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Integrative solution to exploit inbreeding in dense SNP chip and exome data.", "sc:name": "FSuite", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genestat.cephb.fr/software/index.php/FSuite" } \ No newline at end of file diff --git a/data/fsweight/fsweightbioschemas.jsonld b/data/fsweight/fsweightbioschemas.jsonld index bacc1e9b5c293..1dd4cefc46a15 100644 --- a/data/fsweight/fsweightbioschemas.jsonld +++ b/data/fsweight/fsweightbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software for inferring the function of proteins based on its indirect interaction partners. Its sensitivity and precision are superior to Neighbour Counting, Chi2, PRODISTIN, Functional Flow, and Markov Random Field approaches. It can also be used for ranking the reliability of individual protein interactions.", "sc:name": "FSWeight", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.comp.nus.edu.sg/~wongls/projects/functionprediction/index.html" } \ No newline at end of file diff --git a/data/ft-comar/ft-comarbioschemas.jsonld b/data/ft-comar/ft-comarbioschemas.jsonld index bdb9e8c3322f4..529f1fa84b823 100644 --- a/data/ft-comar/ft-comarbioschemas.jsonld +++ b/data/ft-comar/ft-comarbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Fault Tolerance Reconstruction of 3D Structure from Protein Contact Maps.", "sc:name": "FT-COMAR", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", diff --git a/data/ftmap/ftmapbioschemas.jsonld b/data/ftmap/ftmapbioschemas.jsonld index b1c9181ddf920..a9ffd3194592c 100644 --- a/data/ftmap/ftmapbioschemas.jsonld +++ b/data/ftmap/ftmapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "FTMAP is a webserver that globally samples the surface of a target protein using small organic molecules as probes to identify and predict binding hot spots. Users can also input small molecule probes.", "sc:name": "FTMAP", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://ftmap.bu.edu/param" } \ No newline at end of file diff --git a/data/ftprod/ftprodbioschemas.jsonld b/data/ftprod/ftprodbioschemas.jsonld index a10cb16334832..e292adff9265b 100644 --- a/data/ftprod/ftprodbioschemas.jsonld +++ b/data/ftprod/ftprodbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Plugin for VMD designed to characterize and identify cross-structural ‘hot spots’ in proteins. The program identifies these druggable hot spots by docking a series of small molecular probes onto the protein surfaces. It combines these output structures, clusters them, and displays them visually for easy comparison.", "sc:name": "FTProd", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://amarolab.ucsd.edu/ftprod/" } \ No newline at end of file diff --git a/data/fuento/fuentobioschemas.jsonld b/data/fuento/fuentobioschemas.jsonld index 57d3331491e25..81075bb522ce6 100644 --- a/data/fuento/fuentobioschemas.jsonld +++ b/data/fuento/fuentobioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/fuento", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Bojan Zagrovic", - "Anton A. Polyansky" + "Anton A. Polyansky", + "Bojan Zagrovic" ], "sc:additionalType": "Command-line tool", "sc:description": "Functional enrichment tool for bioinformatic analysis.", "sc:name": "Fuento", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/DavidWeichselbaum/fuento" } \ No newline at end of file diff --git a/data/fugue/fuguebioschemas.jsonld b/data/fugue/fuguebioschemas.jsonld index 6c08d5c7572c3..16a5b7adab303 100644 --- a/data/fugue/fuguebioschemas.jsonld +++ b/data/fugue/fuguebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure.", "sc:name": "FUGUE", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://mizuguchilab.org/fugue/" } \ No newline at end of file diff --git a/data/fuma/fumabioschemas.jsonld b/data/fuma/fumabioschemas.jsonld index d68952e1664aa..034eaf968f188 100644 --- a/data/fuma/fumabioschemas.jsonld +++ b/data/fuma/fumabioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Program that reports identical fusion genes based on gene-name annotations.", "sc:name": "FuMa", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/ErasmusMC-Bioinformatics/fuma" } \ No newline at end of file diff --git a/data/fun/funbioschemas.jsonld b/data/fun/funbioschemas.jsonld index 0b34d5ec4e04c..2b6679f0a5fa1 100644 --- a/data/fun/funbioschemas.jsonld +++ b/data/fun/funbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "FUn", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://doc.gdb.tools/fun/" } \ No newline at end of file diff --git a/data/funcassociate/funcassociatebioschemas.jsonld b/data/funcassociate/funcassociatebioschemas.jsonld index 2f1c707176846..b37102d3936b8 100644 --- a/data/funcassociate/funcassociatebioschemas.jsonld +++ b/data/funcassociate/funcassociatebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. The program takes a list of genes as input and produces a ranked list of the Gene Ontology terms enriched in an input list.", "sc:name": "FuncAssociate", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://llama.mshri.on.ca/funcassociate/" } \ No newline at end of file diff --git a/data/funcepimod/funcepimodbioschemas.jsonld b/data/funcepimod/funcepimodbioschemas.jsonld index 5a40bba2f09c0..5e324d4a6aedf 100644 --- a/data/funcepimod/funcepimodbioschemas.jsonld +++ b/data/funcepimod/funcepimodbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Novel functional supervised algorithm for the integrative analysis of Infinium 450k DNA methylation and matched or unmatched gene expression data.", "sc:name": "FuncEpiMod", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://sourceforge.net/projects/funepimod/" } \ No newline at end of file diff --git a/data/funcexplorer/funcexplorerbioschemas.jsonld b/data/funcexplorer/funcexplorerbioschemas.jsonld index 53182cdc753d2..cd7d979e3768b 100644 --- a/data/funcexplorer/funcexplorerbioschemas.jsonld +++ b/data/funcexplorer/funcexplorerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "FuncExplorer", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://biit.cs.ut.ee/funcexplorer" } \ No newline at end of file diff --git a/data/funchip/funchipbioschemas.jsonld b/data/funchip/funchipbioschemas.jsonld index d58c9c6f5e97d..785cbb6300b57 100644 --- a/data/funchip/funchipbioschemas.jsonld +++ b/data/funchip/funchipbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "FunChIP", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/FunChIP.html", "sc:version": "1.0.0" diff --git a/data/funcisnp/funcisnpbioschemas.jsonld b/data/funcisnp/funcisnpbioschemas.jsonld index f6d82a582614f..e38bd10ef742a 100644 --- a/data/funcisnp/funcisnpbioschemas.jsonld +++ b/data/funcisnp/funcisnpbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Simon G. Coetzee", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "It integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.", "sc:license": "GPL-3.0", "sc:name": "FunciSNP", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/FunciSNP.html", "sc:version": "1.16.0" diff --git a/data/funcluster/funclusterbioschemas.jsonld b/data/funcluster/funclusterbioschemas.jsonld index 3bb0e7c613c9a..05f2eab69962c 100644 --- a/data/funcluster/funclusterbioschemas.jsonld +++ b/data/funcluster/funclusterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Genomic data analysis tool designed to perform a functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, functional analysis allows to detect co-regulated biological processes (i.e. represented by annotating genomic themes) through a specifically designed co-clustering procedure involving biological annotations and gene expression data.", "sc:name": "FunCluster", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://corneliu.henegar.info/FunCluster.htm" diff --git a/data/funcoup/funcoupbioschemas.jsonld b/data/funcoup/funcoupbioschemas.jsonld index ff9a1f47d858c..a4c728731736a 100644 --- a/data/funcoup/funcoupbioschemas.jsonld +++ b/data/funcoup/funcoupbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Global networks of functional coupling in eukaryotes from comprehensive data integration.", "sc:name": "FunCoup", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "bils.se", "sc:url": "http://funcoup.sbc.su.se/", diff --git a/data/funcpatch/funcpatchbioschemas.jsonld b/data/funcpatch/funcpatchbioschemas.jsonld index f8a417a95c550..814917d5ec3d9 100644 --- a/data/funcpatch/funcpatchbioschemas.jsonld +++ b/data/funcpatch/funcpatchbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool was developed for inferring conserved functional regions in protein tertiary structures.", "sc:name": "FuncPatch", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://info.mcmaster.ca/yifei/FuncPatch/" } \ No newline at end of file diff --git a/data/funcprop/funcpropbioschemas.jsonld b/data/funcprop/funcpropbioschemas.jsonld index dc5227f121ba8..b15c49bd79a81 100644 --- a/data/funcprop/funcpropbioschemas.jsonld +++ b/data/funcprop/funcpropbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Novel label propagation techniques applied to many different types of gene and protein data in order to predict protein function via Gene Ontology annotations.", "sc:name": "FunCProp", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bonneaulab.bio.nyu.edu/funcprop.html" } \ No newline at end of file diff --git a/data/functional_heatmap/functional_heatmapbioschemas.jsonld b/data/functional_heatmap/functional_heatmapbioschemas.jsonld index e8c91751265a5..a55610468a795 100644 --- a/data/functional_heatmap/functional_heatmapbioschemas.jsonld +++ b/data/functional_heatmap/functional_heatmapbioschemas.jsonld @@ -13,9 +13,9 @@ "@id": "https://bio.tools/Functional_Heatmap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Joshua Williams", "Ruoting Yang", - "Daniel Watson", - "Joshua Williams" + "Daniel Watson" ], "sc:additionalType": "Web application", "sc:citation": [ @@ -28,10 +28,10 @@ "sc:description": "Automated and interactive pattern recognition tool to integrate time with multi-omics assays.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_0531" }, { - "@id": "edam:operation_0531" + "@id": "edam:operation_3501" } ], "sc:name": "Functional Heatmap", diff --git a/data/functionannotator/functionannotatorbioschemas.jsonld b/data/functionannotator/functionannotatorbioschemas.jsonld index 1f33ab758629e..d29755e5d88bb 100644 --- a/data/functionannotator/functionannotatorbioschemas.jsonld +++ b/data/functionannotator/functionannotatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Versatile and efficient web tool for non-model organism annotation.", "sc:name": "FunctionAnnotator", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://fa.cgu.edu.tw/" } \ No newline at end of file diff --git a/data/functree/functreebioschemas.jsonld b/data/functree/functreebioschemas.jsonld index b4d32d0430da5..ac10095cf703d 100644 --- a/data/functree/functreebioschemas.jsonld +++ b/data/functree/functreebioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:25974630", "pmcid:PMC4431737", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0126967" - } + }, + "pubmed:25974630" ], "sc:description": "A web-based application for analyzing and visualizing large-scale omics data, including but not limited to genomic, metagenomic, and transcriptomic data.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "FuncTree", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://bioviz.tokyo/functree/" } diff --git a/data/funel/funelbioschemas.jsonld b/data/funel/funelbioschemas.jsonld index d96dfa0107692..fffe8e6f9f9dc 100644 --- a/data/funel/funelbioschemas.jsonld +++ b/data/funel/funelbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/funel", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jaume Bacardit", - "Nicola Lazzarini" + "Nicola Lazzarini", + "Jaume Bacardit" ], "sc:additionalType": "Command-line tool", "sc:author": "Nicola Lazzarini", diff --git a/data/funfold2/funfold2bioschemas.jsonld b/data/funfold2/funfold2bioschemas.jsonld index 4360b75806eff..fd02b6ba8b8a3 100644 --- a/data/funfold2/funfold2bioschemas.jsonld +++ b/data/funfold2/funfold2bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server that integrates protein-ligand binding and quality assessment protocols for the prediction of protein function from sequence via structure.", "sc:name": "FunFOLD2", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html" } \ No newline at end of file diff --git a/data/fungap/fungapbioschemas.jsonld b/data/fungap/fungapbioschemas.jsonld index 0a65f12f42a27..d003bd2157ae4 100644 --- a/data/fungap/fungapbioschemas.jsonld +++ b/data/fungap/fungapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Fungal Genome Annotation Pipeline using evidence-based gene model evaluation.", "sc:name": "FunGAP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/CompSynBioLab-KoreaUniv/FunGAP" } \ No newline at end of file diff --git a/data/fungenes/fungenesbioschemas.jsonld b/data/fungenes/fungenesbioschemas.jsonld index e8bcb524e3cdf..da7c745c90ef2 100644 --- a/data/fungenes/fungenesbioschemas.jsonld +++ b/data/fungenes/fungenesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Freeware", "sc:name": "FunGenES", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://biit.cs.ut.ee/fungenes/" diff --git a/data/fungifun/fungifunbioschemas.jsonld b/data/fungifun/fungifunbioschemas.jsonld index 9a6565b390a49..e109014b8b591 100644 --- a/data/fungifun/fungifunbioschemas.jsonld +++ b/data/fungifun/fungifunbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/fungifun", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Steffen Priebe", - "Jörg Linde" + "Jörg Linde", + "Steffen Priebe" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:25294921", "sc:description": "Assign functional annotations to fungal genes or proteins. Based on different classification methods like FunCat (Functional Catalogue), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes), it categorizes genes and proteins for fungal species on different levels and conducts an enrichment analysis.", "sc:name": "FungiFun 2.2.8 BETA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://elbe.hki-jena.de/fungifun/fungifun.php" } \ No newline at end of file diff --git a/data/funmap/funmapbioschemas.jsonld b/data/funmap/funmapbioschemas.jsonld index be337f9e87972..b50b06327f52c 100644 --- a/data/funmap/funmapbioschemas.jsonld +++ b/data/funmap/funmapbioschemas.jsonld @@ -12,14 +12,14 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:12196415", - "pmcid:PMC1462199" + "pmcid:PMC1462199", + "pubmed:12196415" ], "sc:description": "The Funmap package is developed to identify quantitative trait loci (QTL) for a longitudinal, or vectorized, phenotypic trait as based on the Funmap model", "sc:name": "Funmap", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://statgen.psu.edu/software/funmap.html", diff --git a/data/funmap2/funmap2bioschemas.jsonld b/data/funmap2/funmap2bioschemas.jsonld index ef30357dcefdf..50de7c45abfa6 100644 --- a/data/funmap2/funmap2bioschemas.jsonld +++ b/data/funmap2/funmap2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.7717/peerj.7008", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Funmap2", "@type": "sc:SoftwareApplication", @@ -27,25 +31,21 @@ "@id": "edam:operation_3196" }, { - "@id": "edam:operation_0282" + "@id": "edam:operation_3232" }, { - "@id": "edam:operation_3232" + "@id": "edam:operation_0282" } ], "sc:license": "GPL-3.0", "sc:name": "Funmap2", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/wzhy2000/Funmap2", "sc:version": "2.4.2" - }, - { - "@id": "https://doi.org/10.7717/peerj.7008", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/funmappone/funmapponebioschemas.jsonld b/data/funmappone/funmapponebioschemas.jsonld index b804c540de8fb..4b002dfcc1e4a 100644 --- a/data/funmappone/funmapponebioschemas.jsonld +++ b/data/funmappone/funmapponebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "FunMappOne", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/Greco-Lab/FunMappOne" } \ No newline at end of file diff --git a/data/funpat/funpatbioschemas.jsonld b/data/funpat/funpatbioschemas.jsonld index 9786911dc75be..eeb9e63a4231c 100644 --- a/data/funpat/funpatbioschemas.jsonld +++ b/data/funpat/funpatbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R package designed to provide: a useful tool to analyze time series genomic data; a computational pipeline which integrates gene selection, clustering and functional annotations into a single framework to identify the main temporal patterns associated to functional groups of differentially expressed genes; an easy way to exploit different types of annotations from currently available databases; a user-friendly organization and visualization of the outcome.", "sc:name": "FunPat", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://sysbiobig.dei.unipd.it/?q=Software#FunPat", diff --git a/data/funsip/funsipbioschemas.jsonld b/data/funsip/funsipbioschemas.jsonld index 55137d42847cf..14da124747ade 100644 --- a/data/funsip/funsipbioschemas.jsonld +++ b/data/funsip/funsipbioschemas.jsonld @@ -11,14 +11,14 @@ "@id": "https://bio.tools/funsip", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "A modular and extensible classifier for the prediction of functional sites in DNA.", "sc:name": "FunSiP", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/supplementary_data/mibel/FunSiP/", diff --git a/data/funsys/funsysbioschemas.jsonld b/data/funsys/funsysbioschemas.jsonld index c21d4581ac259..be71ab4a7e675 100644 --- a/data/funsys/funsysbioschemas.jsonld +++ b/data/funsys/funsysbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software that can be used to analyse differential expression data from RNAseq and can integrate these analyses with data from proteomic studies.", "sc:name": "FunSys", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://sourceforge.net/projects/funsysufpa/" } \ No newline at end of file diff --git a/data/funtaxis/funtaxisbioschemas.jsonld b/data/funtaxis/funtaxisbioschemas.jsonld index 2703fc71da4ab..f53577758bf61 100644 --- a/data/funtaxis/funtaxisbioschemas.jsonld +++ b/data/funtaxis/funtaxisbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Funtaxis", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Department of Molecular Medicine, University of Padua", "sc:url": "http://www.medcomp.medicina.unipd.it/funtaxis", diff --git a/data/funtoonorm/funtoonormbioschemas.jsonld b/data/funtoonorm/funtoonormbioschemas.jsonld index dc4cbf70e61b6..1a780617b4cf2 100644 --- a/data/funtoonorm/funtoonormbioschemas.jsonld +++ b/data/funtoonorm/funtoonormbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The R package which provides a function for normalization of Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K) data when there are samples from multiple tissues or cell types.", "sc:name": "funtooNorm", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/GreenwoodLab/funtooNorm" } \ No newline at end of file diff --git a/data/funtree/funtreebioschemas.jsonld b/data/funtree/funtreebioschemas.jsonld index 0b13e6422ca34..40ae38899361a 100644 --- a/data/funtree/funtreebioschemas.jsonld +++ b/data/funtree/funtreebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH.", "sc:name": "FunTree", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.ebi.ac.uk/thornton-srv/databases/FunTree/" } \ No newline at end of file diff --git a/data/fusenet/fusenetbioschemas.jsonld b/data/fusenet/fusenetbioschemas.jsonld index fc1f482eb5ef1..2db0eecf62f2c 100644 --- a/data/fusenet/fusenetbioschemas.jsonld +++ b/data/fusenet/fusenetbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Markov network formulation that infers networks from a collection of nonidentically distributed datasets.", "sc:name": "FuseNet", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/marinkaz/fusenet" } \ No newline at end of file diff --git a/data/fusion/fusionbioschemas.jsonld b/data/fusion/fusionbioschemas.jsonld index 283842fe26ba3..7abf3ceeeaf53 100644 --- a/data/fusion/fusionbioschemas.jsonld +++ b/data/fusion/fusionbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Fusion", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://fusion.cebitec.uni-bielefeld.de" } \ No newline at end of file diff --git a/data/fusion_protein/fusion_proteinbioschemas.jsonld b/data/fusion_protein/fusion_proteinbioschemas.jsonld index 9b1ecea9bc09a..d9d0d05069077 100644 --- a/data/fusion_protein/fusion_proteinbioschemas.jsonld +++ b/data/fusion_protein/fusion_proteinbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Fragment-free probabilistic graphical model for conformational sampling in continuous space and assess its accuracy using ‘blind’ protein targets with a length up to 250 residues from the CASP11 structure prediction exercise.", "sc:name": "FUSION", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://protein.rnet.missouri.edu/FUSION/" } \ No newline at end of file diff --git a/data/fusionhunter/fusionhunterbioschemas.jsonld b/data/fusionhunter/fusionhunterbioschemas.jsonld index b295d19e4f882..22814d5a3b95d 100644 --- a/data/fusionhunter/fusionhunterbioschemas.jsonld +++ b/data/fusionhunter/fusionhunterbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/fusionhunter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jian Ma", - "Yang Li" + "Yang Li", + "Jian Ma" ], "sc:additionalType": "Command-line tool", "sc:description": "An open-source software tool that identifies gene fusions in RNA-Seq data.", diff --git a/data/fusionmap/fusionmapbioschemas.jsonld b/data/fusionmap/fusionmapbioschemas.jsonld index 00d73f61e5dbb..b86f1e9b22bc9 100644 --- a/data/fusionmap/fusionmapbioschemas.jsonld +++ b/data/fusionmap/fusionmapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "FusionMap", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.arrayserver.com/wiki/index.php?title=FusionMap" } \ No newline at end of file diff --git a/data/fusionseq/fusionseqbioschemas.jsonld b/data/fusionseq/fusionseqbioschemas.jsonld index e50e61913581b..a23caac4a7436 100644 --- a/data/fusionseq/fusionseqbioschemas.jsonld +++ b/data/fusionseq/fusionseqbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "CC-BY-NC-4.0", "sc:name": "FusionSeq", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://rnaseq.gersteinlab.org/fusionseq/" } \ No newline at end of file diff --git a/data/fusorsv/fusorsvbioschemas.jsonld b/data/fusorsv/fusorsvbioschemas.jsonld index 9c75df62397ed..9f8df0883c41d 100644 --- a/data/fusorsv/fusorsvbioschemas.jsonld +++ b/data/fusorsv/fusorsvbioschemas.jsonld @@ -9,30 +9,22 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13059-018-1404-6", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0002-1905-0732", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/fusorsv", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Charles Lee", { "@id": "https://orcid.org/0000-0002-1905-0732" - } + }, + "Charles Lee" ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5859555", { "@id": "https://doi.org/10.1186/s13059-018-1404-6" }, - "pubmed:29559002", - "pmcid:PMC5859555" + "pubmed:29559002" ], "sc:description": "A data fusion method for multi source (VCF4.0+) structural variation analysis.", "sc:featureList": { @@ -40,10 +32,18 @@ }, "sc:name": "FusorSV", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/timothyjamesbecker/FusorSV" + }, + { + "@id": "https://doi.org/10.1186/s13059-018-1404-6", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-1905-0732", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/fuzznuc/fuzznucbioschemas.jsonld b/data/fuzznuc/fuzznucbioschemas.jsonld index 3488bfafaca1b..bdc70a2b2b0d1 100644 --- a/data/fuzznuc/fuzznucbioschemas.jsonld +++ b/data/fuzznuc/fuzznucbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:contributor": [ "UK MRC", "EMBOSS Contributors", - "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Search for patterns in nucleotide sequences.", "sc:funder": [ @@ -27,8 +27,8 @@ "sc:name": "fuzznuc", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/fuzzpro/fuzzprobioschemas.jsonld b/data/fuzzpro/fuzzprobioschemas.jsonld index 27c64af9f494a..095759b593024 100644 --- a/data/fuzzpro/fuzzprobioschemas.jsonld +++ b/data/fuzzpro/fuzzprobioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "Wellcome Trust", "UK MRC", - "UK BBSRC" + "Wellcome Trust", + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Search for patterns in protein sequences.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", + "UK BBSRC", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "fuzzpro", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/fuzzpro.html", "sc:version": "r6" diff --git a/data/fuzztran/fuzztranbioschemas.jsonld b/data/fuzztran/fuzztranbioschemas.jsonld index f0a359b6fdc5f..1dbf15b1e803e 100644 --- a/data/fuzztran/fuzztranbioschemas.jsonld +++ b/data/fuzztran/fuzztranbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", - "UK MRC", "Wellcome Trust", + "UK MRC", "EMBOSS Contributors" ], "sc:description": "Search for patterns in protein sequences (translated).", "sc:funder": [ + "Wellcome Trust", "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "fuzztran", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/fuzzyclust/fuzzyclustbioschemas.jsonld b/data/fuzzyclust/fuzzyclustbioschemas.jsonld index 3e5e648490df0..2ac3d38f0d544 100644 --- a/data/fuzzyclust/fuzzyclustbioschemas.jsonld +++ b/data/fuzzyclust/fuzzyclustbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-9708-6722", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/fuzzyclust", "@type": "sc:SoftwareApplication", @@ -24,13 +20,17 @@ "sc:description": "A simple shiny app for fuzzy c-means clustering to multi-variate data. The parameters of the algorithm are calculated automatically or can be chosen from validation indices.", "sc:name": "FuzzyClust", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "bmb.sdu.dk", "sc:url": "http://computproteomics.bmb.sdu.dk/Apps/FuzzyClust", "sc:version": "1" + }, + { + "@id": "http://orcid.org/0000-0002-9708-6722", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/g-blastn/g-blastnbioschemas.jsonld b/data/g-blastn/g-blastnbioschemas.jsonld index 0584c04ea1ec1..077a3959e271c 100644 --- a/data/g-blastn/g-blastnbioschemas.jsonld +++ b/data/g-blastn/g-blastnbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/g-blastn", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Zhao Kaiyong", - "Xiaowen Chu" + "Xiaowen Chu", + "Zhao Kaiyong" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:24463183", diff --git a/data/g-language_api/g-language_apibioschemas.jsonld b/data/g-language_api/g-language_apibioschemas.jsonld index b207353e59832..f3c9b50679e04 100644 --- a/data/g-language_api/g-language_apibioschemas.jsonld +++ b/data/g-language_api/g-language_apibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Set of Perl libraries for genome sequence analysis.", "sc:name": "G-language API", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.g-language.org/wiki/rest", "sc:version": "1" diff --git a/data/g-language_gae/g-language_gaebioschemas.jsonld b/data/g-language_gae/g-language_gaebioschemas.jsonld index 5c562930b237e..7e359fd5e27f3 100644 --- a/data/g-language_gae/g-language_gaebioschemas.jsonld +++ b/data/g-language_gae/g-language_gaebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "G-language GAE", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.g-language.org/wiki/soap/" } \ No newline at end of file diff --git a/data/g-links/g-linksbioschemas.jsonld b/data/g-links/g-linksbioschemas.jsonld index fd253363f43ed..3046c0bd52420 100644 --- a/data/g-links/g-linksbioschemas.jsonld +++ b/data/g-links/g-linksbioschemas.jsonld @@ -16,28 +16,28 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pmcid:PMC4670005", + "pubmed:26673001", { "@id": "https://doi.org/10.12688/F1000RESEARCH.5754.2" - }, - "pubmed:26673001" + } ], "sc:description": "A gateway server for querying and retrieving gene annotation data", "sc:featureList": [ { - "@id": "edam:operation_2422" + "@id": "edam:operation_0362" }, { "@id": "edam:operation_3436" }, { - "@id": "edam:operation_0362" + "@id": "edam:operation_2422" } ], "sc:license": "MIT", "sc:name": "G-Links", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.g-language.org/wiki/glinks" diff --git a/data/g-onramp/g-onrampbioschemas.jsonld b/data/g-onramp/g-onrampbioschemas.jsonld index 6c084c59aa75c..75400788969f2 100644 --- a/data/g-onramp/g-onrampbioschemas.jsonld +++ b/data/g-onramp/g-onrampbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Jeremy Goecks", - "Wilson Leung", + "Luke Sargent", "Sarah C.R. Elgin", - "Luke Sargent" + "Wilson Leung" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:31070714", @@ -22,9 +22,9 @@ "sc:license": "Unlicense", "sc:name": "G-OnRamp", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://gonramp.wustl.edu/" } \ No newline at end of file diff --git a/data/g-sesame/g-sesamebioschemas.jsonld b/data/g-sesame/g-sesamebioschemas.jsonld index ad2bef921cf04..085c4ea34e0c1 100644 --- a/data/g-sesame/g-sesamebioschemas.jsonld +++ b/data/g-sesame/g-sesamebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.", "sc:name": "G-SESAME", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioinformatics.clemson.edu/G-SESAME" } \ No newline at end of file diff --git a/data/g-sqz/g-sqzbioschemas.jsonld b/data/g-sqz/g-sqzbioschemas.jsonld index 695ce4bd58f4b..8fe781ed7f81d 100644 --- a/data/g-sqz/g-sqzbioschemas.jsonld +++ b/data/g-sqz/g-sqzbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "G-SQZ", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cs.gettysburg.edu/~lalvsa01/gsqz/project.html" } \ No newline at end of file diff --git a/data/g2d/g2dbioschemas.jsonld b/data/g2d/g2dbioschemas.jsonld index 5562780dfc159..c2d955c0d554c 100644 --- a/data/g2d/g2dbioschemas.jsonld +++ b/data/g2d/g2dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Scans a human genomic region for genes related to an inherited disease. The server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.", "sc:name": "G2D", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.ogic.ca/projects/g2d_2/" } \ No newline at end of file diff --git a/data/g2p/g2pbioschemas.jsonld b/data/g2p/g2pbioschemas.jsonld index b5eefdc19688d..cc48787f35768 100644 --- a/data/g2p/g2pbioschemas.jsonld +++ b/data/g2p/g2pbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Unlicense", "sc:name": "G2P", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/XiaoleiLiuBio/G2P" } \ No newline at end of file diff --git a/data/g3viz/g3vizbioschemas.jsonld b/data/g3viz/g3vizbioschemas.jsonld index e3d9656a70f69..7026fac2104fa 100644 --- a/data/g3viz/g3vizbioschemas.jsonld +++ b/data/g3viz/g3vizbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "G3viz", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://cran.r-project.org/package=g3viz" } \ No newline at end of file diff --git a/data/ga4gh_beacon/ga4gh_beaconbioschemas.jsonld b/data/ga4gh_beacon/ga4gh_beaconbioschemas.jsonld index 60467697d012d..722c4275e8463 100644 --- a/data/ga4gh_beacon/ga4gh_beaconbioschemas.jsonld +++ b/data/ga4gh_beacon/ga4gh_beaconbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/ga4gh_beacon", "@type": "sc:SoftwareApplication", "sc:additionalType": [ + "Database portal", "Web API", - "Web application", - "Database portal" + "Web application" ], "sc:citation": "pubmed:27284183", "sc:description": "A global search engine for genetic mutations.", "sc:name": "GA4GH Beacon", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://beacon-network.org//#/" } \ No newline at end of file diff --git a/data/ga4ghclient/ga4ghclientbioschemas.jsonld b/data/ga4ghclient/ga4ghclientbioschemas.jsonld index ca0d7b4f6be47..32b8c180d9397 100644 --- a/data/ga4ghclient/ga4ghclientbioschemas.jsonld +++ b/data/ga4ghclient/ga4ghclientbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "GA4GHclient", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GA4GHclient.html", "sc:version": "1.4.0" diff --git a/data/ga4ghshiny/ga4ghshinybioschemas.jsonld b/data/ga4ghshiny/ga4ghshinybioschemas.jsonld index a4778160c5c5f..7bc356c12722c 100644 --- a/data/ga4ghshiny/ga4ghshinybioschemas.jsonld +++ b/data/ga4ghshiny/ga4ghshinybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "GA4GHshiny", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GA4GHshiny.html", "sc:version": "1.2.0" diff --git a/data/gadem/gadembioschemas.jsonld b/data/gadem/gadembioschemas.jsonld index a203094cae548..6459f582c304e 100644 --- a/data/gadem/gadembioschemas.jsonld +++ b/data/gadem/gadembioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Unbiased de novo motif discovery tool implementing an expectation-maximization (EM) algorithm.", "sc:name": "GADEM", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.niehs.nih.gov/research/resources/software/biostatistics/gadem/index.cfm" } \ No newline at end of file diff --git a/data/gads/gadsbioschemas.jsonld b/data/gads/gadsbioschemas.jsonld index dd229a718eb02..d6dc008f36d40 100644 --- a/data/gads/gadsbioschemas.jsonld +++ b/data/gads/gadsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software for Genetic Analyses of quantitative traits Distributed with Spike on the base of large pedigrees without loops.", "sc:name": "GADS", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mga.bionet.nsc.ru/soft/index.html" } \ No newline at end of file diff --git a/data/gaev/gaevbioschemas.jsonld b/data/gaev/gaevbioschemas.jsonld index 9e9cef78c63ff..7b6b003052d50 100644 --- a/data/gaev/gaevbioschemas.jsonld +++ b/data/gaev/gaevbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/gaev", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Script", - "Command-line tool" + "Command-line tool", + "Script" ], "sc:description": "Gene Annotation Easy Viewer. It integrates the gene annotation data from the KEGG (Kyoto Encyclopedia of Genes and Genomes) Automatic Annotation Server and generates an easy-to-read table that summarizes the query gene name, the KO (KEGG Orthology) number, name of gene orthologs, functional definition of the ortholog, and the functional pathways that query gene has been mapped to.", "sc:license": "MIT", diff --git a/data/gag/gagbioschemas.jsonld b/data/gag/gagbioschemas.jsonld index 5dcf1f1b0a0c9..39c7ef3e0256a 100644 --- a/data/gag/gagbioschemas.jsonld +++ b/data/gag/gagbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "GAG", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/genomeannotation/GAG" diff --git a/data/gag_builder/gag_builderbioschemas.jsonld b/data/gag_builder/gag_builderbioschemas.jsonld index e454595fcd044..3d36661d33446 100644 --- a/data/gag_builder/gag_builderbioschemas.jsonld +++ b/data/gag_builder/gag_builderbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "GAG builder", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://glycan-builder.cermav.cnrs.fr/gag/" } \ No newline at end of file diff --git a/data/gaga/gagabioschemas.jsonld b/data/gaga/gagabioschemas.jsonld index 90eb20f84ae7e..0983f385ac87c 100644 --- a/data/gaga/gagabioschemas.jsonld +++ b/data/gaga/gagabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "gaga", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gaga.html", "sc:version": "2.20.0" diff --git a/data/gage/gagebioschemas.jsonld b/data/gage/gagebioschemas.jsonld index f4ea9e659e232..28e36130bba42 100644 --- a/data/gage/gagebioschemas.jsonld +++ b/data/gage/gagebioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Weijun Luo", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:19473525", + "pmcid:PMC2696452", { "@id": "https://doi.org/10.1186/1471-2105-10-161" }, - "pmcid:PMC2696452" + "pubmed:19473525" ], "sc:description": "Published method for gene set (enrichment or GSEA) or pathway analysis. It is generally applicable independent of microarray or RNA-Seq data attributes and consistently achieves superior performance over other frequently used methods. We provide functions for basic analysis, result processing and presentation. We have also built pipeline routines for of multiple analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies.", "sc:featureList": [ @@ -40,8 +40,8 @@ "sc:license": "GPL-2.0", "sc:name": "gage", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gage.html", diff --git a/data/gaggle/gagglebioschemas.jsonld b/data/gaggle/gagglebioschemas.jsonld index cf3c5a4e306bf..7a25136cf4119 100644 --- a/data/gaggle/gagglebioschemas.jsonld +++ b/data/gaggle/gagglebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christopher Bare", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package contains functions enabling data exchange between R and Gaggle enabled bioinformatics software, including Cytoscape, Firegoose and Gaggle Genome Browser.", "sc:license": "GPL-2.0", "sc:name": "gaggle", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gaggle.html", diff --git a/data/gaia/gaiabioschemas.jsonld b/data/gaia/gaiabioschemas.jsonld index c784f41210a50..39ee5667fba53 100644 --- a/data/gaia/gaiabioschemas.jsonld +++ b/data/gaia/gaiabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "gaia", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gaia.html", "sc:version": "2.18.0" diff --git a/data/galactosemia_proteins_database/galactosemia_proteins_databasebioschemas.jsonld b/data/galactosemia_proteins_database/galactosemia_proteins_databasebioschemas.jsonld index 98e00f02c8cc0..2f971e8e8bf90 100644 --- a/data/galactosemia_proteins_database/galactosemia_proteins_databasebioschemas.jsonld +++ b/data/galactosemia_proteins_database/galactosemia_proteins_databasebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Unlicense", "sc:name": "Galactosemia Proteins Database", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "ELIXIR-ITA-SALERNO", diff --git a/data/galaxy/galaxybioschemas.jsonld b/data/galaxy/galaxybioschemas.jsonld index 4d647f9f6a1b2..6986bc59fd890 100644 --- a/data/galaxy/galaxybioschemas.jsonld +++ b/data/galaxy/galaxybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "AFL-3.0", "sc:name": "Galaxy", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://usegalaxy.org/" } \ No newline at end of file diff --git a/data/galaxy_australia/galaxy_australiabioschemas.jsonld b/data/galaxy_australia/galaxy_australiabioschemas.jsonld index edd1eb81b4eab..d9a01a7402851 100644 --- a/data/galaxy_australia/galaxy_australiabioschemas.jsonld +++ b/data/galaxy_australia/galaxy_australiabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/galaxy_australia", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:description": "Galaxy Australia is a hosted instance of the Galaxy web-based platform for data intensive biological research, for all Australian researchers.\nIn addition to being accessible through a web interface, Galaxy Australia can also be accessed programmatically, through shell scripts and other programs via an API", "sc:name": "Galaxy Australia API", diff --git a/data/galaxy_tools/galaxy_toolsbioschemas.jsonld b/data/galaxy_tools/galaxy_toolsbioschemas.jsonld index 7edf1de22c89b..11fde50234746 100644 --- a/data/galaxy_tools/galaxy_toolsbioschemas.jsonld +++ b/data/galaxy_tools/galaxy_toolsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "AFL-2.0", "sc:name": "Galaxy Tools", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools" } \ No newline at end of file diff --git a/data/galaxydock/galaxydockbioschemas.jsonld b/data/galaxydock/galaxydockbioschemas.jsonld index 6cc798019abd0..065fce45cab23 100644 --- a/data/galaxydock/galaxydockbioschemas.jsonld +++ b/data/galaxydock/galaxydockbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand using Conformational Space Annealing.", "sc:name": "GalaxyDock", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://galaxy.seoklab.org/softwares/galaxydock.html" } \ No newline at end of file diff --git a/data/galaxyhomomer/galaxyhomomerbioschemas.jsonld b/data/galaxyhomomer/galaxyhomomerbioschemas.jsonld index 37bed5ec409ab..f92e255ea0cad 100644 --- a/data/galaxyhomomer/galaxyhomomerbioschemas.jsonld +++ b/data/galaxyhomomer/galaxyhomomerbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKX246", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/galaxyhomomer", "@type": "sc:SoftwareApplication", @@ -26,45 +22,49 @@ ], "edam:has_output": [ { - "@id": "edam:data_1460" + "@id": "edam:data_1537" }, { - "@id": "edam:data_1537" + "@id": "edam:data_1460" } ], "sc:additionalType": "Web application", "sc:applicationSubCategory": [ - { - "@id": "edam:topic_0082" - }, { "@id": "edam:topic_3300" }, { "@id": "edam:topic_0736" + }, + { + "@id": "edam:topic_0082" } ], "sc:citation": [ - "pubmed:28387820", { "@id": "https://doi.org/10.1093/NAR/GKX246" }, - "pmcid:PMC5570155" + "pmcid:PMC5570155", + "pubmed:28387820" ], "sc:description": "Protein oligomer structure prediction from a monomer sequence or structure. It carries out template-based modeling, ab initio docking or both depending on the availability of proper oligomer templates.", "sc:featureList": [ { - "@id": "edam:operation_0478" + "@id": "edam:operation_0267" }, { "@id": "edam:operation_3662" }, { - "@id": "edam:operation_0267" + "@id": "edam:operation_0478" } ], "sc:name": "GalaxyHomomer", "sc:url": "http://galaxy.seoklab.org/homomer" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKX246", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/galaxyrefine/galaxyrefinebioschemas.jsonld b/data/galaxyrefine/galaxyrefinebioschemas.jsonld index 0e90a6493c614..1bba2eb3be3c0 100644 --- a/data/galaxyrefine/galaxyrefinebioschemas.jsonld +++ b/data/galaxyrefine/galaxyrefinebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GalaxyRefine", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://galaxy.seoklab.org/refine" } \ No newline at end of file diff --git a/data/galaxysite/galaxysitebioschemas.jsonld b/data/galaxysite/galaxysitebioschemas.jsonld index 98bf13088e896..37a6732379a76 100644 --- a/data/galaxysite/galaxysitebioschemas.jsonld +++ b/data/galaxysite/galaxysitebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "GalaxySite is a web server for ligand-binding site prediction by using molecular docking.", "sc:name": "GalaxySite", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://galaxy.seoklab.org/site" } \ No newline at end of file diff --git a/data/gametes/gametesbioschemas.jsonld b/data/gametes/gametesbioschemas.jsonld index 35cc83792a678..eac59c50d52b5 100644 --- a/data/gametes/gametesbioschemas.jsonld +++ b/data/gametes/gametesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "User-friendly software package and algorithm which generates complex biallelic single nucleotide polymorphism (SNP) disease models for simulation studies.", "sc:name": "GAMETES", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://sourceforge.net/projects/gametes/?source=navbar" } \ No newline at end of file diff --git a/data/gaml/gamlbioschemas.jsonld b/data/gaml/gamlbioschemas.jsonld index cb5e90ebb4010..caa3a22cdc898 100644 --- a/data/gaml/gamlbioschemas.jsonld +++ b/data/gaml/gamlbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/gaml", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Broňa Brejová", - "Tomáš Vinař" + "Tomáš Vinař", + "Broňa Brejová" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:26042154", "sc:description": "Prototype genome assembly tool based on maximizing likelihood of the assembly in a model encompaasing error rate, insert length and other features of indvidual sequencing technologies.", "sc:name": "GAML", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://compbio.fmph.uniba.sk/gaml/" } \ No newline at end of file diff --git a/data/gamola2/gamola2bioschemas.jsonld b/data/gamola2/gamola2bioschemas.jsonld index ea536deaafa82..e36f5a26e1db1 100644 --- a/data/gamola2/gamola2bioschemas.jsonld +++ b/data/gamola2/gamola2bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes.", "sc:name": "GAMOLA2", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://drive.google.com/file/d/0B_fIEHIR2oaabVlzcF9NUTlnbjQ/view" } \ No newline at end of file diff --git a/data/gamp/gampbioschemas.jsonld b/data/gamp/gampbioschemas.jsonld index 3e5e53c67a808..dddfc4ed8bee4 100644 --- a/data/gamp/gampbioschemas.jsonld +++ b/data/gamp/gampbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Conduct “global analysis” of DNA methylation data, particularly from the Illumina 450k Infinium platform. Instead of examining the effect of individual CpGs, the idea is to compare the overall profile or distribution of CpG measurements across individuals.", "sc:name": "GAMP", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://research.fhcrc.org/wu/en/software.html#GAMP" } \ No newline at end of file diff --git a/data/ganesh/ganeshbioschemas.jsonld b/data/ganesh/ganeshbioschemas.jsonld index a125081a1bcc5..efad4566c76d3 100644 --- a/data/ganesh/ganeshbioschemas.jsonld +++ b/data/ganesh/ganeshbioschemas.jsonld @@ -24,9 +24,9 @@ "sc:description": "A software to cluster expression data by Gibbs sampling procedure.", "sc:name": "GaneSh", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/GaneSh", diff --git a/data/gap/gapbioschemas.jsonld b/data/gap/gapbioschemas.jsonld index 623effe710d9a..e165ccf0d543c 100644 --- a/data/gap/gapbioschemas.jsonld +++ b/data/gap/gapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Distinguish between amyloid fibril-forming and amorphous ß-aggregating hexapeptides with almost 100 percent accuracies in validation tests performed using non-redundant datasets.", "sc:name": "GAP", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.iitm.ac.in/bioinfo/GAP/" diff --git a/data/gapit/gapitbioschemas.jsonld b/data/gapit/gapitbioschemas.jsonld index 3d01b96582959..019dcc383f74e 100644 --- a/data/gapit/gapitbioschemas.jsonld +++ b/data/gapit/gapitbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Not licensed", "sc:name": "GAPIT", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.maizegenetics.net/gapit" } \ No newline at end of file diff --git a/data/gapp/gappbioschemas.jsonld b/data/gapp/gappbioschemas.jsonld index 4c98bef0ceadc..a7e2673807c81 100644 --- a/data/gapp/gappbioschemas.jsonld +++ b/data/gapp/gappbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5098048", - "pubmed:27630248", { "@id": "https://doi.org/10.1074/MCP.M116.060046" - } + }, + "pubmed:27630248" ], "sc:description": "A Proteogenomic tool for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.", "sc:featureList": [ @@ -36,8 +36,8 @@ ], "sc:name": "GAPP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/gappproteogenomic/" } diff --git a/data/gaprediction/gapredictionbioschemas.jsonld b/data/gaprediction/gapredictionbioschemas.jsonld index 6e914b022ffcc..1bc373cd4b833 100644 --- a/data/gaprediction/gapredictionbioschemas.jsonld +++ b/data/gaprediction/gapredictionbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "GAprediction", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GAprediction.html", "sc:version": "1.0.0" diff --git a/data/gapsplit/gapsplitbioschemas.jsonld b/data/gapsplit/gapsplitbioschemas.jsonld index 4187bea97ad20..1194efbd5da0c 100644 --- a/data/gapsplit/gapsplitbioschemas.jsonld +++ b/data/gapsplit/gapsplitbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "Gapsplit", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/jensenlab/gapsplit" } \ No newline at end of file diff --git a/data/garfield/garfieldbioschemas.jsonld b/data/garfield/garfieldbioschemas.jsonld index f06ce27d69fb3..27d65e3abba8a 100644 --- a/data/garfield/garfieldbioschemas.jsonld +++ b/data/garfield/garfieldbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Valentina Iotchkova", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Method that leverages GWAS findings with regulatory or functional annotations to find features relevant to a phenotype. It performs greedy pruning of GWAS SNPs and then annotates them based on functional information overlap. Next, it quantifies Fold Enrichment (FE) at various GWAS significance cutoffs and assesses them by permutation testing, while matching for MAF, distance to nearest transcription start site and number of LD proxies.", "sc:license": "GPL-3.0", "sc:name": "garfield", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/garfield.html", diff --git a/data/garlic_homozygosity/garlic_homozygositybioschemas.jsonld b/data/garlic_homozygosity/garlic_homozygositybioschemas.jsonld index a297ae5040b53..a3ca4ec17eb84 100644 --- a/data/garlic_homozygosity/garlic_homozygositybioschemas.jsonld +++ b/data/garlic_homozygosity/garlic_homozygositybioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GARLIC", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/szpiech/garlic" } \ No newline at end of file diff --git a/data/garn/garnbioschemas.jsonld b/data/garn/garnbioschemas.jsonld index 9e0c2ac0a19df..36878d887e3e2 100644 --- a/data/garn/garnbioschemas.jsonld +++ b/data/garn/garnbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/garn", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Johanne Cohen", - "Melanie Boudard" + "Melanie Boudard", + "Johanne Cohen" ], "sc:additionalType": "Desktop application", "sc:description": "Coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.", "sc:name": "GARN2", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://garn.lri.fr/" } \ No newline at end of file diff --git a/data/garnier/garnierbioschemas.jsonld b/data/garnier/garnierbioschemas.jsonld index 153d2fc197bf1..6097af4b1edb3 100644 --- a/data/garnier/garnierbioschemas.jsonld +++ b/data/garnier/garnierbioschemas.jsonld @@ -13,15 +13,15 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:description": "Predict protein secondary structure using GOR method.", "sc:funder": [ - "UK MRC", "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "garnier", diff --git a/data/gars/garsbioschemas.jsonld b/data/gars/garsbioschemas.jsonld index 74dc47dba8c21..4a2c5dd03ddd0 100644 --- a/data/gars/garsbioschemas.jsonld +++ b/data/gars/garsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "GARS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GARS.html", diff --git a/data/gasoline/gasolinebioschemas.jsonld b/data/gasoline/gasolinebioschemas.jsonld index 60a5789d8cd21..e1753af3018b2 100644 --- a/data/gasoline/gasolinebioschemas.jsonld +++ b/data/gasoline/gasolinebioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.4537.2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/gasoline", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Giovanni Micale", "sc:additionalType": "Plug-in", "sc:citation": [ - "pubmed:25324964", "pmcid:PMC4197741", + "pubmed:25324964", { "@id": "https://doi.org/10.12688/F1000RESEARCH.4537.2" } @@ -28,20 +24,24 @@ "sc:description": "Multiple local alignments of PPI (protein-protein interaction) networks. It is based on the homonymous greedy and stochastic algorithm. It starts with the identification of sets of similar nodes, called seeds of the alignment and then alignments are then extended in a greedy manner and finally refined.", "sc:featureList": [ { - "@id": "edam:operation_0495" + "@id": "edam:operation_0277" }, { - "@id": "edam:operation_0277" + "@id": "edam:operation_0495" } ], "sc:name": "GASOLINE", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/GMicale/GASOLINE", "sc:version": "2.0" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.4537.2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gass-web/gass-webbioschemas.jsonld b/data/gass-web/gass-webbioschemas.jsonld index aa476690cd929..4b6aecc94e2b3 100644 --- a/data/gass-web/gass-webbioschemas.jsonld +++ b/data/gass-web/gass-webbioschemas.jsonld @@ -17,10 +17,6 @@ "@id": "http://orcid.org/0000-0002-3004-2119", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1093/nar/gkx337", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/gass-web", "@type": "sc:SoftwareApplication", @@ -34,11 +30,11 @@ ], "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC5570142", { "@id": "https://doi.org/10.1093/nar/gkx337" }, - "pubmed:28459991", - "pmcid:PMC5570142" + "pubmed:28459991" ], "sc:description": "Web version of GASS (Genetic Active Site Search). Method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures.", "sc:featureList": { @@ -46,6 +42,10 @@ }, "sc:name": "GASS-WEB", "sc:url": "http://gass.unifei.edu.br/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkx337", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gasv/gasvbioschemas.jsonld b/data/gasv/gasvbioschemas.jsonld index 9d0caa6d5e16c..f736e494576bd 100644 --- a/data/gasv/gasvbioschemas.jsonld +++ b/data/gasv/gasvbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "GASV", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://compbio.cs.brown.edu/projects/gasv/" } \ No newline at end of file diff --git a/data/gat/gatbioschemas.jsonld b/data/gat/gatbioschemas.jsonld index d36fab021e958..9f82049a9a199 100644 --- a/data/gat/gatbioschemas.jsonld +++ b/data/gat/gatbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "GAT", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/AndreasHeger/gat" } \ No newline at end of file diff --git a/data/gatb/gatbbioschemas.jsonld b/data/gatb/gatbbioschemas.jsonld index 3519ffb77e1b7..bdcea8b02bdfe 100644 --- a/data/gatb/gatbbioschemas.jsonld +++ b/data/gatb/gatbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "C++ library of high level functions designed to benefit from recent advances in NGS data structures for handling huge datasets of sequencing data.", "sc:name": "GATB", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://gatb.inria.fr/" } \ No newline at end of file diff --git a/data/gatekeeper/gatekeeperbioschemas.jsonld b/data/gatekeeper/gatekeeperbioschemas.jsonld index 821e5ae00d98f..6417360823eea 100644 --- a/data/gatekeeper/gatekeeperbioschemas.jsonld +++ b/data/gatekeeper/gatekeeperbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Mohammed Alser", - "Onur Mutlu", - "Can Alkan" + "Can Alkan", + "Onur Mutlu" ], "sc:additionalType": "Command-line tool", "sc:description": "Fast Alignment Filter for DNA Short Read Mapping.", diff --git a/data/gatk-lodn/gatk-lodnbioschemas.jsonld b/data/gatk-lodn/gatk-lodnbioschemas.jsonld index fda2bb64d58f4..f52aa185a0e2a 100644 --- a/data/gatk-lodn/gatk-lodnbioschemas.jsonld +++ b/data/gatk-lodn/gatk-lodnbioschemas.jsonld @@ -9,23 +9,23 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-3185-7456", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-016-1190-7", "@type": "sc:CreativeWork" }, + { + "@id": "http://orcid.org/0000-0003-3185-7456", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/gatk-lodn", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Ítalo Faria do Valle", { "@id": "http://orcid.org/0000-0003-3185-7456" }, - "Gastone Castellani", - "Ítalo Faria do Valle" + "Gastone Castellani" ], "edam:has_input": { "@id": "edam:data_1234" @@ -38,11 +38,11 @@ "@id": "edam:topic_2533" }, "sc:citation": [ + "pubmed:28185561", + "pmcid:PMC5123378", { "@id": "https://doi.org/10.1186/s12859-016-1190-7" - }, - "pubmed:28185561", - "pmcid:PMC5123378" + } ], "sc:description": "This method increases specificity and sensitivity of GATK results for mutation detection.", "sc:featureList": { @@ -52,8 +52,8 @@ "sc:license": "Apache-1.0", "sc:name": "GATK-LODn", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bitbucket.org/BBDA-UNIBO/wes-pipeline" } diff --git a/data/gatk/gatkbioschemas.jsonld b/data/gatk/gatkbioschemas.jsonld index df14e30e7afe8..0c89a34c5aa26 100644 --- a/data/gatk/gatkbioschemas.jsonld +++ b/data/gatk/gatkbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data. The toolkit is well established for germline short variant discovery from whole genome and exome sequencing data. GATK4 expands functionality into copy number and somatic analyses and offers pipeline scripts for workflows. \n\nVersion 4 (GATK4) is open-source at https://github.com/broadinstitute/gatk.", "sc:name": "GATK", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "4.x" diff --git a/data/gatk_base_recalibrator/gatk_base_recalibratorbioschemas.jsonld b/data/gatk_base_recalibrator/gatk_base_recalibratorbioschemas.jsonld index 19785dd39fa85..55539a18ff8cf 100644 --- a/data/gatk_base_recalibrator/gatk_base_recalibratorbioschemas.jsonld +++ b/data/gatk_base_recalibrator/gatk_base_recalibratorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal operating only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors and indicative of poor base quality. This walker generates tables based on various user-specified covariates (such as read group, reported quality score, cycle, and dinucleotide).", "sc:name": "gatk_base_recalibrator", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_depth_of_coverage/gatk_depth_of_coveragebioschemas.jsonld b/data/gatk_depth_of_coverage/gatk_depth_of_coveragebioschemas.jsonld index 025ceafedaebc..dfe41f5191425 100644 --- a/data/gatk_depth_of_coverage/gatk_depth_of_coveragebioschemas.jsonld +++ b/data/gatk_depth_of_coverage/gatk_depth_of_coveragebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score.", "sc:name": "gatk_depth_of_coverage", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_haplotype_caller/gatk_haplotype_callerbioschemas.jsonld b/data/gatk_haplotype_caller/gatk_haplotype_callerbioschemas.jsonld index 37e18167f8f18..20c71e61379b9 100644 --- a/data/gatk_haplotype_caller/gatk_haplotype_callerbioschemas.jsonld +++ b/data/gatk_haplotype_caller/gatk_haplotype_callerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "gatk_haplotype_caller", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_indel_realigner/gatk_indel_realignerbioschemas.jsonld b/data/gatk_indel_realigner/gatk_indel_realignerbioschemas.jsonld index c59e09cb41edc..f96cc38b94000 100644 --- a/data/gatk_indel_realigner/gatk_indel_realignerbioschemas.jsonld +++ b/data/gatk_indel_realigner/gatk_indel_realignerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "gatk_indel_realigner", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_print_reads/gatk_print_readsbioschemas.jsonld b/data/gatk_print_reads/gatk_print_readsbioschemas.jsonld index 733e1e9435b7e..d3ac67ddc500d 100644 --- a/data/gatk_print_reads/gatk_print_readsbioschemas.jsonld +++ b/data/gatk_print_reads/gatk_print_readsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads.", "sc:name": "gatk_print_reads", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_realigner_target_creator/gatk_realigner_target_creatorbioschemas.jsonld b/data/gatk_realigner_target_creator/gatk_realigner_target_creatorbioschemas.jsonld index e595d4408b3f0..17995ca4ba66e 100644 --- a/data/gatk_realigner_target_creator/gatk_realigner_target_creatorbioschemas.jsonld +++ b/data/gatk_realigner_target_creator/gatk_realigner_target_creatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Realigner Target Creator for use in local realignment.", "sc:name": "gatk_realigner_target_creator", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_reduce_reads/gatk_reduce_readsbioschemas.jsonld b/data/gatk_reduce_reads/gatk_reduce_readsbioschemas.jsonld index 733a4451938e9..5cca069732ec7 100644 --- a/data/gatk_reduce_reads/gatk_reduce_readsbioschemas.jsonld +++ b/data/gatk_reduce_reads/gatk_reduce_readsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Reduce the BAM file using read based compression that keeps only essential information for variant calling.", "sc:name": "gatk_reduce_reads", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_unified_genotyper/gatk_unified_genotyperbioschemas.jsonld b/data/gatk_unified_genotyper/gatk_unified_genotyperbioschemas.jsonld index a39cc6eaa1470..9f5135cab9d3d 100644 --- a/data/gatk_unified_genotyper/gatk_unified_genotyperbioschemas.jsonld +++ b/data/gatk_unified_genotyper/gatk_unified_genotyperbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "SNP and indel caller.", "sc:name": "gatk_unified_genotyper", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_validate_variants/gatk_validate_variantsbioschemas.jsonld b/data/gatk_validate_variants/gatk_validate_variantsbioschemas.jsonld index 60a19d7b9056d..523a6d8682c93 100644 --- a/data/gatk_validate_variants/gatk_validate_variantsbioschemas.jsonld +++ b/data/gatk_validate_variants/gatk_validate_variantsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Validate a variants file.", "sc:name": "gatk_validate_variants", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://software.broadinstitute.org/gatk/", diff --git a/data/gatk_variant_annotator/gatk_variant_annotatorbioschemas.jsonld b/data/gatk_variant_annotator/gatk_variant_annotatorbioschemas.jsonld index f668880a75990..a9a7f93777f2f 100644 --- a/data/gatk_variant_annotator/gatk_variant_annotatorbioschemas.jsonld +++ b/data/gatk_variant_annotator/gatk_variant_annotatorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Annotate variant calls with context information. Users can specify which of the available annotations to use.", "sc:name": "gatk_variant_annotator", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://software.broadinstitute.org/gatk/", diff --git a/data/gatk_variant_apply_recalibration/gatk_variant_apply_recalibrationbioschemas.jsonld b/data/gatk_variant_apply_recalibration/gatk_variant_apply_recalibrationbioschemas.jsonld index fdd38be9859fa..03e17d05ecfa1 100644 --- a/data/gatk_variant_apply_recalibration/gatk_variant_apply_recalibrationbioschemas.jsonld +++ b/data/gatk_variant_apply_recalibration/gatk_variant_apply_recalibrationbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Apply cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration.", "sc:name": "gatk_variant_apply_recalibration", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_variant_combine/gatk_variant_combinebioschemas.jsonld b/data/gatk_variant_combine/gatk_variant_combinebioschemas.jsonld index 902dc349108fd..d180e086b5b7a 100644 --- a/data/gatk_variant_combine/gatk_variant_combinebioschemas.jsonld +++ b/data/gatk_variant_combine/gatk_variant_combinebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Combine VCF records from different sources. The tool supports both full merges and set unions. Merge: combines multiple records into a single one; if sample names overlap then they are uniquified. Union: assumes each rod represents the same set of samples (although this is not enforced); using the priority list (if provided), emits a single record instance at every position represented in the rods.", "sc:name": "gatk_variant_combine", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_variant_eval/gatk_variant_evalbioschemas.jsonld b/data/gatk_variant_eval/gatk_variant_evalbioschemas.jsonld index 5de29c4e82657..b733468fe4096 100644 --- a/data/gatk_variant_eval/gatk_variant_evalbioschemas.jsonld +++ b/data/gatk_variant_eval/gatk_variant_evalbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more).", "sc:name": "gatk_variant_eval", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://software.broadinstitute.org/gatk/", diff --git a/data/gatk_variant_filtration/gatk_variant_filtrationbioschemas.jsonld b/data/gatk_variant_filtration/gatk_variant_filtrationbioschemas.jsonld index 81eb91094066b..61a0c522e0e1c 100644 --- a/data/gatk_variant_filtration/gatk_variant_filtrationbioschemas.jsonld +++ b/data/gatk_variant_filtration/gatk_variant_filtrationbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Filter variant calls using a number of user-selectable, parameterizable criteria.", "sc:name": "gatk_variant_filtration", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://software.broadinstitute.org/gatk/", diff --git a/data/gatk_variant_recalibrator/gatk_variant_recalibratorbioschemas.jsonld b/data/gatk_variant_recalibrator/gatk_variant_recalibratorbioschemas.jsonld index a8d35efdc72e3..1e293bc46163e 100644 --- a/data/gatk_variant_recalibrator/gatk_variant_recalibratorbioschemas.jsonld +++ b/data/gatk_variant_recalibrator/gatk_variant_recalibratorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score.", "sc:name": "gatk_variant_recalibrator", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gatk_variant_select/gatk_variant_selectbioschemas.jsonld b/data/gatk_variant_select/gatk_variant_selectbioschemas.jsonld index 44d40d23a0d64..c4590cbdc726a 100644 --- a/data/gatk_variant_select/gatk_variant_selectbioschemas.jsonld +++ b/data/gatk_variant_select/gatk_variant_selectbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion.", "sc:name": "gatk_variant_select", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://software.broadinstitute.org/gatk/", "sc:version": "2.4-9" diff --git a/data/gaucho/gauchobioschemas.jsonld b/data/gaucho/gauchobioschemas.jsonld index 5760943ae3dfd..97feeb234795b 100644 --- a/data/gaucho/gauchobioschemas.jsonld +++ b/data/gaucho/gauchobioschemas.jsonld @@ -22,9 +22,9 @@ "sc:license": "GPL-3.0", "sc:name": "gaucho", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gaucho.html", "sc:version": "1.10.0" diff --git a/data/gazepath/gazepathbioschemas.jsonld b/data/gazepath/gazepathbioschemas.jsonld index e230edc4730dd..555ecad877206 100644 --- a/data/gazepath/gazepathbioschemas.jsonld +++ b/data/gazepath/gazepathbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3758/s13428-017-0909-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gazepath", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Daan van Renswoude", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5880860", - "pubmed:28593606", { "@id": "https://doi.org/10.3758/s13428-017-0909-3" - } + }, + "pmcid:PMC5880860", + "pubmed:28593606" ], "sc:description": "Eye-tracking data must be transformed into fixations and saccades before it can be analyzed. This package provides a non-parametric speed-based approach to do this on a trial basis. The method is especially useful when there are large differences in data quality, as the thresholds are adjusted accordingly.", "sc:featureList": { @@ -34,10 +38,6 @@ ], "sc:url": "https://cran.r-project.org/web/packages/gazepath/index.html", "sc:version": "1.2" - }, - { - "@id": "https://doi.org/10.3758/s13428-017-0909-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gbif_occurrence_ws/gbif_occurrence_wsbioschemas.jsonld b/data/gbif_occurrence_ws/gbif_occurrence_wsbioschemas.jsonld index ec1832bcc523f..ef7616eea3e34 100644 --- a/data/gbif_occurrence_ws/gbif_occurrence_wsbioschemas.jsonld +++ b/data/gbif_occurrence_ws/gbif_occurrence_wsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Web service for occurrence data (specimens, observations) from the global GBIF data portal.", "sc:name": "GBIF occurrence WS", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.gbif.org/developer/summary", "sc:version": "1" diff --git a/data/gbif_taxon_ws/gbif_taxon_wsbioschemas.jsonld b/data/gbif_taxon_ws/gbif_taxon_wsbioschemas.jsonld index 4a9ae814c19c0..6dbd531321ab9 100644 --- a/data/gbif_taxon_ws/gbif_taxon_wsbioschemas.jsonld +++ b/data/gbif_taxon_ws/gbif_taxon_wsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "GBIF taxon WS", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.gbif.org/developer/summary", "sc:version": "1" diff --git a/data/gbis/gbisbioschemas.jsonld b/data/gbis/gbisbioschemas.jsonld index f7a2337d9f7d4..be9ebee26c4ca 100644 --- a/data/gbis/gbisbioschemas.jsonld +++ b/data/gbis/gbisbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GBIS", "sc:operatingSystem": "Linux", "sc:provider": [ - "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben", - "ipk" + "ipk", + "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben" ], "sc:url": "http://gbis.ipk-gatersleben.de", "sc:version": "1" diff --git a/data/gboosting/gboostingbioschemas.jsonld b/data/gboosting/gboostingbioschemas.jsonld index f4546d02b7280..7847e0b242db6 100644 --- a/data/gboosting/gboostingbioschemas.jsonld +++ b/data/gboosting/gboostingbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "gboosting", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sites.google.com/site/bestumich/issues" } \ No newline at end of file diff --git a/data/gbrowse/gbrowsebioschemas.jsonld b/data/gbrowse/gbrowsebioschemas.jsonld index da453b858dde2..1cf37988b08a8 100644 --- a/data/gbrowse/gbrowsebioschemas.jsonld +++ b/data/gbrowse/gbrowsebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GBrowse", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://gmod.org/wiki/GBrowse" } \ No newline at end of file diff --git a/data/gc-profile/gc-profilebioschemas.jsonld b/data/gc-profile/gc-profilebioschemas.jsonld index 6cfc41a8b6a25..36518f8f9ed05 100644 --- a/data/gc-profile/gc-profilebioschemas.jsonld +++ b/data/gc-profile/gc-profilebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.", "sc:name": "GC-Profile", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://tubic.tju.edu.cn/GC-Profile/" } \ No newline at end of file diff --git a/data/gcac/gcacbioschemas.jsonld b/data/gcac/gcacbioschemas.jsonld index be1fb80f2ed62..3304b2b09e53d 100644 --- a/data/gcac/gcacbioschemas.jsonld +++ b/data/gcac/gcacbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "MIT", "sc:name": "GCAC", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://toolshed.g2.bx.psu.edu/repository?repository_id=351af44ceb587e54" } \ No newline at end of file diff --git a/data/gcalignr/gcalignrbioschemas.jsonld b/data/gcalignr/gcalignrbioschemas.jsonld index ad790226474c5..fad43b14abfa7 100644 --- a/data/gcalignr/gcalignrbioschemas.jsonld +++ b/data/gcalignr/gcalignrbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0198311", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/gcalignr", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:29879149", - "pmcid:PMC5991698", { "@id": "https://doi.org/10.1371/journal.pone.0198311" - } + }, + "pmcid:PMC5991698" ], "sc:description": "Simple peak alignment for gas-chromatography data in R.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "GCalignR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/mottensmann/GCalignR" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0198311", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gcapc/gcapcbioschemas.jsonld b/data/gcapc/gcapcbioschemas.jsonld index c1c2e01f32522..0a8831654ffde 100644 --- a/data/gcapc/gcapcbioschemas.jsonld +++ b/data/gcapc/gcapcbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "gcapc", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gcapc.html", "sc:version": "1.4.0" diff --git a/data/gcatest/gcatestbioschemas.jsonld b/data/gcatest/gcatestbioschemas.jsonld index 1aa6dcbec4a1b..e5e5267d705b8 100644 --- a/data/gcatest/gcatestbioschemas.jsonld +++ b/data/gcatest/gcatestbioschemas.jsonld @@ -22,9 +22,9 @@ "sc:license": "GPL-3.0", "sc:name": "gcatest", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gcatest.html", "sc:version": "1.4.0" diff --git a/data/gcmapweb/gcmapwebbioschemas.jsonld b/data/gcmapweb/gcmapwebbioschemas.jsonld index 6edaa12102348..aa06628d6d332 100644 --- a/data/gcmapweb/gcmapwebbioschemas.jsonld +++ b/data/gcmapweb/gcmapwebbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas Sandmann", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:24132929", "sc:description": "This R package provides a graphical user interface for the gCMAP package. It uses the Rook package and can be used either on a local machine, leveraging R's internal web server, or run on a dedicated rApache web server installation. It allows users to search their own data sources and instructions to generate reference datasets from public repositories are included with the package.", "sc:license": "Artistic-2.0", "sc:name": "gCMAPWeb", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gCMAPWeb.html", "sc:version": "1.14.0" diff --git a/data/gcocoa/gcocoabioschemas.jsonld b/data/gcocoa/gcocoabioschemas.jsonld index 4f56e3dc9d2a1..59edc2a01a4e3 100644 --- a/data/gcocoa/gcocoabioschemas.jsonld +++ b/data/gcocoa/gcocoabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Freeware", "sc:name": "gCocoa", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "ELIXIR-EE", diff --git a/data/gcontrol/gcontrolbioschemas.jsonld b/data/gcontrol/gcontrolbioschemas.jsonld index 3939b4d8ba248..faa288eb12a33 100644 --- a/data/gcontrol/gcontrolbioschemas.jsonld +++ b/data/gcontrol/gcontrolbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Computer program for Bayesian analysis of case-control data that controls for population stratification and cryptic relatedness. The program performs these analyses using Markov chain Monte Carlo algorithms.", "sc:name": "GControl", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://wpicr.wpic.pitt.edu/WPICCompGen/bayesian_genomic_control_softwar.htm" } \ No newline at end of file diff --git a/data/gconvert/gconvertbioschemas.jsonld b/data/gconvert/gconvertbioschemas.jsonld index 1bcc8c9e99428..589ad70c000c7 100644 --- a/data/gconvert/gconvertbioschemas.jsonld +++ b/data/gconvert/gconvertbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Freeware", "sc:name": "gConvert", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://biit.cs.ut.ee/gprofiler/gconvert.cgi", diff --git a/data/gcpred/gcpredbioschemas.jsonld b/data/gcpred/gcpredbioschemas.jsonld index 57f46bf7ae902..daf1ee323f260 100644 --- a/data/gcpred/gcpredbioschemas.jsonld +++ b/data/gcpred/gcpredbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Aloysius Wong", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:description": "Web tool for guanylyl cyclase functional centre prediction from amino acid sequence.", "sc:license": "Unlicense", "sc:name": "GCPred", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://gcpred.com/" } \ No newline at end of file diff --git a/data/gcrisprtools/bioconda_gcrisprtools.yaml b/data/gcrisprtools/bioconda_gcrisprtools.yaml index b15018bfe51d2..88e9475e89df3 100644 --- a/data/gcrisprtools/bioconda_gcrisprtools.yaml +++ b/data/gcrisprtools/bioconda_gcrisprtools.yaml @@ -7,7 +7,6 @@ description: Set of tools for evaluating pooled high-throughput screening experi home: https://bioconductor.org/packages/3.10/bioc/html/gCrisprTools.html identifiers: - biotools:gcrisprtools -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-gcrisprtools summary: Suite of Functions for Pooled Crispr Screen QC and Analysis diff --git a/data/gcrisprtools/gcrisprtoolsbioschemas.jsonld b/data/gcrisprtools/gcrisprtoolsbioschemas.jsonld index b6daa97b1fa42..cb387b7d62a88 100644 --- a/data/gcrisprtools/gcrisprtoolsbioschemas.jsonld +++ b/data/gcrisprtools/gcrisprtoolsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "gCrisprTools", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gCrisprTools.html", diff --git a/data/gcrma/gcrmabioschemas.jsonld b/data/gcrma/gcrmabioschemas.jsonld index e818ce5fe9bdd..17be53e5cae4d 100644 --- a/data/gcrma/gcrmabioschemas.jsonld +++ b/data/gcrma/gcrmabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "gcrma", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gcrma.html", "sc:version": "2.46.0" diff --git a/data/gcta/gctabioschemas.jsonld b/data/gcta/gctabioschemas.jsonld index 72a645f35bf5c..c766ebb33a02e 100644 --- a/data/gcta/gctabioschemas.jsonld +++ b/data/gcta/gctabioschemas.jsonld @@ -21,11 +21,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:21167468", "pmcid:PMC3014363", { "@id": "https://doi.org/10.1016/j.ajhg.2010.11.011" - }, - "pubmed:21167468" + } ], "sc:description": "Genome-wide Complex Trait Analysis. Estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.", "sc:featureList": { diff --git a/data/gcua/gcuabioschemas.jsonld b/data/gcua/gcuabioschemas.jsonld index c9c4e3c70cdf4..738f9114d3a19 100644 --- a/data/gcua/gcuabioschemas.jsonld +++ b/data/gcua/gcuabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Differences in codon usage preference among organisms lead to a variety of problems concerning heterologous gene expression but can be overcome by rational gene design and gene synthesis. The gcua tool displays the codon quality either in codon usage frequency values or relative adaptiveness values.", "sc:name": "Graphical Codon Usage Analyser", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://gcua.schoedl.de" } \ No newline at end of file diff --git a/data/gcup/gcupbioschemas.jsonld b/data/gcup/gcupbioschemas.jsonld index 4b2afbc94652a..5a42a7d17a5a8 100644 --- a/data/gcup/gcupbioschemas.jsonld +++ b/data/gcup/gcupbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Rapid GPU-based HIV-1 coreceptor usage prediction for next-generation sequencing.", "sc:name": "gCUP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://www.uni-due.de/~hy0546/gCUP/" } \ No newline at end of file diff --git a/data/gdap/gdapbioschemas.jsonld b/data/gdap/gdapbioschemas.jsonld index 7c097807ff1cb..8539e85b009ec 100644 --- a/data/gdap/gdapbioschemas.jsonld +++ b/data/gdap/gdapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Predicts disulfide bonds for a user-supplied protein sequence. It also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.", "sc:name": "GDAP", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.doe-mbi.ucla.edu/Services/GDAP" diff --git a/data/gdc/gdcbioschemas.jsonld b/data/gdc/gdcbioschemas.jsonld index fb00af097331f..5b96f8f1f3731 100644 --- a/data/gdc/gdcbioschemas.jsonld +++ b/data/gdc/gdcbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Utility designed for compression of genome collections from the same species.", "sc:name": "GDC", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about" } \ No newline at end of file diff --git a/data/gdcrnatools/gdcrnatoolsbioschemas.jsonld b/data/gdcrnatools/gdcrnatoolsbioschemas.jsonld index 563d9b54df785..1c3963d40eec6 100644 --- a/data/gdcrnatools/gdcrnatoolsbioschemas.jsonld +++ b/data/gdcrnatools/gdcrnatoolsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "GDCRNATools", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/devel/bioc/html/GDCRNATools.html", diff --git a/data/gdfuzz3d/gdfuzz3dbioschemas.jsonld b/data/gdfuzz3d/gdfuzz3dbioschemas.jsonld index 5758e21206022..a077b7e063035 100644 --- a/data/gdfuzz3d/gdfuzz3dbioschemas.jsonld +++ b/data/gdfuzz3d/gdfuzz3dbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.", "sc:name": "GDFuzz3D", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://iimcb.genesilico.pl/gdserver/GDFuzz3D/" } \ No newline at end of file diff --git a/data/gdhc/gdhcbioschemas.jsonld b/data/gdhc/gdhcbioschemas.jsonld index 2191f74cb1962..e0d3b686182f9 100644 --- a/data/gdhc/gdhcbioschemas.jsonld +++ b/data/gdhc/gdhcbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Method of hierarchical clustering for high throughput data. Nonlinear relations exist between features of high-throughput data. They reflect critical regulation patterns in the biological system. Clustering based on both linear and nonlinear relations in high throughput data is hampered by the high dimensionality and high noise level in the data.", "sc:name": "GDHC", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://web1.sph.emory.edu/users/tyu8/GDHC/" } \ No newline at end of file diff --git a/data/gdr/gdrbioschemas.jsonld b/data/gdr/gdrbioschemas.jsonld index 740045fbacefc..b061777fc6f15 100644 --- a/data/gdr/gdrbioschemas.jsonld +++ b/data/gdr/gdrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Contains all publically available Rosaceae sequences including annotated peach, strawberry and almond EST sequences and the genetically anchored peach physical map.", "sc:name": "Genome Database for Rosaceae (GDR)", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.rosaceae.org/" } \ No newline at end of file diff --git a/data/gdsctools/gdsctoolsbioschemas.jsonld b/data/gdsctools/gdsctoolsbioschemas.jsonld index dc5cf1a9ef47a..9fd65d3bac1e4 100644 --- a/data/gdsctools/gdsctoolsbioschemas.jsonld +++ b/data/gdsctools/gdsctoolsbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/gdsctools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Thomas Cokelaer", "Julio Saez-Rodriguez", - "Mathew J Garnett" + "Mathew J Garnett", + "Thomas Cokelaer" ], "sc:additionalType": "Command-line tool", "sc:description": "Mining pharmacogenomic interactions in cancer.", "sc:name": "GDSCTools", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://gdsctools.readthedocs.io/en/master/" } \ No newline at end of file diff --git a/data/gdsfmt/gdsfmtbioschemas.jsonld b/data/gdsfmt/gdsfmtbioschemas.jsonld index 5ff99946abf36..2d40d478ad641 100644 --- a/data/gdsfmt/gdsfmtbioschemas.jsonld +++ b/data/gdsfmt/gdsfmtbioschemas.jsonld @@ -30,18 +30,18 @@ "@id": "edam:data_1276" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": { "@id": "edam:topic_3071" }, "sc:citation": [ "pubmed:28334390", + "pmcid:PMC5860110", { "@id": "https://doi.org/10.1093/bioinformatics/btx145" - }, - "pmcid:PMC5860110" + } ], "sc:description": "This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. It offers efficient operations designed for integers of less than 8 bits (single genetic/genomic variant fewer bits than a byte).", "sc:featureList": { @@ -51,8 +51,8 @@ "sc:name": "gdsfmt", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gdsfmt.html", "sc:version": "1.10.0" diff --git a/data/gdt/gdtbioschemas.jsonld b/data/gdt/gdtbioschemas.jsonld index 03e44ef92a4ba..59791165c41e3 100644 --- a/data/gdt/gdtbioschemas.jsonld +++ b/data/gdt/gdtbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software package for genome-wide association analysis.", "sc:name": "GDT", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://people.virginia.edu/~wc9c/GDT/" } \ No newline at end of file diff --git a/data/gdtools_annotate/gdtools_annotatebioschemas.jsonld b/data/gdtools_annotate/gdtools_annotatebioschemas.jsonld index 86cac2955e1d2..ce3dac2889d03 100644 --- a/data/gdtools_annotate/gdtools_annotatebioschemas.jsonld +++ b/data/gdtools_annotate/gdtools_annotatebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "gdtools_annotate", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gdtools_apply/gdtools_applybioschemas.jsonld b/data/gdtools_apply/gdtools_applybioschemas.jsonld index ce98cec5c5843..80413f96b604a 100644 --- a/data/gdtools_apply/gdtools_applybioschemas.jsonld +++ b/data/gdtools_apply/gdtools_applybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "gdtools_apply", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gdtools_gd2gvf/gdtools_gd2gvfbioschemas.jsonld b/data/gdtools_gd2gvf/gdtools_gd2gvfbioschemas.jsonld index 37db035ee70de..a96718516fdef 100644 --- a/data/gdtools_gd2gvf/gdtools_gd2gvfbioschemas.jsonld +++ b/data/gdtools_gd2gvf/gdtools_gd2gvfbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Creates a Genome Variation Format (GVF) file of mutations present in an input Genome Diff file.", "sc:name": "gdtools_gd2gvf", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gdtools_gd2vcf/gdtools_gd2vcfbioschemas.jsonld b/data/gdtools_gd2vcf/gdtools_gd2vcfbioschemas.jsonld index 5bbafdf7c297a..81c98f1ae6ef8 100644 --- a/data/gdtools_gd2vcf/gdtools_gd2vcfbioschemas.jsonld +++ b/data/gdtools_gd2vcf/gdtools_gd2vcfbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "gdtools_gd2vcf", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gdtools_intersect/gdtools_intersectbioschemas.jsonld b/data/gdtools_intersect/gdtools_intersectbioschemas.jsonld index 45316c8bd53a2..593aa429299fe 100644 --- a/data/gdtools_intersect/gdtools_intersectbioschemas.jsonld +++ b/data/gdtools_intersect/gdtools_intersectbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Creates a new Genome Diff file with mutations that are present in ALL input Genome Diff files.", "sc:name": "gdtools_intersect", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gdtools_mutations/gdtools_mutationsbioschemas.jsonld b/data/gdtools_mutations/gdtools_mutationsbioschemas.jsonld index 7916ff102384e..45dac118530fb 100644 --- a/data/gdtools_mutations/gdtools_mutationsbioschemas.jsonld +++ b/data/gdtools_mutations/gdtools_mutationsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predicts mutations from the evidence entries in the input GD file. Any mutation entries (three-letter code lines) already present in the input GD file will be removed.", "sc:name": "gdtools_mutations", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gdtools_normalize/gdtools_normalizebioschemas.jsonld b/data/gdtools_normalize/gdtools_normalizebioschemas.jsonld index 339cccd30ddcf..ff86ac529be93 100644 --- a/data/gdtools_normalize/gdtools_normalizebioschemas.jsonld +++ b/data/gdtools_normalize/gdtools_normalizebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "gdtools_normalize", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gdtools_not-evidence/gdtools_not-evidencebioschemas.jsonld b/data/gdtools_not-evidence/gdtools_not-evidencebioschemas.jsonld index 56f6601725d5f..3ffc6c29d95d6 100644 --- a/data/gdtools_not-evidence/gdtools_not-evidencebioschemas.jsonld +++ b/data/gdtools_not-evidence/gdtools_not-evidencebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Takes a GenomeDiff file and removes all of the entries that are NOT used as evidence by a mutation. Outputs to a new GenomeDiff file if specified. If no output is specified, verbose will still inform what evidence isn't being used.", "sc:name": "gdtools_not-evidence", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gdtools_subtract/gdtools_subtractbioschemas.jsonld b/data/gdtools_subtract/gdtools_subtractbioschemas.jsonld index ffe09194b8c77..67af400ff7a8c 100644 --- a/data/gdtools_subtract/gdtools_subtractbioschemas.jsonld +++ b/data/gdtools_subtract/gdtools_subtractbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Creates a new Genome Diff file that contains all entries that are still present in the input file after removing mutations that are in any of the subtracted Genome Diff files. All evidence and validation entries are retained in the output file.", "sc:name": "gdtools_subtract", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", diff --git a/data/gdtools_union/gdtools_unionbioschemas.jsonld b/data/gdtools_union/gdtools_unionbioschemas.jsonld index 74541b53ec810..21cac51e4e0e6 100644 --- a/data/gdtools_union/gdtools_unionbioschemas.jsonld +++ b/data/gdtools_union/gdtools_unionbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Creates a GD file with entries that exist in any input GD file. Duplicate entries are merged into a single entry.", "sc:name": "gdtools_union", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", diff --git a/data/gdtools_validate/gdtools_validatebioschemas.jsonld b/data/gdtools_validate/gdtools_validatebioschemas.jsonld index a423e17a94e7c..1d274d43ada76 100644 --- a/data/gdtools_validate/gdtools_validatebioschemas.jsonld +++ b/data/gdtools_validate/gdtools_validatebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Validates whether the format of the input Genome Diff files is correct.", "sc:name": "gdtools_validate", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gdtools_vcf2gd/gdtools_vcf2gdbioschemas.jsonld b/data/gdtools_vcf2gd/gdtools_vcf2gdbioschemas.jsonld index 05a562ea5b9fb..6bc4689547703 100644 --- a/data/gdtools_vcf2gd/gdtools_vcf2gdbioschemas.jsonld +++ b/data/gdtools_vcf2gd/gdtools_vcf2gdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Variant Call Format(VCF) to GD.", "sc:name": "gdtools_vcf2gd", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html", "sc:version": "0.26" diff --git a/data/gear-base/gear-basebioschemas.jsonld b/data/gear-base/gear-basebioschemas.jsonld index 8b1543cb47263..90d320b052604 100644 --- a/data/gear-base/gear-basebioschemas.jsonld +++ b/data/gear-base/gear-basebioschemas.jsonld @@ -22,9 +22,9 @@ "sc:license": "Unlicense", "sc:name": "GEAR-base", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://gear-base.com" } \ No newline at end of file diff --git a/data/gec/gecbioschemas.jsonld b/data/gec/gecbioschemas.jsonld index e7b626d6ef743..31255bad6ca96 100644 --- a/data/gec/gecbioschemas.jsonld +++ b/data/gec/gecbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Java-based application developed to address multiple-testing issue with dependent Single-nucleotide polymorphisms (SNPs).  Based on this new measure, several popular multiple-testing methods including Bonferroni, Holm, Simes correction was improved to evaluate significance level of SNP p-values in genome-wide association studies.", "sc:name": "GEC", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://statgenpro.psychiatry.hku.hk/gec/index.php" } \ No newline at end of file diff --git a/data/gecko-csb/gecko-csbbioschemas.jsonld b/data/gecko-csb/gecko-csbbioschemas.jsonld index f747632bea111..ec4afaad708ce 100644 --- a/data/gecko-csb/gecko-csbbioschemas.jsonld +++ b/data/gecko-csb/gecko-csbbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Esteban Pérez-Wohlfeil", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:27116744", "sc:description": "Software aimed at detecting and identifying blocks of large rearrangements taking into account repeats, tandem repeats and duplications, starting with the simple collection of ungapped local alignments produced by GECKO or equivalent software.", "sc:license": "GPL-3.0", "sc:name": "GECKO-CSB", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "uma.es", "sc:url": "http://bitlab-es.com/gecko/template.php#GECKO-CSB", diff --git a/data/gecko-mgv/gecko-mgvbioschemas.jsonld b/data/gecko-mgv/gecko-mgvbioschemas.jsonld index 39ce654f36658..5ef2652445926 100644 --- a/data/gecko-mgv/gecko-mgvbioschemas.jsonld +++ b/data/gecko-mgv/gecko-mgvbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "GECKO-MGV", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "uma.es", diff --git a/data/gecko/geckobioschemas.jsonld b/data/gecko/geckobioschemas.jsonld index 50bfb54b817a1..e0e458de21817 100644 --- a/data/gecko/geckobioschemas.jsonld +++ b/data/gecko/geckobioschemas.jsonld @@ -27,11 +27,11 @@ "@id": "edam:topic_0080" }, "sc:citation": [ - "pubmed:26260162", - "pmcid:PMC4531504", { "@id": "https://doi.org/10.1186/s12859-015-0679-9" - } + }, + "pmcid:PMC4531504", + "pubmed:26260162" ], "sc:description": "Software aimed at pairwise sequence comparison generating high quality results (equivalent to MUMmer) with controlled memory consumption and comparable or faster execution times particularly with long sequences.", "sc:featureList": { diff --git a/data/gecko_conservation/gecko_conservationbioschemas.jsonld b/data/gecko_conservation/gecko_conservationbioschemas.jsonld index 384c022d8994e..9d27ab1164eef 100644 --- a/data/gecko_conservation/gecko_conservationbioschemas.jsonld +++ b/data/gecko_conservation/gecko_conservationbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The software allows for the systematic detection of gene cluster conservation in a large number of genomes. The enhancement over the original Gecko tool is the use of set-distance based gene cluster models that allow for the detection of gene clusters with diverse conservation patterns including gaps and missing genes in cluster occurrences. It is also tolerant of errors in gene homology assignment.", "sc:name": "Gecko", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bibiserv.techfak.uni-bielefeld.de/gecko/" } \ No newline at end of file diff --git a/data/gecont_2/gecont_2bioschemas.jsonld b/data/gecont_2/gecont_2bioschemas.jsonld index 0e440ba4b7ba8..fd42757994389 100644 --- a/data/gecont_2/gecont_2bioschemas.jsonld +++ b/data/gecont_2/gecont_2bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.", "sc:name": "GeConT 2", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://operons.ibt.unam.mx/gctNG/" } \ No newline at end of file diff --git a/data/gecs/gecsbioschemas.jsonld b/data/gecs/gecsbioschemas.jsonld index fc6a568749fef..784d35b1736b7 100644 --- a/data/gecs/gecsbioschemas.jsonld +++ b/data/gecs/gecsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "GECS (Gene Expression to Chemical Structure) is a collection of prediction methods linking genomic or transcriptomic contents of genes to chemical structures of biosynthetic substances. This N-Glycan Prediction Server is based on the repertoire of glycosyltransferases for N-glycan biosynthesis.", "sc:name": "GECS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.genome.jp/tools/gecs" } \ No newline at end of file diff --git a/data/gedevo-m/gedevo-mbioschemas.jsonld b/data/gedevo-m/gedevo-mbioschemas.jsonld index 45cec120b64c8..d2137379313f0 100644 --- a/data/gedevo-m/gedevo-mbioschemas.jsonld +++ b/data/gedevo-m/gedevo-mbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Extension of the idea implemented in GEDEVO to multiple input networks which aims to minimize the sum of GEDs between every pair of input networks.", "sc:name": "GEDEVO-M", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "bmb.sdu.dk", "sc:url": "http://gedevo.compbio.sdu.dk/", diff --git a/data/gedevo/gedevobioschemas.jsonld b/data/gedevo/gedevobioschemas.jsonld index 67f92e892787d..6dad1ec15b90f 100644 --- a/data/gedevo/gedevobioschemas.jsonld +++ b/data/gedevo/gedevobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software tool for solving the network alignment problem. It utilizes the evolutionary computing strategies for solving the so-called Graph Edit Distance problem.", "sc:name": "GEDEVO", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "bmb.sdu.dk", diff --git a/data/geecc/geeccbioschemas.jsonld b/data/geecc/geeccbioschemas.jsonld index c486d147d4623..5dc232b872873 100644 --- a/data/geecc/geeccbioschemas.jsonld +++ b/data/geecc/geeccbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "geecc", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/geecc.html", "sc:version": "1.8.0" diff --git a/data/geecee/geeceebioschemas.jsonld b/data/geecee/geeceebioschemas.jsonld index ff8bc15d26cb2..943417156daa2 100644 --- a/data/geecee/geeceebioschemas.jsonld +++ b/data/geecee/geeceebioschemas.jsonld @@ -13,9 +13,9 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", - "UK MRC", "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:description": "Calculate fractional GC content of nucleic acid sequences.", "sc:funder": [ @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "geecee", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/geist/geistbioschemas.jsonld b/data/geist/geistbioschemas.jsonld index f8295447f4a84..168cb7f3e7308 100644 --- a/data/geist/geistbioschemas.jsonld +++ b/data/geist/geistbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Identify integrations of DNA elements on a genome-wide scale.", "sc:name": "GeIST", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://research.nhgri.nih.gov/software/GeIST/" diff --git a/data/gell/gellbioschemas.jsonld b/data/gell/gellbioschemas.jsonld index 1d218b10f97ed..1a2fe76e144ab 100644 --- a/data/gell/gellbioschemas.jsonld +++ b/data/gell/gellbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "General Likelihood Library for use in phylogenetics. It is intended to provide classes that facilitate investigating new models and techniques.", "sc:name": "GeLL", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://phylo.bio.ku.edu/GeLL/" } \ No newline at end of file diff --git a/data/gelscape_and_gelbank/gelscape_and_gelbankbioschemas.jsonld b/data/gelscape_and_gelbank/gelscape_and_gelbankbioschemas.jsonld index 20d6aedb405dc..225db480df407 100644 --- a/data/gelscape_and_gelbank/gelscape_and_gelbankbioschemas.jsonld +++ b/data/gelscape_and_gelbank/gelscape_and_gelbankbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Platform-independent 1D and 2D gel analysis system that is freely available. Features include the ability to mark spots, to measure spot intensities and to archive gel images and annotations to the public database GelBank. Includes searchable access to GelBank's repository.", "sc:name": "GelScape and GelBank", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.gelscape.ualberta.ca/" } \ No newline at end of file diff --git a/data/gem-trend/gem-trendbioschemas.jsonld b/data/gem-trend/gem-trendbioschemas.jsonld index 4b1dadad6cda4..d00a91775737b 100644 --- a/data/gem-trend/gem-trendbioschemas.jsonld +++ b/data/gem-trend/gem-trendbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data.", "sc:name": "GEM-TREND", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://cgs.pharm.kyoto-u.ac.jp/network/" } \ No newline at end of file diff --git a/data/gem/gembioschemas.jsonld b/data/gem/gembioschemas.jsonld index 78a90cc00e21d..2e0f7cb7947a4 100644 --- a/data/gem/gembioschemas.jsonld +++ b/data/gem/gembioschemas.jsonld @@ -9,54 +9,54 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/bts163", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-0309-6821", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1161-z", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/gem", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Hong Pan", { "@id": "http://orcid.org/0000-0003-0309-6821" - }, - "Hong Pan" + } ], "sc:additionalType": [ "Command-line tool", "Library" ], "sc:citation": [ - "pmcid:PMC3348564", - "pubmed:24626854", - "pubmed:27480116", { "@id": "https://doi.org/10.1186/s12859-016-1161-z" }, - "pubmed:22492648", - "pmcid:PMC4970299", + "pubmed:27480116", + "pmcid:PMC3348564", + "pubmed:24626854", { "@id": "https://doi.org/10.1093/bioinformatics/bts163" - } + }, + "pubmed:22492648", + "pmcid:PMC4970299" ], "sc:description": "Tools for analyzing EWAS, methQTL and GxE genome widely.", "sc:license": "Artistic-2.0", "sc:name": "GEM", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GEM.html", "sc:version": "1.0.0" + }, + { + "@id": "http://orcid.org/0000-0003-0309-6821", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/bts163", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://doi.org/10.1186/s12859-016-1161-z", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gem3/gem3bioschemas.jsonld b/data/gem3/gem3bioschemas.jsonld index 4d6b3bd609e97..8d811c431aeea 100644 --- a/data/gem3/gem3bioschemas.jsonld +++ b/data/gem3/gem3bioschemas.jsonld @@ -13,9 +13,9 @@ "biotools:primaryContact": "Santiago Marco-Sola", "sc:additionalType": "Command-line tool", "sc:author": [ + "Santiago Marco-Sola", "Alejandro Chacon", - "Simon Heath", - "Santiago Marco-Sola" + "Simon Heath" ], "sc:citation": "pubmed:23103880", "sc:contributor": "Paolo Ribeca", @@ -23,8 +23,8 @@ "sc:license": "GPL-3.0", "sc:name": "GEM-Mapper v3", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/smarco/gem3-mapper", "sc:version": "v3.6" diff --git a/data/gemma/gemmabioschemas.jsonld b/data/gemma/gemmabioschemas.jsonld index f10ff48dacac7..9f48bd725bb19 100644 --- a/data/gemma/gemmabioschemas.jsonld +++ b/data/gemma/gemmabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Gemma is an open source database, analysis software system and web site for expression data re-use and meta-analysis. It currently contains analyzed data from over 3300 expression profiling studies, yielding billions of data points that can be searched and explored. Gemma offers web-based access to differential expression results and coexpression data in a meta-analysis framework.", "sc:name": "Gemma", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://chibi.ubc.ca/Gemma" } \ No newline at end of file diff --git a/data/gemmapper/gemmapperbioschemas.jsonld b/data/gemmapper/gemmapperbioschemas.jsonld index 2edbbbf2b850c..3f6b6fc2ef706 100644 --- a/data/gemmapper/gemmapperbioschemas.jsonld +++ b/data/gemmapper/gemmapperbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "The GEM (GEnome Multi-tool) Library (GEM Mapper)", "sc:operatingSystem": "Linux", "sc:provider": [ - "Lab Roderic Guigo Group", - "crg.eu" + "crg.eu", + "Lab Roderic Guigo Group" ], "sc:url": "https://sourceforge.net/projects/gemlibrary/", "sc:version": "1" diff --git a/data/gemmer/gemmerbioschemas.jsonld b/data/gemmer/gemmerbioschemas.jsonld index 178c08471b979..ca85611222fb5 100644 --- a/data/gemmer/gemmerbioschemas.jsonld +++ b/data/gemmer/gemmerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "GEMMER", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://gemmer.barberislab.com" diff --git a/data/gemoma/gemomabioschemas.jsonld b/data/gemoma/gemomabioschemas.jsonld index c13677dc5de77..815d29424d1db 100644 --- a/data/gemoma/gemomabioschemas.jsonld +++ b/data/gemoma/gemomabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GeMoMa", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.jstacs.de/index.php/GeMoMa" } \ No newline at end of file diff --git a/data/gemreads/gemreadsbioschemas.jsonld b/data/gemreads/gemreadsbioschemas.jsonld index 62088ccf36670..e805632fde86d 100644 --- a/data/gemreads/gemreadsbioschemas.jsonld +++ b/data/gemreads/gemreadsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Simulate Illumina and 454 reads.", "sc:name": "gemreads", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://sourceforge.net/projects/gemsim/", "sc:version": "1.6" diff --git a/data/gems/gemsbioschemas.jsonld b/data/gems/gemsbioschemas.jsonld index ace3c0379da31..00e9ee4e119bc 100644 --- a/data/gems/gemsbioschemas.jsonld +++ b/data/gems/gemsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for biclustering microarray data. It is available as a web tool and as a standalone command-line program.", "sc:name": "GEMS", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://genomics10.bu.edu/terrence/gems/" } \ No newline at end of file diff --git a/data/gems_disease/gems_diseasebioschemas.jsonld b/data/gems_disease/gems_diseasebioschemas.jsonld index fa801b30aac30..b5c2d806da196 100644 --- a/data/gems_disease/gems_diseasebioschemas.jsonld +++ b/data/gems_disease/gems_diseasebioschemas.jsonld @@ -25,11 +25,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4458858", + "pubmed:26064082", { "@id": "https://doi.org/10.18637/jss.v064.i10" - }, - "pubmed:26064082", - "pmcid:PMC4458858" + } ], "sc:description": "gems is a tool that simulates disease progression in patients and predicts the effect of different interventions on patient outcome.", "sc:featureList": { diff --git a/data/gemse/gemsebioschemas.jsonld b/data/gemse/gemsebioschemas.jsonld index 9fccd465aade4..bf5a1789bda60 100644 --- a/data/gemse/gemsebioschemas.jsonld +++ b/data/gemse/gemsebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "GeMSE", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.bioinformatics.deib.polimi.it/genomic_computing/GeMSE/" diff --git a/data/gemstone/gemstonebioschemas.jsonld b/data/gemstone/gemstonebioschemas.jsonld index 14c7ef8cca580..bf178e13f75ea 100644 --- a/data/gemstone/gemstonebioschemas.jsonld +++ b/data/gemstone/gemstonebioschemas.jsonld @@ -17,15 +17,15 @@ "@id": "https://bio.tools/gemstone", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Suite", - "Web application" + "Web application", + "Suite" ], "sc:citation": [ + "pmcid:PMC5556704", + "pubmed:28521008", { "@id": "https://doi.org/10.1093/nar/gkx398" - }, - "pubmed:28521008", - "pmcid:PMC5556704" + } ], "sc:description": "Germline Mutation Scoring Tool fOr Next-generation sEquencing data. Cloud-based variant prioritization with high-level customization and a comprehensive collection of bioinformatics tools and data libraries.", "sc:featureList": { diff --git a/data/gemtools/gemtoolsbioschemas.jsonld b/data/gemtools/gemtoolsbioschemas.jsonld index dccdc3bc5c5cd..18aeb39a7acbc 100644 --- a/data/gemtools/gemtoolsbioschemas.jsonld +++ b/data/gemtools/gemtoolsbioschemas.jsonld @@ -21,12 +21,12 @@ "sc:license": "GPL-3.0", "sc:name": "GEM-Tools", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "Lab Roderic Guigo Group", - "crg.eu" + "crg.eu", + "Lab Roderic Guigo Group" ], "sc:url": "https://github.com/gemtools/gemtools", "sc:version": "1.7.1" diff --git a/data/gemtools_ancestry/gemtools_ancestrybioschemas.jsonld b/data/gemtools_ancestry/gemtools_ancestrybioschemas.jsonld index 16e7b1be8b9b9..fed2bd1a1260a 100644 --- a/data/gemtools_ancestry/gemtools_ancestrybioschemas.jsonld +++ b/data/gemtools_ancestry/gemtools_ancestrybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Computationally efficient tools for modeling genetic ancestry based in the SNP information.  GemTools is a package of functions to help the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy.", "sc:name": "GemTools", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.compgen.pitt.edu/GemTools/GEM%20Documentation.pdf" } \ No newline at end of file diff --git a/data/gen3d/gen3dbioschemas.jsonld b/data/gen3d/gen3dbioschemas.jsonld index 3a2bf28a4430f..dbc9dfa4c07fc 100644 --- a/data/gen3d/gen3dbioschemas.jsonld +++ b/data/gen3d/gen3dbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Gen3D", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sourceforge.net/projects/gen3d/" } \ No newline at end of file diff --git a/data/gen3va/gen3vabioschemas.jsonld b/data/gen3va/gen3vabioschemas.jsonld index 1216255259bcd..f98c87095cc2d 100644 --- a/data/gen3va/gen3vabioschemas.jsonld +++ b/data/gen3va/gen3vabioschemas.jsonld @@ -9,42 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-016-1321-1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/gen3va", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Avi Ma’ayan", - "Gregory Gundersen" + "Gregory Gundersen", + "Avi Ma’ayan" ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:27846806", - "pmcid:PMC5111283", { "@id": "https://doi.org/10.1186/S12859-016-1321-1" - } + }, + "pubmed:27846806", + "pmcid:PMC5111283" ], "sc:description": "Aggregation and analysis of gene expression signatures from related studies.", "sc:featureList": [ { - "@id": "edam:operation_0315" + "@id": "edam:operation_0338" }, { - "@id": "edam:operation_0338" + "@id": "edam:operation_0315" } ], "sc:license": "GPL-3.0", "sc:name": "GEN3VA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://amp.pharm.mssm.edu/gen3va/" + }, + { + "@id": "https://doi.org/10.1186/S12859-016-1321-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genabel/genabelbioschemas.jsonld b/data/genabel/genabelbioschemas.jsonld index fc4d14d72b642..cd5fe4dd8556d 100644 --- a/data/genabel/genabelbioschemas.jsonld +++ b/data/genabel/genabelbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "GenABEL project developers", "sc:additionalType": [ - "Library", - "Suite" + "Suite", + "Library" ], "sc:description": "Genome-wide association analysis between quantitative or binary traits and SNPs.", "sc:license": "CC-BY-SA-3.0", "sc:name": "GenABEL", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/GenABEL/index.html" } \ No newline at end of file diff --git a/data/genarise/genarisebioschemas.jsonld b/data/genarise/genarisebioschemas.jsonld index 1eb6eebc44452..7ab2dd42d5113 100644 --- a/data/genarise/genarisebioschemas.jsonld +++ b/data/genarise/genarisebioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Eeasy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.", "sc:name": "genArise", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genArise.html", "sc:version": "1.50.0" diff --git a/data/genatlas/genatlasbioschemas.jsonld b/data/genatlas/genatlasbioschemas.jsonld index 08c6f5182650e..50c04ab537b78 100644 --- a/data/genatlas/genatlasbioschemas.jsonld +++ b/data/genatlas/genatlasbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Information on gene mapping and genetic diseases.", "sc:name": "GenAtlas human gene database", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "UNIVERSITE PARIS DESCARTES", "sc:url": "http://www.dsi.univ-paris5.fr/genatlas/" diff --git a/data/genatlasdb/genatlasdbbioschemas.jsonld b/data/genatlasdb/genatlasdbbioschemas.jsonld index af89df499f3c6..5b0f3632c4ef6 100644 --- a/data/genatlasdb/genatlasdbbioschemas.jsonld +++ b/data/genatlasdb/genatlasdbbioschemas.jsonld @@ -11,23 +11,23 @@ "@id": "https://bio.tools/genatlasdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Alexandra Caude", "Claude Mugnier", - "Martine Lemerrer", "Marie-Liesse Chauvet", - "Alexandra Caude" + "Martine Lemerrer" ], "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": "pubmed:9835018", "sc:description": "The Genatlas database provides information on the structure, expression and function of genes, gene mutations and their consequences on diseases.", "sc:license": "Apache-2.0", "sc:name": "Genatlas", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.genatlas.org" } \ No newline at end of file diff --git a/data/genbank/genbankbioschemas.jsonld b/data/genbank/genbankbioschemas.jsonld index 07a9a24f690e9..c8cea671e3a03 100644 --- a/data/genbank/genbankbioschemas.jsonld +++ b/data/genbank/genbankbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A comprehensive database of public nucleotide sequences for more than 300 000 organisms named, from small and large-scale sequencing projects. Data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage.", "sc:name": "GenBank nucleotide sequence database", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "NCBI", "sc:url": "http://www.ncbi.nlm.nih.gov/" diff --git a/data/genbank2gff3/genbank2gff3bioschemas.jsonld b/data/genbank2gff3/genbank2gff3bioschemas.jsonld index 72d6fed4c4ab0..f7b03938bb650 100644 --- a/data/genbank2gff3/genbank2gff3bioschemas.jsonld +++ b/data/genbank2gff3/genbank2gff3bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Convert a GenBank, EMBL or UniProt file into a GFF file.", "sc:name": "genbank2gff3", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/genbankconverters/genbank2GFF3/0.0.3", "sc:version": "0.0.3" diff --git a/data/genbank_to_gene/genbank_to_genebioschemas.jsonld b/data/genbank_to_gene/genbank_to_genebioschemas.jsonld index 85e22a0b54888..ad5ed0adc50af 100644 --- a/data/genbank_to_gene/genbank_to_genebioschemas.jsonld +++ b/data/genbank_to_gene/genbank_to_genebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Convert a Genbank file into the .ffn (gene) file.", "sc:name": "genbank_to_gene", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/genbank_to_gene/genbank_to_gene/0.0.2", "sc:version": "0.0.2" diff --git a/data/genbankr/bioconda_genbankr.yaml b/data/genbankr/bioconda_genbankr.yaml index 10242b77b4e6f..821d9ff871b1c 100644 --- a/data/genbankr/bioconda_genbankr.yaml +++ b/data/genbankr/bioconda_genbankr.yaml @@ -3,7 +3,6 @@ description: Reads Genbank files. home: https://bioconductor.org/packages/3.10/bioc/html/genbankr.html identifiers: - biotools:genbankr -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genbankr summary: Parsing GenBank files into semantically useful objects diff --git a/data/genbankr/genbankrbioschemas.jsonld b/data/genbankr/genbankrbioschemas.jsonld index 8f2068371dd15..62c21a00bdab3 100644 --- a/data/genbankr/genbankrbioschemas.jsonld +++ b/data/genbankr/genbankrbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Gabriel Becker", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Reads Genbank files.", "sc:license": "Artistic-2.0", "sc:name": "genbankr", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genbankr.html", "sc:version": "1.2.0" diff --git a/data/genclip/genclipbioschemas.jsonld b/data/genclip/genclipbioschemas.jsonld index c5d36acb5c012..cd377a95570e6 100644 --- a/data/genclip/genclipbioschemas.jsonld +++ b/data/genclip/genclipbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Literature mining tool that can cluster a list of genes with keywords that are auto-extracted from their up-to-date related literature and then manually curated by the user. It can also generate a group of negative control genes and a group of positive control genes for comparing the cluster results with the analyzed genes to filter out un-specific keywords.", "sc:name": "GenCLiP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://ci.smu.edu.cn" } \ No newline at end of file diff --git a/data/genclust/genclustbioschemas.jsonld b/data/genclust/genclustbioschemas.jsonld index f435148d2605a..177527bd2fa5b 100644 --- a/data/genclust/genclustbioschemas.jsonld +++ b/data/genclust/genclustbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "New genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, compact and easy to update; (b) it can be used naturally in conjunction with data driven internal validation methods.", "sc:name": "GenClust", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.math.unipa.it/~lobosco/genclust/" } \ No newline at end of file diff --git a/data/gencode/gencodebioschemas.jsonld b/data/gencode/gencodebioschemas.jsonld index b34caf7fccc60..8f9e5b854297d 100644 --- a/data/gencode/gencodebioschemas.jsonld +++ b/data/gencode/gencodebioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/GENCODE", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": "pubmed:30357393", "sc:description": "Consortium identifying and classifying all gene features in the human and mouse genomes with high accuracy based on biological evidence, and releasing these annotations for the benefit of biomedical research and genome interpretation.", "sc:license": "Other", "sc:name": "GENCODE", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.gencodegenes.org/" } \ No newline at end of file diff --git a/data/gendbe/gendbebioschemas.jsonld b/data/gendbe/gendbebioschemas.jsonld index 7e0ba6d9ea579..c5f0bfee1b9c4 100644 --- a/data/gendbe/gendbebioschemas.jsonld +++ b/data/gendbe/gendbebioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-2755-6458", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0085568", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gendbe", "@type": "sc:SoftwareApplication", @@ -50,14 +58,6 @@ }, "sc:url": "https://gendbe.computational.bio.uni-giessen.de", "sc:version": "2.4" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0085568", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-2755-6458", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/gendoo/gendoobioschemas.jsonld b/data/gendoo/gendoobioschemas.jsonld index 5f29b81b9afc7..9ee889451bc07 100644 --- a/data/gendoo/gendoobioschemas.jsonld +++ b/data/gendoo/gendoobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.", "sc:name": "Gendoo", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://gendoo.dbcls.jp" } \ No newline at end of file diff --git a/data/gene-clic/gene-clicbioschemas.jsonld b/data/gene-clic/gene-clicbioschemas.jsonld index 5e22b3ca12680..355c5440a558a 100644 --- a/data/gene-clic/gene-clicbioschemas.jsonld +++ b/data/gene-clic/gene-clicbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/gene-clic", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jun S. Liu", + "Sarah E. Calvo", "Vamsi K. Mootha", - "Sarah E. Calvo" + "Jun S. Liu" ], "sc:additionalType": "Command-line tool", "sc:description": "Computational tool for helping users identify new members of a pathway of interest, as well as the RNA expression datasets in which that pathway is relevant.", "sc:name": "CLIC (Clustering by Inferred Co-expression)", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.gene-clic.org/" } \ No newline at end of file diff --git a/data/gene-counter/gene-counterbioschemas.jsonld b/data/gene-counter/gene-counterbioschemas.jsonld index d2275c0176baf..89911595787a4 100644 --- a/data/gene-counter/gene-counterbioschemas.jsonld +++ b/data/gene-counter/gene-counterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression.", "sc:name": "GENE-Counter", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/genecounter/" } \ No newline at end of file diff --git a/data/gene2drug/gene2drugbioschemas.jsonld b/data/gene2drug/gene2drugbioschemas.jsonld index 113b1ccd96a3f..e9ebc7c143b2e 100644 --- a/data/gene2drug/gene2drugbioschemas.jsonld +++ b/data/gene2drug/gene2drugbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Computational tool for pathway-based rational drug repositioning.", "sc:name": "Gene2drug", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://gene2drug.tigem.it/" } \ No newline at end of file diff --git a/data/gene2oligo/gene2oligobioschemas.jsonld b/data/gene2oligo/gene2oligobioschemas.jsonld index a9a36cf61e535..3df82ab7c53f0 100644 --- a/data/gene2oligo/gene2oligobioschemas.jsonld +++ b/data/gene2oligo/gene2oligobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Gene2Oligo", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://berry.engin.umich.edu/gene2oligo/" } \ No newline at end of file diff --git a/data/gene2vec/gene2vecbioschemas.jsonld b/data/gene2vec/gene2vecbioschemas.jsonld index e2cf684f7eca9..c92e8a60aec79 100644 --- a/data/gene2vec/gene2vecbioschemas.jsonld +++ b/data/gene2vec/gene2vecbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12864-018-5370-x", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Gene2vec", "@type": "sc:SoftwareApplication", @@ -36,14 +40,10 @@ "sc:license": "MIT", "sc:name": "Gene2vec", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/jingcheng-du/Gene2vec" - }, - { - "@id": "https://doi.org/10.1186/s12864-018-5370-x", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gene_array_analyzer/gene_array_analyzerbioschemas.jsonld b/data/gene_array_analyzer/gene_array_analyzerbioschemas.jsonld index faafead4cf435..cd25e25e4e50e 100644 --- a/data/gene_array_analyzer/gene_array_analyzerbioschemas.jsonld +++ b/data/gene_array_analyzer/gene_array_analyzerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Gene Array Analyzer (GAA) allow to process CEL files from GeneChip�� Gene 1.0 ST Arrays. Various processing steps and visualizations are implemented to identify alternative splicing events. Three simple steps have to be performed to submit a set of CEL files. After the processing is completed the results can be viewed in the browser.", "sc:name": "Gene Array Analyzer", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://gaa.mpi-bn.mpg.de" } \ No newline at end of file diff --git a/data/gene_expression/gene_expressionbioschemas.jsonld b/data/gene_expression/gene_expressionbioschemas.jsonld index 6ec5ca1b6d2a4..2e09e9818138a 100644 --- a/data/gene_expression/gene_expressionbioschemas.jsonld +++ b/data/gene_expression/gene_expressionbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "See if you can generate and collect three types of protein, then move on to explore the factors that affect protein synthesis in a cell.", "sc:name": "Gene Expression", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://phet.colorado.edu/en/simulation/gene-expression-basics" } \ No newline at end of file diff --git a/data/gene_expression_atlas/gene_expression_atlasbioschemas.jsonld b/data/gene_expression_atlas/gene_expression_atlasbioschemas.jsonld index 68fa3d130b309..bc9aa478f2672 100644 --- a/data/gene_expression_atlas/gene_expression_atlasbioschemas.jsonld +++ b/data/gene_expression_atlas/gene_expression_atlasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.", "sc:name": "Gene Expression Atlas", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.ebi.ac.uk/gxa/" } \ No newline at end of file diff --git a/data/gene_expression_barcode/gene_expression_barcodebioschemas.jsonld b/data/gene_expression_barcode/gene_expression_barcodebioschemas.jsonld index 5fdd0b9c0da29..ed643e9b31c05 100644 --- a/data/gene_expression_barcode/gene_expression_barcodebioschemas.jsonld +++ b/data/gene_expression_barcode/gene_expression_barcodebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database that provides reliable absolute measures of expression for most annotated genes for human and mouse tissue types, including diseased tissue. This is made possible by an algorithm that leverages information from the GEO and ArrayExpress public repositories to build statistical models that permit converting data from a single microarray into expressed/unexpressed calls for each gene. For selected platforms, users may upload data and obtain results.", "sc:name": "Gene Expression Barcode", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://barcode.luhs.org/" } \ No newline at end of file diff --git a/data/gene_graphics/gene_graphicsbioschemas.jsonld b/data/gene_graphics/gene_graphicsbioschemas.jsonld index 710071a5b3645..72ad02bfe8b77 100644 --- a/data/gene_graphics/gene_graphicsbioschemas.jsonld +++ b/data/gene_graphics/gene_graphicsbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/gene_graphics", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rémi Zallot", - "Katherine J Harrison" + "Katherine J Harrison", + "Rémi Zallot" ], "sc:additionalType": "Web application", "sc:description": "Genomic neighborhood data visualization web application.", "sc:name": "Gene Graphics", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://katlabs.cc/genegraphics/" } \ No newline at end of file diff --git a/data/gene_machine/gene_machinebioschemas.jsonld b/data/gene_machine/gene_machinebioschemas.jsonld index 7b73a901e0409..768d8956f4dfd 100644 --- a/data/gene_machine/gene_machinebioschemas.jsonld +++ b/data/gene_machine/gene_machinebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Gene Machine", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://phet.colorado.edu/en/simulation/gene-machine-lac-operon" } \ No newline at end of file diff --git a/data/gene_sculpt_suite/gene_sculpt_suitebioschemas.jsonld b/data/gene_sculpt_suite/gene_sculpt_suitebioschemas.jsonld index 8c8f2a0939264..0cac246c76908 100644 --- a/data/gene_sculpt_suite/gene_sculpt_suitebioschemas.jsonld +++ b/data/gene_sculpt_suite/gene_sculpt_suitebioschemas.jsonld @@ -9,33 +9,33 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-5930-4111", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/Gene_Sculpt_Suite", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jeffrey J. Essner", { "@id": "https://orcid.org/0000-0001-5930-4111" }, - "Stephen C. Ekker" + "Stephen C. Ekker", + "Jeffrey J. Essner" ], "sc:additionalType": [ - "Web application", - "Suite" + "Suite", + "Web application" ], "sc:description": "Set of tools for assisting in highly precise genome editing and engineering.", "sc:license": "GPL-3.0", "sc:name": "Gene Sculpt Suite", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.genesculpt.org" + }, + { + "@id": "https://orcid.org/0000-0001-5930-4111", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/gene_set_builder/gene_set_builderbioschemas.jsonld b/data/gene_set_builder/gene_set_builderbioschemas.jsonld index 6863fb9d9c352..3a10ba57fdfc6 100644 --- a/data/gene_set_builder/gene_set_builderbioschemas.jsonld +++ b/data/gene_set_builder/gene_set_builderbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access.", "sc:name": "Gene Set Builder", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.cisreg.ca/gsb/" } \ No newline at end of file diff --git a/data/gene_set_to_diseases/gene_set_to_diseasesbioschemas.jsonld b/data/gene_set_to_diseases/gene_set_to_diseasesbioschemas.jsonld index 8343561edcd80..bf4e5cc8c8153 100644 --- a/data/gene_set_to_diseases/gene_set_to_diseasesbioschemas.jsonld +++ b/data/gene_set_to_diseases/gene_set_to_diseasesbioschemas.jsonld @@ -12,14 +12,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jean Fred Fontaine", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:description": "Disease enrichment analysis on gene sets.", "sc:name": "Gene set to diseases", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://cbdm.uni-mainz.de/geneset2diseases" diff --git a/data/gene_stacker/gene_stackerbioschemas.jsonld b/data/gene_stacker/gene_stackerbioschemas.jsonld index dfd16b94fdf82..998372995f0d1 100644 --- a/data/gene_stacker/gene_stackerbioschemas.jsonld +++ b/data/gene_stacker/gene_stackerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/gene_stacker", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Open source tool for marker-assisted gene pyramiding.", "sc:license": "Apache-2.0", diff --git a/data/geneanswers/geneanswersbioschemas.jsonld b/data/geneanswers/geneanswersbioschemas.jsonld index c22401bfc230a..dd45a2e6eff3b 100644 --- a/data/geneanswers/geneanswersbioschemas.jsonld +++ b/data/geneanswers/geneanswersbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/geneanswers", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lei Huang", - "Gang Feng" + "Gang Feng", + "Lei Huang" ], "sc:additionalType": [ "Command-line tool", @@ -22,9 +22,9 @@ "sc:license": "GPL-2.0", "sc:name": "GeneAnswers", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneAnswers.html", "sc:version": "2.16.0" diff --git a/data/genease/geneasebioschemas.jsonld b/data/genease/geneasebioschemas.jsonld index e6d6ae99d98d9..a1cd270dad141 100644 --- a/data/genease/geneasebioschemas.jsonld +++ b/data/genease/geneasebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization.", "sc:name": "GENEASE", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://research.cchmc.org/mershalab/GENEASE/login.html" } \ No newline at end of file diff --git a/data/geneattribution/geneattributionbioschemas.jsonld b/data/geneattribution/geneattributionbioschemas.jsonld index c4e366429b442..9c1b3f2bd4891 100644 --- a/data/geneattribution/geneattributionbioschemas.jsonld +++ b/data/geneattribution/geneattributionbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "geneAttribution", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/geneAttribution.html", "sc:version": "1.0.0" diff --git a/data/genebase/genebasebioschemas.jsonld b/data/genebase/genebasebioschemas.jsonld index 136a3c234e482..41148a3681200 100644 --- a/data/genebase/genebasebioschemas.jsonld +++ b/data/genebase/genebasebioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Maria Chiara Pelleri", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:28025344", { "@id": "https://doi.org/10.1093/database/baw153" }, - "pubmed:28025344", "pmcid:PMC5199132" ], "sc:contributor": { diff --git a/data/genebreak/genebreakbioschemas.jsonld b/data/genebreak/genebreakbioschemas.jsonld index bc141e7af8a46..1ed60ecc6ce8d 100644 --- a/data/genebreak/genebreakbioschemas.jsonld +++ b/data/genebreak/genebreakbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Evert van den Broek", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Recurrent breakpoint gene detection on copy number aberration profiles.", "sc:license": "GPL-2.0", "sc:name": "GeneBreak", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneBreak.html", "sc:version": "1.4.0" diff --git a/data/genecards/genecardsbioschemas.jsonld b/data/genecards/genecardsbioschemas.jsonld index 76880e1c11cf9..e8ba29ca501bb 100644 --- a/data/genecards/genecardsbioschemas.jsonld +++ b/data/genecards/genecardsbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "GeneCards", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.genecards.org/" } \ No newline at end of file diff --git a/data/genecite/genecitebioschemas.jsonld b/data/genecite/genecitebioschemas.jsonld index 75707b0066472..3c2de7c646b5d 100644 --- a/data/genecite/genecitebioschemas.jsonld +++ b/data/genecite/genecitebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Generalized query application that allows you to specify sophisticated sets of queries and generates a table of the number of bio-related records found for each query. The table can be presented as a Web page or in a standard spreadsheet format that will allow you to view the full output of only those queries that generate an interesting number of records.", "sc:name": "GeneCite", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.bioinformatics.org/wrair/" } \ No newline at end of file diff --git a/data/geneck/geneckbioschemas.jsonld b/data/geneck/geneckbioschemas.jsonld index 4a1e3b2ab4137..d103e209a40ef 100644 --- a/data/geneck/geneckbioschemas.jsonld +++ b/data/geneck/geneckbioschemas.jsonld @@ -15,26 +15,26 @@ "biotools:primaryContact": "Minzhe Zhang", "sc:additionalType": "Web service", "sc:citation": [ + "pmcid:PMC6323745", { "@id": "https://doi.org/10.1186/s12859-018-2560-0" }, - "pubmed:30616521", - "pmcid:PMC6323745" + "pubmed:30616521" ], "sc:description": "GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information.", "sc:featureList": [ { - "@id": "edam:operation_1781" + "@id": "edam:operation_0277" }, { - "@id": "edam:operation_0277" + "@id": "edam:operation_1781" } ], "sc:license": "GPL-3.0", "sc:name": "GeNeCK", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://lce.biohpc.swmed.edu/geneck", diff --git a/data/geneclassifiers/geneclassifiersbioschemas.jsonld b/data/geneclassifiers/geneclassifiersbioschemas.jsonld index 745a57823b87a..875ee002b0e15 100644 --- a/data/geneclassifiers/geneclassifiersbioschemas.jsonld +++ b/data/geneclassifiers/geneclassifiersbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "geneClassifiers", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/geneClassifiers.html", diff --git a/data/geneclust/geneclustbioschemas.jsonld b/data/geneclust/geneclustbioschemas.jsonld index e07c1e62f0244..082e4618f5d7e 100644 --- a/data/geneclust/geneclustbioschemas.jsonld +++ b/data/geneclust/geneclustbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Kim-Anh Do", - "Paul Roebuck", + "Bradley Broom", "Rumiana Nikolova", - "Bradley Broom" + "Paul Roebuck" ], "sc:additionalType": "Library", "sc:citation": "pubmed:19390667", diff --git a/data/genecodis3/genecodis3bioschemas.jsonld b/data/genecodis3/genecodis3bioschemas.jsonld index efc14740e56e8..147f4802a9657 100644 --- a/data/genecodis3/genecodis3bioschemas.jsonld +++ b/data/genecodis3/genecodis3bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations. Noisy and redundant output data has been removed from enrichment results, and greater comparative analyses are possible.", "sc:name": "GeneCodis3", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://genecodis.cnb.csic.es/" } \ No newline at end of file diff --git a/data/genedb/genedbbioschemas.jsonld b/data/genedb/genedbbioschemas.jsonld index a4a92152e0361..9e8d71c00786f 100644 --- a/data/genedb/genedbbioschemas.jsonld +++ b/data/genedb/genedbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Sequence data and annotation/curation for the whole range of organisms sequenced by the PSU (Sanger Institute Pathogen Sequencing Units).", "sc:name": "GeneDB database", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "Sanger Institute", "sc:url": "http://www.genedb.org/" diff --git a/data/genedistiller/genedistillerbioschemas.jsonld b/data/genedistiller/genedistillerbioschemas.jsonld index 3e42ad13934bf..e96e9e604ea38 100644 --- a/data/genedistiller/genedistillerbioschemas.jsonld +++ b/data/genedistiller/genedistillerbioschemas.jsonld @@ -19,10 +19,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC2587712", + "pubmed:19057649", { "@id": "https://doi.org/10.1371/journal.pone.0003874" - }, - "pubmed:19057649" + } ], "sc:description": "Provides knowledge-driven, fully interactive and intuitive access to multiple data sources. It displays maximum relevant information, while saving the user from drowning in the flood of data. Thus, allowing an interactive and explorative approach to the hunt for the candidate gene.", "sc:featureList": [ @@ -35,9 +35,9 @@ ], "sc:name": "GeneDistiller", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.genedistiller.org" } diff --git a/data/geneexprdataanalyzer/geneexprdataanalyzerbioschemas.jsonld b/data/geneexprdataanalyzer/geneexprdataanalyzerbioschemas.jsonld index bf34f6a75a64c..49a3095c6247f 100644 --- a/data/geneexprdataanalyzer/geneexprdataanalyzerbioschemas.jsonld +++ b/data/geneexprdataanalyzer/geneexprdataanalyzerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization.", "sc:name": "Gene Expression Data Analyzer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinformatics.upmc.edu/GE2/GEDA.html" } \ No newline at end of file diff --git a/data/geneexpressionsignature/geneexpressionsignaturebioschemas.jsonld b/data/geneexpressionsignature/geneexpressionsignaturebioschemas.jsonld index bf8b6a9aa098c..f2c65825801ff 100644 --- a/data/geneexpressionsignature/geneexpressionsignaturebioschemas.jsonld +++ b/data/geneexpressionsignature/geneexpressionsignaturebioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/geneexpressionsignature", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lu Han", "Yang Cao", - "Fei Li" + "Fei Li", + "Lu Han" ], "sc:additionalType": [ "Library", diff --git a/data/genefas/genefasbioschemas.jsonld b/data/genefas/genefasbioschemas.jsonld index 13ec490ee7f6f..da3922027c48a 100644 --- a/data/genefas/genefasbioschemas.jsonld +++ b/data/genefas/genefasbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Java based graphical user interface for prediction of gene function using multiple sources of data.", "sc:name": "GeneFAS", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://digbio.missouri.edu/software/genefas/" } \ No newline at end of file diff --git a/data/genefilter/bioconda_genefilter.yaml b/data/genefilter/bioconda_genefilter.yaml index b9fd7945a6e72..f344bc13d0f14 100644 --- a/data/genefilter/bioconda_genefilter.yaml +++ b/data/genefilter/bioconda_genefilter.yaml @@ -3,7 +3,6 @@ description: Some basic functions for filtering genes. home: https://bioconductor.org/packages/3.10/bioc/html/genefilter.html identifiers: - biotools:genefilter -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genefilter summary: 'genefilter: methods for filtering genes from high-throughput experiments' diff --git a/data/genefilter/genefilterbioschemas.jsonld b/data/genefilter/genefilterbioschemas.jsonld index 46a40edb12c7a..5c446c82d5d23 100644 --- a/data/genefilter/genefilterbioschemas.jsonld +++ b/data/genefilter/genefilterbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Some basic functions for filtering genes.", "sc:license": "Artistic-2.0", "sc:name": "genefilter", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genefilter.html", "sc:version": "1.56.0" diff --git a/data/genefisher/genefisherbioschemas.jsonld b/data/genefisher/genefisherbioschemas.jsonld index 9f19ff8e808c3..27f244dde3518 100644 --- a/data/genefisher/genefisherbioschemas.jsonld +++ b/data/genefisher/genefisherbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Genefisher", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bibiserv.techfak.uni-bielefeld.de/genefisher/" } \ No newline at end of file diff --git a/data/genefisher2/genefisher2bioschemas.jsonld b/data/genefisher2/genefisher2bioschemas.jsonld index f1897bb31d24e..245855c4c095f 100644 --- a/data/genefisher2/genefisher2bioschemas.jsonld +++ b/data/genefisher2/genefisher2bioschemas.jsonld @@ -11,27 +11,27 @@ "@id": "https://bio.tools/genefisher2", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", "Web application", - "Web API" + "Web API", + "Command-line tool" ], "sc:author": [ - "Daniel Hagemeier", "Thomas Gatter", - "Chris Schleiermacher" + "Chris Schleiermacher", + "Daniel Hagemeier" ], "sc:citation": "pubmed:8877506", "sc:description": "Based on the assumption that genes with related function from different organisms show high sequence similarity, degenerate primers can be designed from sequences of homologues genes. It is an interactive web-based program for designing degenerate primers.", "sc:name": "genefisher2", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ + "CeBiTec", "BiBiServ", - "Bielefeld University", - "CeBiTec" + "Bielefeld University" ], "sc:url": "http://bibiserv.cebitec.uni-bielefeld.de/genefisher2", "sc:version": "1" diff --git a/data/genefu/genefubioschemas.jsonld b/data/genefu/genefubioschemas.jsonld index b6445fa954284..19fadc55e1534 100644 --- a/data/genefu/genefubioschemas.jsonld +++ b/data/genefu/genefubioschemas.jsonld @@ -24,8 +24,8 @@ "sc:license": "Artistic-2.0", "sc:name": "genefu", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genefu.html", diff --git a/data/genega/genegabioschemas.jsonld b/data/genega/genegabioschemas.jsonld index add70df5d5ea3..7b04bc586178b 100644 --- a/data/genega/genegabioschemas.jsonld +++ b/data/genega/genegabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "GeneGA", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneGA.html", "sc:version": "1.24.0" diff --git a/data/genegeneinter/genegeneinterbioschemas.jsonld b/data/genegeneinter/genegeneinterbioschemas.jsonld index ff7b10be5dd68..858a7f1e0d87d 100644 --- a/data/genegeneinter/genegeneinterbioschemas.jsonld +++ b/data/genegeneinter/genegeneinterbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/genegeneinter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Magalie Houee-Bigot", - "Mathieu Emily" + "Mathieu Emily", + "Magalie Houee-Bigot" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results.", "sc:license": "GPL-2.0", "sc:name": "GeneGeneInteR", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneGeneInteR.html", "sc:version": "1.0.0" diff --git a/data/genegenie/genegeniebioschemas.jsonld b/data/genegenie/genegeniebioschemas.jsonld index cf5349ba73a2d..4edb46f976c39 100644 --- a/data/genegenie/genegeniebioschemas.jsonld +++ b/data/genegenie/genegeniebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "GeneGenie is an optimised oligomer design web server for doing directed evolution.", "sc:name": "GeneGenie", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://g.gene-genie.appspot.com" diff --git a/data/genehummus/genehummusbioschemas.jsonld b/data/genehummus/genehummusbioschemas.jsonld index 905cb98ca3e1c..8c02fd8c6cbd1 100644 --- a/data/genehummus/genehummusbioschemas.jsonld +++ b/data/genehummus/genehummusbioschemas.jsonld @@ -9,29 +9,25 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12864-019-5952-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/geneHummus", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jose V. Die", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6639926", "pubmed:31319791", { "@id": "https://doi.org/10.1186/s12864-019-5952-2" - } + }, + "pmcid:PMC6639926" ], "sc:description": "R package to define gene families and their expression in legumes and beyond.", "sc:featureList": [ { - "@id": "edam:operation_0553" + "@id": "edam:operation_3478" }, { - "@id": "edam:operation_3478" + "@id": "edam:operation_0553" }, { "@id": "edam:operation_0552" @@ -45,6 +41,10 @@ ], "sc:url": "https://cran.r-project.org/package=geneHummus", "sc:version": "1.0.11" + }, + { + "@id": "https://doi.org/10.1186/s12864-019-5952-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/geneid/geneidbioschemas.jsonld b/data/geneid/geneidbioschemas.jsonld index edac80611e8ee..2d760a8c49a7d 100644 --- a/data/geneid/geneidbioschemas.jsonld +++ b/data/geneid/geneidbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-6261-7370", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/geneid", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Francisco Camara", - "Support" + "Support", + "Francisco Camara" ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": "Roderic Guigo", "sc:citation": "pubmed:18428791", @@ -33,16 +37,12 @@ "sc:name": "Geneid", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "Centre for Genomic Regulation (CRG), Parc de Recerca Biomedica (PRBB)", "sc:url": "http://genome.crg.es/software/geneid/index.html", "sc:version": "1.4.4" - }, - { - "@id": "http://orcid.org/0000-0001-6261-7370", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/geneimprint/geneimprintbioschemas.jsonld b/data/geneimprint/geneimprintbioschemas.jsonld index 853340ffb5e0f..9a8c892608b3d 100644 --- a/data/geneimprint/geneimprintbioschemas.jsonld +++ b/data/geneimprint/geneimprintbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr. Randy L. Jirtle", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": "pubmed:10094809", "sc:description": "Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed.", "sc:name": "Geneimprint", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.geneimprint.com/site/genes-by-species" } \ No newline at end of file diff --git a/data/geneious/geneiousbioschemas.jsonld b/data/geneious/geneiousbioschemas.jsonld index a30b6a3735b46..d47b679ad2cea 100644 --- a/data/geneious/geneiousbioschemas.jsonld +++ b/data/geneious/geneiousbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research.", "sc:name": "Geneious", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.geneious.com" } \ No newline at end of file diff --git a/data/genemania/genemaniabioschemas.jsonld b/data/genemania/genemaniabioschemas.jsonld index 6a96c2877b4f1..a1f695b0f7947 100644 --- a/data/genemania/genemaniabioschemas.jsonld +++ b/data/genemania/genemaniabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.", "sc:name": "GeneMANIA", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.genemania.org" diff --git a/data/genemark/genemarkbioschemas.jsonld b/data/genemark/genemarkbioschemas.jsonld index b8de3ce595de7..18d491fd6cce0 100644 --- a/data/genemark/genemarkbioschemas.jsonld +++ b/data/genemark/genemarkbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/genemark", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Suite", - "Web application" + "Web application", + "Suite" ], "sc:description": "A family of gene prediction programs: Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes; Gene Prediction in Eukaryotes; Gene Prediction in Transcripts; Gene Prediction in Viruses, Phages and Plasmids.", "sc:name": "GeneMark", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://exon.gatech.edu/GeneMark/" } \ No newline at end of file diff --git a/data/genematcher/genematcherbioschemas.jsonld b/data/genematcher/genematcherbioschemas.jsonld index fa5b332d81cbd..b9340f331280e 100644 --- a/data/genematcher/genematcherbioschemas.jsonld +++ b/data/genematcher/genematcherbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web site designed to enable connections between clinicians and researchers from around the world who share an interest in the same gene or genes.", "sc:name": "GeneMatcher", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://www.genematcher.org/" } \ No newline at end of file diff --git a/data/genemeta/bioconda_genemeta.yaml b/data/genemeta/bioconda_genemeta.yaml index ca5e52298701d..53c7964ebff1f 100644 --- a/data/genemeta/bioconda_genemeta.yaml +++ b/data/genemeta/bioconda_genemeta.yaml @@ -4,7 +4,6 @@ description: A collection of meta-analysis tools for analysing high throughput e home: https://bioconductor.org/packages/3.10/bioc/html/GeneMeta.html identifiers: - biotools:genemeta -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genemeta summary: MetaAnalysis for High Throughput Experiments diff --git a/data/genemeta/genemetabioschemas.jsonld b/data/genemeta/genemetabioschemas.jsonld index 448ef9e56448d..9012fc2b2c045 100644 --- a/data/genemeta/genemetabioschemas.jsonld +++ b/data/genemeta/genemetabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A collection of meta-analysis tools for analysing high throughput experimental data.", "sc:license": "Artistic-2.0", "sc:name": "GeneMeta", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneMeta.html", "sc:version": "1.46.0" diff --git a/data/genenet/genenetbioschemas.jsonld b/data/genenet/genenetbioschemas.jsonld index c2b171650cbce..fa92eee988d25 100644 --- a/data/genenet/genenetbioschemas.jsonld +++ b/data/genenet/genenetbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GeneNet", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://strimmerlab.org/software/genenet/index.html" } \ No newline at end of file diff --git a/data/genenet_toolbox/genenet_toolboxbioschemas.jsonld b/data/genenet_toolbox/genenet_toolboxbioschemas.jsonld index 8a52db70766ea..81086bd16aea2 100644 --- a/data/genenet_toolbox/genenet_toolboxbioschemas.jsonld +++ b/data/genenet_toolbox/genenet_toolboxbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "GeneNet Toolbox", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://avigailtaylor.github.io/gntat14/" } \ No newline at end of file diff --git a/data/genenetval/genenetvalbioschemas.jsonld b/data/genenetval/genenetvalbioschemas.jsonld index da316a21653bf..93c9dbc7ba2cf 100644 --- a/data/genenetval/genenetvalbioschemas.jsonld +++ b/data/genenetval/genenetvalbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Java application for network analysis. The application uses the metabolic pathways stored in kegg to rate the validity of an input network.", "sc:name": "GeneNetVal", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://fgomezvela.github.io/GeneNetVal/" } \ No newline at end of file diff --git a/data/genenetworkbuilder/genenetworkbuilderbioschemas.jsonld b/data/genenetworkbuilder/genenetworkbuilderbioschemas.jsonld index a2ccd71aae696..a227ee9c59ead 100644 --- a/data/genenetworkbuilder/genenetworkbuilderbioschemas.jsonld +++ b/data/genenetworkbuilder/genenetworkbuilderbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "GeneNetworkBuilder", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneNetworkBuilder.html", "sc:version": "1.16.0" diff --git a/data/geneoverlap/geneoverlapbioschemas.jsonld b/data/geneoverlap/geneoverlapbioschemas.jsonld index 9776ba2d06197..8dc42c13213a1 100644 --- a/data/geneoverlap/geneoverlapbioschemas.jsonld +++ b/data/geneoverlap/geneoverlapbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "GeneOverlap", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneOverlap.html", "sc:version": "1.10.0" diff --git a/data/genepainter/genepainterbioschemas.jsonld b/data/genepainter/genepainterbioschemas.jsonld index 7baddbad509a7..e0d9b21bd4531 100644 --- a/data/genepainter/genepainterbioschemas.jsonld +++ b/data/genepainter/genepainterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Standalone tool for mapping gene structures onto protein multiple sequence alignments (MSA). Gene structures, as provided by WebScipio, are aligned with respect to the exact positions of the introns (down to nucleotide level) and intron phase. Output can be viewed in various formats, ranging from plain text to graphical output formats.", "sc:name": "GenePainter", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.motorprotein.de/genepainter.html" } \ No newline at end of file diff --git a/data/genepalette/genepalettebioschemas.jsonld b/data/genepalette/genepalettebioschemas.jsonld index 3b2d4fb654c25..7a918662b70ba 100644 --- a/data/genepalette/genepalettebioschemas.jsonld +++ b/data/genepalette/genepalettebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Genome sequence visualization and navigation. Users can download from NCBI’s GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites, etc. can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization.", "sc:name": "GenePalette", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.genepalette.org" } \ No newline at end of file diff --git a/data/genepattern/genepatternbioschemas.jsonld b/data/genepattern/genepatternbioschemas.jsonld index bc5a8c5562a0b..87baa62863728 100644 --- a/data/genepattern/genepatternbioschemas.jsonld +++ b/data/genepattern/genepatternbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/genepattern", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Workbench" + "Workbench", + "Web application" ], "sc:citation": "pubmed:16857664", "sc:description": "GenePattern provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis.", "sc:license": "Proprietary", "sc:name": "GenePattern", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.broad.mit.edu/cancer/software/genepattern/download/" } \ No newline at end of file diff --git a/data/genepattern_notebook/genepattern_notebookbioschemas.jsonld b/data/genepattern_notebook/genepattern_notebookbioschemas.jsonld index ca959a5e7fcee..225c51dddbdeb 100644 --- a/data/genepattern_notebook/genepattern_notebookbioschemas.jsonld +++ b/data/genepattern_notebook/genepattern_notebookbioschemas.jsonld @@ -9,12 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-9926-5209", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.12688/F1000RESEARCH.16338.1", "@type": "sc:CreativeWork" }, { - "@id": "https://orcid.org/0000-0001-9926-5209", + "@id": "https://orcid.org/0000-0002-8718-8848", "@type": "schema:Person" }, { @@ -31,35 +35,31 @@ "sc:additionalType": "Suite", "sc:citation": [ "pubmed:31105932", - "pmcid:PMC6498745", { "@id": "https://doi.org/10.12688/F1000RESEARCH.16338.1" - } + }, + "pmcid:PMC6498745" ], "sc:description": "Analysis of copy number variation using Illumina Infinium DNA methylation arrays.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3219" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_3219" } ], "sc:license": "Unlicense", "sc:name": "GenePattern notebook", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.genepattern-notebook.org/" - }, - { - "@id": "https://orcid.org/0000-0002-8718-8848", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/geneplast/bioconda_geneplast.yaml b/data/geneplast/bioconda_geneplast.yaml index 656e7332fffe1..40f5353042d48 100644 --- a/data/geneplast/bioconda_geneplast.yaml +++ b/data/geneplast/bioconda_geneplast.yaml @@ -7,7 +7,6 @@ description: Geneplast is designed for evolutionary and plasticity analysis base home: https://bioconductor.org/packages/3.10/bioc/html/geneplast.html identifiers: - biotools:geneplast -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-geneplast diff --git a/data/geneplast/geneplastbioschemas.jsonld b/data/geneplast/geneplastbioschemas.jsonld index 967a13c42302b..1d3186853242d 100644 --- a/data/geneplast/geneplastbioschemas.jsonld +++ b/data/geneplast/geneplastbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mauro Castro", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This tool is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.", "sc:license": "GPL-2.0", diff --git a/data/geneplotter/bioconda_geneplotter.yaml b/data/geneplotter/bioconda_geneplotter.yaml index 469a66720e2b2..d8c3c3a2b16be 100644 --- a/data/geneplotter/bioconda_geneplotter.yaml +++ b/data/geneplotter/bioconda_geneplotter.yaml @@ -3,7 +3,6 @@ description: Functions for plotting genomic data home: https://bioconductor.org/packages/3.10/bioc/html/geneplotter.html identifiers: - biotools:geneplotter -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-geneplotter summary: Graphics related functions for Bioconductor diff --git a/data/genepopedit/genepopeditbioschemas.jsonld b/data/genepopedit/genepopeditbioschemas.jsonld index 5cf47d11b107c..88aebe2223c08 100644 --- a/data/genepopedit/genepopeditbioschemas.jsonld +++ b/data/genepopedit/genepopeditbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "genepopedit", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/rystanley/genepopedit" } \ No newline at end of file diff --git a/data/geneprof/geneprofbioschemas.jsonld b/data/geneprof/geneprofbioschemas.jsonld index c0fe026a53fe8..1465cc436d3a4 100644 --- a/data/geneprof/geneprofbioschemas.jsonld +++ b/data/geneprof/geneprofbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GeneProf", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.geneprof.org/GeneProf/" } \ No newline at end of file diff --git a/data/generecommender/generecommenderbioschemas.jsonld b/data/generecommender/generecommenderbioschemas.jsonld index 8000e722cfb23..c185cf6a16f4c 100644 --- a/data/generecommender/generecommenderbioschemas.jsonld +++ b/data/generecommender/generecommenderbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Greg Hather", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.", "sc:license": "GPL-2.0", "sc:name": "geneRecommender", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/geneRecommender.html", "sc:version": "1.46.0" diff --git a/data/generecon/genereconbioschemas.jsonld b/data/generecon/genereconbioschemas.jsonld index 04b0c0778eb08..07e6614d81669 100644 --- a/data/generecon/genereconbioschemas.jsonld +++ b/data/generecon/genereconbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A coalescent based tool for fine-scale association mapping.", "sc:name": "GeneRecon", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "birc.au.dk", "sc:url": "http://www.daimi.au.dk/~mailund/GeneRecon/", diff --git a/data/generegionscan/generegionscanbioschemas.jsonld b/data/generegionscan/generegionscanbioschemas.jsonld index 404f583444c36..44be2536e6bf0 100644 --- a/data/generegionscan/generegionscanbioschemas.jsonld +++ b/data/generegionscan/generegionscanbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-0708-9530", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/generegionscan", "@type": "sc:SoftwareApplication", @@ -16,14 +20,14 @@ "@id": "http://orcid.org/0000-0003-0708-9530" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC2712334", { "@id": "https://doi.org/10.1093/bioinformatics/btp279" }, + "pmcid:PMC2712334", "pubmed:19398447" ], "sc:description": "A package with focus on analysis of discrete regions of the genome using Affymetrix data, including additional information about the sequence of each probe and the probe set it is derived from. It includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.", @@ -34,16 +38,12 @@ "sc:name": "GeneRegionScan", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneRegionScan.html", "sc:version": "1.30.0" }, - { - "@id": "http://orcid.org/0000-0003-0708-9530", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1093/bioinformatics/btp279", "@type": "sc:CreativeWork" diff --git a/data/generxcluster/generxclusterbioschemas.jsonld b/data/generxcluster/generxclusterbioschemas.jsonld index 6e81ec1659bb0..49cf402035aa5 100644 --- a/data/generxcluster/generxclusterbioschemas.jsonld +++ b/data/generxcluster/generxclusterbioschemas.jsonld @@ -14,15 +14,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Charles Berry", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pmcid:PMC4029028", "pubmed:24489369", { "@id": "https://doi.org/10.1093/bioinformatics/btu035" - } + }, + "pmcid:PMC4029028" ], "sc:description": "This package provides functions for exploring genomic insertion sites originating from two different sources.", "sc:featureList": { @@ -31,9 +31,9 @@ "sc:license": "GPL-2.0", "sc:name": "geneRxCluster", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/geneRxCluster.html", "sc:version": "1.10.0" diff --git a/data/genes2wordcloud/genes2wordcloudbioschemas.jsonld b/data/genes2wordcloud/genes2wordcloudbioschemas.jsonld index 9b4d06bace08c..a5d5f433cfabc 100644 --- a/data/genes2wordcloud/genes2wordcloudbioschemas.jsonld +++ b/data/genes2wordcloud/genes2wordcloudbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies.", "sc:name": "Genes2WordCloud", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.maayanlab.net/G2W/create_wordcloud.php" } \ No newline at end of file diff --git a/data/genes_by_isoelectric_point/genes_by_isoelectric_pointbioschemas.jsonld b/data/genes_by_isoelectric_point/genes_by_isoelectric_pointbioschemas.jsonld index 3458b3caf3aa4..adc7827598aec 100644 --- a/data/genes_by_isoelectric_point/genes_by_isoelectric_pointbioschemas.jsonld +++ b/data/genes_by_isoelectric_point/genes_by_isoelectric_pointbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Web service that retrieves all genes whose protein product has an isoelectric point in a range that user specify.", "sc:name": "Genes by Isoelectric Point", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mango.ctegd.uga.edu/jkissingLab/contact.html", "sc:version": "1" diff --git a/data/geneseeker/geneseekerbioschemas.jsonld b/data/geneseeker/geneseekerbioschemas.jsonld index e92ae0e68ee36..c37008d83b7f3 100644 --- a/data/geneseeker/geneseekerbioschemas.jsonld +++ b/data/geneseeker/geneseekerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GeneSeeker", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.cmbi.ru.nl/GeneSeeker/" } \ No newline at end of file diff --git a/data/geneselectmmd/geneselectmmdbioschemas.jsonld b/data/geneselectmmd/geneselectmmdbioschemas.jsonld index ba3b64d814093..60fd98bf0a40d 100644 --- a/data/geneselectmmd/geneselectmmdbioschemas.jsonld +++ b/data/geneselectmmd/geneselectmmdbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Weiliang Qiu", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Gene selection based on a mixture of marginal distributions.", "sc:license": "GPL-2.0", "sc:name": "GeneSelectMMD", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneSelectMMD.html", "sc:version": "2.18.0" diff --git a/data/geneselector/geneselectorbioschemas.jsonld b/data/geneselector/geneselectorbioschemas.jsonld index 094bd6ab0b61a..ffac655c18084 100644 --- a/data/geneselector/geneselectorbioschemas.jsonld +++ b/data/geneselector/geneselectorbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "GeneSelector", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneSelector.html", diff --git a/data/geneseqer/geneseqerbioschemas.jsonld b/data/geneseqer/geneseqerbioschemas.jsonld index e49725b66a100..d86a1e731e3cc 100644 --- a/data/geneseqer/geneseqerbioschemas.jsonld +++ b/data/geneseqer/geneseqerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GeneSeqer", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.plantgdb.org/search/misc/PublicPlantSeq.php" } \ No newline at end of file diff --git a/data/geneseqtofamily/geneseqtofamilybioschemas.jsonld b/data/geneseqtofamily/geneseqtofamilybioschemas.jsonld index 5d5adf48958f4..5cb5c91d999dd 100644 --- a/data/geneseqtofamily/geneseqtofamilybioschemas.jsonld +++ b/data/geneseqtofamily/geneseqtofamilybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "GeneSeqToFamily", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily", "sc:version": "0.1.0" diff --git a/data/geneshelf/geneshelfbioschemas.jsonld b/data/geneshelf/geneshelfbioschemas.jsonld index 34e01217a1091..c16dcf4c5e830 100644 --- a/data/geneshelf/geneshelfbioschemas.jsonld +++ b/data/geneshelf/geneshelfbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool builds upon a zoomable grid display to represent two categorical dimensions. It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts.", "sc:name": "GeneShelf", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://hcil.snu.ac.kr/research/geneshelf" } \ No newline at end of file diff --git a/data/geneshot/geneshotbioschemas.jsonld b/data/geneshot/geneshotbioschemas.jsonld index de764eb7097f5..109bccc72e5de 100644 --- a/data/geneshot/geneshotbioschemas.jsonld +++ b/data/geneshot/geneshotbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-6904-1017", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/Geneshot", "@type": "sc:SoftwareApplication", @@ -20,29 +24,29 @@ ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31114885", { "@id": "https://doi.org/10.1093/NAR/GKZ393" }, + "pubmed:31114885", "pmcid:PMC6602493" ], "sc:description": "search engine for ranking genes from arbitrary text queries | Submit biomedical terms to receive ranked lists of relevant genes | Submit any search terms to Geneshot to receive prioritized genes that are most relevant to the search terms. Geneshot finds publications that mention both the search terms and genes. It then prioritizes these genes using various methods: 1) list of genes from publications; 2) predicted genes using gene-gene similarity matrices derived from a variety of resources ( ARCHS4 : Enrichr : Tagger : AutoRIF : GeneRIF ) | Examples: Wound healing : Hair loss : Trichostatin A : Glioblastoma : Diabetes", "sc:featureList": [ - { - "@id": "edam:operation_3463" - }, { "@id": "edam:operation_2436" }, { "@id": "edam:operation_2454" + }, + { + "@id": "edam:operation_3463" } ], "sc:license": "Apache-2.0", "sc:name": "Geneshot", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://amp.pharm.mssm.edu/geneshot" @@ -50,10 +54,6 @@ { "@id": "https://doi.org/10.1093/NAR/GKZ393", "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0002-6904-1017", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/genesigdb/genesigdbbioschemas.jsonld b/data/genesigdb/genesigdbbioschemas.jsonld index 47b003e374204..45831e77f4569 100644 --- a/data/genesigdb/genesigdbbioschemas.jsonld +++ b/data/genesigdb/genesigdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Manually curated database of gene expression signatures. It focuses on cancer, development, and stem cell gene signatures and was constructed from thousands of publications from which we manually transcribe gene signatures. Gene signatures are mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. It provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene.", "sc:name": "GeneSigDB", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://compbio.dfci.harvard.edu/genesigdb" } \ No newline at end of file diff --git a/data/genesilico/genesilicobioschemas.jsonld b/data/genesilico/genesilicobioschemas.jsonld index 8265a4b36160d..6fcf894414f04 100644 --- a/data/genesilico/genesilicobioschemas.jsonld +++ b/data/genesilico/genesilicobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "GeneSilico is a protein structure prediction meta-server that gives access to various fold-recognition servers.", "sc:name": "GeneSilico", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://genesilico.pl/meta2/" } \ No newline at end of file diff --git a/data/genesis/genesisbioschemas.jsonld b/data/genesis/genesisbioschemas.jsonld index c02a83834e31a..5852df1c43612 100644 --- a/data/genesis/genesisbioschemas.jsonld +++ b/data/genesis/genesisbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Matthew P. Conomos", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a PCA on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry.", "sc:license": "GPL-3.0", "sc:name": "GENESIS", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GENESIS.html", "sc:version": "2.4.0" diff --git a/data/genesis_microarray/genesis_microarraybioschemas.jsonld b/data/genesis_microarray/genesis_microarraybioschemas.jsonld index aa0ec3f0f613f..8ee8774209a96 100644 --- a/data/genesis_microarray/genesis_microarraybioschemas.jsonld +++ b/data/genesis_microarray/genesis_microarraybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Various tools for microarray data analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support vector machines.", "sc:name": "Genesis", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://genome.tugraz.at/genesisclient/genesisclient_description.shtml" } \ No newline at end of file diff --git a/data/genesmash/genesmashbioschemas.jsonld b/data/genesmash/genesmashbioschemas.jsonld index 9a01e3bbe6a92..43f916ea631dd 100644 --- a/data/genesmash/genesmashbioschemas.jsonld +++ b/data/genesmash/genesmashbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Collates data from bioinformatics resources and provides automated gene-centric annotations.", "sc:name": "geneSmash", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://app1.bioinformatics.mdanderson.org/genesmash/_design/basic/api.html", "sc:version": "1" diff --git a/data/genesnps/genesnpsbioschemas.jsonld b/data/genesnps/genesnpsbioschemas.jsonld index 891de2aa7982d..3005bdd6a7968 100644 --- a/data/genesnps/genesnpsbioschemas.jsonld +++ b/data/genesnps/genesnpsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Gene-centric map of the genome structure, coding sequences, and identified allelic variation in genes being targeted for a role in disease susceptibility by the NIEHS (National Institute of Evironmental Health Sciences). This database provides a graphical view of all available SNP data including allele frequencies and genotypes in select populations. This information is key in selecting the polymorphic sites needed to examine disease risk in human population studies.", "sc:name": "GeneSNPs", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.genome.utah.edu/genesnps/" } \ No newline at end of file diff --git a/data/genestitch/genestitchbioschemas.jsonld b/data/genestitch/genestitchbioschemas.jsonld index b576c05a29fdd..b7e3687418c05 100644 --- a/data/genestitch/genestitchbioschemas.jsonld +++ b/data/genestitch/genestitchbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/genestitch", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yuzhen Ye", - "Yu-Wei Wu" + "Yu-Wei Wu", + "Yuzhen Ye" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:22962453", diff --git a/data/genestructuretools/genestructuretoolsbioschemas.jsonld b/data/genestructuretools/genestructuretoolsbioschemas.jsonld index fdb625f6fd2be..57fff14525e35 100644 --- a/data/genestructuretools/genestructuretoolsbioschemas.jsonld +++ b/data/genestructuretools/genestructuretoolsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "GeneStructureTools", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneStructureTools.html", "sc:version": "1.0.0" diff --git a/data/genesurrounder/genesurrounderbioschemas.jsonld b/data/genesurrounder/genesurrounderbioschemas.jsonld index 65c82c8b13dd1..4b8d0a81238d1 100644 --- a/data/genesurrounder/genesurrounderbioschemas.jsonld +++ b/data/genesurrounder/genesurrounderbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-019-2829-Y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GeneSurrounder", "@type": "sc:SoftwareApplication", @@ -22,32 +18,36 @@ ], "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6503437", { "@id": "https://doi.org/10.1186/S12859-019-2829-Y" }, - "pubmed:31060502" + "pubmed:31060502", + "pmcid:PMC6503437" ], "sc:description": "Network-based identification of disease genes in expression data.", "sc:featureList": [ { - "@id": "edam:operation_0277" + "@id": "edam:operation_3463" }, { "@id": "edam:operation_2436" }, { - "@id": "edam:operation_3463" + "@id": "edam:operation_0277" } ], "sc:license": "Unlicense", "sc:name": "GeneSurrounder", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://github.com/sahildshah1/gene-surrounder" + }, + { + "@id": "https://doi.org/10.1186/S12859-019-2829-Y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genesysv/genesysvbioschemas.jsonld b/data/genesysv/genesysvbioschemas.jsonld index 08febaf417e65..9549b766fad1c 100644 --- a/data/genesysv/genesysvbioschemas.jsonld +++ b/data/genesysv/genesysvbioschemas.jsonld @@ -9,32 +9,28 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2636-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GenESysV", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Center for Computational Research", "sc:additionalType": "Web service", "sc:citation": [ + "pmcid:PMC6357466", { "@id": "https://doi.org/10.1186/s12859-019-2636-5" }, - "pmcid:PMC6357466", "pubmed:30704396" ], "sc:description": "Genome exploration open source tool for variants generated from high-throughput sequencing projects.", "sc:featureList": [ { - "@id": "edam:operation_2422" + "@id": "edam:operation_3227" }, { "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3227" + "@id": "edam:operation_2422" } ], "sc:license": "GPL-2.0", @@ -44,6 +40,10 @@ "Linux" ], "sc:url": "https://github.com/ubccr/genesysv" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2636-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genetalk/genetalkbioschemas.jsonld b/data/genetalk/genetalkbioschemas.jsonld index 3f4e2a8633584..6c8c2bb8d9b49 100644 --- a/data/genetalk/genetalkbioschemas.jsonld +++ b/data/genetalk/genetalkbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-based platform, that can filter, reduce and prioritize human sequence variants from NGS data and assist in the interpretation of personal variants in clinical context.", "sc:name": "GeneTalk", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.gene-talk.de" } \ No newline at end of file diff --git a/data/genetclassifier/genetclassifierbioschemas.jsonld b/data/genetclassifier/genetclassifierbioschemas.jsonld index e635c37e743fb..5410bf991a811 100644 --- a/data/genetclassifier/genetclassifierbioschemas.jsonld +++ b/data/genetclassifier/genetclassifierbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-6104-7134", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/1471-2164-16-S5-S3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/genetclassifier", "@type": "sc:SoftwareApplication", @@ -24,15 +16,15 @@ "@id": "http://orcid.org/0000-0001-6104-7134" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pmcid:PMC4460584", - "pubmed:26040557", { "@id": "https://doi.org/10.1186/1471-2164-16-S5-S3" - } + }, + "pmcid:PMC4460584", + "pubmed:26040557" ], "sc:description": "Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.", "sc:featureList": { @@ -41,12 +33,20 @@ "sc:license": "GPL-2.0", "sc:name": "geNetClassifier", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/geNetClassifier.html", "sc:version": "1.14.0" + }, + { + "@id": "https://doi.org/10.1186/1471-2164-16-S5-S3", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-6104-7134", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/genetests/genetestsbioschemas.jsonld b/data/genetests/genetestsbioschemas.jsonld index 9685fbef18c3f..28c92bf1c5acd 100644 --- a/data/genetests/genetestsbioschemas.jsonld +++ b/data/genetests/genetestsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons.", "sc:name": "GeneTests", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.geneclinics.org/" } \ No newline at end of file diff --git a/data/genetic_revision/genetic_revisionbioschemas.jsonld b/data/genetic_revision/genetic_revisionbioschemas.jsonld index 57c7c54edd6ec..6ed051358dd65 100644 --- a/data/genetic_revision/genetic_revisionbioschemas.jsonld +++ b/data/genetic_revision/genetic_revisionbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Allows searching information in GenBank and also in other NCBI databases through the interactive orchestration of NCBI Web services.", "sc:name": "Genetic Revision", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://zti.polsl.pl/dmrozek/science/sgb/sgb.htm" } \ No newline at end of file diff --git a/data/geneticsdesign/bioconda_geneticsdesign.yaml b/data/geneticsdesign/bioconda_geneticsdesign.yaml index ce0b35c438422..a38938baf49f2 100644 --- a/data/geneticsdesign/bioconda_geneticsdesign.yaml +++ b/data/geneticsdesign/bioconda_geneticsdesign.yaml @@ -4,7 +4,6 @@ description: This package contains functions useful for designing genetics studi home: https://bioconductor.org/packages/3.10/bioc/html/GeneticsDesign.html identifiers: - biotools:geneticsdesign -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-geneticsdesign diff --git a/data/geneticsdesign/geneticsdesignbioschemas.jsonld b/data/geneticsdesign/geneticsdesignbioschemas.jsonld index d5e1b0a892b71..046d612e9b79e 100644 --- a/data/geneticsdesign/geneticsdesignbioschemas.jsonld +++ b/data/geneticsdesign/geneticsdesignbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "The R Genetics Project", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package contains functions useful for designing genetics studies, including power and sample-size calculations.", "sc:license": "GPL-2.0", "sc:name": "GeneticsDesign", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneticsDesign.html", "sc:version": "1.42.0" diff --git a/data/geneticsped/geneticspedbioschemas.jsonld b/data/geneticsped/geneticspedbioschemas.jsonld index 447e9a457060f..2ca41ea973d3d 100644 --- a/data/geneticsped/geneticspedbioschemas.jsonld +++ b/data/geneticsped/geneticspedbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David Henderson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities.", "sc:license": "GPL-2.0", "sc:name": "GeneticsPed", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GeneticsPed.html", diff --git a/data/genetier/genetierbioschemas.jsonld b/data/genetier/genetierbioschemas.jsonld index 7c703ef4e9ade..73dc03fbb4417 100644 --- a/data/genetier/genetierbioschemas.jsonld +++ b/data/genetier/genetierbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool replaces the knowledge-based inference traditionally used in candidate disease gene prioritization, instead using experimental data from tissue-specific gene expression data sets.", "sc:name": "GeneTIER", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://dna2.leeds.ac.uk:8080/expression/index.jsp" } \ No newline at end of file diff --git a/data/genetrail/genetrailbioschemas.jsonld b/data/genetrail/genetrailbioschemas.jsonld index 08409f2784fc1..e0751c6370eef 100644 --- a/data/genetrail/genetrailbioschemas.jsonld +++ b/data/genetrail/genetrailbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GeneTrail", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://genetrail.bioinf.uni-sb.de/index.php" } \ No newline at end of file diff --git a/data/genetrail2/genetrail2bioschemas.jsonld b/data/genetrail2/genetrail2bioschemas.jsonld index 1d5146b49ce36..b06955f9fad4c 100644 --- a/data/genetrail2/genetrail2bioschemas.jsonld +++ b/data/genetrail2/genetrail2bioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Prof. Dr. Hans-Peter Lenhof", "sc:additionalType": [ - "Web API", - "Web application" + "Web application", + "Web API" ], "sc:citation": "pubmed:26787660", "sc:description": "GeneTrail 2 is a web-interface providing access to different tools for the statistical analysis of molecular signatures. GeneTrail2 allows the integrated analysis of transcriptomic, miRNomic, genomic, and proteomic datasets. It offers multiple statistical tests, a large number of predefined reference sets, as well as a comprehensive collection of biological categories and enables direct comparisons between the computed results.", "sc:name": "GeneTrail2", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "lumc.nl", "sc:url": "http://genetrail2.bioinf.uni-sb.de/", diff --git a/data/genetree/genetreebioschemas.jsonld b/data/genetree/genetreebioschemas.jsonld index 20702a03fa152..d2cbfde0bf447 100644 --- a/data/genetree/genetreebioschemas.jsonld +++ b/data/genetree/genetreebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Genetree", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.stats.ox.ac.uk/~griff/software.html" } \ No newline at end of file diff --git a/data/genevalidator/genevalidatorbioschemas.jsonld b/data/genevalidator/genevalidatorbioschemas.jsonld index 6eafea2f15524..7b44882baf99c 100644 --- a/data/genevalidator/genevalidatorbioschemas.jsonld +++ b/data/genevalidator/genevalidatorbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btw015", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-3140-2809", "@type": "schema:Person" @@ -34,23 +30,23 @@ "Command-line tool" ], "sc:applicationSubCategory": [ - { - "@id": "edam:topic_0080" - }, { "@id": "edam:topic_0654" }, { "@id": "edam:topic_0219" + }, + { + "@id": "edam:topic_0080" } ], "sc:author": "WurmLab", "sc:citation": [ + "pubmed:26787666", + "pmcid:PMC4866521", { "@id": "https://doi.org/10.1093/bioinformatics/btw015" - }, - "pmcid:PMC4866521", - "pubmed:26787666" + } ], "sc:description": "Tool to identify problematic gene predictions based on comparisons between gene predictions and similar sequences in public databases (e.g., SwissProt).", "sc:featureList": { @@ -60,23 +56,27 @@ "sc:license": "AGPL-3.0", "sc:name": "GeneValidator", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:softwareHelp": [ { - "@id": "https://github.com/wurmlab/genevalidator/blob/master/README.md#introduction" + "@id": "https://wurmlab.github.io/tools/genevalidator/" }, { - "@id": "https://github.com/wurmlab/genevalidator/blob/master/README.md" + "@id": "https://github.com/wurmlab/genevalidator/blob/master/README.md#introduction" }, { - "@id": "https://wurmlab.github.io/tools/genevalidator/" + "@id": "https://github.com/wurmlab/genevalidator/blob/master/README.md" } ], "sc:url": "https://wurmlab.github.io/tools/genevalidator/", "sc:version": "1.6.12" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btw015", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genevestigator/genevestigatorbioschemas.jsonld b/data/genevestigator/genevestigatorbioschemas.jsonld index ed594de864bb0..31f1061bb6c07 100644 --- a/data/genevestigator/genevestigatorbioschemas.jsonld +++ b/data/genevestigator/genevestigatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "High performance search engine for gene expression. It integrates thousands of manually curated, well described public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts such as diseases, drugs, tissues, cancers, cell lines or genotypes. The high diversity of curated experiments allows the tool to project your genes or your data against a broad spectrum of reference profiles and datasets.", "sc:name": "Genevestigator", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.genevestigator.com/" } \ No newline at end of file diff --git a/data/genevetter/genevetterbioschemas.jsonld b/data/genevetter/genevetterbioschemas.jsonld index 4821edb13b6b8..b7655076d98b9 100644 --- a/data/genevetter/genevetterbioschemas.jsonld +++ b/data/genevetter/genevetterbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btv432", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GeneVetter", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Web service" ], "sc:citation": [ + "pmcid:PMC4643620", { "@id": "https://doi.org/10.1093/bioinformatics/btv432" }, - "pubmed:26209433", - "pmcid:PMC4643620" + "pubmed:26209433" ], "sc:description": "Investigation of the background prevalence (rare, protein altering variants that could be classified as pathogenic) of exonic variation.", "sc:featureList": [ @@ -43,11 +39,15 @@ "sc:license": "Other", "sc:name": "GeneVetter", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://genevetter.org/" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv432", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/geneview/geneviewbioschemas.jsonld b/data/geneview/geneviewbioschemas.jsonld index e86204769c0fb..1bf7628103c5d 100644 --- a/data/geneview/geneviewbioschemas.jsonld +++ b/data/geneview/geneviewbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Webserver that lets you search scientific articles using keywords and identifiers for specific biological entities. It has advanced features like: recognizing biological entities like genes and SNPs.", "sc:name": "GeneView", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bc3.informatik.hu-berlin.de/" diff --git a/data/geneweaver/geneweaverbioschemas.jsonld b/data/geneweaver/geneweaverbioschemas.jsonld index 2cb86de7cc556..3958dab728f1b 100644 --- a/data/geneweaver/geneweaverbioschemas.jsonld +++ b/data/geneweaver/geneweaverbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Curated repository of genomic experimental results with an accompanying tool set for dynamic integration of these data sets, enabling users to interactively address questions about sets of biological functions and their relations to sets of genes.", "sc:name": "GeneWeaver", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ontologicaldiscovery.org/" } \ No newline at end of file diff --git a/data/genewise/genewisebioschemas.jsonld b/data/genewise/genewisebioschemas.jsonld index 085840c148e35..868cf11b0326d 100644 --- a/data/genewise/genewisebioschemas.jsonld +++ b/data/genewise/genewisebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Compare a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.", "sc:name": "GeneWise", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/psa/genewise/", diff --git a/data/genexpi/genexpibioschemas.jsonld b/data/genexpi/genexpibioschemas.jsonld index c1f00d4b3bdcd..91ace981850fa 100644 --- a/data/genexpi/genexpibioschemas.jsonld +++ b/data/genexpi/genexpibioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Martin Modrák", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC5899412", + "pubmed:29653518", { "@id": "https://doi.org/10.1186/s12859-018-2138-x" - }, - "pubmed:29653518", - "pmcid:PMC5899412" + } ], "sc:description": "Tool to infer or validate genetic networks based on expression time series data.", "sc:featureList": { @@ -36,8 +36,8 @@ "sc:name": "Genexpi", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/cas-bioinf/genexpi/wiki" } diff --git a/data/genextender/genextenderbioschemas.jsonld b/data/genextender/genextenderbioschemas.jsonld index 603da701d1d57..0617cd2b185a4 100644 --- a/data/genextender/genextenderbioschemas.jsonld +++ b/data/genextender/genextenderbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bohdan Khomtchouk", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This tool annotates a histone modification ChIP-seq peak input file with functionally important genomic features (e.g., genes associated with peaks) based on optimization calculations. It extends the boundaries of every gene in a genome by some distance in DNA base pairs, incorporating cis-regulatory elements (CREs), such as enhancers and promoters, as well as downstream elements that are important to the function of the gene relative to an epigenetic histone modification ChIP-seq dataset.", "sc:license": "GPL-3.0", diff --git a/data/geneyenta/geneyentabioschemas.jsonld b/data/geneyenta/geneyentabioschemas.jsonld index 7139ecdb2634f..3da0f53551148 100644 --- a/data/geneyenta/geneyentabioschemas.jsonld +++ b/data/geneyenta/geneyentabioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/GeneYenta", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web API", - "Web application" + "Web application", + "Web API" ], "sc:author": [ - "Zach Maurer", - "David Arenillas" + "David Arenillas", + "Zach Maurer" ], "sc:citation": "pubmed:25703386", "sc:description": "Tool for clinicians to make connections to share genetic data by being matched using phenotype data. It aims to create a portal for clinicians to enter phenotypic case data for individuals who have had exome sequencing without a genetic diagnosis.", "sc:name": "GeneYenta", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://geneyenta.com/accounts/home/" } \ No newline at end of file diff --git a/data/genezilla/genezillabioschemas.jsonld b/data/genezilla/genezillabioschemas.jsonld index 9350fee4bda94..94459302c3a1c 100644 --- a/data/genezilla/genezillabioschemas.jsonld +++ b/data/genezilla/genezillabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Highly reconfigurable gene finder written in C++. Graph-theoretic representations of the high scoring open reading frames are provided, allowing for exploration of sub-optimal gene models. It utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, CAP sites, and will soon model CpG islands as well.", "sc:name": "GeneZilla", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.genezilla.org" } \ No newline at end of file diff --git a/data/geniatagger/geniataggerbioschemas.jsonld b/data/geniatagger/geniataggerbioschemas.jsonld index 88f29c4180c6b..bc5da1d6d8a2b 100644 --- a/data/geniatagger/geniataggerbioschemas.jsonld +++ b/data/geniatagger/geniataggerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Analyze English sentences and output the base forms, part-of-speech tags, chunk tags, and named entity tags. The tagger is specifically tuned for biomedical text such as MEDLINE abstracts.", "sc:name": "geniatagger", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.nactem.ac.uk/tsujii/GENIA/tagger/", "sc:version": "1" diff --git a/data/genie/geniebioschemas.jsonld b/data/genie/geniebioschemas.jsonld index 3364cdaa14a72..66d0f1e7f511f 100644 --- a/data/genie/geniebioschemas.jsonld +++ b/data/genie/geniebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Genes prioritization for topics of interest using gene-related PubMed abstracts.", "sc:name": "Genie", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://cbdm.uni-mainz.de/medlineranker" } \ No newline at end of file diff --git a/data/genie3/genie3bioschemas.jsonld b/data/genie3/genie3bioschemas.jsonld index ba5137193f055..f816c26a624d7 100644 --- a/data/genie3/genie3bioschemas.jsonld +++ b/data/genie3/genie3bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Algorithm for the inference of gene regulatory networks from expression data. It decomposes the prediction of a regulatory network between p genes into p different regression problems. In each of the regression problems, the expression pattern of one of the genes (target gene) is predicted from the expression patterns of all the other genes (input genes), using tree-based ensemble methods Random Forests or Extra-Trees.", "sc:name": "GENIE3", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/vahuynh/GENIE3" } \ No newline at end of file diff --git a/data/genie_cbdm/genie_cbdmbioschemas.jsonld b/data/genie_cbdm/genie_cbdmbioschemas.jsonld index fa28fdbabf61d..25d891854f949 100644 --- a/data/genie_cbdm/genie_cbdmbioschemas.jsonld +++ b/data/genie_cbdm/genie_cbdmbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Genie", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cbdm-01.zdv.uni-mainz.de/~jfontain/cms/?page_id=6" } \ No newline at end of file diff --git a/data/genio/geniobioschemas.jsonld b/data/genio/geniobioschemas.jsonld index 52a325ba7e21f..7765cec7c4afd 100644 --- a/data/genio/geniobioschemas.jsonld +++ b/data/genio/geniobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2027-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GenIO", "@type": "sc:SoftwareApplication", @@ -21,19 +17,19 @@ "Web application" ], "sc:citation": [ - "pmcid:PMC5787240", "pubmed:29374474", { "@id": "https://doi.org/10.1186/s12859-018-2027-3" - } + }, + "pmcid:PMC5787240" ], "sc:description": "Genomic Input Output (GenIO) identifies the most probable variants causing a rare disease, using the genomic and clinical information provided by a medical practitioner.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_3229" }, { - "@id": "edam:operation_3229" + "@id": "edam:operation_3196" } ], "sc:license": "GPL-3.0", @@ -45,6 +41,10 @@ ], "sc:url": "https://bioinformatics.ibioba-mpsp-conicet.gov.ar/GenIO/index.php", "sc:version": "1.0" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2027-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genlib/genlibbioschemas.jsonld b/data/genlib/genlibbioschemas.jsonld index 36b0a260b7c87..dacbda7af911b 100644 --- a/data/genlib/genlibbioschemas.jsonld +++ b/data/genlib/genlibbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-015-0581-5", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/genlib", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC4431039", - "pubmed:25971991", { "@id": "https://doi.org/10.1186/s12859-015-0581-5" - } + }, + "pubmed:25971991" ], "sc:description": "GENLIB is an R package that can be used to analyze genealogical data.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "GPL-3.0", "sc:name": "GENLIB", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/GENLIB/index.html", "sc:version": "1.0.6" - }, - { - "@id": "https://doi.org/10.1186/s12859-015-0581-5", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genmr/genmrbioschemas.jsonld b/data/genmr/genmrbioschemas.jsonld index 6d71681a1d70c..25df56b602850 100644 --- a/data/genmr/genmrbioschemas.jsonld +++ b/data/genmr/genmrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for generating 3D protein structures using input sequence data, NOE-based distance restraints or NMR chemical shifts. Output is a set of PDB coordinates for the input protein.", "sc:name": "GeNMR", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.genmr.ca" } \ No newline at end of file diff --git a/data/genn/gennbioschemas.jsonld b/data/genn/gennbioschemas.jsonld index 2c998489a7d58..c5c60ae447051 100644 --- a/data/genn/gennbioschemas.jsonld +++ b/data/genn/gennbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:26740369", + "pmcid:PMC4703976", { "@id": "https://doi.org/10.1038/SREP18854" - }, - "pmcid:PMC4703976", - "pubmed:26740369" + } ], "sc:description": "Code generation framework for accelerated brain simulations.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "GeNN", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://genn-team.github.io/genn/" } diff --git a/data/gennon-h/gennon-hbioschemas.jsonld b/data/gennon-h/gennon-hbioschemas.jsonld index ca7094676f297..65c2eb4980b0e 100644 --- a/data/gennon-h/gennon-hbioschemas.jsonld +++ b/data/gennon-h/gennon-hbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-13-216", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gennon-h", "@type": "sc:SoftwareApplication", @@ -25,10 +29,10 @@ }, "sc:citation": [ "pmcid:PMC3532078", + "pubmed:22928840", { "@id": "https://doi.org/10.1186/1471-2105-13-216" - }, - "pubmed:22928840" + } ], "sc:description": "Software designed to generate multiple sequence alignments of DNA evolving on any phylogenetic tree.", "sc:featureList": { @@ -40,10 +44,6 @@ "sc:provider": "crg.eu", "sc:url": "http://genome.crg.es/cgi-bin/phylo_mod_sel/AlgGenNonH.pl", "sc:version": "1" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-13-216", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/geno2pheno/geno2phenobioschemas.jsonld b/data/geno2pheno/geno2phenobioschemas.jsonld index aafec99c5f161..8f1f3712902d2 100644 --- a/data/geno2pheno/geno2phenobioschemas.jsonld +++ b/data/geno2pheno/geno2phenobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for the prediction of HIV phenotypic drug resistance and coreceptor usage from genotype.", "sc:name": "Geno2pheno", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.geno2pheno.org/" } \ No newline at end of file diff --git a/data/genocn/genocnbioschemas.jsonld b/data/genocn/genocnbioschemas.jsonld index 01d19c0128802..82b2418af5ea4 100644 --- a/data/genocn/genocnbioschemas.jsonld +++ b/data/genocn/genocnbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "genoCN", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genoCN.html", diff --git a/data/genocrypt/genocryptbioschemas.jsonld b/data/genocrypt/genocryptbioschemas.jsonld index 5fe3a3301a312..bb5283af0f93d 100644 --- a/data/genocrypt/genocryptbioschemas.jsonld +++ b/data/genocrypt/genocryptbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Method for identifying genetic relatives without compromising privacy by taking advantage of novel cryptographic techniques customized for secure and private comparison of genetic information.", "sc:name": "GenoCrypt beta", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://genetics.cs.ucla.edu/crypto/" diff --git a/data/genogam/genogambioschemas.jsonld b/data/genogam/genogambioschemas.jsonld index 5856ce773b4d0..0d0f7a0f3a203 100644 --- a/data/genogam/genogambioschemas.jsonld +++ b/data/genogam/genogambioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "GenoGAM", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenoGAM.html", "sc:version": "1.2.1" diff --git a/data/genolist/genolistbioschemas.jsonld b/data/genolist/genolistbioschemas.jsonld index 15bafc94557b2..33ac72a481ceb 100644 --- a/data/genolist/genolistbioschemas.jsonld +++ b/data/genolist/genolistbioschemas.jsonld @@ -9,15 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkm1042", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/genolist", "@type": "sc:SoftwareApplication", "edam:has_input": [ { - "@id": "edam:data_2739" + "@id": "edam:data_1868" }, { - "@id": "edam:data_1868" + "@id": "edam:data_2739" }, { "@id": "edam:data_1026" @@ -25,19 +29,19 @@ ], "edam:has_output": [ { - "@id": "edam:data_3028" + "@id": "edam:data_0916" }, { - "@id": "edam:data_0916" + "@id": "edam:data_3028" } ], "sc:additionalType": "Database portal", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0621" + "@id": "edam:topic_0797" }, { - "@id": "edam:topic_0797" + "@id": "edam:topic_0621" } ], "sc:citation": [ @@ -53,15 +57,11 @@ }, "sc:name": "GenoList comparative analysis of microbial genomes", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genolist.pasteur.fr/GenoList" - }, - { - "@id": "https://doi.org/10.1093/nar/gkm1042", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genoma/genomabioschemas.jsonld b/data/genoma/genomabioschemas.jsonld index 84995766b37e1..70dc5f3ecbfb2 100644 --- a/data/genoma/genomabioschemas.jsonld +++ b/data/genoma/genomabioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/Genoma", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "Database of genomic data related to marine species of biological interest. It allows analyses of reference genome annotations, organising the resources in an integrated way", "sc:license": "Unlicense", "sc:name": "Genoma", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioinfo.szn.it/genoma/" } \ No newline at end of file diff --git a/data/genomation/genomationbioschemas.jsonld b/data/genomation/genomationbioschemas.jsonld index 48e678e58dd6e..c4aeeeaae8b60 100644 --- a/data/genomation/genomationbioschemas.jsonld +++ b/data/genomation/genomationbioschemas.jsonld @@ -21,27 +21,27 @@ } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:25417204", "sc:description": "A package for summary and annotation of genomic intervals. The genomic intervals represent regions with a defined chromosomic position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals.", "sc:license": "Artistic-2.0", "sc:name": "genomation", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genomation.html", "sc:version": "1.6.0" }, { - "@id": "http://orcid.org/0000-0003-3606-6792", + "@id": "http://orcid.org/0000-0002-0468-0117", "@type": "schema:Person" }, { - "@id": "http://orcid.org/0000-0002-0468-0117", + "@id": "http://orcid.org/0000-0003-3606-6792", "@type": "schema:Person" } ] diff --git a/data/genomatix_genegrid/genomatix_genegridbioschemas.jsonld b/data/genomatix_genegrid/genomatix_genegridbioschemas.jsonld index 12b4024db4c52..7c487221d4d87 100644 --- a/data/genomatix_genegrid/genomatix_genegridbioschemas.jsonld +++ b/data/genomatix_genegrid/genomatix_genegridbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/genomatix_genegrid", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Contact Form", - "GeneGrid Support" + "GeneGrid Support", + "Contact Form" ], "sc:additionalType": "Web application", "sc:description": "Quickly reduce millions of variants obtained from Next Generation Sequencing to the few or even the single relevant one(s). It annotates SNPs and enables to perform trio analyses, compare case and control sets and identify somatic SNPs. The interaction with the Genomatix Pathway System enables to explore networks of affected genes and allows for an in-depth assessment of the biological background of variants under investigation.", "sc:license": "Proprietary", "sc:name": "GeneGrid", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://genegrid.genomatix.com/grid/home" } \ No newline at end of file diff --git a/data/genome_artist/genome_artistbioschemas.jsonld b/data/genome_artist/genome_artistbioschemas.jsonld index ff88a5a22ccf2..0453255f27519 100644 --- a/data/genome_artist/genome_artistbioschemas.jsonld +++ b/data/genome_artist/genome_artistbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Alexandru Al. Ecovoiu", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC4744444", + "pubmed:26855675", { "@id": "https://doi.org/10.1186/s13100-016-0061-0" - }, - "pmcid:PMC4744444", - "pubmed:26855675" + } ], "sc:description": "Genome ARTIST is a pairwise gapped aligner tool which works out issues in mapping the hits of artificial transposons at nucleotide lever accuracy in insertion mutagenesis experiments.", "sc:featureList": { diff --git a/data/genome_classifier/genome_classifierbioschemas.jsonld b/data/genome_classifier/genome_classifierbioschemas.jsonld index 5ce66009bab9b..3aa0264ae3052 100644 --- a/data/genome_classifier/genome_classifierbioschemas.jsonld +++ b/data/genome_classifier/genome_classifierbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Python/pyrex implementation of the Bayesian classifier of genomic signatures.", "sc:name": "Genome Classifier", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://sandberg.cmb.ki.se/genomeclass/" } \ No newline at end of file diff --git a/data/genome_maps/genome_mapsbioschemas.jsonld b/data/genome_maps/genome_mapsbioschemas.jsonld index c53f5e9bacdbf..048868288aafe 100644 --- a/data/genome_maps/genome_mapsbioschemas.jsonld +++ b/data/genome_maps/genome_mapsbioschemas.jsonld @@ -15,14 +15,14 @@ "sc:description": "Open source and high-performance HTML5 web-based genome browser. It allows to browse several genomes and annotations by fetching data from CellBase high-performance REST web services. Custom data (BAMs, VCFs, ...) can also be loaded from remote servers and local disk by using OpenCGA server.", "sc:name": "Genome Maps", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ "cipf.es", - "http://bioinfo.cipf.es", - "Computational Genomics Department. Prince Felipe Research Center (CIPF)" + "Computational Genomics Department. Prince Felipe Research Center (CIPF)", + "http://bioinfo.cipf.es" ], "sc:url": "http://www.genomemaps.org/", "sc:version": "3" diff --git a/data/genome_projector/genome_projectorbioschemas.jsonld b/data/genome_projector/genome_projectorbioschemas.jsonld index baaef49e13e86..1fd4b7a400e12 100644 --- a/data/genome_projector/genome_projectorbioschemas.jsonld +++ b/data/genome_projector/genome_projectorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Genome Projector", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.g-language.org/GenomeProjector/" } \ No newline at end of file diff --git a/data/genome_trax/genome_traxbioschemas.jsonld b/data/genome_trax/genome_traxbioschemas.jsonld index 17a9e2c33e3bc..033b2603a99ff 100644 --- a/data/genome_trax/genome_traxbioschemas.jsonld +++ b/data/genome_trax/genome_traxbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A search tool for finding variants from specific chromosome coordinates. It is possible to integrate the results in NGS pipeline.", "sc:name": "Genome Trax", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.biobase-international.com/product/genome-trax" } \ No newline at end of file diff --git a/data/genome_uplot/genome_uplotbioschemas.jsonld b/data/genome_uplot/genome_uplotbioschemas.jsonld index 7b2462131534f..bc0995156f02d 100644 --- a/data/genome_uplot/genome_uplotbioschemas.jsonld +++ b/data/genome_uplot/genome_uplotbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Visualize chromosomal abnormalities in the Human Genome using a U-shape layout.", "sc:name": "Genome U-Plot", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/gaitat/GenomeUPlot" } \ No newline at end of file diff --git a/data/genomebrowse/genomebrowsebioschemas.jsonld b/data/genomebrowse/genomebrowsebioschemas.jsonld index acdd881034225..f73508b463db3 100644 --- a/data/genomebrowse/genomebrowsebioschemas.jsonld +++ b/data/genomebrowse/genomebrowsebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A free genome browser for exploring sequencing pile-up and coverage data with numerous annotation tracks hosted on the cloud.", "sc:name": "GenomeBrowse", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.goldenhelix.com/GenomeBrowse/index.html" } \ No newline at end of file diff --git a/data/genomecrispr/genomecrisprbioschemas.jsonld b/data/genomecrispr/genomecrisprbioschemas.jsonld index 46969070ca09a..00e5fa156a5c6 100644 --- a/data/genomecrispr/genomecrisprbioschemas.jsonld +++ b/data/genomecrispr/genomecrisprbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkw997", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/genomecrispr", "@type": "sc:SoftwareApplication", @@ -33,20 +29,20 @@ } ], "sc:citation": [ + "pubmed:27789686", "pmcid:PMC5210668", { "@id": "https://doi.org/10.1093/nar/gkw997" - }, - "pubmed:27789686" + } ], "sc:contributor": "Michael Boutros", "sc:description": "Database for high-throughput screening experiments performed by using the CRISPR/Cas9 system. A dynamic web interface guides users through the process of finding information about published CRISPR screens. The database holds detailed data about observed hits and phenotypes. Moreover, it provides knowledge about performance of individual single guide RNAs (sgRNAs) used under various experimental conditions.", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_2421" }, { - "@id": "edam:operation_2421" + "@id": "edam:operation_0337" }, { "@id": "edam:operation_2422" @@ -55,6 +51,10 @@ "sc:name": "GenomeCRISPR", "sc:operatingSystem": "Linux", "sc:url": "http://genomecrispr.dkfz.de" + }, + { + "@id": "https://doi.org/10.1093/nar/gkw997", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genomed3plot/genomed3plotbioschemas.jsonld b/data/genomed3plot/genomed3plotbioschemas.jsonld index 038c5d43f292a..67ce6c2929aa7 100644 --- a/data/genomed3plot/genomed3plotbioschemas.jsonld +++ b/data/genomed3plot/genomed3plotbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "SVG based genome viewer written in javascript using D3.", "sc:name": "GenomeD3Plot", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/brinkmanlab/GenomeD3Plot" } \ No newline at end of file diff --git a/data/genomedata/genomedatabioschemas.jsonld b/data/genomedata/genomedatabioschemas.jsonld index cf13204ea719b..1c941be02fb15 100644 --- a/data/genomedata/genomedatabioschemas.jsonld +++ b/data/genomedata/genomedatabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Genomedata", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://noble.gs.washington.edu/proj/genomedata/" } \ No newline at end of file diff --git a/data/genomedisco/genomediscobioschemas.jsonld b/data/genomedisco/genomediscobioschemas.jsonld index c63274a703e7d..ca9f92c7b690f 100644 --- a/data/genomedisco/genomediscobioschemas.jsonld +++ b/data/genomedisco/genomediscobioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Software for comparing contact maps from HiC, CaptureC and other 3D genome data.", "sc:name": "GenomeDISCO", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/kundajelab/genomedisco" } \ No newline at end of file diff --git a/data/genomeflow/genomeflowbioschemas.jsonld b/data/genomeflow/genomeflowbioschemas.jsonld index 981aa1456bb62..2909b573f85a6 100644 --- a/data/genomeflow/genomeflowbioschemas.jsonld +++ b/data/genomeflow/genomeflowbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Graphical tool for modeling and analyzing 3D genome structure.", "sc:name": "GenomeFlow", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/jianlin-cheng/GenomeFlow" } \ No newline at end of file diff --git a/data/genomegraphs/genomegraphsbioschemas.jsonld b/data/genomegraphs/genomegraphsbioschemas.jsonld index f94633c2839f7..e303076c625ba 100644 --- a/data/genomegraphs/genomegraphsbioschemas.jsonld +++ b/data/genomegraphs/genomegraphsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Steffen Durinck", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Genomic data analyses requires integrated visualization of known genomic information and new experimental data. This tool uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. Genomic information is plotted together with your data. Plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.", "sc:license": "Artistic-2.0", "sc:name": "GenomeGraphs", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html", "sc:version": "1.34.0" diff --git a/data/genomeinfodb/bioconda_genomeinfodb.yaml b/data/genomeinfodb/bioconda_genomeinfodb.yaml index 878730d3670ee..5c0ccc5d44e35 100644 --- a/data/genomeinfodb/bioconda_genomeinfodb.yaml +++ b/data/genomeinfodb/bioconda_genomeinfodb.yaml @@ -6,7 +6,6 @@ description: Contains data and functions that define and allow translation betwe home: https://bioconductor.org/packages/3.10/bioc/html/GenomeInfoDb.html identifiers: - biotools:genomeinfodb -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genomeinfodb summary: Utilities for manipulating chromosome names, including modifying them to diff --git a/data/genomeinfodb/genomeinfodbbioschemas.jsonld b/data/genomeinfodb/genomeinfodbbioschemas.jsonld index 63e129b0cd3ce..926aa3494c674 100644 --- a/data/genomeinfodb/genomeinfodbbioschemas.jsonld +++ b/data/genomeinfodb/genomeinfodbbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "GenomeInfoDb", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html", "sc:version": "1.10.2" diff --git a/data/genomeintervals/bioconda_genomeintervals.yaml b/data/genomeintervals/bioconda_genomeintervals.yaml index 3e358ab018467..286f9c959b08f 100644 --- a/data/genomeintervals/bioconda_genomeintervals.yaml +++ b/data/genomeintervals/bioconda_genomeintervals.yaml @@ -5,7 +5,6 @@ description: 'This package defines classes for representing genomic intervals an home: https://bioconductor.org/packages/3.10/bioc/html/genomeIntervals.html identifiers: - biotools:genomeintervals -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genomeintervals summary: Operations on genomic intervals diff --git a/data/genomeintervals/genomeintervalsbioschemas.jsonld b/data/genomeintervals/genomeintervalsbioschemas.jsonld index 05e4a625b6f2e..4d026af1a00e0 100644 --- a/data/genomeintervals/genomeintervalsbioschemas.jsonld +++ b/data/genomeintervals/genomeintervalsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Julien Gagneur", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package 'girafe'.", "sc:license": "Artistic-2.0", "sc:name": "genomeIntervals", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genomeIntervals.html", "sc:version": "1.30.0" diff --git a/data/genomemasker/genomemaskerbioschemas.jsonld b/data/genomemasker/genomemaskerbioschemas.jsonld index 99c19173a4a6a..ffc14938de618 100644 --- a/data/genomemasker/genomemaskerbioschemas.jsonld +++ b/data/genomemasker/genomemaskerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10 000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.", "sc:name": "GenomeMasker", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinfo.ut.ee/?page_id=167" } \ No newline at end of file diff --git a/data/genomenet/genomenetbioschemas.jsonld b/data/genomenet/genomenetbioschemas.jsonld index 74ca18afab72c..240503cabb926 100644 --- a/data/genomenet/genomenetbioschemas.jsonld +++ b/data/genomenet/genomenetbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (i.e. Blast, Motif, Clustal W).", "sc:name": "GenomeNet", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.genome.ad.jp/" } \ No newline at end of file diff --git a/data/genomepartitioner/genomepartitionerbioschemas.jsonld b/data/genomepartitioner/genomepartitionerbioschemas.jsonld index 63a9418005f4a..039a4f8ed2932 100644 --- a/data/genomepartitioner/genomepartitionerbioschemas.jsonld +++ b/data/genomepartitioner/genomepartitionerbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/genomepartitioner", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Matthias Christen", - "Beat Christen" + "Beat Christen", + "Matthias Christen" ], "sc:additionalType": "Web application", "sc:description": "Tool that permits multi-level partitioning of large scale DNA constructs for synthetic biology applications. The partitioning algorithm fragments large DNA sequences into smaller, fabricable DNA blocks sharing flanking homologies for in vitro and in vivo DNA assembly. Overlapping homology regions between adjacent DNA blocks are optimized to remove hairpin, sequence repeats and any pattern that interferes with the DNA assembly process. Segments, blocks and sub-blocks that build the blueprint for hierarchical DNA assembly are listed in a GenBank output file.", "sc:name": "GenomePartitioner", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://christenlab.ethz.ch/GenomePartitioner/upload_form_v6.php" } \ No newline at end of file diff --git a/data/genomernai/genomernaibioschemas.jsonld b/data/genomernai/genomernaibioschemas.jsonld index 293bde2d0d33b..5c5fdfc8c7b3d 100644 --- a/data/genomernai/genomernaibioschemas.jsonld +++ b/data/genomernai/genomernaibioschemas.jsonld @@ -13,17 +13,17 @@ "sc:additionalType": "Database portal", "sc:author": [ "Benedikt Rauscher", - "Michael Boutros", "Oliver Pelz", + "Michael Boutros", "Esther Schmidt" ], "sc:citation": "pubmed:23193271", "sc:description": "This database makes available RNAi phenotype data extracted from the literature, or submitted by data producers directly, for human and Drosophila. It also provides RNAi reagent information, along with an assessment as to their efficiency and specificity.", "sc:name": "GenomeRNAi", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ "German Cancer Research Center", diff --git a/data/genomes/genomesbioschemas.jsonld b/data/genomes/genomesbioschemas.jsonld index 080513b56e07e..59235528a65bc 100644 --- a/data/genomes/genomesbioschemas.jsonld +++ b/data/genomes/genomesbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "genomes", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genomes.html", diff --git a/data/genometester/genometesterbioschemas.jsonld b/data/genometester/genometesterbioschemas.jsonld index cf703ed9ae566..5bf5fcdf2dc36 100644 --- a/data/genometester/genometesterbioschemas.jsonld +++ b/data/genometester/genometesterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GenomeTester", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://bioinfo.ut.ee/genometester", diff --git a/data/genometools/genometoolsbioschemas.jsonld b/data/genometools/genometoolsbioschemas.jsonld index 42b911b34ed60..b1d28befc2c97 100644 --- a/data/genometools/genometoolsbioschemas.jsonld +++ b/data/genometools/genometoolsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "GenomeTools", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://genometools.org/" } \ No newline at end of file diff --git a/data/genometrafac/genometrafacbioschemas.jsonld b/data/genometrafac/genometrafacbioschemas.jsonld index 06a21f07b5372..cd1033bba8035 100644 --- a/data/genometrafac/genometrafacbioschemas.jsonld +++ b/data/genometrafac/genometrafacbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Comparative genomics based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq gene orthologs.", "sc:name": "GenomeTraFaC", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://genometrafac.cchmc.org/genome-trafac/index.jsp" } \ No newline at end of file diff --git a/data/genometricorr/genometricorrbioschemas.jsonld b/data/genometricorr/genometricorrbioschemas.jsonld index 4f8eca8b840dc..bc77d0f5a6087 100644 --- a/data/genometricorr/genometricorrbioschemas.jsonld +++ b/data/genometricorr/genometricorrbioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1002529", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/genometricorr", "@type": "sc:SoftwareApplication", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:22693437", "pmcid:PMC3364938", + "pubmed:22693437", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1002529" } @@ -23,10 +27,10 @@ "sc:description": "Performs several carefully chosen spatial tests of independence on genome-wide data and determines the correlation of genome-wide data with other datasets or known biological features.", "sc:featureList": [ { - "@id": "edam:operation_2451" + "@id": "edam:operation_3731" }, { - "@id": "edam:operation_3731" + "@id": "edam:operation_2451" }, { "@id": "edam:operation_3465" @@ -34,16 +38,12 @@ ], "sc:name": "GenometriCorr", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://genometricorr.sourceforge.net", "sc:version": "1.1.19" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1002529", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genomeview/genomeviewbioschemas.jsonld b/data/genomeview/genomeviewbioschemas.jsonld index 83beebcbc648d..08a14e05aba8e 100644 --- a/data/genomeview/genomeviewbioschemas.jsonld +++ b/data/genomeview/genomeviewbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "GenomeView", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "PSB", "sc:url": "http://genomeview.org", diff --git a/data/genomicalignments/genomicalignmentsbioschemas.jsonld b/data/genomicalignments/genomicalignmentsbioschemas.jsonld index 45a6bc8cdca13..8fbe7f4c54a02 100644 --- a/data/genomicalignments/genomicalignmentsbioschemas.jsonld +++ b/data/genomicalignments/genomicalignmentsbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "BioConductor Package Maintainer", "edam:has_input": [ { - "@id": "edam:data_1270" + "@id": "edam:data_1383" }, { - "@id": "edam:data_1383" + "@id": "edam:data_1270" } ], "edam:has_output": [ @@ -46,10 +46,10 @@ "sc:description": "Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.", "sc:featureList": [ { - "@id": "edam:operation_3563" + "@id": "edam:operation_2478" }, { - "@id": "edam:operation_2478" + "@id": "edam:operation_3563" }, { "@id": "edam:operation_3230" @@ -59,8 +59,8 @@ "sc:name": "GenomicAlignments", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html", "sc:version": "1.10.0" diff --git a/data/genomicdatacommons/genomicdatacommonsbioschemas.jsonld b/data/genomicdatacommons/genomicdatacommonsbioschemas.jsonld index 480ef6b800a77..b91f941298d83 100644 --- a/data/genomicdatacommons/genomicdatacommonsbioschemas.jsonld +++ b/data/genomicdatacommons/genomicdatacommonsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "GenomicDataCommons", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenomicDataCommons.html", diff --git a/data/genomicfeatures/genomicfeaturesbioschemas.jsonld b/data/genomicfeatures/genomicfeaturesbioschemas.jsonld index bb6e09bd9a957..5b3b813dd84db 100644 --- a/data/genomicfeatures/genomicfeaturesbioschemas.jsonld +++ b/data/genomicfeatures/genomicfeaturesbioschemas.jsonld @@ -14,14 +14,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "edam:has_input": [ - { - "@id": "edam:data_1050" - }, { "@id": "edam:data_3134" }, { "@id": "edam:data_1270" + }, + { + "@id": "edam:data_1050" } ], "edam:has_output": [ @@ -32,33 +32,33 @@ "@id": "edam:data_1017" }, { - "@id": "edam:data_2048" + "@id": "edam:data_3134" }, { - "@id": "edam:data_3134" + "@id": "edam:data_2048" } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { "@id": "edam:topic_3071" }, { - "@id": "edam:topic_3170" + "@id": "edam:topic_3169" }, { - "@id": "edam:topic_3169" + "@id": "edam:topic_3170" } ], "sc:citation": [ + "pmcid:PMC3738458", + "pubmed:23950696", { "@id": "https://doi.org/10.1371/journal.pcbi.1003118" - }, - "pmcid:PMC3738458", - "pubmed:23950696" + } ], "sc:description": "A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and CDS of a given organism, from either the UCSC Genome Browser or a BioMart database. This information is then stored in a local database that keeps track of the relationship between transcripts, exons, CDS and genes.", "sc:featureList": [ @@ -72,9 +72,9 @@ "sc:license": "Artistic-2.0", "sc:name": "GenomicFeatures", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html", "sc:version": "1.26.2" diff --git a/data/genomicfiles/bioconda_genomicfiles.yaml b/data/genomicfiles/bioconda_genomicfiles.yaml index 22bb0a4821b94..17951a3917c44 100644 --- a/data/genomicfiles/bioconda_genomicfiles.yaml +++ b/data/genomicfiles/bioconda_genomicfiles.yaml @@ -5,7 +5,6 @@ description: This package provides infrastructure for parallel computations dist home: https://bioconductor.org/packages/3.10/bioc/html/GenomicFiles.html identifiers: - biotools:genomicfiles -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genomicfiles summary: Distributed computing by file or by range diff --git a/data/genomicfiles/genomicfilesbioschemas.jsonld b/data/genomicfiles/genomicfilesbioschemas.jsonld index 28ac666f65c3e..8e2039915151b 100644 --- a/data/genomicfiles/genomicfilesbioschemas.jsonld +++ b/data/genomicfiles/genomicfilesbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "GenomicFiles", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenomicFiles.html", "sc:version": "1.10.3" diff --git a/data/genomicinteractions/genomicinteractionsbioschemas.jsonld b/data/genomicinteractions/genomicinteractionsbioschemas.jsonld index f18599e2e31ad..93e71f39d1434 100644 --- a/data/genomicinteractions/genomicinteractionsbioschemas.jsonld +++ b/data/genomicinteractions/genomicinteractionsbioschemas.jsonld @@ -22,9 +22,9 @@ "sc:license": "GPL-3.0", "sc:name": "GenomicInteractions", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenomicInteractions.html", "sc:version": "1.8.1" diff --git a/data/genomicranges/genomicrangesbioschemas.jsonld b/data/genomicranges/genomicrangesbioschemas.jsonld index 146a1906d639d..69b3a1f9db713 100644 --- a/data/genomicranges/genomicrangesbioschemas.jsonld +++ b/data/genomicranges/genomicrangesbioschemas.jsonld @@ -50,8 +50,8 @@ "sc:license": "Artistic-2.0", "sc:name": "GenomicRanges", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html", diff --git a/data/genomics_virtual_lab/genomics_virtual_labbioschemas.jsonld b/data/genomics_virtual_lab/genomics_virtual_labbioschemas.jsonld index 37484d973cd74..33e463385cb20 100644 --- a/data/genomics_virtual_lab/genomics_virtual_labbioschemas.jsonld +++ b/data/genomics_virtual_lab/genomics_virtual_labbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Genomics Virtual Lab", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "The University of Queensland (RCC)", diff --git a/data/genomictuples/genomictuplesbioschemas.jsonld b/data/genomictuples/genomictuplesbioschemas.jsonld index 7cce33dacecf4..c90635c0f33da 100644 --- a/data/genomictuples/genomictuplesbioschemas.jsonld +++ b/data/genomictuples/genomictuplesbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Peter Hickey", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges BioConductor package.", "sc:license": "Artistic-2.0", "sc:name": "GenomicTuples", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenomicTuples.html", "sc:version": "1.8.2" diff --git a/data/genomicus/genomicusbioschemas.jsonld b/data/genomicus/genomicusbioschemas.jsonld index 29e1ff0c28e71..b49e96bb28499 100644 --- a/data/genomicus/genomicusbioschemas.jsonld +++ b/data/genomicus/genomicusbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-7032-5650", - "@type": "schema:Person" - }, - { - "@id": "http://orcid.org/0000-0002-8209-173X", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/GENOMICUS", "@type": "sc:SoftwareApplication", @@ -29,12 +21,20 @@ } ], "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.", "sc:name": "GENOMICUS", "sc:url": "http://www.genomicus.biologie.ens.fr/genomicus/" + }, + { + "@id": "http://orcid.org/0000-0002-8209-173X", + "@type": "schema:Person" + }, + { + "@id": "http://orcid.org/0000-0001-7032-5650", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/genominator/bioconda_genominator.yaml b/data/genominator/bioconda_genominator.yaml index ab0eb7f144513..d317d24dff085 100644 --- a/data/genominator/bioconda_genominator.yaml +++ b/data/genominator/bioconda_genominator.yaml @@ -3,7 +3,6 @@ description: Tools for storing, accessing, analyzing and visualizing genomic dat home: https://bioconductor.org/packages/3.10/bioc/html/Genominator.html identifiers: - biotools:genominator -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genominator summary: Analyze, manage and store genomic data diff --git a/data/genominator/genominatorbioschemas.jsonld b/data/genominator/genominatorbioschemas.jsonld index c1ed0387dd0ff..86ada24cbe8d6 100644 --- a/data/genominator/genominatorbioschemas.jsonld +++ b/data/genominator/genominatorbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "Genominator", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Genominator.html", "sc:version": "1.28.0" diff --git a/data/genomix/genomixbioschemas.jsonld b/data/genomix/genomixbioschemas.jsonld index dd33220942b19..c74c25e78fc17 100644 --- a/data/genomix/genomixbioschemas.jsonld +++ b/data/genomix/genomixbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Parallel genome assembly system built from the ground up with scalability in mind. It can assemble large and high-coverage genomes from fastq files in a short time and produces assemblies similar to Velvet or Ray in quality.", "sc:name": "Genomix", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/uci-cbcl/genomix", "sc:version": "0.2.11" diff --git a/data/genomorama/genomoramabioschemas.jsonld b/data/genomorama/genomoramabioschemas.jsonld index 3292dc281b27e..c8a5f71d8ac4a 100644 --- a/data/genomorama/genomoramabioschemas.jsonld +++ b/data/genomorama/genomoramabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Genomorama", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://public.lanl.gov/jgans/genomorama/" } \ No newline at end of file diff --git a/data/genonets/genonetsbioschemas.jsonld b/data/genonets/genonetsbioschemas.jsonld index 240b198168465..7a164221ff9ba 100644 --- a/data/genonets/genonetsbioschemas.jsonld +++ b/data/genonets/genonetsbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/genonets", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "A genotype network is a graph in which vertices represent genotypes that have the same phenotype. This tool provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network; (iii) multiple interactive visualizations.", "sc:name": "Genonets", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://ieu-genonets.uzh.ch" } \ No newline at end of file diff --git a/data/genosa/genosabioschemas.jsonld b/data/genosa/genosabioschemas.jsonld index 6045a816f20b1..f7ea1652fd5bc 100644 --- a/data/genosa/genosabioschemas.jsonld +++ b/data/genosa/genosabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GeNOSA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://140.113.239.45/GeNOSA/" } \ No newline at end of file diff --git a/data/genoset/bioconda_genoset.yaml b/data/genoset/bioconda_genoset.yaml index 84bb19ad576f8..a914f14eb66ea 100644 --- a/data/genoset/bioconda_genoset.yaml +++ b/data/genoset/bioconda_genoset.yaml @@ -7,7 +7,6 @@ description: GenoSet provides an extension of the RangedSummarizedExperiment cla home: https://bioconductor.org/packages/3.10/bioc/html/genoset.html identifiers: - biotools:genoset -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genoset summary: A RangedSummarizedExperiment with methods for copy number analysis diff --git a/data/genoset/genosetbioschemas.jsonld b/data/genoset/genosetbioschemas.jsonld index ce1ee8340998d..90b13dc520a7c 100644 --- a/data/genoset/genosetbioschemas.jsonld +++ b/data/genoset/genosetbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "genoset", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genoset.html", "sc:version": "1.30.0" diff --git a/data/genotom/genotombioschemas.jsonld b/data/genotom/genotombioschemas.jsonld index 3f1afcf197e5e..9ded02cb5858b 100644 --- a/data/genotom/genotombioschemas.jsonld +++ b/data/genotom/genotombioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "A multigenome platform with information on genomes and gene annotations from different tomato cultivars. This platform includes genomes from Heinz 1706, Lucariello and Corbarino (tomato landaraces) with related genome browsers and transcriptomic data. It gives free access to the recently sequenced Italian tomato varieties and offers tools for their comparative analysis. (Tranchida-Lombardo et al., ‎2017; https://doi.org/10.1093/dnares/dsx045)", "sc:name": "Genotom", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://cab.unina.it/genotom/", "sc:version": "1" diff --git a/data/genotypeeval/genotypeevalbioschemas.jsonld b/data/genotypeeval/genotypeevalbioschemas.jsonld index 89dfedb1138f4..51fb4e6615d52 100644 --- a/data/genotypeeval/genotypeevalbioschemas.jsonld +++ b/data/genotypeeval/genotypeevalbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Takes in a gVCF or VCF and reports metrics to assess quality of calls.", "sc:name": "genotypeeval", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/genotypeeval.html", "sc:version": "1.4.0" diff --git a/data/genovar/genovarbioschemas.jsonld b/data/genovar/genovarbioschemas.jsonld index 2da72bc2222e2..ab1649eef9af2 100644 --- a/data/genovar/genovarbioschemas.jsonld +++ b/data/genovar/genovarbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Genovar", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://genovar.sourceforge.net/" } \ No newline at end of file diff --git a/data/genowap/genowapbioschemas.jsonld b/data/genowap/genowapbioschemas.jsonld index 9d9783cd0be7f..d0ceb37798661 100644 --- a/data/genowap/genowapbioschemas.jsonld +++ b/data/genowap/genowapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Post-GWAS prioritization method that integrates genomic functional annotation and GWAS test statistics. After prioritization, real disease-associated loci become easier to be identified.", "sc:name": "GenoWAP", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://genocanyon.med.yale.edu/GenoWAP" diff --git a/data/genphen/genphenbioschemas.jsonld b/data/genphen/genphenbioschemas.jsonld index c18085b615455..e3674c0ae8aa7 100644 --- a/data/genphen/genphenbioschemas.jsonld +++ b/data/genphen/genphenbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Simo Kitanovski", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This tool conducts genetic association studies by using statistical learning techniques such as random forests and support vector machines, as well as Bayesian inference with hierarchical models. It alleviates the multiple hypothesis problems and the need for P value corrections, which often lead to massive numbers of false negatives.", "sc:license": "GPL-2.0", diff --git a/data/genprobis/genprobisbioschemas.jsonld b/data/genprobis/genprobisbioschemas.jsonld index 6e18fd98cbd90..8180b922cd33a 100644 --- a/data/genprobis/genprobisbioschemas.jsonld +++ b/data/genprobis/genprobisbioschemas.jsonld @@ -21,19 +21,19 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5570222", { "@id": "https://doi.org/10.1093/nar/gkx420" }, - "pubmed:28498966" + "pubmed:28498966", + "pmcid:PMC5570222" ], "sc:description": "Maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein–protein, protein–nucleic acid, protein–compound, and protein–metal ion binding sites. Binding sites are defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach", "sc:featureList": [ { - "@id": "edam:operation_0417" + "@id": "edam:operation_2575" }, { - "@id": "edam:operation_2575" + "@id": "edam:operation_0417" } ], "sc:name": "GenProBiS", diff --git a/data/gens/gensbioschemas.jsonld b/data/gens/gensbioschemas.jsonld index 5a4d14b2bd734..b94bd86ed421f 100644 --- a/data/gens/gensbioschemas.jsonld +++ b/data/gens/gensbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GENS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sourceforge.net/projects/gensim/" } \ No newline at end of file diff --git a/data/genscalpel/genscalpelbioschemas.jsonld b/data/genscalpel/genscalpelbioschemas.jsonld index ca5128ecdfa39..d41e83bfd06cf 100644 --- a/data/genscalpel/genscalpelbioschemas.jsonld +++ b/data/genscalpel/genscalpelbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Program designed for specified-sequence retrieval and extraction from large-scale sequence sets in NCBI GenBank flatfile format.", "sc:name": "GenScalpel", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://code.google.com/archive/p/genscalpel/" } \ No newline at end of file diff --git a/data/genscan/genscanbioschemas.jsonld b/data/genscan/genscanbioschemas.jsonld index edc828b974295..9f16e076290dd 100644 --- a/data/genscan/genscanbioschemas.jsonld +++ b/data/genscan/genscanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Identify complete exon/intron structures of genes in genomic DNA. Novel features of the program include the capacity to predict multiple genes in a sequence, to deal with partial as well as complete genes, and to predict consistent sets of genes occurring on either or both DNA strands.", "sc:name": "GENSCAN", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://genes.mit.edu/GENSCANinfo.html" diff --git a/data/gensearchngs/gensearchngsbioschemas.jsonld b/data/gensearchngs/gensearchngsbioschemas.jsonld index eaa2a5292955d..41a3170c870af 100644 --- a/data/gensearchngs/gensearchngsbioschemas.jsonld +++ b/data/gensearchngs/gensearchngsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "GensearchNGS", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.phenosystems.com/www/index.php/products/gensearchngs" } \ No newline at end of file diff --git a/data/genskew/genskewbioschemas.jsonld b/data/genskew/genskewbioschemas.jsonld index cfda667b9a0cd..68c109a9b43da 100644 --- a/data/genskew/genskewbioschemas.jsonld +++ b/data/genskew/genskewbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/genskew", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:description": "G+C skew plot of microbial genomes.", "sc:name": "GenSkew", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "AT-CUBE", "sc:url": "http://genskew.csb.univie.ac.at/", diff --git a/data/genssi/genssibioschemas.jsonld b/data/genssi/genssibioschemas.jsonld index b486e90318e78..20f85cc4c36d2 100644 --- a/data/genssi/genssibioschemas.jsonld +++ b/data/genssi/genssibioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/genssi", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jan Hasenauer", - "Thomas Ligon" + "Thomas Ligon", + "Jan Hasenauer" ], "sc:additionalType": "Plug-in", "sc:description": "Generating Series for testing Structural Identifiability.", diff --git a/data/gentree/gentreebioschemas.jsonld b/data/gentree/gentreebioschemas.jsonld index d95e48c16c1ff..e172b56301cf9 100644 --- a/data/gentree/gentreebioschemas.jsonld +++ b/data/gentree/gentreebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1101/gr.238733.118", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GenTree", "@type": "sc:SoftwareApplication", @@ -22,19 +18,19 @@ "Web application" ], "sc:citation": [ + "pubmed:30862647", + "pmcid:PMC6442393", { "@id": "https://doi.org/10.1101/gr.238733.118" - }, - "pubmed:30862647", - "pmcid:PMC6442393" + } ], "sc:description": "Integrated resource for analyzing the evolution and function of primate-specific coding genes.", "sc:featureList": [ { - "@id": "edam:operation_0487" + "@id": "edam:operation_3766" }, { - "@id": "edam:operation_3766" + "@id": "edam:operation_0487" }, { "@id": "edam:operation_3501" @@ -43,11 +39,15 @@ "sc:license": "Other", "sc:name": "GenTree", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://gentree.ioz.ac.cn/index.php" + }, + { + "@id": "https://doi.org/10.1101/gr.238733.118", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/genvisr/genvisrbioschemas.jsonld b/data/genvisr/genvisrbioschemas.jsonld index ddf10222a034f..47aa7e819294a 100644 --- a/data/genvisr/genvisrbioschemas.jsonld +++ b/data/genvisr/genvisrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btw325", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/genvisr", "@type": "sc:SoftwareApplication", @@ -33,17 +37,13 @@ "sc:license": "GPL-3.0", "sc:name": "GenVisR", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GenVisR.html", "sc:version": "1.4.1" }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btw325", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-1928-7139", "@type": "schema:Person" diff --git a/data/geodis/geodisbioschemas.jsonld b/data/geodis/geodisbioschemas.jsonld index a4cbb78cd5370..7739a51737bc9 100644 --- a/data/geodis/geodisbioschemas.jsonld +++ b/data/geodis/geodisbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GEODIS", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://darwin.uvigo.es/software/geodis.html" } \ No newline at end of file diff --git a/data/geometadb/geometadbbioschemas.jsonld b/data/geometadb/geometadbbioschemas.jsonld index 44ce4a1758b28..3f93be6015acd 100644 --- a/data/geometadb/geometadbbioschemas.jsonld +++ b/data/geometadb/geometadbbioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btn520", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/geometadb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jack Zhu", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pubmed:18842599", @@ -31,16 +35,12 @@ "sc:license": "Artistic-2.0", "sc:name": "GEOmetadb", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GEOmetadb.html", "sc:version": "1.34.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btn520", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/geometree/geometreebioschemas.jsonld b/data/geometree/geometreebioschemas.jsonld index a6fa5b9ba12a0..37caa16d802ff 100644 --- a/data/geometree/geometreebioschemas.jsonld +++ b/data/geometree/geometreebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Python program to compute the geodesic path between two phylogenetic trees.", "sc:name": "GeoMeTree", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cibiv.at/software/geometree/" } \ No newline at end of file diff --git a/data/geoquery/geoquerybioschemas.jsonld b/data/geoquery/geoquerybioschemas.jsonld index 94bd81a48a10d..9b1793454be6f 100644 --- a/data/geoquery/geoquerybioschemas.jsonld +++ b/data/geoquery/geoquerybioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "GEOquery", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GEOquery.html", "sc:version": "2.40.0" diff --git a/data/geosearch/geosearchbioschemas.jsonld b/data/geosearch/geosearchbioschemas.jsonld index 9ba0a289c5bfd..7ae5eaea74f7e 100644 --- a/data/geosearch/geosearchbioschemas.jsonld +++ b/data/geosearch/geosearchbioschemas.jsonld @@ -16,16 +16,16 @@ "Library" ], "sc:author": [ - "Hongkai Ji", - "Zhicheng Ji" + "Zhicheng Ji", + "Hongkai Ji" ], "sc:description": "Extendable search engine for NCBI GEO (Gene Expression Omnibus). Instead of directly searching the term, it can find all the gene names contained in the search term and search all the alias of the gene names simultaneously in GEO database. It also provides other functions such as summarizing common biology keywords in the search results.", "sc:license": "GPL-2.0", "sc:name": "GEOsearch", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "BioConductor", "sc:url": "http://bioconductor.org/packages/release/bioc/html/GEOsearch.html", diff --git a/data/geosubmission/bioconda_geosubmission.yaml b/data/geosubmission/bioconda_geosubmission.yaml index ad30ac1824819..721d30c1dc102 100644 --- a/data/geosubmission/bioconda_geosubmission.yaml +++ b/data/geosubmission/bioconda_geosubmission.yaml @@ -4,7 +4,6 @@ description: Helps to easily submit a microarray dataset and the associated samp home: https://bioconductor.org/packages/3.10/bioc/html/GEOsubmission.html identifiers: - biotools:geosubmission -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-geosubmission diff --git a/data/geosubmission/geosubmissionbioschemas.jsonld b/data/geosubmission/geosubmissionbioschemas.jsonld index cf7d10497772f..779041f13cf3c 100644 --- a/data/geosubmission/geosubmissionbioschemas.jsonld +++ b/data/geosubmission/geosubmissionbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "GEOsubmission", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GEOsubmission.html", "sc:version": "1.26.0" diff --git a/data/gep2pep/gep2pepbioschemas.jsonld b/data/gep2pep/gep2pepbioschemas.jsonld index 725ea941d28ea..30debabe6f0ae 100644 --- a/data/gep2pep/gep2pepbioschemas.jsonld +++ b/data/gep2pep/gep2pepbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "gep2pep", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gep2pep.html", "sc:version": "1.0.0" diff --git a/data/gepard/gepardbioschemas.jsonld b/data/gepard/gepardbioschemas.jsonld index b9d1a0ac89624..18282c36dd43f 100644 --- a/data/gepard/gepardbioschemas.jsonld +++ b/data/gepard/gepardbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Genome pair rapid dotter.", "sc:name": "Gepard", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "AT-CUBE", "sc:url": "http://www.helmholtz-muenchen.de/icb/gepard", diff --git a/data/gepat/gepatbioschemas.jsonld b/data/gepat/gepatbioschemas.jsonld index eaf11ba8326d3..e680b075cb57d 100644 --- a/data/gepat/gepatbioschemas.jsonld +++ b/data/gepat/gepatbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "GEPAT", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://gepat.sourceforge.net/" } \ No newline at end of file diff --git a/data/gephex/gephexbioschemas.jsonld b/data/gephex/gephexbioschemas.jsonld index fc0642c42cfdc..2e739d20aa181 100644 --- a/data/gephex/gephexbioschemas.jsonld +++ b/data/gephex/gephexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GePhEx", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://gephex.ega-archive.org/" } \ No newline at end of file diff --git a/data/gepia/gepiabioschemas.jsonld b/data/gepia/gepiabioschemas.jsonld index 32a5453d96b73..81b3f54f93e28 100644 --- a/data/gepia/gepiabioschemas.jsonld +++ b/data/gepia/gepiabioschemas.jsonld @@ -14,22 +14,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC5570223", { "@id": "https://doi.org/10.1093/NAR/GKX247" }, - "pubmed:28407145", - "pmcid:PMC5570223" + "pubmed:28407145" ], "sc:description": "Gene Expression Profiling Interactive Analysis. Interactive and customizable functions including differential expression analysis, profiling plotting, correlation analysis, patient survival analysis, similar gene detection and dimensionality reduction analysis.", "sc:featureList": [ { - "@id": "edam:operation_0314" + "@id": "edam:operation_3463" }, { "@id": "edam:operation_0313" }, { - "@id": "edam:operation_3463" + "@id": "edam:operation_0314" } ], "sc:name": "GEPIA", diff --git a/data/germ-line_v_genes/germ-line_v_genesbioschemas.jsonld b/data/germ-line_v_genes/germ-line_v_genesbioschemas.jsonld index 6afcb6977bfa0..fecb09805f33a 100644 --- a/data/germ-line_v_genes/germ-line_v_genesbioschemas.jsonld +++ b/data/germ-line_v_genes/germ-line_v_genesbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "An integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.", "sc:name": "germ-line V genes", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.vbase2.org/" } \ No newline at end of file diff --git a/data/germonline/germonlinebioschemas.jsonld b/data/germonline/germonlinebioschemas.jsonld index e481654a69a5f..782f718a0be09 100644 --- a/data/germonline/germonlinebioschemas.jsonld +++ b/data/germonline/germonlinebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "High-throughput expression data relevant for germline development and fertility across species.", "sc:name": "Gametogenesis and reproductive tissue expression", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.germonline.org/" diff --git a/data/geross/gerossbioschemas.jsonld b/data/geross/gerossbioschemas.jsonld index 3a77ba49ae67e..744a668a19f5d 100644 --- a/data/geross/gerossbioschemas.jsonld +++ b/data/geross/gerossbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Other", "sc:name": "GerOSS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://www.geross.de/Default_en.aspx" diff --git a/data/geseq/geseqbioschemas.jsonld b/data/geseq/geseqbioschemas.jsonld index 84097508c8e4a..27e5ee1ec7518 100644 --- a/data/geseq/geseqbioschemas.jsonld +++ b/data/geseq/geseqbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkx391", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/geseq", "@type": "sc:SoftwareApplication", @@ -26,11 +22,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28486635", "pmcid:PMC5570176", { "@id": "https://doi.org/10.1093/nar/gkx391" - } + }, + "pubmed:28486635" ], "sc:description": "Rapid and accurate annotation of organellar genome sequences, in particular chloroplast genomes.", "sc:featureList": [ @@ -44,11 +40,15 @@ "sc:name": "GeSeq", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://chlorobox.mpimp-golm.mpg.de/geseq.html", "sc:version": "1.55" + }, + { + "@id": "https://doi.org/10.1093/nar/gkx391", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gespa/gespabioschemas.jsonld b/data/gespa/gespabioschemas.jsonld index da8db1a40e8d5..63265cb64d09c 100644 --- a/data/gespa/gespabioschemas.jsonld +++ b/data/gespa/gespabioschemas.jsonld @@ -18,8 +18,8 @@ { "@id": "https://doi.org/10.1186/S12859-015-0673-2" }, - "pmcid:PMC4513380", - "pubmed:26206375" + "pubmed:26206375", + "pmcid:PMC4513380" ], "sc:description": "Classifying nsSNPs to predict disease association.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "GESPA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/gespa/" }, diff --git a/data/gesper/gesperbioschemas.jsonld b/data/gesper/gesperbioschemas.jsonld index b97b52d507a50..38c6d0b69f6b2 100644 --- a/data/gesper/gesperbioschemas.jsonld +++ b/data/gesper/gesperbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Fabian Schmich", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Estimates gene-specific phenotypes from off-target confounded RNAi screens. The phenotype of each siRNA is modeled based on on-targeted and off-targeted genes, using a regularized linear regression model.", "sc:license": "GPL-3.0", "sc:name": "gespeR", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gespeR.html", "sc:version": "1.6.0" diff --git a/data/gess/gessbioschemas.jsonld b/data/gess/gessbioschemas.jsonld index 5c2a7a5612d72..701c21a8086c1 100644 --- a/data/gess/gessbioschemas.jsonld +++ b/data/gess/gessbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/gess", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Victor Jin", - "Zhenqing Ye" + "Zhenqing Ye", + "Victor Jin" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:24369421", "sc:description": "Novel computational method for de novo detection of skipping event sites from raw RNA-seq reads without prior knowledge of gene annotations, as well as for determining the dominant isoform generated from such sites.", "sc:name": "GESS", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://compbio.uthscsa.edu/GESS_Web/" } \ No newline at end of file diff --git a/data/getdifference/getdifferencebioschemas.jsonld b/data/getdifference/getdifferencebioschemas.jsonld index ff21048e89b9d..ff94cfac63786 100644 --- a/data/getdifference/getdifferencebioschemas.jsonld +++ b/data/getdifference/getdifferencebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Gets all the regions of the genome, except the one given or get all the elements from the first set which does not ovelap with the second set (at the nucleotide level).", "sc:name": "getdifference", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getdifferentialexpression/getdifferentialexpressionbioschemas.jsonld b/data/getdifferentialexpression/getdifferentialexpressionbioschemas.jsonld index 10c06995a087b..5921a0a0b067a 100644 --- a/data/getdifferentialexpression/getdifferentialexpressionbioschemas.jsonld +++ b/data/getdifferentialexpression/getdifferentialexpressionbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file.", "sc:name": "getdifferentialexpression", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getdistance/getdistancebioschemas.jsonld b/data/getdistance/getdistancebioschemas.jsonld index 1fd7336b72b1c..b4dc4128bfa2b 100644 --- a/data/getdistance/getdistancebioschemas.jsonld +++ b/data/getdistance/getdistancebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Give the distances between every data from the first input set and the data from the second input set.", "sc:name": "getdistance", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getdistribution/getdistributionbioschemas.jsonld b/data/getdistribution/getdistributionbioschemas.jsonld index e2f1998342e19..6988decaa6448 100644 --- a/data/getdistribution/getdistributionbioschemas.jsonld +++ b/data/getdistribution/getdistributionbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Get the distribution of the genomic coordinates on a genome.", "sc:name": "getdistribution", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", diff --git a/data/getexons/getexonsbioschemas.jsonld b/data/getexons/getexonsbioschemas.jsonld index 8d850af928b83..521e65ac954a9 100644 --- a/data/getexons/getexonsbioschemas.jsonld +++ b/data/getexons/getexonsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Get the exons of a set of transcripts.", "sc:name": "getexons", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", diff --git a/data/getflanking/getflankingbioschemas.jsonld b/data/getflanking/getflankingbioschemas.jsonld index 637701aae46ae..655139e404c86 100644 --- a/data/getflanking/getflankingbioschemas.jsonld +++ b/data/getflanking/getflankingbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Get the flanking regions of a set of reference.", "sc:name": "getflanking", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getintrons/getintronsbioschemas.jsonld b/data/getintrons/getintronsbioschemas.jsonld index bdde80ffabfd7..41912374626a2 100644 --- a/data/getintrons/getintronsbioschemas.jsonld +++ b/data/getintrons/getintronsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "getintrons", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getletterdistribution1/getletterdistribution1bioschemas.jsonld b/data/getletterdistribution1/getletterdistribution1bioschemas.jsonld index cf702ea2e7bfe..f51c10c6c6d4b 100644 --- a/data/getletterdistribution1/getletterdistribution1bioschemas.jsonld +++ b/data/getletterdistribution1/getletterdistribution1bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Calculate distribution for each nucleotide per position for all short reads (S-MART).", "sc:name": "getletterdistribution1", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getnumber/getnumberbioschemas.jsonld b/data/getnumber/getnumberbioschemas.jsonld index 08b8b93d166d4..5f6beefa58e5e 100644 --- a/data/getnumber/getnumberbioschemas.jsonld +++ b/data/getnumber/getnumberbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster.", "sc:name": "getnumber", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getorf/getorfbioschemas.jsonld b/data/getorf/getorfbioschemas.jsonld index 006c097b3694a..f2a5bc21490a5 100644 --- a/data/getorf/getorfbioschemas.jsonld +++ b/data/getorf/getorfbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "EMBOSS Contributors", - "UK BBSRC" + "UK MRC", + "EMBOSS Contributors" ], "sc:description": "Find and extract open reading frames (ORFs).", "sc:funder": [ + "UK MRC", "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "getorf", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/getreaddistribution/getreaddistributionbioschemas.jsonld b/data/getreaddistribution/getreaddistributionbioschemas.jsonld index 9da74b27ebdbf..2159c7ee53e1b 100644 --- a/data/getreaddistribution/getreaddistributionbioschemas.jsonld +++ b/data/getreaddistribution/getreaddistributionbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Plot the number of identical reads and give the most represented.", "sc:name": "getreaddistribution", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getsequence/getsequencebioschemas.jsonld b/data/getsequence/getsequencebioschemas.jsonld index e86e9a16b71b1..9b6dfbbc7d591 100644 --- a/data/getsequence/getsequencebioschemas.jsonld +++ b/data/getsequence/getsequencebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Get a single sequence in a FASTA file.", "sc:name": "getsequence", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", diff --git a/data/getsizes/getsizesbioschemas.jsonld b/data/getsizes/getsizesbioschemas.jsonld index 507cec15eeff9..0d056b38f8d57 100644 --- a/data/getsizes/getsizesbioschemas.jsonld +++ b/data/getsizes/getsizesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Get the sizes of a set of genomic coordinates.", "sc:name": "getsizes", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getwigdata/getwigdatabioschemas.jsonld b/data/getwigdata/getwigdatabioschemas.jsonld index 4dbc8422b45bc..09f46d342f0ea 100644 --- a/data/getwigdata/getwigdatabioschemas.jsonld +++ b/data/getwigdata/getwigdatabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "getwigdata", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getwigdistance/getwigdistancebioschemas.jsonld b/data/getwigdistance/getwigdistancebioschemas.jsonld index 01186e987bdb0..e84dcd7edcaac 100644 --- a/data/getwigdistance/getwigdistancebioschemas.jsonld +++ b/data/getwigdistance/getwigdistancebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome).", "sc:name": "getwigdistance", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/getwigprofile/getwigprofilebioschemas.jsonld b/data/getwigprofile/getwigprofilebioschemas.jsonld index a3a38a3b0b681..1ea88732b7fd5 100644 --- a/data/getwigprofile/getwigprofilebioschemas.jsonld +++ b/data/getwigprofile/getwigprofilebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).", "sc:name": "getwigprofile", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/gfapy/gfapybioschemas.jsonld b/data/gfapy/gfapybioschemas.jsonld index 1f79f1527936a..debe7bdcfb98d 100644 --- a/data/gfapy/gfapybioschemas.jsonld +++ b/data/gfapy/gfapybioschemas.jsonld @@ -12,14 +12,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Giorgio Gonnella", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Flexible and extensible software library for handling sequence graphs in Python.", "sc:name": "GfaPy", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ggonnella/gfapy" } \ No newline at end of file diff --git a/data/gfasparse/gfasparsebioschemas.jsonld b/data/gfasparse/gfasparsebioschemas.jsonld index f8d892433601d..02ecd4d3eea70 100644 --- a/data/gfasparse/gfasparsebioschemas.jsonld +++ b/data/gfasparse/gfasparsebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/gfasparse", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Suleiman Ali Khan", - "Eemeli Leppäaho" + "Eemeli Leppäaho", + "Suleiman Ali Khan" ], "sc:additionalType": "Library", "sc:citation": "pubmed:25161239", diff --git a/data/gfbio/gfbiobioschemas.jsonld b/data/gfbio/gfbiobioschemas.jsonld index 11738ea8ca629..ae48e440c75e3 100644 --- a/data/gfbio/gfbiobioschemas.jsonld +++ b/data/gfbio/gfbiobioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/gfbio", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", "Web service", + "Web application", "Web API" ], "sc:description": "The German Federation for Biological Data was established as a sustainable, national infrastructure to facilitate data sharing for the biological environmental sciences. It supports the complete life cycle of research data management, from planning, through acquisition, to publication. Research data are constantly increasing in both size and complexity, offering not only new analytical possibilities, but also posing new challenges to data processing, integration and safeguarding.", "sc:funder": "Deutsche Forschungsgemeinschaft (DFG)", "sc:name": "GFBio", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.gfbio.org" } \ No newline at end of file diff --git a/data/gff-ex/gff-exbioschemas.jsonld b/data/gff-ex/gff-exbioschemas.jsonld index 26482a734d9cd..8930bced7528e 100644 --- a/data/gff-ex/gff-exbioschemas.jsonld +++ b/data/gff-ex/gff-exbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1756-0500-7-315", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gff-ex", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dinesh Gupta", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:24885931", - "pmcid:PMC4045924", { "@id": "https://doi.org/10.1186/1756-0500-7-315" - } + }, + "pmcid:PMC4045924", + "pubmed:24885931" ], "sc:description": "Automated feature-based extraction of sequences from a GFF file.", "sc:featureList": { @@ -28,10 +32,6 @@ "sc:name": "GFF-Ex", "sc:operatingSystem": "Linux", "sc:url": "http://bioinfo.icgeb.res.in/gff/" - }, - { - "@id": "https://doi.org/10.1186/1756-0500-7-315", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gffcompare/gffcomparebioschemas.jsonld b/data/gffcompare/gffcomparebioschemas.jsonld index 647babcb0ef0c..3b8e4086b23ff 100644 --- a/data/gffcompare/gffcomparebioschemas.jsonld +++ b/data/gffcompare/gffcomparebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "gffcompare", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://ccb.jhu.edu/software/stringtie/gff.shtml" } \ No newline at end of file diff --git a/data/gflasso/gflassobioschemas.jsonld b/data/gflasso/gflassobioschemas.jsonld index 20516f76ab506..1031b6d3a3766 100644 --- a/data/gflasso/gflassobioschemas.jsonld +++ b/data/gflasso/gflassobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software for association analysis that searches for genetic variations influencing a group of correlated traits.", "sc:name": "GFlasso", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.sailing.cs.cmu.edu/main/?page_id=462" } \ No newline at end of file diff --git a/data/gfsat/gfsatbioschemas.jsonld b/data/gfsat/gfsatbioschemas.jsonld index 67df2cc06301a..08a6d24def02f 100644 --- a/data/gfsat/gfsatbioschemas.jsonld +++ b/data/gfsat/gfsatbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/gfsat", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Desktop application" + "Desktop application", + "Web application" ], "sc:citation": "pubmed:23628645", "sc:description": "Web tool that can be used to Analysis the functional similarity of genes in the forms of “two genes”, “two gene groups “, and “pairwise gene groups” based on GO Annotation(GOA) and GO semantic similarity measurements.", "sc:name": "GFSAT", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://118.178.236.158/GFSAT/index.php" } \ No newline at end of file diff --git a/data/gganatogram/gganatogrambioschemas.jsonld b/data/gganatogram/gganatogrambioschemas.jsonld index cf2075948cc4a..04693eb5c2cea 100644 --- a/data/gganatogram/gganatogrambioschemas.jsonld +++ b/data/gganatogram/gganatogrambioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/f1000research.16409.2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/gganatogram", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jesper Maag", "sc:additionalType": [ - "Library", - "Web application" + "Web application", + "Library" ], "sc:citation": [ { "@id": "https://doi.org/10.12688/f1000research.16409.2" }, - "pubmed:30467523", - "pmcid:PMC6208569" + "pmcid:PMC6208569", + "pubmed:30467523" ], "sc:description": "R package for modular visualisation of anatograms and tissues based on ggplot2.", "sc:featureList": [ @@ -39,10 +35,14 @@ ], "sc:name": "gganatogram", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/jespermaag/gganatogram" + }, + { + "@id": "https://doi.org/10.12688/f1000research.16409.2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ggb/ggbbioschemas.jsonld b/data/ggb/ggbbioschemas.jsonld index 9b71cc3fc7e13..0817bfff102f9 100644 --- a/data/ggb/ggbbioschemas.jsonld +++ b/data/ggb/ggbbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "The GGB (Gaggle Genome Browser) is an open source software tool for visualizing high-density data plotted against coordinates on the genome. Tiling arrays, ChIP-chip, and high-throughput sequencing are a few potential use-cases. The genome browser is designed to gracefully handle large datasets, allow easy import of user data, and interoperate with other bioinformatics tools through the Gaggle framework.", "sc:name": "GGB", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://gaggle.systemsbiology.net/docs/geese/genomebrowser/", diff --git a/data/ggbase/bioconda_ggbase.yaml b/data/ggbase/bioconda_ggbase.yaml index b9e79abc18b67..8e36e01774e0a 100644 --- a/data/ggbase/bioconda_ggbase.yaml +++ b/data/ggbase/bioconda_ggbase.yaml @@ -3,7 +3,6 @@ description: infrastructure home: https://bioconductor.org/packages/3.10/bioc/html/GGBase.html identifiers: - biotools:ggbase -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-ggbase summary: GGBase infrastructure for genetics of gene expression package GGtools diff --git a/data/ggbase/ggbasebioschemas.jsonld b/data/ggbase/ggbasebioschemas.jsonld index 8ab59b84a6a69..180201b07f5dd 100644 --- a/data/ggbase/ggbasebioschemas.jsonld +++ b/data/ggbase/ggbasebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "GGBase", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GGBase.html", "sc:version": "3.36.0" diff --git a/data/ggbio/ggbiobioschemas.jsonld b/data/ggbio/ggbiobioschemas.jsonld index 2682f324ae7a4..6c9ec39e74642 100644 --- a/data/ggbio/ggbiobioschemas.jsonld +++ b/data/ggbio/ggbiobioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/gb-2012-13-8-r77", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ggbio", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Lawrence", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pmcid:PMC4053745", "pubmed:22937822", { "@id": "https://doi.org/10.1186/gb-2012-13-8-r77" - }, - "pmcid:PMC4053745" + } ], "sc:description": "The package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, those often asked of high throughput genomics data. All core BioConductor appropriate data structures are supported. The package supports detailed views of genomic regions and genome-wide overviews. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.", "sc:featureList": { @@ -31,16 +35,12 @@ "sc:license": "Artistic-2.0", "sc:name": "ggbio", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ggbio.html", "sc:version": "1.22.3" - }, - { - "@id": "https://doi.org/10.1186/gb-2012-13-8-r77", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ggcyto/bioconda_ggcyto.yaml b/data/ggcyto/bioconda_ggcyto.yaml index 524a20f8973a5..8e6171f2c46f3 100644 --- a/data/ggcyto/bioconda_ggcyto.yaml +++ b/data/ggcyto/bioconda_ggcyto.yaml @@ -6,7 +6,6 @@ description: With the dedicated fortify method implemented for flowSet, ncdfFlow home: https://bioconductor.org/packages/3.10/bioc/html/ggcyto.html identifiers: - biotools:ggcyto -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-ggcyto summary: Visualize Cytometry data with ggplot diff --git a/data/ggd-lasso/ggd-lassobioschemas.jsonld b/data/ggd-lasso/ggd-lassobioschemas.jsonld index 5d4b689be0de2..599a0f14748ea 100644 --- a/data/ggd-lasso/ggd-lassobioschemas.jsonld +++ b/data/ggd-lasso/ggd-lassobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Robust approach for eQTL mapping.", "sc:name": "GGD-Lasso", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.cs.unc.edu/~weicheng/" } \ No newline at end of file diff --git a/data/ggea/ggeabioschemas.jsonld b/data/ggea/ggeabioschemas.jsonld index ced51a58c11ee..2b29938fccd13 100644 --- a/data/ggea/ggeabioschemas.jsonld +++ b/data/ggea/ggeabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Intuitive method to detect consistently and coherently enriched gene sets, based on prior knowledge derived from directed gene regulatory networks.", "sc:name": "GGEA", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://drupal.bio.ifi.lmu.de/en/GGEA/index.html" diff --git a/data/ggms/ggmsbioschemas.jsonld b/data/ggms/ggmsbioschemas.jsonld index 9bcbb5c678e24..00f5e0681b71a 100644 --- a/data/ggms/ggmsbioschemas.jsonld +++ b/data/ggms/ggmsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Unlicense", "sc:name": "GGMs", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/V-Bernal/GGM-Shrinkage" diff --git a/data/ggost/ggostbioschemas.jsonld b/data/ggost/ggostbioschemas.jsonld index a3aa3194b9c7e..f96d9eeee5c11 100644 --- a/data/ggost/ggostbioschemas.jsonld +++ b/data/ggost/ggostbioschemas.jsonld @@ -15,8 +15,8 @@ "Jüri Reimand" ], "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Central tool of the g:Profiler web server. It maps a user provided gene list to various sources of functional information and determines significantly enriched pathways, processes and other annotations.", "sc:license": "Freeware", diff --git a/data/ggplot2/ggplot2bioschemas.jsonld b/data/ggplot2/ggplot2bioschemas.jsonld index 9ae94c7443b55..dde59b68b4d7c 100644 --- a/data/ggplot2/ggplot2bioschemas.jsonld +++ b/data/ggplot2/ggplot2bioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Plotting system for R, based on the grammar of graphics.", "sc:name": "ggplot2", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://ggplot2.org/" diff --git a/data/ggrna/ggrnabioschemas.jsonld b/data/ggrna/ggrnabioschemas.jsonld index 78929933f3927..98ae4457497c5 100644 --- a/data/ggrna/ggrnabioschemas.jsonld +++ b/data/ggrna/ggrnabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Google-like, ultrafast search engine for genes and transcripts. Users input gene names, IDs, gene descriptions, annotations or sequence and are returned relevant RefSeq transcripts.", "sc:name": "GGRNA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://GGRNA.dbcls.jp/" } \ No newline at end of file diff --git a/data/ggseqlogo/ggseqlogobioschemas.jsonld b/data/ggseqlogo/ggseqlogobioschemas.jsonld index 3a53e10b2199f..29a67ff9f8448 100644 --- a/data/ggseqlogo/ggseqlogobioschemas.jsonld +++ b/data/ggseqlogo/ggseqlogobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ggseqlogo", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/ggseqlogo/" } \ No newline at end of file diff --git a/data/ggtools/ggtoolsbioschemas.jsonld b/data/ggtools/ggtoolsbioschemas.jsonld index 10da716cbfdd3..23302d9f58432 100644 --- a/data/ggtools/ggtoolsbioschemas.jsonld +++ b/data/ggtools/ggtoolsbioschemas.jsonld @@ -14,31 +14,31 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "VJ Carey", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:19349284", { "@id": "https://doi.org/10.1093/bioinformatics/btp169" }, + "pubmed:19349284", "pmcid:PMC2682516" ], "sc:description": "Software and data for analyses in genetics of gene expression and/or DNA methylation.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_3204" }, { - "@id": "edam:operation_3204" + "@id": "edam:operation_2495" } ], "sc:license": "Artistic-2.0", "sc:name": "GGtools", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GGtools.html", "sc:version": "5.10.0" diff --git a/data/ggtree/ggtreebioschemas.jsonld b/data/ggtree/ggtreebioschemas.jsonld index 59cb039222fe6..3c87bc501eb72 100644 --- a/data/ggtree/ggtreebioschemas.jsonld +++ b/data/ggtree/ggtreebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "ggtree", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ggtree.html", diff --git a/data/ghost/ghostbioschemas.jsonld b/data/ghost/ghostbioschemas.jsonld index b12ef22cebde4..068b692289e2a 100644 --- a/data/ghost/ghostbioschemas.jsonld +++ b/data/ghost/ghostbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software package for global biological network alignment. It computes alignments based on a novel spectral signature for comparing the topological similarity of nodes across networks.", "sc:name": "GHOST", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.cs.cmu.edu/~ckingsf/software/ghost/index.html" } \ No newline at end of file diff --git a/data/giant/giantbioschemas.jsonld b/data/giant/giantbioschemas.jsonld index b0fa0ba787cd0..63db0dd27f706 100644 --- a/data/giant/giantbioschemas.jsonld +++ b/data/giant/giantbioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC3897944", - "pubmed:24423161", { "@id": "https://doi.org/10.1186/1471-2105-15-12" - } + }, + "pubmed:24423161" ], "sc:description": "Pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "GIANT", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://giant.hgc.jp/" }, diff --git a/data/giardiadb/giardiadbbioschemas.jsonld b/data/giardiadb/giardiadbbioschemas.jsonld index 034e63884dc5b..4a3ee81650ced 100644 --- a/data/giardiadb/giardiadbbioschemas.jsonld +++ b/data/giardiadb/giardiadbbioschemas.jsonld @@ -27,8 +27,8 @@ "@id": "edam:topic_0621" }, "sc:citation": [ - "pmcid:PMC2686445", "pubmed:18824479", + "pmcid:PMC2686445", { "@id": "https://doi.org/10.1093/nar/gkn631" } @@ -39,8 +39,8 @@ }, "sc:name": "Giardia genome resources (GiardiaDB)", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://giardiadb.org/giardiadb/" diff --git a/data/gibbscluster/gibbsclusterbioschemas.jsonld b/data/gibbscluster/gibbsclusterbioschemas.jsonld index 4c74a31fbfd52..d80f469496e73 100644 --- a/data/gibbscluster/gibbsclusterbioschemas.jsonld +++ b/data/gibbscluster/gibbsclusterbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-8036-2647", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/gibbscluster", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Web application" ], "sc:citation": [ + "pubmed:28407089", { "@id": "https://doi.org/10.1093/NAR/GKX248" }, - "pmcid:PMC5570237", - "pubmed:28407089" + "pmcid:PMC5570237" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-8036-2647" @@ -34,18 +30,22 @@ "sc:description": "Simultaneous alignment and clustering of peptide data. It takes as input a set of peptide sequences and clusters them into meaningful groups. It returns the optimal number of clusters it identified, together with the sequence alignment and sequence motif characterizing each cluster.", "sc:featureList": [ { - "@id": "edam:operation_3629" + "@id": "edam:operation_0238" }, { "@id": "edam:operation_3432" }, { - "@id": "edam:operation_0238" + "@id": "edam:operation_3629" } ], "sc:name": "GibbsCluster", "sc:url": "http://www.cbs.dtu.dk/services/GibbsCluster-2.0" }, + { + "@id": "http://orcid.org/0000-0002-8036-2647", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/NAR/GKX248", "@type": "sc:CreativeWork" diff --git a/data/gidb/gidbbioschemas.jsonld b/data/gidb/gidbbioschemas.jsonld index 2caf8fa71b13b..458901e9c6a86 100644 --- a/data/gidb/gidbbioschemas.jsonld +++ b/data/gidb/gidbbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/DATABASE/BAZ051", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GIDB", "@type": "sc:SoftwareApplication", @@ -21,15 +17,15 @@ "Xiaoyan Zhang" ], "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ - "pmcid:PMC6517830", + "pubmed:31089686", { "@id": "https://doi.org/10.1093/DATABASE/BAZ051" }, - "pubmed:31089686" + "pmcid:PMC6517830" ], "sc:description": "Knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal (GI) cancer.", "sc:featureList": { @@ -38,11 +34,15 @@ "sc:license": "Unlicense", "sc:name": "GIDB", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bmtongji.cn/GIDB/index.html" + }, + { + "@id": "https://doi.org/10.1093/DATABASE/BAZ051", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gidetector/gidetectorbioschemas.jsonld b/data/gidetector/gidetectorbioschemas.jsonld index 5403ba06df354..cdd97874ee9d0 100644 --- a/data/gidetector/gidetectorbioschemas.jsonld +++ b/data/gidetector/gidetectorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GIDetector", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www5.esu.edu/cpsc/bioinfo/software/GIDetector/" } \ No newline at end of file diff --git a/data/giggle/gigglebioschemas.jsonld b/data/giggle/gigglebioschemas.jsonld index 762e7492b4514..c7beb4a79270e 100644 --- a/data/giggle/gigglebioschemas.jsonld +++ b/data/giggle/gigglebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "GIGGLE", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/ryanlayer/giggle" } \ No newline at end of file diff --git a/data/gigwa/gigwabioschemas.jsonld b/data/gigwa/gigwabioschemas.jsonld index 8c8de2373a3a6..ea879f1aecd88 100644 --- a/data/gigwa/gigwabioschemas.jsonld +++ b/data/gigwa/gigwabioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ051", "@type": "sc:CreativeWork" }, + { + "@id": "https://doi.org/10.1186/s13742-016-0131-8", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0001-7429-2091", "@type": "schema:Person" @@ -25,16 +29,16 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31077313", + { + "@id": "https://doi.org/10.1186/s13742-016-0131-8" + }, { "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ051" }, "pubmed:27267926", - "pmcid:PMC4897896", + "pubmed:31077313", "pmcid:PMC6511067", - { - "@id": "https://doi.org/10.1186/s13742-016-0131-8" - } + "pmcid:PMC4897896" ], "sc:description": "The Gigwa application, which stands for “Genotype Investigator for Genome-Wide Analyses”, provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time. Gigwa provides the means to export filtered data into several popular formats and features connectivity not only with online genomic tools, but also with standalone software such as FlapJack or IGV. Additionnally, Gigwa-hosted datasets are interoperable via two standard REST APIs: GA4GH and BrAPI.", "sc:featureList": [ @@ -42,28 +46,24 @@ "@id": "edam:operation_3695" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_2409" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_2409" + "@id": "edam:operation_3196" } ], "sc:license": "AGPL-3.0", "sc:name": "Gigwa", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.southgreen.fr/content/gigwa", "sc:version": "2.2" - }, - { - "@id": "https://doi.org/10.1186/s13742-016-0131-8", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/giira/giirabioschemas.jsonld b/data/giira/giirabioschemas.jsonld index bf1ea8ca1474e..f246cd8db5121 100644 --- a/data/giira/giirabioschemas.jsonld +++ b/data/giira/giirabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment.", "sc:name": "GIIRA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://sourceforge.net/projects/giira/" } \ No newline at end of file diff --git a/data/gimli/gimlibioschemas.jsonld b/data/gimli/gimlibioschemas.jsonld index 91b3245c45043..331419f697101 100644 --- a/data/gimli/gimlibioschemas.jsonld +++ b/data/gimli/gimlibioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-14-54", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gimli", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:23413997", - "pmcid:PMC3651325", { "@id": "https://doi.org/10.1186/1471-2105-14-54" - } + }, + "pmcid:PMC3651325", + "pubmed:23413997" ], "sc:description": "Open source and high-performance biomedical name recognition.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "NCSA", "sc:name": "Gimli", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/BMDSoftware/neji" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-14-54", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gina/ginabioschemas.jsonld b/data/gina/ginabioschemas.jsonld index 74b732c5b2746..0b3c87d91a220 100644 --- a/data/gina/ginabioschemas.jsonld +++ b/data/gina/ginabioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0160439", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gina", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Juan Zalapa", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC4986961", { "@id": "https://doi.org/10.1371/journal.pone.0160439" }, - "pubmed:27529547", - "pmcid:PMC4986961" + "pubmed:27529547" ], "sc:description": "GiNA is an open-source software which is a simple tool for measuring horticultural traits such as shape- and color-related parameters of fruits, vegetables, and seeds for horticultural phenotyping.", "sc:featureList": { @@ -31,15 +35,11 @@ "sc:license": "GPL-3.0", "sc:name": "GiNA", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/GiNA/index.html", "sc:version": "1.0.1" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0160439", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/giniclust2/giniclust2bioschemas.jsonld b/data/giniclust2/giniclust2bioschemas.jsonld index d37a7a7624a6e..7cbb33085d466 100644 --- a/data/giniclust2/giniclust2bioschemas.jsonld +++ b/data/giniclust2/giniclust2bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "GiniClust2", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/dtsoucas/GiniClust2" } \ No newline at end of file diff --git a/data/ginkgo/ginkgobioschemas.jsonld b/data/ginkgo/ginkgobioschemas.jsonld index b48fb0a800b62..45d85117f0d46 100644 --- a/data/ginkgo/ginkgobioschemas.jsonld +++ b/data/ginkgo/ginkgobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-2-Clause", "sc:name": "Ginkgo", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://qb.cshl.edu/ginkgo" diff --git a/data/ginkgo_simulation/ginkgo_simulationbioschemas.jsonld b/data/ginkgo_simulation/ginkgo_simulationbioschemas.jsonld index ee3785ec006a0..cb16a7f4acad1 100644 --- a/data/ginkgo_simulation/ginkgo_simulationbioschemas.jsonld +++ b/data/ginkgo_simulation/ginkgo_simulationbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Agent-based forward-time simulation to produce gene genealogies and incidence (occurrence) data for multiple populations of multiple species in a spatially-explicit and environmentally-heterogenous framework.", "sc:name": "Ginkgo", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://phylo.bio.ku.edu/ginkgo/index.html" } \ No newline at end of file diff --git a/data/ginsim/ginsimbioschemas.jsonld b/data/ginsim/ginsimbioschemas.jsonld index 49f282b4fd1ee..fab9df580988f 100644 --- a/data/ginsim/ginsimbioschemas.jsonld +++ b/data/ginsim/ginsimbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GINsim", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://ginsim.org/", "sc:version": "3.0" diff --git a/data/gips/gipsbioschemas.jsonld b/data/gips/gipsbioschemas.jsonld index 61e1d03043e21..a74bfef08fd66 100644 --- a/data/gips/gipsbioschemas.jsonld +++ b/data/gips/gipsbioschemas.jsonld @@ -21,18 +21,18 @@ "@id": "https://bio.tools/gips", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Weitao Wang", { "@id": "http://orcid.org/0000-0002-1196-6826" - } + }, + "Weitao Wang" ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4825123", "pubmed:26842621", { "@id": "https://doi.org/10.1104/pp.15.01327" - } + }, + "pmcid:PMC4825123" ], "sc:description": "Software which considers a range of experimental and analysis choices in sequencing-based forward genetics studies within an integrated probabilistic framework, which enables direct gene cloning from the sequencing of several unrelated mutants of the same phenotype without the need to create segregation populations.", "sc:featureList": { @@ -40,9 +40,9 @@ }, "sc:name": "GIPS", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/synergy-zju/gips/wiki" } diff --git a/data/girafe/girafebioschemas.jsonld b/data/girafe/girafebioschemas.jsonld index 0b0abf9593978..cbeb149b80ed7 100644 --- a/data/girafe/girafebioschemas.jsonld +++ b/data/girafe/girafebioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-1471-1295", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btq531", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/girafe", "@type": "sc:SoftwareApplication", @@ -39,14 +47,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/girafe.html", "sc:version": "1.26.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btq531", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-1471-1295", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/gispa/gispabioschemas.jsonld b/data/gispa/gispabioschemas.jsonld index c8e7912cafa5f..b9286de5426d8 100644 --- a/data/gispa/gispabioschemas.jsonld +++ b/data/gispa/gispabioschemas.jsonld @@ -17,11 +17,11 @@ }, "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC4838358", "pubmed:26826710", { "@id": "https://doi.org/10.1093/nar/gkv1503" - }, - "pmcid:PMC4838358" + } ], "sc:description": "It is a method intended for the researchers who are interested in defining gene sets with similar, a priori specified molecular profile.", "sc:featureList": { @@ -30,20 +30,20 @@ "sc:license": "GPL-2.0", "sc:name": "GISPA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GISPA.html", "sc:version": "1.4.0" }, - { - "@id": "https://doi.org/10.1093/nar/gkv1503", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-9029-3737", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gkv1503", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/give/givebioschemas.jsonld b/data/give/givebioschemas.jsonld index f4dbe47994c05..24f015095d1b2 100644 --- a/data/give/givebioschemas.jsonld +++ b/data/give/givebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "GIVE", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://zhong-lab-ucsd.github.io/GIVE_homepage/" diff --git a/data/gk_arrays/gk_arraysbioschemas.jsonld b/data/gk_arrays/gk_arraysbioschemas.jsonld index fafe7e2e2c36f..411f3aec25fb8 100644 --- a/data/gk_arrays/gk_arraysbioschemas.jsonld +++ b/data/gk_arrays/gk_arraysbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Gk arrays", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.atgc-montpellier.fr/gkarrays" } \ No newline at end of file diff --git a/data/glad/gladbioschemas.jsonld b/data/glad/gladbioschemas.jsonld index 3d8e9a5a6c5db..bbddbf3764597 100644 --- a/data/glad/gladbioschemas.jsonld +++ b/data/glad/gladbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Philippe Hupe", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.", "sc:license": "GPL-2.0", "sc:name": "GLAD", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GLAD.html", "sc:version": "2.38.0" diff --git a/data/glad_tumor/glad_tumorbioschemas.jsonld b/data/glad_tumor/glad_tumorbioschemas.jsonld index f9433a9583aaf..8c811cf11c6f2 100644 --- a/data/glad_tumor/glad_tumorbioschemas.jsonld +++ b/data/glad_tumor/glad_tumorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Mixed-membership classification model that simultaneously learns a sparse biomarker signature for each subtype as well as a distribution over subtypes for each sample.", "sc:name": "GLaD", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://genomics.wpi.edu/glad/" } \ No newline at end of file diff --git a/data/glamm/glammbioschemas.jsonld b/data/glamm/glammbioschemas.jsonld index e9ce7bcbfef12..6c008f21cf85e 100644 --- a/data/glamm/glammbioschemas.jsonld +++ b/data/glamm/glammbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Web server for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic data and investigating the construction of novel, transgenic pathways.", "sc:name": "GLAMM", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://glamm.lbl.gov" } \ No newline at end of file diff --git a/data/glanet/glanetbioschemas.jsonld b/data/glanet/glanetbioschemas.jsonld index 90d3e548b4cb7..3ecfaafa691e1 100644 --- a/data/glanet/glanetbioschemas.jsonld +++ b/data/glanet/glanetbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Burçak Otlu", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "Genomic loci annotation and enrichment tool.", "sc:license": "Unlicense", "sc:name": "GLANET", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/burcakotlu/GLANET" } \ No newline at end of file diff --git a/data/glass/glassbioschemas.jsonld b/data/glass/glassbioschemas.jsonld index 3ddba840a14ee..e371965aa1eb4 100644 --- a/data/glass/glassbioschemas.jsonld +++ b/data/glass/glassbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "GLASS (GLobal Alignment SyStem) is a tool for aligning pairs of homologous sequences. It is designed for aligning long, divergent sequences, that contain blocks of moderate to strong homology, such as orthologous/paralogous pairs of genes", "sc:name": "GLASS", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://groups.csail.mit.edu/cb/crossspecies/" } \ No newline at end of file diff --git a/data/glassgo/glassgobioschemas.jsonld b/data/glassgo/glassgobioschemas.jsonld index 6b684ff29878c..cf9636f5e4e61 100644 --- a/data/glassgo/glassgobioschemas.jsonld +++ b/data/glassgo/glassgobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "GLobal Automated sRNA Search go, combines iterative BLAST searches, pairwise identity filtering, and structure based clustering in an automated prediction pipeline to find sRNA homologs from scratch. The web server provides predefined parameter sets for a non-expert usage as well as enables a manual setup of the query parameters. The returned GLASSgo result is in FASTA format, whereby the first entry represents the input sequence.", "sc:name": "GLASSgo", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://rna.informatik.uni-freiburg.de/GLASSgo/Input.jsp" } \ No newline at end of file diff --git a/data/glimma/glimmabioschemas.jsonld b/data/glimma/glimmabioschemas.jsonld index c5b9d06cc9d2f..4fa681444955b 100644 --- a/data/glimma/glimmabioschemas.jsonld +++ b/data/glimma/glimmabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Shian Su", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.", "sc:license": "GPL-3.0", "sc:name": "Glimma", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Glimma.html", "sc:version": "1.2.1" diff --git a/data/glint/glintbioschemas.jsonld b/data/glint/glintbioschemas.jsonld index 6d48a8412f28e..fda495891f7a5 100644 --- a/data/glint/glintbioschemas.jsonld +++ b/data/glint/glintbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/glint", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Eran Halperin", - "Elior Rahmani" + "Elior Rahmani", + "Eran Halperin" ], "sc:additionalType": "Command-line tool", "sc:description": "User-friendly toolset for the analysis of high-throughput DNA-methylation array data.", diff --git a/data/globalancova/globalancovabioschemas.jsonld b/data/globalancova/globalancovabioschemas.jsonld index d18916b9aac2a..dae6b7ef84c50 100644 --- a/data/globalancova/globalancovabioschemas.jsonld +++ b/data/globalancova/globalancovabioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Manuela Hummel", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "We give the following arguments in support this approach: After normalization, gene-expression-data appears symmetrical and outliers are no problem, least squares should be robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals can’t be expected. Application of ordinary least squares gives unbiased, no longer optimal estimates.", "sc:license": "GPL-2.0", "sc:name": "GlobalAncova", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GlobalAncova.html", diff --git a/data/globalseq/globalseqbioschemas.jsonld b/data/globalseq/globalseqbioschemas.jsonld index 4ac3de083d3e4..819b88ba3da85 100644 --- a/data/globalseq/globalseqbioschemas.jsonld +++ b/data/globalseq/globalseqbioschemas.jsonld @@ -9,43 +9,43 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-016-0961-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/globalseq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Armin Rauschenberger", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pubmed:26951498", + "pmcid:PMC4782413", { "@id": "https://doi.org/10.1186/s12859-016-0961-5" - }, - "pubmed:26951498", - "pmcid:PMC4782413" + } ], "sc:description": "The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size.", "sc:featureList": [ { - "@id": "edam:operation_3659" + "@id": "edam:operation_2238" }, { - "@id": "edam:operation_2238" + "@id": "edam:operation_3659" } ], "sc:license": "GPL-3.0", "sc:name": "globalSeq", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/globalSeq.html", "sc:version": "1.2.0" + }, + { + "@id": "https://doi.org/10.1186/s12859-016-0961-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/globaltest/globaltestbioschemas.jsonld b/data/globaltest/globaltestbioschemas.jsonld index 828f22ddb715b..3c9e4ec276233 100644 --- a/data/globaltest/globaltestbioschemas.jsonld +++ b/data/globaltest/globaltestbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "globaltest", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/globaltest.html", "sc:version": "5.28.0" diff --git a/data/globetrotter/globetrotterbioschemas.jsonld b/data/globetrotter/globetrotterbioschemas.jsonld index d11a9f0c0294e..cc741d97a514e 100644 --- a/data/globetrotter/globetrotterbioschemas.jsonld +++ b/data/globetrotter/globetrotterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Not licensed", "sc:name": "GLOBETROTTER", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://paintmychromosomes.com/" diff --git a/data/globplot/globplotbioschemas.jsonld b/data/globplot/globplotbioschemas.jsonld index 8581358ba1c96..0cc6a1b4784b1 100644 --- a/data/globplot/globplotbioschemas.jsonld +++ b/data/globplot/globplotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.", "sc:name": "GlobPlot", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://globplot.embl.de/" } \ No newline at end of file diff --git a/data/globplotter/globplotterbioschemas.jsonld b/data/globplotter/globplotterbioschemas.jsonld index a88b4c17047e4..f39602374cecc 100644 --- a/data/globplotter/globplotterbioschemas.jsonld +++ b/data/globplotter/globplotterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "GlobPlotter", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://globplot.embl.de", "sc:version": "1" diff --git a/data/glossary/glossarybioschemas.jsonld b/data/glossary/glossarybioschemas.jsonld index 349ceb0c42edc..d038944bfa796 100644 --- a/data/glossary/glossarybioschemas.jsonld +++ b/data/glossary/glossarybioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/GLOSSary", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "16S subunit related sequences database, identified from metagenomic efforts as part of the Tara Oceans project. It includes a BLAST search tool. The analysis system incorporates the SILVA collection, allowing comparative analyses to identify unclassified sequences and their geographical distribution.", "sc:license": "Unlicense", "sc:name": "GLOSSary", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinfo.szn.it/glossary/" } \ No newline at end of file diff --git a/data/glue/gluebioschemas.jsonld b/data/glue/gluebioschemas.jsonld index b98d8762e5a29..97ed3e907b7e2 100644 --- a/data/glue/gluebioschemas.jsonld +++ b/data/glue/gluebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2459-9", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GLUE", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6299651", "pubmed:30563445", { "@id": "https://doi.org/10.1186/s12859-018-2459-9" - } + }, + "pmcid:PMC6299651" ], "sc:description": "GLUE (Genes Linked by Underlying Evolution) is data-centric bioinformatics environment for virus sequence data, with a focus on variation, evolution and sequence interpretation.", "sc:featureList": [ @@ -34,20 +30,24 @@ "@id": "edam:operation_0499" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_0564" }, { - "@id": "edam:operation_0564" + "@id": "edam:operation_3196" } ], "sc:license": "AGPL-3.0", "sc:name": "GLUE", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://tools.glue.cvr.ac.uk/#/home" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2459-9", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/glutton/gluttonbioschemas.jsonld b/data/glutton/gluttonbioschemas.jsonld index 5ef8190d7848d..48f92da335e38 100644 --- a/data/glutton/gluttonbioschemas.jsonld +++ b/data/glutton/gluttonbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "Glutton", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/YeeHo/Glutton" } \ No newline at end of file diff --git a/data/glycan_array_dashboard/glycan_array_dashboardbioschemas.jsonld b/data/glycan_array_dashboard/glycan_array_dashboardbioschemas.jsonld index f66139c21b4ad..e155d68799886 100644 --- a/data/glycan_array_dashboard/glycan_array_dashboardbioschemas.jsonld +++ b/data/glycan_array_dashboard/glycan_array_dashboardbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "GLycan Array Dashboard", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://glycotoolkit.com/Tools/GLAD/", diff --git a/data/glycananalyzer/glycananalyzerbioschemas.jsonld b/data/glycananalyzer/glycananalyzerbioschemas.jsonld index 6e2c435bc0588..5180b693435de 100644 --- a/data/glycananalyzer/glycananalyzerbioschemas.jsonld +++ b/data/glycananalyzer/glycananalyzerbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/GlycanAnalyzer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Christopher H. Taron", "Prof. Pauline M. Rudd", - "Dr. Ian Walsh" + "Dr. Ian Walsh", + "Dr. Christopher H. Taron" ], "sc:additionalType": "Web application", "sc:author": "Dr. Ian Walsh", diff --git a/data/glycanmass/glycanmassbioschemas.jsonld b/data/glycanmass/glycanmassbioschemas.jsonld index af073a60f13a1..5ec73e7c5f48f 100644 --- a/data/glycanmass/glycanmassbioschemas.jsonld +++ b/data/glycanmass/glycanmassbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Calculate the mass of an oligosaccharide structure.", "sc:name": "GlycanMass", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://web.expasy.org/glycanmass/" } \ No newline at end of file diff --git a/data/glycodigest/glycodigestbioschemas.jsonld b/data/glycodigest/glycodigestbioschemas.jsonld index 1701ae7618702..9cca61650d5f7 100644 --- a/data/glycodigest/glycodigestbioschemas.jsonld +++ b/data/glycodigest/glycodigestbioschemas.jsonld @@ -23,15 +23,15 @@ "ExPASy helpdesk" ], "sc:additionalType": [ - "Web application", - "Desktop application" + "Desktop application", + "Web application" ], "sc:citation": [ { "@id": "https://doi.org/10.1093/bioinformatics/btu425" }, - "pmcid:PMC4609004", - "pubmed:25015990" + "pubmed:25015990", + "pmcid:PMC4609004" ], "sc:description": "Tool that simulates the action of these exoglycosidases on released oligosaccharides. It assists glycobiologists in designing enzyme mixtures that can be used to guide the precise determination of glycan structures.", "sc:featureList": { @@ -39,9 +39,9 @@ }, "sc:name": "GlycoDigest", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.glycodigest.org/" }, diff --git a/data/glycofragment/glycofragmentbioschemas.jsonld b/data/glycofragment/glycofragmentbioschemas.jsonld index ed3fbec4ad568..86957fada595d 100644 --- a/data/glycofragment/glycofragmentbioschemas.jsonld +++ b/data/glycofragment/glycofragmentbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool that takes the sequence of a carbohydrate structure as input, and calculates all theoretically possible fragments which are likely to occur in mass spectra.", "sc:name": "GlycoFragment", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.glycosciences.de/tools/GlycoFragments/fragment.php4" } \ No newline at end of file diff --git a/data/glycomod/glycomodbioschemas.jsonld b/data/glycomod/glycomodbioschemas.jsonld index c596efb2de249..2ad08d1ebc74d 100644 --- a/data/glycomod/glycomodbioschemas.jsonld +++ b/data/glycomod/glycomodbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides.", "sc:name": "GlycoMod", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://web.expasy.org/glycomod/" diff --git a/data/glyconnect/glyconnectbioschemas.jsonld b/data/glyconnect/glyconnectbioschemas.jsonld index 412dffc3b7f84..0d9d3dc91e721 100644 --- a/data/glyconnect/glyconnectbioschemas.jsonld +++ b/data/glyconnect/glyconnectbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "GlyConnect", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://glyconnect.expasy.org/" } \ No newline at end of file diff --git a/data/glycosciences/glycosciencesbioschemas.jsonld b/data/glycosciences/glycosciencesbioschemas.jsonld index 0133af0af1dfe..aa04e579d759b 100644 --- a/data/glycosciences/glycosciencesbioschemas.jsonld +++ b/data/glycosciences/glycosciencesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Carbohydrate structure database.", "sc:name": "Glycosciences", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.glycosciences.de/sweetdb/index.php" } \ No newline at end of file diff --git a/data/glycoviewer/glycoviewerbioschemas.jsonld b/data/glycoviewer/glycoviewerbioschemas.jsonld index 6cb003af8f183..926203914fdbe 100644 --- a/data/glycoviewer/glycoviewerbioschemas.jsonld +++ b/data/glycoviewer/glycoviewerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Visualisation tool for representing a set of glycan structures as a summary figure of all structural features using icons and colours recommended by the Consortium for Functional Glycomics (CFG).", "sc:name": "GlycoViewer", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.glycoviewer.babs.unsw.edu.au" } \ No newline at end of file diff --git a/data/glycresoft/glycresoftbioschemas.jsonld b/data/glycresoft/glycresoftbioschemas.jsonld index 9caaa48a9e31c..94741e8c08d26 100644 --- a/data/glycresoft/glycresoftbioschemas.jsonld +++ b/data/glycresoft/glycresoftbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "GlycReSoft", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.bumc.bu.edu/msr/glycresoft/", "sc:version": "0.3.7" diff --git a/data/glydin/glydinbioschemas.jsonld b/data/glydin/glydinbioschemas.jsonld index 959d820082aa5..c17fc7fbf02e7 100644 --- a/data/glydin/glydinbioschemas.jsonld +++ b/data/glydin/glydinbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Glydin' compiles and maps information relative to glycoepitopes (glycan determinants) as published in the literature or reported in databases. The output is an interactive network of strucutrally related glycan sub-structures.", "sc:name": "Glydin", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://glycoproteome.expasy.org/epitopes/" } \ No newline at end of file diff --git a/data/glynest_and_casper/glynest_and_casperbioschemas.jsonld b/data/glynest_and_casper/glynest_and_casperbioschemas.jsonld index 85eb26c0d129f..1b1bff8591515 100644 --- a/data/glynest_and_casper/glynest_and_casperbioschemas.jsonld +++ b/data/glynest_and_casper/glynest_and_casperbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "GlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure.", "sc:name": "GlyNest and CASPER", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.glycosciences.de/sweetdb/start.php?action=form_shift_estimation" diff --git a/data/glynsight/glynsightbioschemas.jsonld b/data/glynsight/glynsightbioschemas.jsonld index ced64596907d3..44820c977597d 100644 --- a/data/glynsight/glynsightbioschemas.jsonld +++ b/data/glynsight/glynsightbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web interface to upload, visualize and interactively compare glycan expression profiles. The tool can process N- or O-linked glycan expression data.", "sc:name": "Glynsight", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://glycoproteome.expasy.org/glynsight/" diff --git a/data/glys3/glys3bioschemas.jsonld b/data/glys3/glys3bioschemas.jsonld index 0d74fb7f7de1e..e165441469df7 100644 --- a/data/glys3/glys3bioschemas.jsonld +++ b/data/glys3/glys3bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "GlyS3 matches any substructure such as glycan determinants to a large collection of structures recorded in UniCarbKB, SugarBind or GlycomeDB.", "sc:name": "GlyS3", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://glycoproteome.expasy.org/substructuresearch" } \ No newline at end of file diff --git a/data/gma/gmabioschemas.jsonld b/data/gma/gmabioschemas.jsonld index c5bd5158ddee6..cd82ba9d88428 100644 --- a/data/gma/gmabioschemas.jsonld +++ b/data/gma/gmabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "GMA", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/chaoning/GMA" } \ No newline at end of file diff --git a/data/gmap_build/gmap_buildbioschemas.jsonld b/data/gmap_build/gmap_buildbioschemas.jsonld index 6cf7d86775d5c..62541e301b966 100644 --- a/data/gmap_build/gmap_buildbioschemas.jsonld +++ b/data/gmap_build/gmap_buildbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A database genome index for GMAP and GSNAP.", "sc:name": "gmap_build", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://research-pub.gene.com/gmap/", "sc:version": "2013-01-23" diff --git a/data/gmap_iit_store/gmap_iit_storebioschemas.jsonld b/data/gmap_iit_store/gmap_iit_storebioschemas.jsonld index 193f16f6a4606..6bb3d5bfda0ad 100644 --- a/data/gmap_iit_store/gmap_iit_storebioschemas.jsonld +++ b/data/gmap_iit_store/gmap_iit_storebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Create a map store for known genes or SNPs.", "sc:name": "gmap_iit_store", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://research-pub.gene.com/gmap/", diff --git a/data/gmapr/gmaprbioschemas.jsonld b/data/gmapr/gmaprbioschemas.jsonld index b0ea3e581718b..f945f46915618 100644 --- a/data/gmapr/gmaprbioschemas.jsonld +++ b/data/gmapr/gmaprbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "gmapR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gmapR.html", "sc:version": "1.16.0" diff --git a/data/gmata/gmatabioschemas.jsonld b/data/gmata/gmatabioschemas.jsonld index 6fad10b21a438..6f624c9b3aec0 100644 --- a/data/gmata/gmatabioschemas.jsonld +++ b/data/gmata/gmatabioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Xuewen Wang", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5020087", "pubmed:27679641", { "@id": "https://doi.org/10.3389/fpls.2016.01350" - } + }, + "pmcid:PMC5020087" ], "sc:description": "Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrates SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "GMATA", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://sourceforge.net/projects/gmata/", "sc:version": "v21" diff --git a/data/gmato/gmatobioschemas.jsonld b/data/gmato/gmatobioschemas.jsonld index 1ce2afc4c0294..297517fdf1d91 100644 --- a/data/gmato/gmatobioschemas.jsonld +++ b/data/gmato/gmatobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "GMATo", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sourceforge.net/projects/gmato/", "sc:version": "1.2" diff --git a/data/gmd-r/gmd-rbioschemas.jsonld b/data/gmd-r/gmd-rbioschemas.jsonld index c3a6225adffba..b6bb4a871562c 100644 --- a/data/gmd-r/gmd-rbioschemas.jsonld +++ b/data/gmd-r/gmd-rbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Package for non-parametric distance measurement between two discrete frequency distributions.", "sc:name": "GMD", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "binf.ku.dk", diff --git a/data/gmd/gmdbioschemas.jsonld b/data/gmd/gmdbioschemas.jsonld index 0669e116ac40a..d8286690699fb 100644 --- a/data/gmd/gmdbioschemas.jsonld +++ b/data/gmd/gmdbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Database which facilitates the search and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS).", "sc:name": "Golm Metabolome Database (GMD)", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://gmd.mpimp-golm.mpg.de/REST/default.aspx", diff --git a/data/gmdr/gmdrbioschemas.jsonld b/data/gmdr/gmdrbioschemas.jsonld index d3a542ab60aa2..9c5580ae722a1 100644 --- a/data/gmdr/gmdrbioschemas.jsonld +++ b/data/gmdr/gmdrbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-2.0", "sc:name": "GMDR", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.ssg.uab.edu/gmdr/" diff --git a/data/gmrp/bioconda_gmrp.yaml b/data/gmrp/bioconda_gmrp.yaml index b1b975daeecf0..489a4fccbbdeb 100644 --- a/data/gmrp/bioconda_gmrp.yaml +++ b/data/gmrp/bioconda_gmrp.yaml @@ -5,7 +5,6 @@ description: Perform Mendelian randomization analysis of multiple SNPs to determ home: https://bioconductor.org/packages/3.10/bioc/html/GMRP.html identifiers: - biotools:gmrp -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-gmrp diff --git a/data/gmrp/gmrpbioschemas.jsonld b/data/gmrp/gmrpbioschemas.jsonld index 428ba5d7bf62e..114d363cdfca5 100644 --- a/data/gmrp/gmrpbioschemas.jsonld +++ b/data/gmrp/gmrpbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "GMRP", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GMRP.html", "sc:version": "1.2.0" diff --git a/data/gms/gmsbioschemas.jsonld b/data/gms/gmsbioschemas.jsonld index b75845e4b97e1..2be8f0ed4b057 100644 --- a/data/gms/gmsbioschemas.jsonld +++ b/data/gms/gmsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Mapping of NGS reads onto genomes, transcriptomes and splice-junction libraries. It is a client-server based solution and can be controlled through an intuitive GUI or via command-line. It covers different tasks such as, as genomic positioning, SNP detection, splice analyses and genomic enrichments.", "sc:name": "Genomatix Mining Station (GMS)", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.genomatix.de/en/index.html" diff --git a/data/gmt/gmtbioschemas.jsonld b/data/gmt/gmtbioschemas.jsonld index 9180769fc37cc..fa76a41bfb708 100644 --- a/data/gmt/gmtbioschemas.jsonld +++ b/data/gmt/gmtbioschemas.jsonld @@ -15,30 +15,30 @@ "biotools:primaryContact": "Saskia Hiltemann", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6377400", - "pubmed:30597007", { "@id": "https://doi.org/10.1093/gigascience/giy166" - } + }, + "pmcid:PMC6377400", + "pubmed:30597007" ], "sc:description": "Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur.", "sc:featureList": [ - { - "@id": "edam:operation_3431" - }, { "@id": "edam:operation_3192" }, { "@id": "edam:operation_3797" + }, + { + "@id": "edam:operation_3431" } ], "sc:license": "Unlicense", "sc:name": "GmT", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://galaxyproject.org/use/gmt/" }, diff --git a/data/gna/gnabioschemas.jsonld b/data/gna/gnabioschemas.jsonld index 14fbb109e11b4..9e5043f4764a3 100644 --- a/data/gna/gnabioschemas.jsonld +++ b/data/gna/gnabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computer tool for the qualitative modeling and simulation of genetic regulatory networks. It assists you in constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data. Moreover, it allows you to simulate the qualitative behavior of the network in response to external perturbations.", "sc:name": "GNA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ibis.inrialpes.fr/article122.html" } \ No newline at end of file diff --git a/data/gnat/gnatbioschemas.jsonld b/data/gnat/gnatbioschemas.jsonld index 31949fb9b3a1e..d82f99afdda1b 100644 --- a/data/gnat/gnatbioschemas.jsonld +++ b/data/gnat/gnatbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Open source MATLAB-based toolbox. It provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks.", "sc:name": "GNAT", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sourceforge.net/projects/gnatmatlab/" } \ No newline at end of file diff --git a/data/gnat_nmr/gnat_nmrbioschemas.jsonld b/data/gnat_nmr/gnat_nmrbioschemas.jsonld index a2a6704e47803..a6406aa7aabd3 100644 --- a/data/gnat_nmr/gnat_nmrbioschemas.jsonld +++ b/data/gnat_nmr/gnat_nmrbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1002/mrc.4717", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/gnat_nmr", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pmcid:PMC6001793", + "pubmed:29396867", { "@id": "https://doi.org/10.1002/mrc.4717" - }, - "pubmed:29396867" + } ], "sc:description": "Software package intended primarily for the processing of multicomponent high resolution NMR datasets such as those acquired in diffusion, relaxation and kinetic experiments.", "sc:featureList": { @@ -37,6 +33,10 @@ "Mac" ], "sc:url": "https://www.nmr.chemistry.manchester.ac.uk/?q=node/430" + }, + { + "@id": "https://doi.org/10.1002/mrc.4717", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gnc/gncbioschemas.jsonld b/data/gnc/gncbioschemas.jsonld index c054c204ade99..c080146f0f745 100644 --- a/data/gnc/gncbioschemas.jsonld +++ b/data/gnc/gncbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/gnc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Francisco Gómez Vela", + "Norberto Díaz-Díaz", "José Antonio Lagares", - "Norberto Díaz-Díaz" + "Francisco Gómez Vela" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:25935118", diff --git a/data/gnomad/gnomadbioschemas.jsonld b/data/gnomad/gnomadbioschemas.jsonld index 22d92447538dc..a78f4be1e5052 100644 --- a/data/gnomad/gnomadbioschemas.jsonld +++ b/data/gnomad/gnomadbioschemas.jsonld @@ -9,19 +9,23 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/nature19057", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gnomad", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ "pmcid:PMC5018207", + "pubmed:27535533", { "@id": "https://doi.org/10.1038/nature19057" - }, - "pubmed:27535533" + } ], "sc:description": "Genome Aggregation Database (gnomAD) - browser that aggregates exome and whole-genome sequencing data from a wide variety of large-scale sequencing projects. It enables search of genetic variation information by gene, variant or region.", "sc:featureList": [ @@ -29,10 +33,10 @@ "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2421" + "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_2421" }, { "@id": "edam:operation_3197" @@ -41,15 +45,11 @@ "sc:license": "ODbL-1.0", "sc:name": "gnomAD", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://gnomad.broadinstitute.org/" - }, - { - "@id": "https://doi.org/10.1038/nature19057", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gnpis/gnpisbioschemas.jsonld b/data/gnpis/gnpisbioschemas.jsonld index 74a8fc201b64f..42d2e80158c27 100644 --- a/data/gnpis/gnpisbioschemas.jsonld +++ b/data/gnpis/gnpisbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/gnpis", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "A multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information and genomic data for species of agronomical interest. It is used by both large international projects and plant science departments at the French National Institute for Agricultural Research.", "sc:license": "CC-BY-4.0", "sc:name": "Genetic and Genomic Information System (GnpIS)", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/gnpis", "sc:version": "18.2" diff --git a/data/go-elite/go-elitebioschemas.jsonld b/data/go-elite/go-elitebioschemas.jsonld index 45c29d390cb86..cd79f1b998603 100644 --- a/data/go-elite/go-elitebioschemas.jsonld +++ b/data/go-elite/go-elitebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "GO-Elite is designed to identify a minimal non-redundant set of biological Ontology terms or pathways to describe a particular set of genes or metabolites.", "sc:name": "GO-Elite", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.genmapp.org/go_elite/", "sc:version": "1.2.5" diff --git a/data/go2msig/go2msigbioschemas.jsonld b/data/go2msig/go2msigbioschemas.jsonld index 15c493ecf21d6..91f49456fd0b5 100644 --- a/data/go2msig/go2msigbioschemas.jsonld +++ b/data/go2msig/go2msigbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "GO2MSIG generates collections of gene sets in MSigDB format based on the Gene Ontology (GO) project hierarchy and gene association data, for use with the Gene Set Enrichment Analysis (GSEA) implementation available at the Broad Institute. This enables rapid creation of gene set collections for multiple species.", "sc:name": "GO2MSIG", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.bioinformatics.org/go2msig/", diff --git a/data/go_feat/go_featbioschemas.jsonld b/data/go_feat/go_featbioschemas.jsonld index e4de98fecd650..96678e826590b 100644 --- a/data/go_feat/go_featbioschemas.jsonld +++ b/data/go_feat/go_featbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "GO FEAT", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://computationalbiology.ufpa.br/gofeat/" } \ No newline at end of file diff --git a/data/go_term_finder/go_term_finderbioschemas.jsonld b/data/go_term_finder/go_term_finderbioschemas.jsonld index d8ecaca6afd12..6c508f61bfbc7 100644 --- a/data/go_term_finder/go_term_finderbioschemas.jsonld +++ b/data/go_term_finder/go_term_finderbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A tool for finding significant GO terms shared among a list of genes from your organism of choice.", "sc:name": "Generic GO Term Finder", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://go.princeton.edu/cgi-bin/GOTermFinder" } \ No newline at end of file diff --git a/data/go_term_mapper/go_term_mapperbioschemas.jsonld b/data/go_term_mapper/go_term_mapperbioschemas.jsonld index 777acf1b8306b..c15d21fc9d0a2 100644 --- a/data/go_term_mapper/go_term_mapperbioschemas.jsonld +++ b/data/go_term_mapper/go_term_mapperbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A tool for mapping the granular GO annotations for genes in a list to a set of broader, high-level GO parents terms.", "sc:name": "Generic GO Term Mapper", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://go.princeton.edu/cgi-bin/GOTermMapper" diff --git a/data/goa_gubbar/goa_gubbarbioschemas.jsonld b/data/goa_gubbar/goa_gubbarbioschemas.jsonld index b9ecd4c654bf3..9450b08c6b72e 100644 --- a/data/goa_gubbar/goa_gubbarbioschemas.jsonld +++ b/data/goa_gubbar/goa_gubbarbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "goa_gubbar", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ms-utils.org/goa_gubbar/index.html" } \ No newline at end of file diff --git a/data/gobyweb/gobywebbioschemas.jsonld b/data/gobyweb/gobywebbioschemas.jsonld index 5bd17f13e8b73..c468407a9ee8e 100644 --- a/data/gobyweb/gobywebbioschemas.jsonld +++ b/data/gobyweb/gobywebbioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0069666", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gobyweb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:23936070", "pmcid:PMC3720652", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0069666" - } + }, + "pubmed:23936070" ], "sc:description": "Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_3204" }, { - "@id": "edam:operation_3204" + "@id": "edam:operation_2495" } ], "sc:name": "GobyWeb", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://campagnelab.org/software/gobyweb/" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0069666", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/godef/godefbioschemas.jsonld b/data/godef/godefbioschemas.jsonld index c08232d764129..defc80093fbe8 100644 --- a/data/godef/godefbioschemas.jsonld +++ b/data/godef/godefbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "Wellcome Trust", + "UK MRC", "UK BBSRC", "EMBOSS Contributors" ], "sc:description": "Find GO ontology terms by definition.", "sc:funder": [ - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "godef", diff --git a/data/godmd/godmdbioschemas.jsonld b/data/godmd/godmdbioschemas.jsonld index 5b0a140227c9a..2fa5c71358068 100644 --- a/data/godmd/godmdbioschemas.jsonld +++ b/data/godmd/godmdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web portal for determining pathways for conformational transitions in macromolecules based on the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell-Demon sampling techniques.", "sc:name": "GOdMD", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mmb.irbbarcelona.org/GOdMD" } \ No newline at end of file diff --git a/data/goexpress/goexpressbioschemas.jsonld b/data/goexpress/goexpressbioschemas.jsonld index a63c44131b8c8..a07198637e042 100644 --- a/data/goexpress/goexpressbioschemas.jsonld +++ b/data/goexpress/goexpressbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Kevin Rue-Albrecht", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples.", "sc:license": "GPL-3.0", diff --git a/data/gofish/gofishbioschemas.jsonld b/data/gofish/gofishbioschemas.jsonld index f0bfa4173d1b7..a363d5c70a9ea 100644 --- a/data/gofish/gofishbioschemas.jsonld +++ b/data/gofish/gofishbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GoFish", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://llama.mshri.on.ca/gofish/GoFishWelcome.html" } \ No newline at end of file diff --git a/data/gofuncr/gofuncrbioschemas.jsonld b/data/gofuncr/gofuncrbioschemas.jsonld index 4932467ebff3e..72ee061ca5060 100644 --- a/data/gofuncr/gofuncrbioschemas.jsonld +++ b/data/gofuncr/gofuncrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "GOfuncR", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GOfuncR.html", diff --git a/data/gofunction/gofunctionbioschemas.jsonld b/data/gofunction/gofunctionbioschemas.jsonld index dc9cff2d9fbd1..0c40dee4a1a79 100644 --- a/data/gofunction/gofunctionbioschemas.jsonld +++ b/data/gofunction/gofunctionbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "GOFunction", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GOFunction.html", diff --git a/data/gold/goldbioschemas.jsonld b/data/gold/goldbioschemas.jsonld index 809d66c54f95f..02345f1b7ed87 100644 --- a/data/gold/goldbioschemas.jsonld +++ b/data/gold/goldbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This tool has proven success in virtual screening, lead optimisation, and identifying the correct binding mode of active molecules. It enables to make confident binding mode predictions, and achieve high database enrichments. It reliably identifies the correct binding mode for a large range of test set cases.", "sc:name": "GOLD", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/" } \ No newline at end of file diff --git a/data/golden_helix/golden_helixbioschemas.jsonld b/data/golden_helix/golden_helixbioschemas.jsonld index bbb8d55ef39e5..b6df8577c3f0b 100644 --- a/data/golden_helix/golden_helixbioschemas.jsonld +++ b/data/golden_helix/golden_helixbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/golden_helix", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Customer Support", - "General" + "General", + "Customer Support" ], "sc:additionalType": "Workflow", "sc:description": "Bioinformatic software provider and analytic service provider.", "sc:name": "Golden Helix", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.goldenhelix.com" diff --git a/data/goldenmutagenesis/goldenmutagenesisbioschemas.jsonld b/data/goldenmutagenesis/goldenmutagenesisbioschemas.jsonld index 1b0839da61187..cff069ecf9625 100644 --- a/data/goldenmutagenesis/goldenmutagenesisbioschemas.jsonld +++ b/data/goldenmutagenesis/goldenmutagenesisbioschemas.jsonld @@ -17,8 +17,8 @@ "@id": "https://bio.tools/GoldenMutagenesis", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", - "Web application" + "Web application", + "Library" ], "sc:author": { "@id": "https://orcid.org/0000-0001-5444-9282" @@ -30,9 +30,9 @@ "sc:license": "LGPL-3.0", "sc:name": "GoldenMutagenesis", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://msbi.ipb-halle.de/GoldenMutagenesisWeb", "sc:version": "1.1.1" diff --git a/data/goldilocks/goldilocksbioschemas.jsonld b/data/goldilocks/goldilocksbioschemas.jsonld index 230a9b21263b7..1e2cb6ce73507 100644 --- a/data/goldilocks/goldilocksbioschemas.jsonld +++ b/data/goldilocks/goldilocksbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btw116", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/goldilocks", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Samuel M. Nicholls", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27153673", "pmcid:PMC4920124", { "@id": "https://doi.org/10.1093/bioinformatics/btw116" - }, - "pubmed:27153673" + } ], "sc:description": "Goldilocks is a Python package providing functionality for collecting summary statistics, identifying shifts in variation, discovering outlier regions and locating and extracting interesting regions from one or more arbitrary genomes for further analysis, for a user-provided definition of interesting.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "MIT", "sc:name": "Goldilocks", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/SamStudio8/goldilocks" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btw116", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gomapman/gomapmanbioschemas.jsonld b/data/gomapman/gomapmanbioschemas.jsonld index df99d2cc1728c..b5c933dfc3d70 100644 --- a/data/gomapman/gomapmanbioschemas.jsonld +++ b/data/gomapman/gomapmanbioschemas.jsonld @@ -13,12 +13,12 @@ "sc:additionalType": "Database portal", "sc:author": "Živa Ramšak", "sc:contributor": [ - "Kristina Gruden", - "Ana Rotter", - "Igor Mozetič", "Matej Korbar", + "Kristina Gruden", "Björn Usadel", - "Špela Baebler" + "Špela Baebler", + "Igor Mozetič", + "Ana Rotter" ], "sc:description": "GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.", "sc:license": "CC-BY-NC-SA-3.0", diff --git a/data/gominer_ws/gominer_wsbioschemas.jsonld b/data/gominer_ws/gominer_wsbioschemas.jsonld index 74a1f5f19ac23..48bcc077f4dc7 100644 --- a/data/gominer_ws/gominer_wsbioschemas.jsonld +++ b/data/gominer_ws/gominer_wsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A tool for biological interpretation of microarray data.", "sc:name": "GOMiner WS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://discover.nci.nih.gov/gominer/goservice.jsp", "sc:version": "1" diff --git a/data/gomodeler/gomodelerbioschemas.jsonld b/data/gomodeler/gomodelerbioschemas.jsonld index 1eb2235769235..cc419d4a95e5d 100644 --- a/data/gomodeler/gomodelerbioschemas.jsonld +++ b/data/gomodeler/gomodelerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Conduct a hypothesis driven interrogation of their functional genomics datasets.", "sc:name": "GOModeler", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://agbase.hpc.msstate.edu/cgi-bin/tools/GOModeler.cgi" } \ No newline at end of file diff --git a/data/goname/gonamebioschemas.jsonld b/data/goname/gonamebioschemas.jsonld index 4b2fe39e134c0..da084f45e86fd 100644 --- a/data/goname/gonamebioschemas.jsonld +++ b/data/goname/gonamebioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK BBSRC", "Wellcome Trust", - "UK MRC", "EMBOSS Contributors", - "UK BBSRC" + "UK MRC" ], "sc:description": "Find GO ontology terms by name.", "sc:funder": [ - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "goname", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ diff --git a/data/gonet/gonetbioschemas.jsonld b/data/gonet/gonetbioschemas.jsonld index c5e60547eebe1..31c6976239cbf 100644 --- a/data/gonet/gonetbioschemas.jsonld +++ b/data/gonet/gonetbioschemas.jsonld @@ -9,39 +9,39 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2533-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GOnet", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mikhail Pomaznoy", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC6286514", + "pubmed:30526489", { "@id": "https://doi.org/10.1186/s12859-018-2533-3" - }, - "pubmed:30526489", - "pmcid:PMC6286514" + } ], "sc:description": "Tool for interactive Gene Ontology analysis.", "sc:featureList": [ { - "@id": "edam:operation_2422" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_2422" } ], "sc:license": "LGPL-3.0", "sc:name": "GOnet", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://tools.dice-database.org/GOnet/" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2533-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/googlegenomics/googlegenomicsbioschemas.jsonld b/data/googlegenomics/googlegenomicsbioschemas.jsonld index 33535453ccf9a..727e398a28e5b 100644 --- a/data/googlegenomics/googlegenomicsbioschemas.jsonld +++ b/data/googlegenomics/googlegenomicsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Siddhartha Bagaria", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An R package to interact with the homonimous API.", "sc:license": "Apache-2.0", "sc:name": "GoogleGenomics", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GoogleGenomics.html", "sc:version": "1.6.0" diff --git a/data/gopher/gopherbioschemas.jsonld b/data/gopher/gopherbioschemas.jsonld index 32c3aff840518..6180688dbd573 100644 --- a/data/gopher/gopherbioschemas.jsonld +++ b/data/gopher/gopherbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "The Jackson Laboratory", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC6332836", - "pubmed:30642251", { "@id": "https://doi.org/10.1186/s12864-018-5376-4" - } + }, + "pmcid:PMC6332836", + "pubmed:30642251" ], "sc:description": "Generator of probes for capture Hi-C experiments at high resolution.", "sc:featureList": [ @@ -37,8 +37,8 @@ "sc:license": "Other", "sc:name": "GOPHER", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/TheJacksonLaboratory/Gopher" diff --git a/data/goplot/goplotbioschemas.jsonld b/data/goplot/goplotbioschemas.jsonld index 0e9ea046f952f..ff5e79861560f 100644 --- a/data/goplot/goplotbioschemas.jsonld +++ b/data/goplot/goplotbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R package for implementation of multilayered visualizations for enhanced graphical representation of functional analysis data.", "sc:name": "GOplot", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://wencke.github.io/" } \ No newline at end of file diff --git a/data/gopro/goprobioschemas.jsonld b/data/gopro/goprobioschemas.jsonld index f7a72dfdabdcd..9b6c9f57a6d9d 100644 --- a/data/gopro/goprobioschemas.jsonld +++ b/data/gopro/goprobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lidia Chrabaszcz", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 group.", "sc:license": "GPL-3.0", diff --git a/data/goprofiles/goprofilesbioschemas.jsonld b/data/goprofiles/goprofilesbioschemas.jsonld index a98c20f715c0b..61e23e520d227 100644 --- a/data/goprofiles/goprofilesbioschemas.jsonld +++ b/data/goprofiles/goprofilesbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alex Sanchez", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.", "sc:license": "GPL-2.0", "sc:name": "goProfiles", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/goProfiles.html", "sc:version": "1.36.0" diff --git a/data/gorgon/gorgonbioschemas.jsonld b/data/gorgon/gorgonbioschemas.jsonld index 87af2c5ba8ad4..9ff709e015038 100644 --- a/data/gorgon/gorgonbioschemas.jsonld +++ b/data/gorgon/gorgonbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.", "sc:name": "Gorgon", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://gorgon.wustl.edu/" } \ No newline at end of file diff --git a/data/gorilla/gorillabioschemas.jsonld b/data/gorilla/gorillabioschemas.jsonld index b2a98d541a256..d5bac93d7de7f 100644 --- a/data/gorilla/gorillabioschemas.jsonld +++ b/data/gorilla/gorillabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Tool for identifying and visualizing enriched GO terms in ranked lists of genes.", "sc:name": "GOrilla", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://cbl-gorilla.cs.technion.ac.il" } \ No newline at end of file diff --git a/data/gorth/gorthbioschemas.jsonld b/data/gorth/gorthbioschemas.jsonld index d8daae5bd385c..4179a45fbd324 100644 --- a/data/gorth/gorthbioschemas.jsonld +++ b/data/gorth/gorthbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Freeware", "sc:name": "gOrth", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://biit.cs.ut.ee/gprofiler/gorth.cgi", diff --git a/data/gosemsim/gosemsimbioschemas.jsonld b/data/gosemsim/gosemsimbioschemas.jsonld index 73347a9f38bc4..e46e0737353de 100644 --- a/data/gosemsim/gosemsimbioschemas.jsonld +++ b/data/gosemsim/gosemsimbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-6485-8781", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/gosemsim", "@type": "sc:SoftwareApplication", @@ -29,11 +25,15 @@ "sc:name": "GOSemSim", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GOSemSim.html", "sc:version": "2.0.3" + }, + { + "@id": "http://orcid.org/0000-0002-6485-8781", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/goseq/goseqbioschemas.jsonld b/data/goseq/goseqbioschemas.jsonld index 5b0be1318c24a..40a323ae5219f 100644 --- a/data/goseq/goseqbioschemas.jsonld +++ b/data/goseq/goseqbioschemas.jsonld @@ -17,14 +17,14 @@ "Anthony Hawkins" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:20132535", { "@id": "https://doi.org/10.1186/gb-2010-11-2-r14" }, + "pubmed:20132535", "pmcid:PMC2872874" ], "sc:description": "Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.", @@ -34,8 +34,8 @@ "sc:license": "GPL-2.0", "sc:name": "GOseq", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/goseq.html", diff --git a/data/gosim/gosimbioschemas.jsonld b/data/gosim/gosimbioschemas.jsonld index a0dafc2745b83..301f19407db7f 100644 --- a/data/gosim/gosimbioschemas.jsonld +++ b/data/gosim/gosimbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Holger Froehlich", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package implements several functions useful for computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis.", "sc:license": "GPL-2.0", "sc:name": "GOSim", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GOSim.html", "sc:version": "1.12.0" diff --git a/data/gossto/gosstobioschemas.jsonld b/data/gossto/gosstobioschemas.jsonld index 954a30e2cbd97..ef3b74220f359 100644 --- a/data/gossto/gosstobioschemas.jsonld +++ b/data/gossto/gosstobioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU144" }, - "pubmed:24659104", - "pmcid:PMC4103586" + "pmcid:PMC4103586", + "pubmed:24659104" ], "sc:description": "Calculating semantic similarities on the Gene Ontology.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "GOssTo", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.paccanarolab.org/gosstoweb/" } diff --git a/data/gostag/gostagbioschemas.jsonld b/data/gostag/gostagbioschemas.jsonld index 521deddbfb8ed..3649f7482335a 100644 --- a/data/gostag/gostagbioschemas.jsonld +++ b/data/gostag/gostagbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "goSTAG", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/goSTAG.html", "sc:version": "1.4.0" diff --git a/data/gostats/gostatsbioschemas.jsonld b/data/gostats/gostatsbioschemas.jsonld index b6a2ddc42ed84..2a83ec4142fc1 100644 --- a/data/gostats/gostatsbioschemas.jsonld +++ b/data/gostats/gostatsbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Artistic-2.0", "sc:name": "GOstats", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GOstats.html", diff --git a/data/gosummaries/gosummariesbioschemas.jsonld b/data/gosummaries/gosummariesbioschemas.jsonld index 08698436f62a3..c55f08a714a39 100644 --- a/data/gosummaries/gosummariesbioschemas.jsonld +++ b/data/gosummaries/gosummariesbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Visualizes the GO enrichment results as word clouds and arranges them together with figures of experimental data. This allows us to draw informative summary plots for analyses such as differential expression or clustering, where for each gene list we display its behaviour in the experiment alongside with its GO annotations.", "sc:name": "GOsummaries", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://raivokolde.github.io/GOsummaries/", diff --git a/data/gothic/gothicbioschemas.jsonld b/data/gothic/gothicbioschemas.jsonld index acfb8cdf09e34..10503005c4c47 100644 --- a/data/gothic/gothicbioschemas.jsonld +++ b/data/gothic/gothicbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Borbala Mifsud", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.", "sc:license": "GPL-3.0", "sc:name": "GOTHiC", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GOTHiC.html", "sc:version": "1.10.0" diff --git a/data/gotools/bioconda_gotools.yaml b/data/gotools/bioconda_gotools.yaml index fa04086c0ee20..075df8e930885 100644 --- a/data/gotools/bioconda_gotools.yaml +++ b/data/gotools/bioconda_gotools.yaml @@ -4,7 +4,6 @@ description: Wraper functions for description/comparison of oligo ID list using home: https://bioconductor.org/packages/3.10/bioc/html/goTools.html identifiers: - biotools:gotools -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-gotools diff --git a/data/gotools/gotoolsbioschemas.jsonld b/data/gotools/gotoolsbioschemas.jsonld index 0ee0e58f1fd55..9924999f87172 100644 --- a/data/gotools/gotoolsbioschemas.jsonld +++ b/data/gotools/gotoolsbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Agnes Paquet", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Wraper functions for description/comparison of oligo ID list using Gene Ontology database.", "sc:license": "GPL-2.0", "sc:name": "goTools", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/goTools.html", diff --git a/data/gotrapper/gotrapperbioschemas.jsonld b/data/gotrapper/gotrapperbioschemas.jsonld index de00c10a2a8c1..ac973fbfcce3c 100644 --- a/data/gotrapper/gotrapperbioschemas.jsonld +++ b/data/gotrapper/gotrapperbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2581-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GOTrapper", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hezha Hassan", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:30634902", "pmcid:PMC6330489", { "@id": "https://doi.org/10.1186/s12859-018-2581-8" - } + }, + "pubmed:30634902" ], "sc:description": "Tool to navigate through branches of gene ontology hierarchy.", "sc:featureList": [ @@ -31,10 +27,10 @@ "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_2495" } ], "sc:license": "GPL-3.0", @@ -45,6 +41,10 @@ "Linux" ], "sc:url": "https://github.com/BioGeneTools/GOTrapper" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2581-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gowinda/gowindabioschemas.jsonld b/data/gowinda/gowindabioschemas.jsonld index 6f13530f04e1c..167030fa4cd32 100644 --- a/data/gowinda/gowindabioschemas.jsonld +++ b/data/gowinda/gowindabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MPL-2.0", "sc:name": "Gowinda", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://code.google.com/p/gowinda/" } \ No newline at end of file diff --git a/data/gpa/gpabioschemas.jsonld b/data/gpa/gpabioschemas.jsonld index 48e3a5aba3315..d6c49cc2bcfbf 100644 --- a/data/gpa/gpabioschemas.jsonld +++ b/data/gpa/gpabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data.", "sc:name": "GPA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://dongjunchung.github.io/GPA/" } \ No newline at end of file diff --git a/data/gpart/gpartbioschemas.jsonld b/data/gpart/gpartbioschemas.jsonld index f7be59e7a1d32..e63d48286011a 100644 --- a/data/gpart/gpartbioschemas.jsonld +++ b/data/gpart/gpartbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "gpart", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://bioconductor.org/packages/gpart" } \ No newline at end of file diff --git a/data/gpcr-modsim/gpcr-modsimbioschemas.jsonld b/data/gpcr-modsim/gpcr-modsimbioschemas.jsonld index 1c28cd4735997..a6f2abaf27dfb 100644 --- a/data/gpcr-modsim/gpcr-modsimbioschemas.jsonld +++ b/data/gpcr-modsim/gpcr-modsimbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs).", "sc:name": "GPCR-ModSim", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://open.gpcr-modsim.org/" } \ No newline at end of file diff --git a/data/gpcr-ssfe/gpcr-ssfebioschemas.jsonld b/data/gpcr-ssfe/gpcr-ssfebioschemas.jsonld index 6ff9a74a59090..3754ea215d4ac 100644 --- a/data/gpcr-ssfe/gpcr-ssfebioschemas.jsonld +++ b/data/gpcr-ssfe/gpcr-ssfebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/gpcr-ssfe", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", + "Suite", "Database portal", - "Suite" + "Web application" ], "sc:description": "GPCR-Sequence-Structure-Feature-Extractor (SSFE). Provides template suggestions and homology models of Class A GPCRs. Identifies key sequence and structural motifs in Class A GPCRs to guide template selection and build homology models.", "sc:name": "GPCR-SSFE", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ssfa-7tmr.de/ssfe2/", "sc:version": "2.0" diff --git a/data/gpcr_sarfari_blast_search/gpcr_sarfari_blast_searchbioschemas.jsonld b/data/gpcr_sarfari_blast_search/gpcr_sarfari_blast_searchbioschemas.jsonld index 2171a5e1a9891..43823258c89d0 100644 --- a/data/gpcr_sarfari_blast_search/gpcr_sarfari_blast_searchbioschemas.jsonld +++ b/data/gpcr_sarfari_blast_search/gpcr_sarfari_blast_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "BLAST search of against GPCR domains stored in GPCR SARfari.", "sc:name": "GPCR SARfari BLAST Search", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "https://www.ebi.ac.uk/chembl/sarfari/gpcrsarfari/protein", diff --git a/data/gpcr_sarfari_small_molecule_search/gpcr_sarfari_small_molecule_searchbioschemas.jsonld b/data/gpcr_sarfari_small_molecule_search/gpcr_sarfari_small_molecule_searchbioschemas.jsonld index 501c9b53a7f51..439e81b46f577 100644 --- a/data/gpcr_sarfari_small_molecule_search/gpcr_sarfari_small_molecule_searchbioschemas.jsonld +++ b/data/gpcr_sarfari_small_molecule_search/gpcr_sarfari_small_molecule_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Search against small molecules stored in GPCR SARfari database.", "sc:name": "GPCR SARfari Small Molecule Search", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "https://www.ebi.ac.uk/chembl/sarfari/gpcrsarfari/compound", diff --git a/data/gpcrautomodel/gpcrautomodelbioschemas.jsonld b/data/gpcrautomodel/gpcrautomodelbioschemas.jsonld index dff075f8cb672..d2f9fe21dc726 100644 --- a/data/gpcrautomodel/gpcrautomodelbioschemas.jsonld +++ b/data/gpcrautomodel/gpcrautomodelbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Allows the user to upload a GPCR sequence, choose a ligand in a library and obtain the 3D structure of the free receptor and ligand-receptor complex.", "sc:name": "GPCRautomodel", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://genome.jouy.inra.fr/GPCRautomodel" } \ No newline at end of file diff --git a/data/gpcrdb/gpcrdbbioschemas.jsonld b/data/gpcrdb/gpcrdbbioschemas.jsonld index 564e124ec5b06..c941141fc0c0e 100644 --- a/data/gpcrdb/gpcrdbbioschemas.jsonld +++ b/data/gpcrdb/gpcrdbbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/gpcrdb", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", "Web service", + "Database portal", "Web application" ], "sc:description": "Contains data, diagrams and web tools for G protein-coupled receptors (GPCRs). Users can browse all GPCR crystal structures and the largest collections of mutants. Diagrams can be produced and downloaded to illustrate receptor residues (snake-plot and helix box diagrams) and relationships (phylogenetic trees).", "sc:name": "GPCRDB", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "GPCRDB", diff --git a/data/gpcrhmm/gpcrhmmbioschemas.jsonld b/data/gpcrhmm/gpcrhmmbioschemas.jsonld index 02b8df429473e..0d844a4e6e3af 100644 --- a/data/gpcrhmm/gpcrhmmbioschemas.jsonld +++ b/data/gpcrhmm/gpcrhmmbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "A hidden Markov model for GPCR detection.", "sc:name": "GPCRHMM", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "bils.se", "sc:url": "http://gpcrhmm.sbc.su.se/", diff --git a/data/gpcrpred/gpcrpredbioschemas.jsonld b/data/gpcrpred/gpcrpredbioschemas.jsonld index c9c887a568c46..ee9563ece6baa 100644 --- a/data/gpcrpred/gpcrpredbioschemas.jsonld +++ b/data/gpcrpred/gpcrpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.", "sc:name": "GPCRpred", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/gpcrpred/" } \ No newline at end of file diff --git a/data/gpcrs/gpcrsbioschemas.jsonld b/data/gpcrs/gpcrsbioschemas.jsonld index 4629659dd28dc..6123ef2081f51 100644 --- a/data/gpcrs/gpcrsbioschemas.jsonld +++ b/data/gpcrs/gpcrsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "GPCR family profiles, mutation data (in various formats), ligand binding data, sequence annotations and cross-references to other databases.", "sc:name": "GPCRs", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://gpcrdb.org/" } \ No newline at end of file diff --git a/data/gpcrsclass/gpcrsclassbioschemas.jsonld b/data/gpcrsclass/gpcrsclassbioschemas.jsonld index 6a813bf2dd539..614d5b89b1be7 100644 --- a/data/gpcrsclass/gpcrsclassbioschemas.jsonld +++ b/data/gpcrsclass/gpcrsclassbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for predicting amine-binding receptors based on a protein sequence provided by the user.", "sc:name": "GPCRsclass", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/gpcrsclass/" } \ No newline at end of file diff --git a/data/gpgpufragfold/gpgpufragfoldbioschemas.jsonld b/data/gpgpufragfold/gpgpufragfoldbioschemas.jsonld index 84ce4f892b547..4e8fe008476a6 100644 --- a/data/gpgpufragfold/gpgpufragfoldbioschemas.jsonld +++ b/data/gpgpufragfold/gpgpufragfoldbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "GPUFRAGFOLD is a CUDA ACELERATED Protein Structure Prediction Tool.", "sc:name": "GPGPUFRAGFOLD", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioinfadmin.cs.ucl.ac.uk/downloads/gpufragfold/", "sc:version": "0.1" diff --git a/data/gpi-anchor_biosynthesis/gpi-anchor_biosynthesisbioschemas.jsonld b/data/gpi-anchor_biosynthesis/gpi-anchor_biosynthesisbioschemas.jsonld index 119b19bffcaf9..e7ccbd0d6b90c 100644 --- a/data/gpi-anchor_biosynthesis/gpi-anchor_biosynthesisbioschemas.jsonld +++ b/data/gpi-anchor_biosynthesis/gpi-anchor_biosynthesisbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1002/MGG3.743", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0001-9713-7107", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/GPI-anchor_biosynthesis", "@type": "sc:SoftwareApplication", @@ -24,23 +16,23 @@ "@id": "https://orcid.org/0000-0001-9713-7107" }, "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ - "pubmed:31127708", { "@id": "https://doi.org/10.1002/MGG3.743" }, + "pubmed:31127708", "pmcid:PMC6625143" ], "sc:description": "Inherited glycophosphatidylinositol deficiency variant database.", "sc:featureList": [ { - "@id": "edam:operation_0417" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_0417" }, { "@id": "edam:operation_3225" @@ -49,11 +41,19 @@ "sc:license": "Unlicense", "sc:name": "GPI-anchor biosynthesis", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.gpibiosynthesis.org" + }, + { + "@id": "https://orcid.org/0000-0001-9713-7107", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1002/MGG3.743", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gplink/gplinkbioschemas.jsonld b/data/gplink/gplinkbioschemas.jsonld index fff0f39193395..eb426c2b52672 100644 --- a/data/gplink/gplinkbioschemas.jsonld +++ b/data/gplink/gplinkbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1086/519795", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/gplink", "@type": "sc:SoftwareApplication", "sc:additionalType": "Workbench", "sc:citation": [ "pubmed:17701901", - "pmcid:PMC1950838", { "@id": "https://doi.org/10.1086/519795" - } + }, + "pmcid:PMC1950838" ], "sc:description": "gPLINKis a Java program that provides a simple form interface to the more commonly-usedPLINKcommands (i.e. instead of using the command line options).gPLINKprovides menus and dialogs to create validPLINKcommands, executes them, keeps a record of all commands run in a project, keeps track of input and output files, allows annotation of result files and facilitates integration withHaploview.", "sc:featureList": { @@ -32,6 +28,10 @@ "sc:name": "gPLINK", "sc:operatingSystem": "Linux", "sc:url": "http://zzz.bwh.harvard.edu/plink/gplink.shtml" + }, + { + "@id": "https://doi.org/10.1086/519795", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gpls/gplsbioschemas.jsonld b/data/gpls/gplsbioschemas.jsonld index 0da121c9dd675..39bac363aa12f 100644 --- a/data/gpls/gplsbioschemas.jsonld +++ b/data/gpls/gplsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.", "sc:license": "Artistic-2.0", diff --git a/data/gpm/gpmbioschemas.jsonld b/data/gpm/gpmbioschemas.jsonld index 086a2b92ffa0a..482690a02996a 100644 --- a/data/gpm/gpmbioschemas.jsonld +++ b/data/gpm/gpmbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-8030-5346", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/gpm", "@type": "sc:SoftwareApplication", @@ -21,11 +17,11 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5048067", - "pubmed:27318200", { "@id": "https://doi.org/10.1093/bioinformatics/btw370" - } + }, + "pubmed:27318200", + "pmcid:PMC5048067" ], "sc:description": "Genome Puzzle Master (GPM) enables the integration of additional genomic signposts to edit and build ‘new-gen-assemblies’ that result in high-quality ‘annotation-ready’ pseudomolecules.", "sc:featureList": { @@ -36,6 +32,10 @@ "sc:operatingSystem": "Linux", "sc:url": "https://github.com/Jianwei-Zhang/LIMS" }, + { + "@id": "http://orcid.org/0000-0001-8030-5346", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/bioinformatics/btw370", "@type": "sc:CreativeWork" diff --git a/data/gpmaw_lite/gpmaw_litebioschemas.jsonld b/data/gpmaw_lite/gpmaw_litebioschemas.jsonld index 400dc93de050b..42ecbfc76aef2 100644 --- a/data/gpmaw_lite/gpmaw_litebioschemas.jsonld +++ b/data/gpmaw_lite/gpmaw_litebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "GPMAW lite is a protein bioinformatics tool to perform basic bioinformatics calculations on any protein amino acid sequence, including predicted molecular weight, molar absorbance and extinction coefficient, isoelectric point and hydrophobicity index, as well as amino acid composition and protease digest.", "sc:name": "GPMAW lite", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.alphalyse.com/gpmaw_lite.html" } \ No newline at end of file diff --git a/data/gpmdb_api/gpmdb_apibioschemas.jsonld b/data/gpmdb_api/gpmdb_apibioschemas.jsonld index f179ab2d1cc90..271f5be3f4bdb 100644 --- a/data/gpmdb_api/gpmdb_apibioschemas.jsonld +++ b/data/gpmdb_api/gpmdb_apibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A REST API used to access mass spectrometry-based experimental proteomics data and information stored in GPMDB.", "sc:name": "GPMDB API", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://wiki.thegpm.org/wiki/GPMDB_REST", "sc:version": "1" diff --git a/data/gppat/gppatbioschemas.jsonld b/data/gppat/gppatbioschemas.jsonld index af0972d30e353..bfb36f04760f8 100644 --- a/data/gppat/gppatbioschemas.jsonld +++ b/data/gppat/gppatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web server for comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments", "sc:name": "GPPAT", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://protein.cau.edu.cn/gppat/" diff --git a/data/gprege/gpregebioschemas.jsonld b/data/gprege/gpregebioschemas.jsonld index f9bb8e75cd591..0c4e8d5e37ad2 100644 --- a/data/gprege/gpregebioschemas.jsonld +++ b/data/gprege/gpregebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-12-180", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/gprege", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Command-line tool" ], "sc:citation": [ - "pubmed:21599902", + "pmcid:PMC3116489", { "@id": "https://doi.org/10.1186/1471-2105-12-180" }, - "pmcid:PMC3116489" + "pubmed:21599902" ], "sc:description": "The software fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP kernel is initialised wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimised via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance.", "sc:featureList": { @@ -36,11 +32,15 @@ "sc:name": "gprege", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gprege.html", "sc:version": "1.18.0" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-12-180", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gprofile_r/gprofile_rbioschemas.jsonld b/data/gprofile_r/gprofile_rbioschemas.jsonld index f3aac075b3249..3a38bf91ad2c9 100644 --- a/data/gprofile_r/gprofile_rbioschemas.jsonld +++ b/data/gprofile_r/gprofile_rbioschemas.jsonld @@ -11,21 +11,21 @@ "@id": "https://bio.tools/gprofile_r", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jaak Vilo", - "Jüri Reimand" + "Jüri Reimand", + "Jaak Vilo" ], "sc:additionalType": [ - "Suite", - "Library" + "Library", + "Suite" ], "sc:citation": "pubmed:27098042", "sc:description": "gProfileR performs functional enrichment analysis, gene identifier conversion and mapping homologous genes across related organisms via the 'g:Profiler' toolkit. The tool performs statistical enrichment analysis to find over-representation of information like Gene Ontology terms, biological pathways, regulatory DNA elements, human disease gene annotations, and protein-protein interaction networks. The basic input is a list of genes.", "sc:license": "GPL-2.0", "sc:name": "gProfileR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/gProfileR/index.html", "sc:version": "0.6.1" diff --git a/data/gprotpred/gprotpredbioschemas.jsonld b/data/gprotpred/gprotpredbioschemas.jsonld index 9471d4a1cb4b2..5ac917a6051dc 100644 --- a/data/gprotpred/gprotpredbioschemas.jsonld +++ b/data/gprotpred/gprotpredbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Detection of distinct Galpha families, Gbeta and Ggamma subunits of heterotrimeric G-proteins using profile Hidden Markov Models (pHMMs).", "sc:name": "GprotPRED", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://aias.biol.uoa.gr/GprotPRED/" diff --git a/data/gps-sumo/gps-sumobioschemas.jsonld b/data/gps-sumo/gps-sumobioschemas.jsonld index 9ee6ee9665d48..748fda802d1eb 100644 --- a/data/gps-sumo/gps-sumobioschemas.jsonld +++ b/data/gps-sumo/gps-sumobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/gps-sumo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yu Xue", - "Jian Ren" + "Jian Ren", + "Yu Xue" ], "sc:additionalType": "Web application", "sc:description": "GPS-SUMO (small ubiquitin-like modifiers) is a tool for the prediction of sumoylation sites and SUMO-interaction motifs in proteins.", diff --git a/data/gps/gpsbioschemas.jsonld b/data/gps/gpsbioschemas.jsonld index 1b465738e62ed..b6db064f01cc9 100644 --- a/data/gps/gpsbioschemas.jsonld +++ b/data/gps/gpsbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "GPS", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://groups.csail.mit.edu/cgs/onePageGPS/" } \ No newline at end of file diff --git a/data/gpsdb/gpsdbbioschemas.jsonld b/data/gpsdb/gpsdbbioschemas.jsonld index 69112b7a5caf1..fdedf5bd3512b 100644 --- a/data/gpsdb/gpsdbbioschemas.jsonld +++ b/data/gpsdb/gpsdbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GPSDB", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://gpsdb.expasy.org/" } \ No newline at end of file diff --git a/data/gpseq/gpseqbioschemas.jsonld b/data/gpseq/gpseqbioschemas.jsonld index b45cf63886e57..f1cf95e6c5935 100644 --- a/data/gpseq/gpseqbioschemas.jsonld +++ b/data/gpseq/gpseqbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons", "sc:name": "GPSeq", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www-rcf.usc.edu/%7Eliangche/software.html" } \ No newline at end of file diff --git a/data/gpu-cassert/gpu-cassertbioschemas.jsonld b/data/gpu-cassert/gpu-cassertbioschemas.jsonld index 6008acbdc3ecd..f51002b6756e0 100644 --- a/data/gpu-cassert/gpu-cassertbioschemas.jsonld +++ b/data/gpu-cassert/gpu-cassertbioschemas.jsonld @@ -25,8 +25,8 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:24481593", "pmcid:PMC3936136", + "pubmed:24481593", { "@id": "https://doi.org/10.1007/s00894-014-2067-1" } diff --git a/data/gpuam/gpuambioschemas.jsonld b/data/gpuam/gpuambioschemas.jsonld index 74a7162f9afd6..b88dafd33c39c 100644 --- a/data/gpuam/gpuambioschemas.jsonld +++ b/data/gpuam/gpuambioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "GPUAM", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/gpuam/binaries.git" } \ No newline at end of file diff --git a/data/grabb/grabbbioschemas.jsonld b/data/grabb/grabbbioschemas.jsonld index 9aca33634174a..e2704742c5846 100644 --- a/data/grabb/grabbbioschemas.jsonld +++ b/data/grabb/grabbbioschemas.jsonld @@ -18,11 +18,11 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4911045", - "pubmed:27308864", { "@id": "https://doi.org/10.1371/journal.pcbi.1004753" - } + }, + "pmcid:PMC4911045", + "pubmed:27308864" ], "sc:description": "Genome Region Assembly by Baiting. Assemble selected regions of the genome or transcriptome using reference sequences and NGS data.", "sc:featureList": { diff --git a/data/graemlin/graemlinbioschemas.jsonld b/data/graemlin/graemlinbioschemas.jsonld index 92fb04cb00393..13fd0fd3402f5 100644 --- a/data/graemlin/graemlinbioschemas.jsonld +++ b/data/graemlin/graemlinbioschemas.jsonld @@ -15,16 +15,16 @@ "Serafim Batzoglou's lab" ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:16899655", "sc:description": "Tool for aligning multiple global protein interaction networks; it also supports search for homology between a query module of proteins and a database of interaction networks.", "sc:name": "Graemlin", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://graemlin.stanford.edu/" } \ No newline at end of file diff --git a/data/graftm/graftmbioschemas.jsonld b/data/graftm/graftmbioschemas.jsonld index 1e351315488c9..dbb7b46a3ffaa 100644 --- a/data/graftm/graftmbioschemas.jsonld +++ b/data/graftm/graftmbioschemas.jsonld @@ -9,25 +9,29 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gky174", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/graftm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Gene W Tyson", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6007438", - "pubmed:29562347", { "@id": "https://doi.org/10.1093/nar/gky174" - } + }, + "pubmed:29562347", + "pmcid:PMC6007438" ], "sc:description": "Scalable, phylogenetically informed classification of genes within metagenomes.", "sc:featureList": [ { - "@id": "edam:operation_0415" + "@id": "edam:operation_2995" }, { - "@id": "edam:operation_2995" + "@id": "edam:operation_0415" } ], "sc:license": "GPL-3.0", @@ -37,10 +41,6 @@ "Linux" ], "sc:url": "https://pypi.org/project/graftm/" - }, - { - "@id": "https://doi.org/10.1093/nar/gky174", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gramm-x/gramm-xbioschemas.jsonld b/data/gramm-x/gramm-xbioschemas.jsonld index 0b590de1dd423..f11cf64e6afa5 100644 --- a/data/gramm-x/gramm-xbioschemas.jsonld +++ b/data/gramm-x/gramm-xbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "GRAMM-X is a protein docking server.", "sc:name": "GRAMM-X", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://vakser.bioinformatics.ku.edu/resources/gramm/grammx" } \ No newline at end of file diff --git a/data/granar/granarbioschemas.jsonld b/data/granar/granarbioschemas.jsonld index c34f0e4754a4e..ae0580845dcb7 100644 --- a/data/granar/granarbioschemas.jsonld +++ b/data/granar/granarbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "GRANAR", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://granar.github.io" } \ No newline at end of file diff --git a/data/granvil/granvilbioschemas.jsonld b/data/granvil/granvilbioschemas.jsonld index fe52102a5cca6..cc1e95c4e73a4 100644 --- a/data/granvil/granvilbioschemas.jsonld +++ b/data/granvil/granvilbioschemas.jsonld @@ -27,20 +27,20 @@ "sc:description": "GRANVIL (Gene- or Region-based ANalysis of Variants of Intermediate and Low frequency) - performs rare-variant analysis of binary or quantitative phenotypes. The method is based on accumulation of minor alleles of rare or uncommon markers discovered through dense genotyping or resequencing data. Association analyses are based on gene- or other pre-defined regions, determined by analyst.", "sc:featureList": [ { - "@id": "edam:operation_1812" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3791" + "@id": "edam:operation_1812" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3791" } ], "sc:name": "GRANVIL", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.geenivaramu.ee/en/tools/granvil" } diff --git a/data/grape_database/grape_databasebioschemas.jsonld b/data/grape_database/grape_databasebioschemas.jsonld index 95d959997e42d..e2036688c6698 100644 --- a/data/grape_database/grape_databasebioschemas.jsonld +++ b/data/grape_database/grape_databasebioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-9571-0747", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/1471-2229-14-99", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/grape_database", "@type": "sc:SoftwareApplication", @@ -25,10 +17,10 @@ }, "sc:additionalType": "Database portal", "sc:citation": [ + "pmcid:PMC4108029", { "@id": "https://doi.org/10.1186/1471-2229-14-99" }, - "pmcid:PMC4108029", "pubmed:24739459" ], "sc:description": "Database which provides several ways to access to the grape genomic data: as a blast search page, a genome browser and a direct link to download the data.", @@ -37,12 +29,20 @@ }, "sc:name": "Grape Database", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://genomes.cribi.unipd.it/grape/" + }, + { + "@id": "https://doi.org/10.1186/1471-2229-14-99", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-9571-0747", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/grape_rna/grape_rnabioschemas.jsonld b/data/grape_rna/grape_rnabioschemas.jsonld index 1536f875924fb..d7d3049358c13 100644 --- a/data/grape_rna/grape_rnabioschemas.jsonld +++ b/data/grape_rna/grape_rnabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/grape_rna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Roderic Guigó", - "Maik Röder" + "Maik Röder", + "Roderic Guigó" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:23329413", diff --git a/data/graph-gpa/graph-gpabioschemas.jsonld b/data/graph-gpa/graph-gpabioschemas.jsonld index b6db20fec1edd..731a58f6689e6 100644 --- a/data/graph-gpa/graph-gpabioschemas.jsonld +++ b/data/graph-gpa/graph-gpabioschemas.jsonld @@ -18,11 +18,11 @@ ], "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5347371", "pubmed:28212402", { "@id": "https://doi.org/10.1371/journal.pcbi.1005388" - }, - "pmcid:PMC5347371" + } ], "sc:description": "Graphical model for prioritizing GWAS results and investigating pleiotropic architecture. Fit graph-GPA models, implement association mapping, and generate a phenotype graph.", "sc:featureList": { diff --git a/data/graph/bioconda_graph.yaml b/data/graph/bioconda_graph.yaml index 2a19b196aed57..888da34a9a1b6 100644 --- a/data/graph/bioconda_graph.yaml +++ b/data/graph/bioconda_graph.yaml @@ -3,7 +3,6 @@ description: A package that implements some simple graph handling capabilities. home: https://bioconductor.org/packages/3.10/bioc/html/graph.html identifiers: - biotools:graph -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-graph summary: 'graph: A package to handle graph data structures' diff --git a/data/graph/graphbioschemas.jsonld b/data/graph/graphbioschemas.jsonld index 71cf72cea2588..f110e6ea94f28 100644 --- a/data/graph/graphbioschemas.jsonld +++ b/data/graph/graphbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A package that implements some simple graph handling capabilities.", "sc:license": "Artistic-2.0", diff --git a/data/graph_peak_caller/graph_peak_callerbioschemas.jsonld b/data/graph_peak_caller/graph_peak_callerbioschemas.jsonld index 1ac52b0ce7282..ff2453a32a51f 100644 --- a/data/graph_peak_caller/graph_peak_callerbioschemas.jsonld +++ b/data/graph_peak_caller/graph_peak_callerbioschemas.jsonld @@ -19,19 +19,19 @@ "biotools:primaryContact": "Biomedical Informatics Research Group (BMI)", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6396939", "pubmed:30779737", { "@id": "https://doi.org/10.1371/journal.pcbi.1006731" - }, - "pmcid:PMC6396939" + } ], "sc:description": "Tool for calling transcription factor peaks on graph-based reference genomes using ChIP-seq data.", "sc:featureList": [ { - "@id": "edam:operation_0487" + "@id": "edam:operation_3215" }, { - "@id": "edam:operation_3215" + "@id": "edam:operation_0487" }, { "@id": "edam:operation_3222" @@ -40,8 +40,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "Graph Peak Caller", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/uio-bmi/graph_peak_caller" } diff --git a/data/graphalignment/graphalignmentbioschemas.jsonld b/data/graphalignment/graphalignmentbioschemas.jsonld index e88934ead8cd0..a2805e4a2f251 100644 --- a/data/graphalignment/graphalignmentbioschemas.jsonld +++ b/data/graphalignment/graphalignmentbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Joern P. Meier", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pmcid:PMC1544158", + "pubmed:16835301", { "@id": "https://doi.org/10.1073/pnas.0602294103" - }, - "pubmed:16835301", - "pmcid:PMC1544158" + } ], "sc:description": "An extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores.", "sc:featureList": { diff --git a/data/graphat/graphatbioschemas.jsonld b/data/graphat/graphatbioschemas.jsonld index f0b06016a4627..8b3b520d9f5ff 100644 --- a/data/graphat/graphatbioschemas.jsonld +++ b/data/graphat/graphatbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "GraphAT", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GraphAT.html", "sc:version": "1.46.0" diff --git a/data/graphite/graphitebioschemas.jsonld b/data/graphite/graphitebioschemas.jsonld index ab4ec0a5e30e9..6f00b6845df91 100644 --- a/data/graphite/graphitebioschemas.jsonld +++ b/data/graphite/graphitebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-13-20", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/graphite", "@type": "sc:SoftwareApplication", @@ -32,13 +28,17 @@ "sc:license": "AGPL-3.0", "sc:name": "graphite", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://www.bioconductor.org/packages/release/bioc/html/graphite.html", "sc:version": "1.12.0" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-13-20", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/graphiteweb/graphitewebbioschemas.jsonld b/data/graphiteweb/graphitewebbioschemas.jsonld index cc6421f6b5cb9..109ccdb584b05 100644 --- a/data/graphiteweb/graphitewebbioschemas.jsonld +++ b/data/graphiteweb/graphitewebbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web tool for for pathway analysis and network visualization for gene expression data from microarray and RNA-seq experiments.", "sc:name": "GraphiteWeb", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://graphiteweb.bio.unipd.it/" diff --git a/data/graphkernels/graphkernelsbioschemas.jsonld b/data/graphkernels/graphkernelsbioschemas.jsonld index 886bd7c6969ee..81b4690619a61 100644 --- a/data/graphkernels/graphkernelsbioschemas.jsonld +++ b/data/graphkernels/graphkernelsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "graphkernels", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/graphkernels/index.html" } \ No newline at end of file diff --git a/data/graphprot/graphprotbioschemas.jsonld b/data/graphprot/graphprotbioschemas.jsonld index 3899b4e96586e..2e21bff8216be 100644 --- a/data/graphprot/graphprotbioschemas.jsonld +++ b/data/graphprot/graphprotbioschemas.jsonld @@ -18,8 +18,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:24451197", "pmcid:PMC4053806", + "pubmed:24451197", { "@id": "https://doi.org/10.1186/gb-2014-15-1-r17" } diff --git a/data/graphtyper/graphtyperbioschemas.jsonld b/data/graphtyper/graphtyperbioschemas.jsonld index 4988f23635220..f4106a3a4f2cc 100644 --- a/data/graphtyper/graphtyperbioschemas.jsonld +++ b/data/graphtyper/graphtyperbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Graphtyper", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/DecodeGenetics/graphtyper" } \ No newline at end of file diff --git a/data/graphweb/graphwebbioschemas.jsonld b/data/graphweb/graphwebbioschemas.jsonld index 9fe29ae1c7873..11396f96b0c2a 100644 --- a/data/graphweb/graphwebbioschemas.jsonld +++ b/data/graphweb/graphwebbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Jüri Reimand", - "Laur Tooming", - "Jaak Vilo" + "Jaak Vilo", + "Laur Tooming" ], "sc:additionalType": "Web application", "sc:description": "Public web server for graph-based analysis of biological networks that: analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; integrates multiple diverse datasets into global networks; incorporates multispecies data; filters nodes and edges; detects gene modules from networks; interprets discovered modules.", "sc:license": "Freeware", "sc:name": "GraphWeb", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://biit.cs.ut.ee/graphweb", diff --git a/data/grapple/grapplebioschemas.jsonld b/data/grapple/grapplebioschemas.jsonld index 22248282300e9..b2ce389e45ee3 100644 --- a/data/grapple/grapplebioschemas.jsonld +++ b/data/grapple/grapplebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GraPPLE", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://grapple.mpimp-golm.mpg.de/" } \ No newline at end of file diff --git a/data/grcalculator/grcalculatorbioschemas.jsonld b/data/grcalculator/grcalculatorbioschemas.jsonld index 7383d4e8fab85..b654066f19c76 100644 --- a/data/grcalculator/grcalculatorbioschemas.jsonld +++ b/data/grcalculator/grcalculatorbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12885-017-3689-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/grcalculator", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ "Library" ], "sc:citation": [ - "pmcid:PMC5655815", - "pubmed:29065900", { "@id": "https://doi.org/10.1186/s12885-017-3689-3" - } + }, + "pubmed:29065900", + "pmcid:PMC5655815" ], "sc:description": "Online tool for calculating and mining dose–response data.", "sc:featureList": { @@ -30,15 +34,11 @@ }, "sc:name": "GRcalculator", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.grcalculator.org/grcalculator/" - }, - { - "@id": "https://doi.org/10.1186/s12885-017-3689-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gream/greambioschemas.jsonld b/data/gream/greambioschemas.jsonld index 89289df9a2fba..cb168d3e8bf33 100644 --- a/data/gream/greambioschemas.jsonld +++ b/data/gream/greambioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Kshitish K. Acharya", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC4514817", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0133647" }, - "pubmed:26208093", - "pmcid:PMC4514817" + "pubmed:26208093" ], "sc:description": "A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species", "sc:featureList": { diff --git a/data/great/greatbioschemas.jsonld b/data/great/greatbioschemas.jsonld index 58988e2d62991..0e4646eb8a4e4 100644 --- a/data/great/greatbioschemas.jsonld +++ b/data/great/greatbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Predicts functions of cis-regulatory regions. Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. It assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes.", "sc:name": "GREAT", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bejerano.stanford.edu/great/public/html/" } \ No newline at end of file diff --git a/data/greatscanmultipatterns/greatscanmultipatternsbioschemas.jsonld b/data/greatscanmultipatterns/greatscanmultipatternsbioschemas.jsonld index 93b3f85b88938..31c74ab280749 100644 --- a/data/greatscanmultipatterns/greatscanmultipatternsbioschemas.jsonld +++ b/data/greatscanmultipatterns/greatscanmultipatternsbioschemas.jsonld @@ -19,13 +19,13 @@ "sc:description": "This tool performs, in a systematic way, an automated analysis of regular arrangements in organisms having multiple chromosomes, for different transcription factors (or regulators, conditions) at the same time. It reports and allows identification of periodic regions of target genes for the different conditions, on each chromosome.", "sc:name": "GREAT:SCAN:multipatterns", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ - "issb.genopole.fr", - "Institute of Systems and Synthetic Biology" + "Institute of Systems and Synthetic Biology", + "issb.genopole.fr" ], "sc:url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/index", "sc:version": "1" diff --git a/data/greatscanpatterns/greatscanpatternsbioschemas.jsonld b/data/greatscanpatterns/greatscanpatternsbioschemas.jsonld index c147e1745b519..eaf4a9db36866 100644 --- a/data/greatscanpatterns/greatscanpatternsbioschemas.jsonld +++ b/data/greatscanpatterns/greatscanpatternsbioschemas.jsonld @@ -24,8 +24,8 @@ "Mac" ], "sc:provider": [ - "issb.genopole.fr", - "Institute of Systems and Synthetic Biology" + "Institute of Systems and Synthetic Biology", + "issb.genopole.fr" ], "sc:url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/patterns/", "sc:version": "1" diff --git a/data/green_listed/green_listedbioschemas.jsonld b/data/green_listed/green_listedbioschemas.jsonld index a0b9aee79ec2f..af7b31475ee04 100644 --- a/data/green_listed/green_listedbioschemas.jsonld +++ b/data/green_listed/green_listedbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "Green listed", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://greenlisted.cmm.ki.se/" } \ No newline at end of file diff --git a/data/greenphyldb/greenphyldbbioschemas.jsonld b/data/greenphyldb/greenphyldbbioschemas.jsonld index 392158650cd1f..f1c53ce4134c9 100644 --- a/data/greenphyldb/greenphyldbbioschemas.jsonld +++ b/data/greenphyldb/greenphyldbbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "A database designed for comparative and functional genomics based on complete genomes. It contains full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families.", "sc:name": "GreenPhylDB", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.greenphyl.org/", "sc:version": "v4" diff --git a/data/grein/greinbioschemas.jsonld b/data/grein/greinbioschemas.jsonld index 2afc9e9975ddf..520ac40d141c6 100644 --- a/data/grein/greinbioschemas.jsonld +++ b/data/grein/greinbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/S41598-019-43935-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0003-4510-3102", "@type": "schema:Person" @@ -25,11 +21,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31110304", + "pmcid:PMC6527554", { "@id": "https://doi.org/10.1038/S41598-019-43935-8" - }, - "pubmed:31110304", - "pmcid:PMC6527554" + } ], "sc:description": "Interactive Web Platform for Re-analyzing Gene Expression Omnibus (GEO) RNA-seq Data.", "sc:featureList": [ @@ -46,11 +42,15 @@ "sc:license": "GPL-2.0", "sc:name": "GREIN", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://shiny.ilincs.org/grein" + }, + { + "@id": "https://doi.org/10.1038/S41598-019-43935-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/grenits/grenitsbioschemas.jsonld b/data/grenits/grenitsbioschemas.jsonld index 6b2324089ac20..4a548d7f85a5f 100644 --- a/data/grenits/grenitsbioschemas.jsonld +++ b/data/grenits/grenitsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Edward Morrissey", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.", "sc:license": "GPL-2.0", diff --git a/data/grep_count/grep_countbioschemas.jsonld b/data/grep_count/grep_countbioschemas.jsonld index f2e3ede56d72b..26a718f521a08 100644 --- a/data/grep_count/grep_countbioschemas.jsonld +++ b/data/grep_count/grep_countbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Count or select lines containing a motif of a dataset.", "sc:name": "grep_count", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/grep_count/grep_count/1.0.0", "sc:version": "1.0.0" diff --git a/data/greylistchip/greylistchipbioschemas.jsonld b/data/greylistchip/greylistchipbioschemas.jsonld index 5e3584950fbe6..c2778aff396a9 100644 --- a/data/greylistchip/greylistchipbioschemas.jsonld +++ b/data/greylistchip/greylistchipbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "GreyListChIP", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GreyListChIP.html", "sc:version": "1.6.0" diff --git a/data/gribcg/gribcgbioschemas.jsonld b/data/gribcg/gribcgbioschemas.jsonld index 91ebfa8fa0512..6827194c430ae 100644 --- a/data/gribcg/gribcgbioschemas.jsonld +++ b/data/gribcg/gribcgbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2712-x", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/GRIBCG", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "B. Merritt", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:30866794", "pmcid:PMC6416924", { "@id": "https://doi.org/10.1186/s12859-019-2712-x" - } + }, + "pubmed:30866794" ], "sc:description": "Guide RNA Identifier for Balancer Chromosome Generation (GRIBCG) - software for selection of sgRNAs in the design of balancer chromosomes.", "sc:name": "GRIBCG", @@ -33,6 +29,10 @@ "Windows" ], "sc:url": "https://github.com/bmerritt1762/GRIBCG" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2712-x", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/grid_map/grid_mapbioschemas.jsonld b/data/grid_map/grid_mapbioschemas.jsonld index 5e10dca289b38..712bbc98453f1 100644 --- a/data/grid_map/grid_mapbioschemas.jsonld +++ b/data/grid_map/grid_mapbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Grid Map was designed to display comparative genome mapping data in a grid format. It is a generic Java version of the Oxford Grid display (written for the ACEDB database software package), but can be used to display many kinds of gridded data.", "sc:name": "Grid Map", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://cbr.jic.ac.uk/dicks/software/Grid_Map/index.html", diff --git a/data/gridmos/gridmosbioschemas.jsonld b/data/gridmos/gridmosbioschemas.jsonld index 8437f5a874fe5..1242e7391c31f 100644 --- a/data/gridmos/gridmosbioschemas.jsonld +++ b/data/gridmos/gridmosbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/gridmos", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "AnnaTesei", - "WainerZoli", "GiuliaPaganelli", + "FilippoPiccinini", + "WainerZoli", "AlessandroBevilacqua", - "FilippoPiccinini" + "AnnaTesei" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:25438936", "sc:description": "Open-source software tool conceived to build an image mosaic of a hemocytometer’s grid.", "sc:name": "GridMos", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://sourceforge.net/projects/gridmos/" } \ No newline at end of file diff --git a/data/gridss/gridssbioschemas.jsonld b/data/gridss/gridssbioschemas.jsonld index 17c4ddb931d14..5061bacfa979e 100644 --- a/data/gridss/gridssbioschemas.jsonld +++ b/data/gridss/gridssbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A high-speed next-gen sequencing structural variation caller. It calls variants based on alignment-guided positional de Bruijn graph breakpoint assembly, split read, and read pair evidence.", "sc:name": "GRIDSS", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "unimelb.edu.au", diff --git a/data/grinn/grinnbioschemas.jsonld b/data/grinn/grinnbioschemas.jsonld index 49cdfa4483eb3..f1c05fdc199e5 100644 --- a/data/grinn/grinnbioschemas.jsonld +++ b/data/grinn/grinnbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/grinn", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Pemra Ozbek", - "Onur Serçinoğlu" + "Onur Serçinoğlu", + "Pemra Ozbek" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:29800260", diff --git a/data/grisotto/grisottobioschemas.jsonld b/data/grisotto/grisottobioschemas.jsonld index e6fb3f44209fc..0fee2a00b81d5 100644 --- a/data/grisotto/grisottobioschemas.jsonld +++ b/data/grisotto/grisottobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "GRISOTTO, uncovers motifs using prior information from a set of co-regulated DNA sequences.", "sc:name": "GRISOTTO", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.lx.it.pt/~asmc/software/grisotto.html" } \ No newline at end of file diff --git a/data/grit/gritbioschemas.jsonld b/data/grit/gritbioschemas.jsonld index b59b995c7b42e..dab7568b8618c 100644 --- a/data/grit/gritbioschemas.jsonld +++ b/data/grit/gritbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/grit", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Nathan Boley", - "Susan E Celniker" + "Susan E Celniker", + "Nathan Boley" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:24633242", diff --git a/data/grm/grmbioschemas.jsonld b/data/grm/grmbioschemas.jsonld index d7361c4e0f39a..e2e02501b9918 100644 --- a/data/grm/grmbioschemas.jsonld +++ b/data/grm/grmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Powerful but simple method to remove technical noise and explicitly compute the true gene expression levels based on spike-in ERCC molecules.", "sc:name": "GRM", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://wanglab.ucsd.edu/star/GRM/" diff --git a/data/grmetrics/bioconda_grmetrics.yaml b/data/grmetrics/bioconda_grmetrics.yaml index d21a7be3c63e7..c4f69b3973fad 100644 --- a/data/grmetrics/bioconda_grmetrics.yaml +++ b/data/grmetrics/bioconda_grmetrics.yaml @@ -4,7 +4,6 @@ description: Functions for calculating and visualizing growth-rate inhibition (G home: https://bioconductor.org/packages/3.10/bioc/html/GRmetrics.html identifiers: - biotools:grmetrics -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-grmetrics diff --git a/data/grnsight/grnsightbioschemas.jsonld b/data/grnsight/grnsightbioschemas.jsonld index c740f0c7e37be..60f47ecf3bda3 100644 --- a/data/grnsight/grnsightbioschemas.jsonld +++ b/data/grnsight/grnsightbioschemas.jsonld @@ -16,15 +16,15 @@ ], "sc:additionalType": "Web application", "sc:author": [ - "Jen Shin", - "Eileen Choe", "Mihir Samdarshi", - "Kam D. Dahlquist", - "John David N. Dionisio", - "Nicole A. Anguiano", + "Anindita Varshneya", + "Eileen Choe", "Britain J. Southwick", + "Kam D. Dahlquist", "Ben G. Fitzpatrick", - "Anindita Varshneya" + "John David N. Dionisio", + "Jen Shin", + "Nicole A. Anguiano" ], "sc:contributor": "NSF award 0921038; LMU Rains Research Assistant Program; LMU Summer Undergraduate Research Program", "sc:description": "Web application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.", @@ -32,9 +32,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "GRNsight", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ "Loyola Marymount University", diff --git a/data/gro2mat/gro2matbioschemas.jsonld b/data/gro2mat/gro2matbioschemas.jsonld index ce39bd88f8473..eccf83203f865 100644 --- a/data/gro2mat/gro2matbioschemas.jsonld +++ b/data/gro2mat/gro2matbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Package that allows fast and easy access to Gromacs output files from Matlab.", "sc:name": "Gro2mat", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.stats.ox.ac.uk/research/proteins/resources" diff --git a/data/groc-svs/groc-svsbioschemas.jsonld b/data/groc-svs/groc-svsbioschemas.jsonld index cfa4b44017c1d..7023fbab679cf 100644 --- a/data/groc-svs/groc-svsbioschemas.jsonld +++ b/data/groc-svs/groc-svsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "GROC-SVs", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/grocsvs/grocsvs" } \ No newline at end of file diff --git a/data/grohmm/grohmmbioschemas.jsonld b/data/grohmm/grohmmbioschemas.jsonld index b39acf07d5732..b2586cab6c20b 100644 --- a/data/grohmm/grohmmbioschemas.jsonld +++ b/data/grohmm/grohmmbioschemas.jsonld @@ -13,17 +13,17 @@ "@id": "https://bio.tools/grohmm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Anusha Nagari", - "Venkat Malladi", + "W. Lee Kraus", "Tulip Nandu", - "W. Lee Kraus" + "Venkat Malladi", + "Anusha Nagari" ], "edam:has_input": [ { - "@id": "edam:data_3002" + "@id": "edam:data_0863" }, { - "@id": "edam:data_0863" + "@id": "edam:data_3002" } ], "edam:has_output": [ @@ -34,10 +34,10 @@ "@id": "edam:data_2048" }, { - "@id": "edam:data_2884" + "@id": "edam:data_3002" }, { - "@id": "edam:data_3002" + "@id": "edam:data_2884" } ], "sc:additionalType": [ @@ -46,17 +46,17 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3308" + "@id": "edam:topic_3168" }, { - "@id": "edam:topic_3168" + "@id": "edam:topic_3308" } ], "sc:citation": [ + "pubmed:26173492", { "@id": "https://doi.org/10.1186/s12859-015-0656-3" }, - "pubmed:26173492", "pmcid:PMC4502638" ], "sc:contributor": { @@ -65,18 +65,18 @@ "sc:description": "A pipeline for the analysis of GRO-seq data.", "sc:featureList": [ { - "@id": "edam:operation_2478" + "@id": "edam:operation_0415" }, { - "@id": "edam:operation_0415" + "@id": "edam:operation_2478" } ], "sc:license": "GPL-3.0", "sc:name": "groHMM", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/groHMM.html", "sc:version": "1.8.0" diff --git a/data/gromacs/gromacsbioschemas.jsonld b/data/gromacs/gromacsbioschemas.jsonld index c32f0ec0f7dbe..aaa26ce687cd6 100644 --- a/data/gromacs/gromacsbioschemas.jsonld +++ b/data/gromacs/gromacsbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "GROMACS support", "sc:additionalType": [ + "Command-line tool", "Suite", - "Library", - "Command-line tool" + "Library" ], "sc:description": "Versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.", "sc:license": "LGPL-2.1", diff --git a/data/groot/grootbioschemas.jsonld b/data/groot/grootbioschemas.jsonld index 3a437a4fc2fbe..b2dac846326a7 100644 --- a/data/groot/grootbioschemas.jsonld +++ b/data/groot/grootbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Indexed variation graphs for efficient and accurate resistome profiling.", "sc:name": "GROOT", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/will-rowe/groot" } \ No newline at end of file diff --git a/data/groupedsurv/groupedsurvbioschemas.jsonld b/data/groupedsurv/groupedsurvbioschemas.jsonld index c0f39de8ed7d4..455e5084fcb88 100644 --- a/data/groupedsurv/groupedsurvbioschemas.jsonld +++ b/data/groupedsurv/groupedsurvbioschemas.jsonld @@ -20,8 +20,8 @@ ], "sc:additionalType": "Library", "sc:citation": [ - "pubmed:31138120", "pmcid:PMC6540566", + "pubmed:31138120", { "@id": "https://doi.org/10.1186/S12859-019-2899-X" } @@ -32,10 +32,10 @@ "@id": "edam:operation_3557" }, { - "@id": "edam:operation_3659" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3659" } ], "sc:license": "GPL-2.0", diff --git a/data/grouper/grouperbioschemas.jsonld b/data/grouper/grouperbioschemas.jsonld index 195edb43b8e2a..7562ffde0956d 100644 --- a/data/grouper/grouperbioschemas.jsonld +++ b/data/grouper/grouperbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Graph-based clustering and annotation for improved de novo transcriptome analysis.", "sc:name": "Grouper", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/COMBINE-lab/grouper" } \ No newline at end of file diff --git a/data/grrann/grrannbioschemas.jsonld b/data/grrann/grrannbioschemas.jsonld index 7aa15d7578f4d..06104b52a60be 100644 --- a/data/grrann/grrannbioschemas.jsonld +++ b/data/grrann/grrannbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.", "sc:name": "GRRANN", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/kangtianyu/GRRANN" diff --git a/data/grridge/grridgebioschemas.jsonld b/data/grridge/grridgebioschemas.jsonld index dacb880d3a9b6..afecae4fa7895 100644 --- a/data/grridge/grridgebioschemas.jsonld +++ b/data/grridge/grridgebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "GRridge", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GRridge.html", "sc:version": "1.4.0" diff --git a/data/grtools/grtoolsbioschemas.jsonld b/data/grtools/grtoolsbioschemas.jsonld index 9c52cf7e6046b..e7a5d1f1e3348 100644 --- a/data/grtools/grtoolsbioschemas.jsonld +++ b/data/grtools/grtoolsbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Fabian A. Soto", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:28588513", "pmcid:PMC5440596", { "@id": "https://doi.org/10.3389/fpsyg.2017.00696" - } + }, + "pubmed:28588513" ], "sc:description": "Analysis of perceptual independence using general recognition theory.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "grtools", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/fsotoc/grtools" }, diff --git a/data/gs-lage/gs-lagebioschemas.jsonld b/data/gs-lage/gs-lagebioschemas.jsonld index 980d2ac9d3e75..40fac1b0b07f7 100644 --- a/data/gs-lage/gs-lagebioschemas.jsonld +++ b/data/gs-lage/gs-lagebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "GS-LAGE (Gene Specific Large-scale Analysis of Gene Expression) is a global analysis strategy for large-scale microarray datasets integrated from public databases such as NCBI GEO.", "sc:name": "GS-LAGE", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://lage.sookmyung.ac.kr/" diff --git a/data/gsa-snp/gsa-snpbioschemas.jsonld b/data/gsa-snp/gsa-snpbioschemas.jsonld index 536cd6e1add29..0bcdee70cfe3b 100644 --- a/data/gsa-snp/gsa-snpbioschemas.jsonld +++ b/data/gsa-snp/gsa-snpbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GSA-SNP", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://gsa.muldas.org" } \ No newline at end of file diff --git a/data/gsaa/gsaabioschemas.jsonld b/data/gsaa/gsaabioschemas.jsonld index 00d786b25adbc..aceffebe56bd7 100644 --- a/data/gsaa/gsaabioschemas.jsonld +++ b/data/gsaa/gsaabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Computational method that integrates gene expression analysis with genome wide association studies to determine whether an a priori defined sets of genes shows statistically significant, concordant differences with respect to gene expression profiles and genotypes between two biological states. Gene sets are generally a group of genes that are putatively functionally related, co-regulated, or tightly linked on the same chromosome.", "sc:name": "GSAA", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://gsaa.unc.edu/" } \ No newline at end of file diff --git a/data/gsan/gsanbioschemas.jsonld b/data/gsan/gsanbioschemas.jsonld index 7f7bbf501ead5..bf964aaa4a7e6 100644 --- a/data/gsan/gsanbioschemas.jsonld +++ b/data/gsan/gsanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "GSAn", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://gsan.labri.fr" } \ No newline at end of file diff --git a/data/gsar/gsarbioschemas.jsonld b/data/gsar/gsarbioschemas.jsonld index b9cb1526cfc3a..39a99abf85627 100644 --- a/data/gsar/gsarbioschemas.jsonld +++ b/data/gsar/gsarbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/bts579", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gsar", "@type": "sc:SoftwareApplication", @@ -24,13 +28,13 @@ "@id": "edam:data_2884" }, { - "@id": "edam:data_1669" + "@id": "edam:data_2048" }, { "@id": "edam:data_2600" }, { - "@id": "edam:data_2048" + "@id": "edam:data_1669" } ], "sc:additionalType": [ @@ -39,47 +43,43 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3518" + "@id": "edam:topic_2269" }, { "@id": "edam:topic_3170" }, { - "@id": "edam:topic_2269" + "@id": "edam:topic_3518" }, { "@id": "edam:topic_0203" } ], "sc:citation": [ + "pmcid:PMC3509490", + "pubmed:23044539", { "@id": "https://doi.org/10.1093/bioinformatics/bts579" - }, - "pubmed:23044539", - "pmcid:PMC3509490" + } ], "sc:description": "Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure.", "sc:featureList": [ { - "@id": "edam:operation_3223" + "@id": "edam:operation_3463" }, { - "@id": "edam:operation_3463" + "@id": "edam:operation_3223" } ], "sc:license": "GPL-2.0", "sc:name": "GSAR", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GSAR.html", "sc:version": "1.8.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/bts579", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gsca/gscabioschemas.jsonld b/data/gsca/gscabioschemas.jsonld index 09481200c292d..c130497891ce9 100644 --- a/data/gsca/gscabioschemas.jsonld +++ b/data/gsca/gscabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkv873", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gsca", "@type": "sc:SoftwareApplication", @@ -18,19 +22,19 @@ "Command-line tool" ], "sc:citation": [ + "pmcid:PMC4705686", { "@id": "https://doi.org/10.1093/nar/gkv873" }, - "pubmed:26350211", - "pmcid:PMC4705686" + "pubmed:26350211" ], "sc:description": "This tool takes as input several lists of activated and repressed genes. It then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. Finally, it provides both traditional R functions and an interactive, user-friendly interface.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3501" } ], "sc:license": "GPL-2.0", @@ -41,10 +45,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GSCA.html", "sc:version": "2.4.0" - }, - { - "@id": "https://doi.org/10.1093/nar/gkv873", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gscluster/gsclusterbioschemas.jsonld b/data/gscluster/gsclusterbioschemas.jsonld index 6bb53d9810d4a..08d0b5b5ea47d 100644 --- a/data/gscluster/gsclusterbioschemas.jsonld +++ b/data/gscluster/gsclusterbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1186/S12864-019-5738-6", "@type": "sc:CreativeWork" }, - { - "@id": "https://orcid.org/0000-0003-0239-2899", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/GScluster", "@type": "sc:SoftwareApplication", @@ -40,20 +36,24 @@ "@id": "edam:operation_2492" }, { - "@id": "edam:operation_2436" + "@id": "edam:operation_3432" }, { - "@id": "edam:operation_3432" + "@id": "edam:operation_2436" } ], "sc:license": "MIT", "sc:name": "GScluster", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/unistbig/GScluster" + }, + { + "@id": "https://orcid.org/0000-0003-0239-2899", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/gsds/gsdsbioschemas.jsonld b/data/gsds/gsdsbioschemas.jsonld index 70eb34e271e1a..d7b6983acc6af 100644 --- a/data/gsds/gsdsbioschemas.jsonld +++ b/data/gsds/gsdsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Designed for the visualization of annotated features for genes, and the generation of high-quality figures for publication.", "sc:name": "GSDS", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://gsds.cbi.pku.edu.cn/" } \ No newline at end of file diff --git a/data/gse/gsebioschemas.jsonld b/data/gse/gsebioschemas.jsonld index e168d1a8c5b24..2885da56194ca 100644 --- a/data/gse/gsebioschemas.jsonld +++ b/data/gse/gsebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Database for storing, visualizing, and analyzing ChIP-based transcription factor binding data and gene expression data.", "sc:name": "GSE", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://groups.csail.mit.edu/cgs/gse.html" } \ No newline at end of file diff --git a/data/gsea/gseabioschemas.jsonld b/data/gsea/gseabioschemas.jsonld index e5c1f360b9861..b7c114f7406b1 100644 --- a/data/gsea/gseabioschemas.jsonld +++ b/data/gsea/gseabioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/gsea", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", "Command-line tool", - "Desktop application" + "Desktop application", + "Library" ], "sc:description": "Computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).", "sc:name": "GSEA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.broadinstitute.org/gsea/index.jsp" } \ No newline at end of file diff --git a/data/gseabase/bioconda_gseabase.yaml b/data/gseabase/bioconda_gseabase.yaml index 4a3a4a2044eeb..ac591c8217c37 100644 --- a/data/gseabase/bioconda_gseabase.yaml +++ b/data/gseabase/bioconda_gseabase.yaml @@ -4,7 +4,6 @@ description: This package provides classes and methods to support Gene Set Enric home: https://bioconductor.org/packages/3.10/bioc/html/GSEABase.html identifiers: - biotools:gseabase -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-gseabase summary: Gene set enrichment data structures and methods diff --git a/data/gseabase/gseabasebioschemas.jsonld b/data/gseabase/gseabasebioschemas.jsonld index 9fb4684c36376..187c914059ea7 100644 --- a/data/gseabase/gseabasebioschemas.jsonld +++ b/data/gseabase/gseabasebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).", "sc:license": "Artistic-2.0", "sc:name": "GSEABase", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GSEABase.html", "sc:version": "1.36.0" diff --git a/data/gseabenchmarker/gseabenchmarkerbioschemas.jsonld b/data/gseabenchmarker/gseabenchmarkerbioschemas.jsonld index 20f199dd3e3c6..bc0a3861d3b76 100644 --- a/data/gseabenchmarker/gseabenchmarkerbioschemas.jsonld +++ b/data/gseabenchmarker/gseabenchmarkerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "GSEABenchmarkeR", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GSEABenchmarkeR.html", "sc:version": "1.0.0" diff --git a/data/gsean/gseanbioschemas.jsonld b/data/gsean/gseanbioschemas.jsonld index 103b87fcd0e15..e90a36186f1b8 100644 --- a/data/gsean/gseanbioschemas.jsonld +++ b/data/gsean/gseanbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "gsean", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gsean.html", "sc:version": "1.0.0" diff --git a/data/gsearch/gsearchbioschemas.jsonld b/data/gsearch/gsearchbioschemas.jsonld index 79c86795acfe5..0f2816236e58c 100644 --- a/data/gsearch/gsearchbioschemas.jsonld +++ b/data/gsearch/gsearchbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/gsearch", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kyu-Baek Hwang", - "Taemin Song" + "Taemin Song", + "Kyu-Baek Hwang" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:22730434", diff --git a/data/gsnap/gsnapbioschemas.jsonld b/data/gsnap/gsnapbioschemas.jsonld index 02b828f0bc3c4..71b1929a84c30 100644 --- a/data/gsnap/gsnapbioschemas.jsonld +++ b/data/gsnap/gsnapbioschemas.jsonld @@ -10,11 +10,7 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1186/1471-2105-14-184", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1186/1471-2164-15-264", + "@id": "https://doi.org/10.1093/bioinformatics/btq057", "@type": "sc:CreativeWork" }, { @@ -23,26 +19,26 @@ "biotools:primaryContact": "Thomas Wu", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5792058", + "pubmed:20147302", + { + "@id": "https://doi.org/10.1186/1471-2164-15-264" + }, + "pubmed:24708189", + "pmcid:PMC2844994", + "pmcid:PMC4051166", { "@id": "https://doi.org/10.1186/1471-2105-14-184" }, { "@id": "https://doi.org/10.1038/nmeth.4106" }, - "pubmed:24708189", "pubmed:27941783", - "pubmed:23758764", - "pmcid:PMC5792058", - "pmcid:PMC4051166", - { - "@id": "https://doi.org/10.1186/1471-2164-15-264" - }, - "pubmed:20147302", "pmcid:PMC3694458", { "@id": "https://doi.org/10.1093/bioinformatics/btq057" }, - "pmcid:PMC2844994" + "pubmed:23758764" ], "sc:description": "GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite treated DNA for the study of methylation state.", "sc:name": "GSNAP", @@ -53,11 +49,15 @@ "sc:url": "http://research-pub.gene.com/gmap/" }, { - "@id": "https://doi.org/10.1093/bioinformatics/btq057", + "@id": "https://doi.org/10.1038/nmeth.4106", "@type": "sc:CreativeWork" }, { - "@id": "https://doi.org/10.1038/nmeth.4106", + "@id": "https://doi.org/10.1186/1471-2164-15-264", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-184", "@type": "sc:CreativeWork" } ] diff --git a/data/gsrc/gsrcbioschemas.jsonld b/data/gsrc/gsrcbioschemas.jsonld index aec45861ff473..5c34109f49d2f 100644 --- a/data/gsrc/gsrcbioschemas.jsonld +++ b/data/gsrc/gsrcbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-3.0", "sc:name": "gsrc", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/grafab/gsrc", "sc:version": "1.1.1" diff --git a/data/gsri/bioconda_gsri.yaml b/data/gsri/bioconda_gsri.yaml index ebdcb882105d8..3bad325df2977 100644 --- a/data/gsri/bioconda_gsri.yaml +++ b/data/gsri/bioconda_gsri.yaml @@ -4,7 +4,6 @@ description: The GSRI package estimates the number of differentially expressed g home: https://bioconductor.org/packages/3.10/bioc/html/GSRI.html identifiers: - biotools:gsri -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-gsri diff --git a/data/gsri/gsribioschemas.jsonld b/data/gsri/gsribioschemas.jsonld index df9e56154bb30..e97f1e38e016a 100644 --- a/data/gsri/gsribioschemas.jsonld +++ b/data/gsri/gsribioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Julian Gehring", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package estimates the number of differentially expressed genes in gene sets by using the concept of the gene set regulation index.", "sc:license": "GPL-3.0", diff --git a/data/gst/gstbioschemas.jsonld b/data/gst/gstbioschemas.jsonld index e54b60dafa512..d0b55745d812c 100644 --- a/data/gst/gstbioschemas.jsonld +++ b/data/gst/gstbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "High sensitivity tool, based on proportion tests for linkage analysis using WES data.", "sc:name": "Gene selection tool (GST)", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/YaoZhou89/GST/" } \ No newline at end of file diff --git a/data/gstpred/gstpredbioschemas.jsonld b/data/gstpred/gstpredbioschemas.jsonld index d4d9c467a6dc8..e026c76c82acc 100644 --- a/data/gstpred/gstpredbioschemas.jsonld +++ b/data/gstpred/gstpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-server specially trained for the Glutathione S-transferase protein.The prediction is based on the basis of amino acid composition, dipeptide composition, tripeptide composition by using support vector machines(SVM).", "sc:name": "GSTPred", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/gstpred/" } \ No newline at end of file diff --git a/data/gsuite_hyperbrowser/gsuite_hyperbrowserbioschemas.jsonld b/data/gsuite_hyperbrowser/gsuite_hyperbrowserbioschemas.jsonld index c60c2aaef2ec5..ee35c9613a1c1 100644 --- a/data/gsuite_hyperbrowser/gsuite_hyperbrowserbioschemas.jsonld +++ b/data/gsuite_hyperbrowser/gsuite_hyperbrowserbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "GSuite HyperBrowser", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://hyperbrowser.uio.no/hb/#!mode=basic" } \ No newline at end of file diff --git a/data/gsva/gsvabioschemas.jsonld b/data/gsva/gsvabioschemas.jsonld index 238776a6de61c..c252539f9639d 100644 --- a/data/gsva/gsvabioschemas.jsonld +++ b/data/gsva/gsvabioschemas.jsonld @@ -18,12 +18,12 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Justin Guinney", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC3618321", "pubmed:23323831", + "pmcid:PMC3618321", { "@id": "https://doi.org/10.1186/1471-2105-14-7" } @@ -35,8 +35,8 @@ "sc:license": "GPL-2.0", "sc:name": "GSVA", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/GSVA.html", "sc:version": "1.22.0" diff --git a/data/gtcreator/gtcreatorbioschemas.jsonld b/data/gtcreator/gtcreatorbioschemas.jsonld index c063e0af7e2f8..e5ac7c5feb9d1 100644 --- a/data/gtcreator/gtcreatorbioschemas.jsonld +++ b/data/gtcreator/gtcreatorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GTCreator", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.cvc.uab.es/CVC-Colon/index.php/gtcreator/" } \ No newline at end of file diff --git a/data/gtex/gtexbioschemas.jsonld b/data/gtex/gtexbioschemas.jsonld index 0c364ff952ff3..39591c379a9c6 100644 --- a/data/gtex/gtexbioschemas.jsonld +++ b/data/gtex/gtexbioschemas.jsonld @@ -14,8 +14,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "GTEx contact form", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ "pmcid:PMC4010069", @@ -26,9 +26,6 @@ ], "sc:description": "Genotype-Tissue Expression (GTEx) - database which helps to study the relationship between genetic variation and gene expression in human tissues.", "sc:featureList": [ - { - "@id": "edam:operation_2495" - }, { "@id": "edam:operation_3197" }, @@ -37,6 +34,9 @@ }, { "@id": "edam:operation_3436" + }, + { + "@id": "edam:operation_2495" } ], "sc:name": "GTEx", diff --git a/data/gtfold/gtfoldbioschemas.jsonld b/data/gtfold/gtfoldbioschemas.jsonld index e7ba8b126810e..c18580db3db0a 100644 --- a/data/gtfold/gtfoldbioschemas.jsonld +++ b/data/gtfold/gtfoldbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "GTfold is a fast, scalable multicore code for predicting RNA secondary structure that is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.", "sc:name": "GTfold", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://gtfold.sourceforge.net/", "sc:version": "3.0" diff --git a/data/gtrellis/gtrellisbioschemas.jsonld b/data/gtrellis/gtrellisbioschemas.jsonld index 33c986dbb9d88..45dae2b368707 100644 --- a/data/gtrellis/gtrellisbioschemas.jsonld +++ b/data/gtrellis/gtrellisbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-7395-8709", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-016-1051-4", "@type": "sc:CreativeWork" @@ -30,8 +26,8 @@ "@id": "edam:data_3002" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { @@ -48,30 +44,34 @@ "@id": "http://orcid.org/0000-0002-7395-8709" }, "sc:citation": [ + "pmcid:PMC4835841", { "@id": "https://doi.org/10.1186/s12859-016-1051-4" }, - "pubmed:27089965", - "pmcid:PMC4835841" + "pubmed:27089965" ], "sc:description": "Visualize genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.", "sc:featureList": [ { - "@id": "edam:operation_3208" + "@id": "edam:operation_0362" }, { - "@id": "edam:operation_0362" + "@id": "edam:operation_3208" } ], "sc:license": "GPL-2.0", "sc:name": "gtrellis", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gtrellis.html", "sc:version": "1.6.0" + }, + { + "@id": "http://orcid.org/0000-0002-7395-8709", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/gtz/gtzbioschemas.jsonld b/data/gtz/gtzbioschemas.jsonld index d2e112dfdaaef..174860e7df7cd 100644 --- a/data/gtz/gtzbioschemas.jsonld +++ b/data/gtz/gtzbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/gtz", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Chengkun Wu", - "Zhuo Song" + "Zhuo Song", + "Chengkun Wu" ], "sc:additionalType": "Command-line tool", "sc:description": "A fast compression and cloud transmission tool optimized for FASTQ files.", diff --git a/data/guardd/guarddbioschemas.jsonld b/data/guardd/guarddbioschemas.jsonld index 56830ce6047a5..0eeb54c888676 100644 --- a/data/guardd/guarddbioschemas.jsonld +++ b/data/guardd/guarddbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data.", "sc:name": "GUARDD", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://research.cbc.osu.edu/foster.281/software/#GUARDD" } \ No newline at end of file diff --git a/data/guidance2/guidance2bioschemas.jsonld b/data/guidance2/guidance2bioschemas.jsonld index 643b18eca2c6c..9b0034ec91363 100644 --- a/data/guidance2/guidance2bioschemas.jsonld +++ b/data/guidance2/guidance2bioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKV318", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/guidance2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4489236", "pubmed:25883146", + "pmcid:PMC4489236", { "@id": "https://doi.org/10.1093/NAR/GKV318" } @@ -36,6 +32,10 @@ "Mac" ], "sc:url": "http://guidance.tau.ac.il/ver2/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKV318", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/guidedclustering/guidedclusteringbioschemas.jsonld b/data/guidedclustering/guidedclusteringbioschemas.jsonld index a66a9d669f530..3f757bc2c7fd4 100644 --- a/data/guidedclustering/guidedclusteringbioschemas.jsonld +++ b/data/guidedclustering/guidedclusteringbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An R package for the joint analysis of clinical microarray profiles and additional per gene measurements.", "sc:name": "GuidedClustering", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://compdiag.uni-regensburg.de/software/guidedClustering.shtml" } \ No newline at end of file diff --git a/data/guides/guidesbioschemas.jsonld b/data/guides/guidesbioschemas.jsonld index 3fe3217e51386..882b7035c4be5 100644 --- a/data/guides/guidesbioschemas.jsonld +++ b/data/guides/guidesbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "GUIDES", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://guides.sanjanalab.org/#/" } \ No newline at end of file diff --git a/data/guidescan/guidescanbioschemas.jsonld b/data/guidescan/guidescanbioschemas.jsonld index 5743d494eedb4..8df5428a94452 100644 --- a/data/guidescan/guidescanbioschemas.jsonld +++ b/data/guidescan/guidescanbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/guidescan", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Developers", + "Christina Leslie", "Andrea Ventura", - "Christina Leslie" + "Developers" ], "sc:additionalType": "Web application", "sc:description": "A generalized CRISPR guideRNA design tool.", "sc:name": "GuideScan", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.guidescan.com/", "sc:version": "1.0" diff --git a/data/guideseq/guideseqbioschemas.jsonld b/data/guideseq/guideseqbioschemas.jsonld index a24c9325ac2b7..71c7032302a03 100644 --- a/data/guideseq/guideseqbioschemas.jsonld +++ b/data/guideseq/guideseqbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lihua Julie Zhu", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package implements GUIDE-seq analysis workflow including functions for obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites.", "sc:license": "GPL-2.0", diff --git a/data/guidetopharmacology/guidetopharmacologybioschemas.jsonld b/data/guidetopharmacology/guidetopharmacologybioschemas.jsonld index bbbbc353c5209..121ddc9379a76 100644 --- a/data/guidetopharmacology/guidetopharmacologybioschemas.jsonld +++ b/data/guidetopharmacology/guidetopharmacologybioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkt1143", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/guidetopharmacology", "@type": "sc:SoftwareApplication", @@ -21,40 +25,36 @@ "pmcid:PMC3965070" ], "sc:contributor": [ + "Wellcome Trust", "International Union of Basic and Clinical Pharmacology (IUPHAR)", - "British Pharmacological Society (BPS)", - "Wellcome Trust" + "British Pharmacological Society (BPS)" ], "sc:description": "An expert-curated pharmacological database of drug targets and their ligands.", "sc:featureList": [ { - "@id": "edam:operation_3760" + "@id": "edam:operation_2421" }, { - "@id": "edam:operation_2421" + "@id": "edam:operation_3760" } ], "sc:funder": [ - "International Union of Basic and Clinical Pharmacology (IUPHAR)", "Wellcome Trust", + "International Union of Basic and Clinical Pharmacology (IUPHAR)", "British Pharmacological Society (BPS)" ], "sc:license": "CC-BY-SA-3.0", "sc:name": "IUPHAR BPS Guide to PHARMACOLOGY", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ "The University of Edinburgh", "ed.ac.uk" ], "sc:url": "http://www.guidetopharmacology.org/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkt1143", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/guidock-vnc/guidock-vncbioschemas.jsonld b/data/guidock-vnc/guidock-vncbioschemas.jsonld index f02dc2990ee20..f2815b6178b12 100644 --- a/data/guidock-vnc/guidock-vncbioschemas.jsonld +++ b/data/guidock-vnc/guidock-vncbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "GUIdock-VNC", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/BioDepot/GUIdock-VNC" } \ No newline at end of file diff --git a/data/guidock/guidockbioschemas.jsonld b/data/guidock/guidockbioschemas.jsonld index 242cad49d388a..f00389ac30f70 100644 --- a/data/guidock/guidockbioschemas.jsonld +++ b/data/guidock/guidockbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0152686", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-1754-7577", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1371/journal.pone.0152686", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/guidock", "@type": "sc:SoftwareApplication", @@ -25,11 +25,11 @@ }, "sc:additionalType": "Plug-in", "sc:citation": [ + "pmcid:PMC4821530", + "pubmed:27045593", { "@id": "https://doi.org/10.1371/journal.pone.0152686" - }, - "pubmed:27045593", - "pmcid:PMC4821530" + } ], "sc:description": "GUIdock allows for the facile distribution of a systems biology application along with its graphics environment.", "sc:featureList": { @@ -38,9 +38,9 @@ "sc:license": "MIT", "sc:name": "GUIdock", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/WebDataScience/GUIdock" } diff --git a/data/guild/guildbioschemas.jsonld b/data/guild/guildbioschemas.jsonld index 507c9a1898930..7fb7c12710d29 100644 --- a/data/guild/guildbioschemas.jsonld +++ b/data/guild/guildbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0043557", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-3466-6535", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1371/journal.pone.0043557", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/guild", "@type": "sc:SoftwareApplication", @@ -25,10 +25,10 @@ "@id": "http://orcid.org/0000-0002-3466-6535" }, "sc:citation": [ + "pmcid:PMC3448640", { "@id": "https://doi.org/10.1371/journal.pone.0043557" }, - "pmcid:PMC3448640", "pubmed:23028459" ], "sc:description": "Framework built for the prioritization of disease candidate genes using a priori gene-disease associations and protein interactions. It consists of implementations of 8 algorithms: NetScore, NetZcore, NetShort, NetCombo, fFlow, NetRank, NetWalk and NetProp.", @@ -37,8 +37,8 @@ }, "sc:name": "GUILD", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "upf.edu", "sc:url": "http://sbi.imim.es/web/index.php/research/software/guildsoftware", diff --git a/data/guildify/guildifybioschemas.jsonld b/data/guildify/guildifybioschemas.jsonld index 8dc1f42665876..42df31815d5d1 100644 --- a/data/guildify/guildifybioschemas.jsonld +++ b/data/guildify/guildifybioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-3466-6535", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/guildify", "@type": "sc:SoftwareApplication", @@ -22,16 +18,16 @@ }, "sc:citation": "pubmed:24532728", "sc:contributor": [ - "MICINN/MINECO & FEBS BIO2011-22568", - "Javier Garcia-Garcia" + "Javier Garcia-Garcia", + "MICINN/MINECO & FEBS BIO2011-22568" ], "sc:description": "Uses network-topology based prioritization algorithms in GUILD to score relevance of gene products with respect to given keywords. First, BIANA knowledge base containing data integrated from publicly available major data repositories is queried for gene products associated with the keywords. These gene products are fed to a species-specific interaction network as seed proteins. Finally, a score of relevance for each gene product in the network is calculated by the prioritization algorithm.", "sc:funder": "MICINN/MINECO & FEBS BIO2011-22568", "sc:name": "GUILDify", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ "upf.edu", @@ -39,6 +35,10 @@ ], "sc:url": "http://sbi.imim.es/web/GUILDify.php", "sc:version": "1.0" + }, + { + "@id": "http://orcid.org/0000-0002-3466-6535", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/guitar/guitarbioschemas.jsonld b/data/guitar/guitarbioschemas.jsonld index f1f9c66118040..4d328b0b10b17 100644 --- a/data/guitar/guitarbioschemas.jsonld +++ b/data/guitar/guitarbioschemas.jsonld @@ -24,23 +24,23 @@ "@id": "edam:data_2884" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3170" + "@id": "edam:topic_0080" }, { - "@id": "edam:topic_0080" + "@id": "edam:topic_3170" } ], "sc:citation": [ + "pmcid:PMC4864564", + "pubmed:27239475", { "@id": "https://doi.org/10.1155/2016/8367534" - }, - "pubmed:27239475", - "pmcid:PMC4864564" + } ], "sc:description": "The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.", "sc:featureList": { @@ -49,9 +49,9 @@ "sc:license": "GPL-2.0", "sc:name": "Guitar", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Guitar.html", "sc:version": "1.12.0" diff --git a/data/gunifrac/gunifracbioschemas.jsonld b/data/gunifrac/gunifracbioschemas.jsonld index 33fec15cc600b..dffc0f3507160 100644 --- a/data/gunifrac/gunifracbioschemas.jsonld +++ b/data/gunifrac/gunifracbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GUniFrac", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/GUniFrac/index.html" } \ No newline at end of file diff --git a/data/guugle/guuglebioschemas.jsonld b/data/guugle/guuglebioschemas.jsonld index 0907607605b3c..4f3792f3cc5c3 100644 --- a/data/guugle/guuglebioschemas.jsonld +++ b/data/guugle/guuglebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/guugle", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web API", "Web application", + "Web API", "Command-line tool" ], "sc:author": "Wolfgang Gerlach", @@ -23,9 +23,9 @@ "Linux" ], "sc:provider": [ - "Bielefeld University", + "CeBiTec", "BiBiServ", - "CeBiTec" + "Bielefeld University" ], "sc:url": "http://bibiserv.cebitec.uni-bielefeld.de/guugle", "sc:version": "1.2" diff --git a/data/guv-ap/guv-apbioschemas.jsonld b/data/guv-ap/guv-apbioschemas.jsonld index 76791ea36da9f..2903f476bcb6c 100644 --- a/data/guv-ap/guv-apbioschemas.jsonld +++ b/data/guv-ap/guv-apbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/GUV-AP", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Winfried Römer", - "Yves Mély" + "Yves Mély", + "Winfried Römer" ], "sc:additionalType": "Desktop application", "sc:description": "Multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles.", "sc:license": "Unlicense", "sc:name": "GUV-AP", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/AG-Roemer/GUV-AP", "sc:version": "2.0" diff --git a/data/gvista/gvistabioschemas.jsonld b/data/gvista/gvistabioschemas.jsonld index 4ae684c4287b3..ec8fe07f9a73f 100644 --- a/data/gvista/gvistabioschemas.jsonld +++ b/data/gvista/gvistabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Not licensed", "sc:name": "gVISTA", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://genome.lbl.gov/cgi-bin/GenomeVista" } \ No newline at end of file diff --git a/data/gviz/gvizbioschemas.jsonld b/data/gviz/gvizbioschemas.jsonld index 283b1c82a40b4..77716d6e40900 100644 --- a/data/gviz/gvizbioschemas.jsonld +++ b/data/gviz/gvizbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Florian Hahne", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:27272860", "sc:description": "Genomic data analyses requires integrated visualization of known genomic information and new experimental data. This package uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.", diff --git a/data/gw-sem/gw-sembioschemas.jsonld b/data/gw-sem/gw-sembioschemas.jsonld index c7325a48b7453..90e0d4fc9b6e6 100644 --- a/data/gw-sem/gw-sembioschemas.jsonld +++ b/data/gw-sem/gw-sembioschemas.jsonld @@ -33,8 +33,8 @@ "sc:name": "GW-SEM", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.people.vcu.edu/~bverhulst/GW-SEM/GW-SEM.R" } diff --git a/data/gwama/gwamabioschemas.jsonld b/data/gwama/gwamabioschemas.jsonld index 932b931931d4a..37e3417edbb5d 100644 --- a/data/gwama/gwamabioschemas.jsonld +++ b/data/gwama/gwamabioschemas.jsonld @@ -30,8 +30,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "GWAMA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.geenivaramu.ee/en/tools/gwama", "sc:version": "2.2.2" diff --git a/data/gwar/gwarbioschemas.jsonld b/data/gwar/gwarbioschemas.jsonld index 04af8c53e6e07..2cbab1c78f17d 100644 --- a/data/gwar/gwarbioschemas.jsonld +++ b/data/gwar/gwarbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Robust Analysis and Meta-Analysis of Genome-Wide Association Studies.", "sc:name": "GWAR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.compgen.org/tools/GWAR", "sc:version": "1.0" diff --git a/data/gwas_catalog/gwas_catalogbioschemas.jsonld b/data/gwas_catalog/gwas_catalogbioschemas.jsonld index 7d04f2067a69b..d1e06abaa28c2 100644 --- a/data/gwas_catalog/gwas_catalogbioschemas.jsonld +++ b/data/gwas_catalog/gwas_catalogbioschemas.jsonld @@ -18,21 +18,21 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "GWAS Catalog Support", "sc:additionalType": [ - "Database portal", "Web application", - "Web API" + "Web API", + "Database portal" ], "sc:citation": [ + "pmcid:PMC3965119", { "@id": "https://doi.org/10.1093/nar/gkt1229" }, - "pmcid:PMC3965119", "pubmed:24316577" ], "sc:description": "A catalogue that provides a publicly available manually curated collection of published GWAS assaying at least 100 000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10−5.", "sc:featureList": [ { - "@id": "edam:operation_3459" + "@id": "edam:operation_2429" }, { "@id": "edam:operation_2421" @@ -41,15 +41,15 @@ "@id": "edam:operation_0484" }, { - "@id": "edam:operation_2429" + "@id": "edam:operation_3459" } ], "sc:license": "Apache-2.0", "sc:name": "GWAS catalog", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.ebi.ac.uk/gwas/" } diff --git a/data/gwascat/gwascatbioschemas.jsonld b/data/gwascat/gwascatbioschemas.jsonld index 5da7e70af3d94..2d849c55694a0 100644 --- a/data/gwascat/gwascatbioschemas.jsonld +++ b/data/gwascat/gwascatbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "gwascat", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/gwascat.html", "sc:version": "2.6.0" diff --git a/data/gwasdb/gwasdbbioschemas.jsonld b/data/gwasdb/gwasdbbioschemas.jsonld index 076b28bd81714..51d20ede7ecdf 100644 --- a/data/gwasdb/gwasdbbioschemas.jsonld +++ b/data/gwasdb/gwasdbbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Database for human genetic variants (GV) identified by genome-wide association studies. Contains twenty times more data than the NHGRI GWAS Catalog, manually curated from literature. Also has annotations for each GV.", "sc:name": "GWASdb", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://jjwanglab.org:8080/gwasdb/" } \ No newline at end of file diff --git a/data/gwasinspector/gwasinspectorbioschemas.jsonld b/data/gwasinspector/gwasinspectorbioschemas.jsonld index 27224b0aa22f1..7a4756795c0f3 100644 --- a/data/gwasinspector/gwasinspectorbioschemas.jsonld +++ b/data/gwasinspector/gwasinspectorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "GWASinspector", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://gwasinspector.com/", "sc:version": "1.3.4" diff --git a/data/gwaspi/gwaspibioschemas.jsonld b/data/gwaspi/gwaspibioschemas.jsonld index 945140caa8aea..4c827d04fc4ec 100644 --- a/data/gwaspi/gwaspibioschemas.jsonld +++ b/data/gwaspi/gwaspibioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:author": [ - "Arcadi Navarro Cuartiellas", - "Fernando Muñiz Fernando" + "Fernando Muñiz Fernando", + "Arcadi Navarro Cuartiellas" ], "sc:citation": "pubmed:21586520", "sc:contributor": [ @@ -23,9 +23,9 @@ "sc:description": "User-friendly, multiplatform, desktop-able application for the management and analysis of GWAS data, with a novel approach on database technologies to leverage the most out of commonly available desktop hardware. GWASpi aims to be a start-to-finish GWAS management application, from raw data to results, containing the most common analysis tools.", "sc:name": "Genome Wide Association Study pipeline (GWASpi)", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": [ "upf.edu", diff --git a/data/gwasrapidd/gwasrapiddbioschemas.jsonld b/data/gwasrapidd/gwasrapiddbioschemas.jsonld index d7ac2d1ec2a21..fa1b26dc8ed19 100644 --- a/data/gwasrapidd/gwasrapiddbioschemas.jsonld +++ b/data/gwasrapidd/gwasrapiddbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "gwasrapidd", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/ramiromagno/gwasrapidd" } \ No newline at end of file diff --git a/data/gwastools/gwastoolsbioschemas.jsonld b/data/gwastools/gwastoolsbioschemas.jsonld index 4faaa57f31654..d53072e5589ed 100644 --- a/data/gwastools/gwastoolsbioschemas.jsonld +++ b/data/gwastools/gwastoolsbioschemas.jsonld @@ -13,10 +13,10 @@ "@id": "https://bio.tools/gwastools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Adrienne Stilp", { "@id": "http://orcid.org/0000-0002-7231-9745" - } + }, + "Adrienne Stilp" ], "sc:additionalType": [ "Library", @@ -24,10 +24,10 @@ ], "sc:citation": [ "pmcid:PMC3519456", - "pubmed:23052040", { "@id": "https://doi.org/10.1093/bioinformatics/bts610" - } + }, + "pubmed:23052040" ], "sc:description": "Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.", "sc:featureList": [ @@ -35,10 +35,10 @@ "@id": "edam:operation_3431" }, { - "@id": "edam:operation_0226" + "@id": "edam:operation_2945" }, { - "@id": "edam:operation_2945" + "@id": "edam:operation_0226" } ], "sc:license": "Artistic-2.0", diff --git a/data/gwasurvivr/gwasurvivrbioschemas.jsonld b/data/gwasurvivr/gwasurvivrbioschemas.jsonld index f865521df8d82..aa33aebd22485 100644 --- a/data/gwasurvivr/gwasurvivrbioschemas.jsonld +++ b/data/gwasurvivr/gwasurvivrbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Artistic-2.0", "sc:name": "gwasurvivr", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/gwasurvivr", "sc:version": "1.2.0" diff --git a/data/gwatoolbox/gwatoolboxbioschemas.jsonld b/data/gwatoolbox/gwatoolboxbioschemas.jsonld index 1bc11b8d082e6..bb966de51757f 100644 --- a/data/gwatoolbox/gwatoolboxbioschemas.jsonld +++ b/data/gwatoolbox/gwatoolboxbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "GWAtoolbox is an R-package for fast quality control and data handling of multiple data files obtained from genome-wide association studies (GWAS).", "sc:name": "GWAtoolbox", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.eurac.edu/en/research/health/biomed/services/Pages/GWAtoolbox.aspx", diff --git a/data/gwfasta/gwfastabioschemas.jsonld b/data/gwfasta/gwfastabioschemas.jsonld index a0b2f07631539..9e93e212e380a 100644 --- a/data/gwfasta/gwfastabioschemas.jsonld +++ b/data/gwfasta/gwfastabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "GWFASTA", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/gwfasta/" } \ No newline at end of file diff --git a/data/gwips-viz/gwips-vizbioschemas.jsonld b/data/gwips-viz/gwips-vizbioschemas.jsonld index 8d2b8eb3359eb..a1c75e72c1b16 100644 --- a/data/gwips-viz/gwips-vizbioschemas.jsonld +++ b/data/gwips-viz/gwips-vizbioschemas.jsonld @@ -19,25 +19,25 @@ "sc:additionalType": "Database portal", "sc:author": "Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM", "sc:citation": [ + "pmcid:PMC3965066", + "pubmed:24185699", { "@id": "https://doi.org/10.1093/nar/gkt1035" }, - "pubmed:25736862", - "pubmed:24185699", - "pmcid:PMC3965066" + "pubmed:25736862" ], "sc:contributor": "Science Foundation Ireland", "sc:description": "Specialized ribosome profiling (ribo-seq) browser providing free access to the genomic alignments of ribo-seq reads in conjunction with mRNA-seq controls along with relevant annotation tracks. Based on the UCSC Genome Browser, the tool’s ribo-seq tracks for various organisms allows for cross-species comparison of orthologous genes while the separate tracks for each ribo-seq study enables cross-study comparisons.", "sc:funder": "Science Foundation Ireland", "sc:name": "GWIPS-viz", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "ucc.ie", - "School of Biochemistry & Cell Biology, University College Cork" + "School of Biochemistry & Cell Biology, University College Cork", + "ucc.ie" ], "sc:url": "http://gwips.ucc.ie" } diff --git a/data/gwrm/gwrmbioschemas.jsonld b/data/gwrm/gwrmbioschemas.jsonld index 79b0cf693d20f..3a44e23d52339 100644 --- a/data/gwrm/gwrmbioschemas.jsonld +++ b/data/gwrm/gwrmbioschemas.jsonld @@ -16,15 +16,15 @@ "@id": "http://orcid.org/0000-0001-9795-9610" }, "sc:additionalType": [ - "Command-line tool", - "Plug-in" + "Plug-in", + "Command-line tool" ], "sc:citation": [ + "pubmed:27936064", + "pmcid:PMC5148598", { "@id": "https://doi.org/10.1371/journal.pone.0167570" - }, - "pmcid:PMC5148598", - "pubmed:27936064" + } ], "sc:description": "GWRM is an R package for fitting, describing and validating the generalized Waring regression model.", "sc:featureList": { @@ -33,19 +33,19 @@ "sc:license": "GPL-3.0", "sc:name": "GWRM", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/GWRM/", "sc:version": "2.1.0.3" }, - { - "@id": "http://orcid.org/0000-0001-9795-9610", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1371/journal.pone.0167570", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-9795-9610", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/gxa/gxabioschemas.jsonld b/data/gxa/gxabioschemas.jsonld index c8d19c827e5dd..7f3134e92046d 100644 --- a/data/gxa/gxabioschemas.jsonld +++ b/data/gxa/gxabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data.", "sc:name": "GXA", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "Identifiers.org", "sc:url": "http://www.ebi.ac.uk/gxa" diff --git a/data/gxa_expt/gxa_exptbioschemas.jsonld b/data/gxa_expt/gxa_exptbioschemas.jsonld index 50745e124d205..672d5e8fc50cf 100644 --- a/data/gxa_expt/gxa_exptbioschemas.jsonld +++ b/data/gxa_expt/gxa_exptbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkr913", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/gxa_expt", "@type": "sc:SoftwareApplication", @@ -24,11 +28,11 @@ "@id": "edam:topic_0203" }, "sc:citation": [ - "pmcid:PMC3245177", - "pubmed:22064864", { "@id": "https://doi.org/10.1093/nar/gkr913" - } + }, + "pubmed:22064864", + "pmcid:PMC3245177" ], "sc:description": "Semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.", "sc:featureList": { @@ -36,16 +40,12 @@ }, "sc:name": "GXA Expt", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "Identifiers.org", "sc:url": "http://www.ebi.ac.uk/gxa/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkr913", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/gxd/gxdbioschemas.jsonld b/data/gxd/gxdbioschemas.jsonld index ed96478c1b7db..1e8aac3d10dde 100644 --- a/data/gxd/gxdbioschemas.jsonld +++ b/data/gxd/gxdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Community resource of mouse developmental expression information. It integrates different types of expression data at the transcript and protein level and captures expression information from many different mouse strains and mutants.", "sc:name": "Gene Expression Database (GXD)", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.informatics.jax.org" } \ No newline at end of file diff --git a/data/gxescan/gxescanbioschemas.jsonld b/data/gxescan/gxescanbioschemas.jsonld index 81efc8b8c3999..2edc34aa2a4a5 100644 --- a/data/gxescan/gxescanbioschemas.jsonld +++ b/data/gxescan/gxescanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Detects GxE Interactions in a Genome-wide Association Study", "sc:name": "GxEscan", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://biostats.usc.edu/software" } \ No newline at end of file diff --git a/data/gxna/gxnabioschemas.jsonld b/data/gxna/gxnabioschemas.jsonld index 0cb2abda399f3..b81c4e655e6ee 100644 --- a/data/gxna/gxnabioschemas.jsonld +++ b/data/gxna/gxnabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "GXNA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://statweb.stanford.edu/~serban/gxna/", "sc:version": "2.0" diff --git a/data/gydb/gydbbioschemas.jsonld b/data/gydb/gydbbioschemas.jsonld index d993a4c303224..d86bf5fd6e843 100644 --- a/data/gydb/gydbbioschemas.jsonld +++ b/data/gydb/gydbbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "Gypsy Database (GyDB)", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://gydb.org" } \ No newline at end of file diff --git a/data/gypsum-dl/gypsum-dlbioschemas.jsonld b/data/gypsum-dl/gypsum-dlbioschemas.jsonld index 8c7fbcba62411..2691ddebceaea 100644 --- a/data/gypsum-dl/gypsum-dlbioschemas.jsonld +++ b/data/gypsum-dl/gypsum-dlbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S13321-019-0358-3", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0002-5808-4097", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/Gypsum-DL", "@type": "sc:SoftwareApplication", @@ -25,11 +17,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6534830", + "pubmed:31127411", { "@id": "https://doi.org/10.1186/S13321-019-0358-3" - }, - "pubmed:31127411", - "pmcid:PMC6534830" + } ], "sc:description": "Program for preparing small-molecule libraries for structure-based virtual screening.", "sc:featureList": { @@ -38,10 +30,18 @@ "sc:license": "Apache-2.0", "sc:name": "Gypsum-DL", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://durrantlab.com/gypsum-dl/" + }, + { + "@id": "https://doi.org/10.1186/S13321-019-0358-3", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-5808-4097", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/h-blast/h-blastbioschemas.jsonld b/data/h-blast/h-blastbioschemas.jsonld index c35f98814b987..4c11b240d8de7 100644 --- a/data/h-blast/h-blastbioschemas.jsonld +++ b/data/h-blast/h-blastbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Fast protein sequence alignment toolkit on heterogeneous computers with GPUs .", "sc:name": "H-BLAST", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/Yeyke/H-BLAST" } \ No newline at end of file diff --git a/data/h-blox/h-bloxbioschemas.jsonld b/data/h-blox/h-bloxbioschemas.jsonld index 52badd316cf1a..689e597dca24d 100644 --- a/data/h-blox/h-bloxbioschemas.jsonld +++ b/data/h-blox/h-bloxbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/h-blox", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Gisbert Schneider", - "Jochen Zuegge" + "Jochen Zuegge", + "Gisbert Schneider" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:11449568", @@ -20,8 +20,8 @@ "sc:name": "H-BloX", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://gecco.org.chemie.uni-frankfurt.de/h-blox/hblox.html" } \ No newline at end of file diff --git a/data/h-clust/h-clustbioschemas.jsonld b/data/h-clust/h-clustbioschemas.jsonld index 8a11557cc581e..9d0b6f8e50a14 100644 --- a/data/h-clust/h-clustbioschemas.jsonld +++ b/data/h-clust/h-clustbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Simple clustering method that can be used to rapidly identify a set of tag SNP’s based upon genotype data.", "sc:name": "H-Clust", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://wpicr.wpic.pitt.edu/WPICCompGen/hclust/hclust.htm" } \ No newline at end of file diff --git a/data/h-protection/h-protectionbioschemas.jsonld b/data/h-protection/h-protectionbioschemas.jsonld index a871bfe4724c8..630c50c764ce4 100644 --- a/data/h-protection/h-protectionbioschemas.jsonld +++ b/data/h-protection/h-protectionbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/h-protection", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Galzitskaya Oxana Valerianovna", - "Sokolovskiy Igor Vitalievich" + "Sokolovskiy Igor Vitalievich", + "Galzitskaya Oxana Valerianovna" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:18949078", "sc:description": "Web application for prediction of residue status to be protected or unprotected from hydrogen-deuterium exchange in a protein chain.", "sc:name": "H-Protection", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioinfo.protres.ru/ogp/" diff --git a/data/h-vdw/h-vdwbioschemas.jsonld b/data/h-vdw/h-vdwbioschemas.jsonld index 42b84950bd7cb..996435f66df9f 100644 --- a/data/h-vdw/h-vdwbioschemas.jsonld +++ b/data/h-vdw/h-vdwbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Novel method for quantitatively predicting non-covalent interactions from protein and nucleic acid sequence.", "sc:name": "H-VDW", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.cbi.seu.edu.cn/H-VDW/H-VDW.htm" diff --git a/data/h5vc/h5vcbioschemas.jsonld b/data/h5vc/h5vcbioschemas.jsonld index 03bc6b6d23b18..0c925edfe9905 100644 --- a/data/h5vc/h5vcbioschemas.jsonld +++ b/data/h5vc/h5vcbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "h5vc", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/h5vc.html", "sc:version": "2.14.0" diff --git a/data/haddock/haddockbioschemas.jsonld b/data/haddock/haddockbioschemas.jsonld index 53964bb9f3722..c11744a63d718 100644 --- a/data/haddock/haddockbioschemas.jsonld +++ b/data/haddock/haddockbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7369-1322", + "@type": "schema:Organization" + }, { "@id": "https://bio.tools/haddock", "@type": "sc:SoftwareApplication", @@ -16,8 +20,8 @@ "@id": "http://orcid.org/0000-0001-7369-1322" }, "sc:additionalType": [ - "Web service", "Web application", + "Web service", "Suite" ], "sc:author": { @@ -26,8 +30,8 @@ "sc:description": "High Ambiguity Driven biomolecular DOCKing: an information-driven flexible docking approach for the modeling of biomolecular complexes. It distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. It can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.", "sc:name": "HADDOCK", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "University of Utrecht", @@ -37,10 +41,6 @@ ], "sc:url": "http://www.bonvinlab.org/software/haddock2.2/", "sc:version": "2.2" - }, - { - "@id": "http://orcid.org/0000-0001-7369-1322", - "@type": "schema:Organization" } ] } \ No newline at end of file diff --git a/data/hairpin_annotation/hairpin_annotationbioschemas.jsonld b/data/hairpin_annotation/hairpin_annotationbioschemas.jsonld index 94014adf1ab08..1f05cf4c4b5e5 100644 --- a/data/hairpin_annotation/hairpin_annotationbioschemas.jsonld +++ b/data/hairpin_annotation/hairpin_annotationbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Generates a secondary structure from an RNA sequence and highlights regions of interest using RNAplot", "sc:name": "RNA Folding Annotation", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://srna-workbench.cmp.uea.ac.uk" } \ No newline at end of file diff --git a/data/haloarchaeal_genomes/haloarchaeal_genomesbioschemas.jsonld b/data/haloarchaeal_genomes/haloarchaeal_genomesbioschemas.jsonld index c897cf288b389..88a312428b1a9 100644 --- a/data/haloarchaeal_genomes/haloarchaeal_genomesbioschemas.jsonld +++ b/data/haloarchaeal_genomes/haloarchaeal_genomesbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Shiladitya DasSarma", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:description": "Haloarchaeal genomes database.", "sc:license": "Unlicense", "sc:name": "Haloarchaeal Genomes", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://halo.umbc.edu/" } \ No newline at end of file diff --git a/data/hamap-scan/hamap-scanbioschemas.jsonld b/data/hamap-scan/hamap-scanbioschemas.jsonld index edbcbe1371b6a..7f143bcb9b193 100644 --- a/data/hamap-scan/hamap-scanbioschemas.jsonld +++ b/data/hamap-scan/hamap-scanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Scan several protein sequences or a whole genome (all ORFs) against HAMAP family profiles. Sequences that match HAMAP profiles will be annotated in the UniProtKB format by the associated annotation rules.", "sc:name": "HAMAP-Scan", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://hamap.expasy.org/hamap_scan/" } \ No newline at end of file diff --git a/data/hamap/hamapbioschemas.jsonld b/data/hamap/hamapbioschemas.jsonld index 972ae529ad388..6c314f2df7bf4 100644 --- a/data/hamap/hamapbioschemas.jsonld +++ b/data/hamap/hamapbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-2148-9135", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/hamap", "@type": "sc:SoftwareApplication", @@ -25,10 +21,10 @@ "sc:additionalType": "Database portal", "sc:citation": [ "pmcid:PMC4383873", - "pubmed:25348399", { "@id": "https://doi.org/10.1093/nar/gku1002" - } + }, + "pubmed:25348399" ], "sc:description": "A system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline.", "sc:featureList": [ @@ -51,6 +47,10 @@ "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://hamap.expasy.org" }, + { + "@id": "http://orcid.org/0000-0003-2148-9135", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/nar/gku1002", "@type": "sc:CreativeWork" diff --git a/data/hamdb/hamdbbioschemas.jsonld b/data/hamdb/hamdbbioschemas.jsonld index 837287c12c205..0a6d0e9673969 100644 --- a/data/hamdb/hamdbbioschemas.jsonld +++ b/data/hamdb/hamdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "HAMdb", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://hamdb.scbdd.com/" } \ No newline at end of file diff --git a/data/hammock/hammockbioschemas.jsonld b/data/hammock/hammockbioschemas.jsonld index 13df0115565ae..c316c286f50d7 100644 --- a/data/hammock/hammockbioschemas.jsonld +++ b/data/hammock/hammockbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for peptide sequence clustering. It is able to cluster extremely large amounts of short peptide sequences into groups sharing sequence motifs.", "sc:name": "Hammock", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.recamo.cz/en/software/hammock-cluster-peptides/" } \ No newline at end of file diff --git a/data/hamr/hamrbioschemas.jsonld b/data/hamr/hamrbioschemas.jsonld index b175e51b0a699..f1f4274c0391f 100644 --- a/data/hamr/hamrbioschemas.jsonld +++ b/data/hamr/hamrbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/HAMR", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web service", "Command-line tool", - "Web application" + "Web application", + "Web service" ], "sc:citation": "pubmed:30539546", "sc:description": "HAMR (High-throughput Annotation of Modified Ribonucleotides) - web application that allows you to detect and classify modified nucleotides in RNA-seq data.", "sc:license": "MIT", "sc:name": "HAMR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://tesla.pcbi.upenn.edu/hamr/", "sc:version": "1.2" diff --git a/data/hamster/hamsterbioschemas.jsonld b/data/hamster/hamsterbioschemas.jsonld index d5e34bd52e77f..29b68114df919 100644 --- a/data/hamster/hamsterbioschemas.jsonld +++ b/data/hamster/hamsterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for depicting experiments in a microarray data set as a set of minimum spanning trees.", "sc:name": "HAMSTER", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/rwanwork/Hamster" diff --git a/data/hana/hanabioschemas.jsonld b/data/hana/hanabioschemas.jsonld index beae6713ad299..c9414cf09bb5c 100644 --- a/data/hana/hanabioschemas.jsonld +++ b/data/hana/hanabioschemas.jsonld @@ -15,16 +15,16 @@ "Web application" ], "sc:author": [ + "Miloš Fetter", "Daniel Georgiev", - "Lucie Houdová", - "Miloš Fetter" + "Lucie Houdová" ], "sc:description": "Haplotype analyzer for the Czech population.", "sc:name": "HANA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "University of West Bohemia, Czech Republic", "sc:url": "http://ccy.zcu.cz/registr/CZ-HANA.html", diff --git a/data/hansa/hansabioschemas.jsonld b/data/hansa/hansabioschemas.jsonld index 26a2e54a5677a..13322e1d075f1 100644 --- a/data/hansa/hansabioschemas.jsonld +++ b/data/hansa/hansabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool to predict the deleterious effects of a mutation by using 10 Neutral- Disease Mis-Sense Mutation Discriminatory (NDMSMD) features.", "sc:name": "Hansa", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://hansa.cdfd.org.in:8080/" diff --git a/data/hapassoc/hapassocbioschemas.jsonld b/data/hapassoc/hapassocbioschemas.jsonld index 68d7523afedde..a17c2731c7e0b 100644 --- a/data/hapassoc/hapassocbioschemas.jsonld +++ b/data/hapassoc/hapassocbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "hapassoc", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://stat.sfu.ca/statgen/research/hapassoc.html" } \ No newline at end of file diff --git a/data/hapchat/hapchatbioschemas.jsonld b/data/hapchat/hapchatbioschemas.jsonld index 865c09fe1b0cc..3c7897fdbec98 100644 --- a/data/hapchat/hapchatbioschemas.jsonld +++ b/data/hapchat/hapchatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "HapCHAT", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://hapchat.algolab.eu" } \ No newline at end of file diff --git a/data/hapedit/hapeditbioschemas.jsonld b/data/hapedit/hapeditbioschemas.jsonld index c246a35b74a01..9c88e4ad089fe 100644 --- a/data/hapedit/hapeditbioschemas.jsonld +++ b/data/hapedit/hapeditbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for assessing the accuracy of assembled haplotypes. Editting functions such as breaking erroneous haplotype segments into smaller segments or concatenating haplotype segments are also possible.", "sc:name": "HapEdit", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://embio.yonsei.ac.kr/hapedit" } \ No newline at end of file diff --git a/data/hapevolution/hapevolutionbioschemas.jsonld b/data/hapevolution/hapevolutionbioschemas.jsonld index acc80231ac060..26563264950f8 100644 --- a/data/hapevolution/hapevolutionbioschemas.jsonld +++ b/data/hapevolution/hapevolutionbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "HapEvolution", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.med.mun.ca/PTRG/What-We-Do/Research/PTRG-Research/HapEvolution.aspx" } \ No newline at end of file diff --git a/data/hapfabia/hapfabiabioschemas.jsonld b/data/hapfabia/hapfabiabioschemas.jsonld index afd39b04e3724..7f7050a026dab 100644 --- a/data/hapfabia/hapfabiabioschemas.jsonld +++ b/data/hapfabia/hapfabiabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkt1013", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/hapfabia", "@type": "sc:SoftwareApplication", @@ -24,21 +20,21 @@ }, "edam:has_output": [ { - "@id": "edam:data_2048" + "@id": "edam:data_1276" }, { - "@id": "edam:data_1863" + "@id": "edam:data_2884" }, { - "@id": "edam:data_2884" + "@id": "edam:data_1863" }, { - "@id": "edam:data_1276" + "@id": "edam:data_2048" } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { @@ -49,11 +45,11 @@ } ], "sc:citation": [ + "pubmed:24174545", "pmcid:PMC3905877", { "@id": "https://doi.org/10.1093/nar/gkt1013" - }, - "pubmed:24174545" + } ], "sc:description": "Package to identify very short IBD segments in large sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.", "sc:featureList": { @@ -63,12 +59,16 @@ "sc:name": "hapFabia", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hapFabia.html", "sc:version": "1.16.0" }, + { + "@id": "https://doi.org/10.1093/nar/gkt1013", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0001-7449-2528", "@type": "schema:Person" diff --git a/data/hapflk/hapflkbioschemas.jsonld b/data/hapflk/hapflkbioschemas.jsonld index b7ef8ada0cbbf..2e7913dd7b01f 100644 --- a/data/hapflk/hapflkbioschemas.jsonld +++ b/data/hapflk/hapflkbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Software for the detection of selection signatures based on multiple population genotyping data.", "sc:name": "hapFLK", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://forge-dga.jouy.inra.fr/projects/hapflk", "sc:version": "1.2.1" diff --git a/data/hapflow/hapflowbioschemas.jsonld b/data/hapflow/hapflowbioschemas.jsonld index b8e3be81e2733..e3fe1fa81f551 100644 --- a/data/hapflow/hapflowbioschemas.jsonld +++ b/data/hapflow/hapflowbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/hapflow", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mitchell J Sullivan", - "Issue reporting" + "Issue reporting", + "Mitchell J Sullivan" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:26449930", "sc:description": "Python application for visualising haplotypes present in sequencing data. It identifies variant profiles present and reads and creates an abstract visual representation of these profiles to make haplotypes easier to identify.", "sc:name": "HapFlow", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://mjsull.github.io/HapFlow/" } \ No newline at end of file diff --git a/data/hapler/haplerbioschemas.jsonld b/data/hapler/haplerbioschemas.jsonld index 02d8854d82dca..2f110fb83d0e3 100644 --- a/data/hapler/haplerbioschemas.jsonld +++ b/data/hapler/haplerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/hapler", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Shawn O'Neil", - "Scott J. Emrich" + "Scott J. Emrich", + "Shawn O'Neil" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:22537299", diff --git a/data/haplin/haplinbioschemas.jsonld b/data/haplin/haplinbioschemas.jsonld index 65815068e3a34..8d46156df02f8 100644 --- a/data/haplin/haplinbioschemas.jsonld +++ b/data/haplin/haplinbioschemas.jsonld @@ -15,29 +15,29 @@ "biotools:primaryContact": "Hakon K. Gjessing", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6444579", - "pubmed:30940094", { "@id": "https://doi.org/10.1186/s12859-019-2727-3" - } + }, + "pubmed:30940094", + "pmcid:PMC6444579" ], "sc:description": "R package for power and sample size calculations in genetic association analyses of family triads and unrelated controls.", "sc:featureList": [ - { - "@id": "edam:operation_3454" - }, { "@id": "edam:operation_3196" }, { "@id": "edam:operation_0487" + }, + { + "@id": "edam:operation_3454" } ], "sc:license": "GPL-3.0", "sc:name": "Haplin", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://cran.r-project.org/package=Haplin", diff --git a/data/haplogrep/haplogrepbioschemas.jsonld b/data/haplogrep/haplogrepbioschemas.jsonld index f19f8014db0b4..27a83d6d50d65 100644 --- a/data/haplogrep/haplogrepbioschemas.jsonld +++ b/data/haplogrep/haplogrepbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Web application for finding the corresponding haplogroup to given mtDNA profiles based on Phylotree (mtDNA classification tree).", "sc:name": "HaploGrep", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://haplogrep.uibk.ac.at/" } \ No newline at end of file diff --git a/data/haplohseq/haplohseqbioschemas.jsonld b/data/haplohseq/haplohseqbioschemas.jsonld index 733ab218d373c..8be032ff1ef6f 100644 --- a/data/haplohseq/haplohseqbioschemas.jsonld +++ b/data/haplohseq/haplohseqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Identifies regions of allelic imbalance (AI) in sequencing data obtained from impure samples where AI events exist in a potentially low proportion of cells in the sample.", "sc:name": "hapLOHseq", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sites.google.com/site/integrativecancergenomics/software/haplohseq" } \ No newline at end of file diff --git a/data/haplor/haplorbioschemas.jsonld b/data/haplor/haplorbioschemas.jsonld index 19a3f6d4249fa..94e5343f1609d 100644 --- a/data/haplor/haplorbioschemas.jsonld +++ b/data/haplor/haplorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "haploR", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/izhbannikov/haploR", diff --git a/data/haploscope/haploscopebioschemas.jsonld b/data/haploscope/haploscopebioschemas.jsonld index ddbe2dd36f220..75e0c7c02e33e 100644 --- a/data/haploscope/haploscopebioschemas.jsonld +++ b/data/haploscope/haploscopebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Haploscope", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://haploscope.scheetlabsoftware.org/", "sc:version": "0.4.1" diff --git a/data/haplosuite/haplosuitebioschemas.jsonld b/data/haplosuite/haplosuitebioschemas.jsonld index 7941ce5422246..1f23e11b9b797 100644 --- a/data/haplosuite/haplosuitebioschemas.jsonld +++ b/data/haplosuite/haplosuitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Haplosuite", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.statgen.nus.edu.sg" } \ No newline at end of file diff --git a/data/haploview/haploviewbioschemas.jsonld b/data/haploview/haploviewbioschemas.jsonld index 2b0aa66cfc130..7b6e61a6e2d21 100644 --- a/data/haploview/haploviewbioschemas.jsonld +++ b/data/haploview/haploviewbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "HaploView", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://www.broadinstitute.org/haploview/haploview" } \ No newline at end of file diff --git a/data/haplowser/haplowserbioschemas.jsonld b/data/haplowser/haplowserbioschemas.jsonld index 00625abfa4e54..3e200fb3ad7e2 100644 --- a/data/haplowser/haplowserbioschemas.jsonld +++ b/data/haplowser/haplowserbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "Haplowser", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://haplowser-free-download.softwares7.com/" diff --git a/data/happy/happybioschemas.jsonld b/data/happy/happybioschemas.jsonld index f2a9e10a15c76..7167d5642b0e4 100644 --- a/data/happy/happybioschemas.jsonld +++ b/data/happy/happybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Estimates haplotype-specific odds ratios from genotype data on unrelated cases and controls using unconditional logistic regression. It can adjust for the main effects of relevant covariates and estimate stratum-specific haplotype effects.", "sc:name": "HAPPY", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.hsph.harvard.edu/peter-kraft/software/" } \ No newline at end of file diff --git a/data/hapreads/hapreadsbioschemas.jsonld b/data/hapreads/hapreadsbioschemas.jsonld index 80f1ac3040c65..1efad7a91106f 100644 --- a/data/hapreads/hapreadsbioschemas.jsonld +++ b/data/hapreads/hapreadsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A ILP program for infering haplotypes with shot reads, which finds the most likely haplotypes by approximating local genealogical history as a perfect phylogeny.", "sc:name": "HapReads", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.engr.uconn.edu/~jiz08001/hapreads.html" } \ No newline at end of file diff --git a/data/hapredictor/hapredictorbioschemas.jsonld b/data/hapredictor/hapredictorbioschemas.jsonld index d91c415b4887a..93760d79c0fdc 100644 --- a/data/hapredictor/hapredictorbioschemas.jsonld +++ b/data/hapredictor/hapredictorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "HApredictor is an HA-specific prediction tool which showed disease prediction accuracy comparable to other publicly available prediction software.", "sc:name": "HAPredictor", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#hapredictor" diff --git a/data/harman/harmanbioschemas.jsonld b/data/harman/harmanbioschemas.jsonld index 38e9bd3cb0d31..05c31eb2cf994 100644 --- a/data/harman/harmanbioschemas.jsonld +++ b/data/harman/harmanbioschemas.jsonld @@ -14,30 +14,30 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jason Ross", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pubmed:27585881", + "pmcid:PMC5009651", { "@id": "https://doi.org/10.1186/s12859-016-1212-5" - }, - "pubmed:27585881", - "pmcid:PMC5009651" + } ], "sc:description": "PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.", "sc:featureList": [ { - "@id": "edam:operation_2409" + "@id": "edam:operation_2939" }, { - "@id": "edam:operation_2939" + "@id": "edam:operation_2409" } ], "sc:license": "GPL-3.0", "sc:name": "Harman", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Harman.html", "sc:version": "1.2.0" diff --git a/data/harmony/harmonybioschemas.jsonld b/data/harmony/harmonybioschemas.jsonld index f512d74ebf672..0aa0724af55ba 100644 --- a/data/harmony/harmonybioschemas.jsonld +++ b/data/harmony/harmonybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.", "sc:name": "Harmony", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://caps.ncbs.res.in/harmony/" } \ No newline at end of file diff --git a/data/harsh/harshbioschemas.jsonld b/data/harsh/harshbioschemas.jsonld index 3038c7f7e65da..9a7bfd2bd49d6 100644 --- a/data/harsh/harshbioschemas.jsonld +++ b/data/harsh/harshbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "HARSH (HAplotype inference using Reference and Sequencing tecHnology) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method.", "sc:name": "HARSH", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://genetics.cs.ucla.edu/harsh/", "sc:version": "0.21" diff --git a/data/harshlight/harshlightbioschemas.jsonld b/data/harshlight/harshlightbioschemas.jsonld index e99e138406194..aa3c80bb0112d 100644 --- a/data/harshlight/harshlightbioschemas.jsonld +++ b/data/harshlight/harshlightbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Maurizio Pellegrino", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package is used to detect extended, diffuse and compact blemishes on microarray chips. It automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.", "sc:license": "GPL-2.0", "sc:name": "Harshlight", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Harshlight.html", diff --git a/data/harvester/harvesterbioschemas.jsonld b/data/harvester/harvesterbioschemas.jsonld index c95c014f33814..9af9e34a0637f 100644 --- a/data/harvester/harvesterbioschemas.jsonld +++ b/data/harvester/harvesterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Fast access to public bioinformatic databases and servers for human proteins. Results are returned as a single HTML page that contains the cached and cross-linked output from the following databases/servers: Uniprot/SWISSprot, ensEMBL, BLAST (NCBI), SOURCE, SMART, STRING, PSORT2, CDART, UniGene and SOSUI.", "sc:name": "Harvester", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://harvester.fzk.de/harvester/" } \ No newline at end of file diff --git a/data/hasp/haspbioschemas.jsonld b/data/hasp/haspbioschemas.jsonld index c342fd399d7ec..246f5fd4af5f6 100644 --- a/data/hasp/haspbioschemas.jsonld +++ b/data/hasp/haspbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server designed as a scientific tool for researchers to visualize their phylogenetic, biochemical, and immunological HA data in the three-dimensional context of the HA structure, in the hopes that the context may help researchers better interpret their data and generate new hypotheses.", "sc:name": "HASP", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://exon.niaid.nih.gov/HASP.html" } \ No newline at end of file diff --git a/data/hatseq/hatseqbioschemas.jsonld b/data/hatseq/hatseqbioschemas.jsonld index 8420c54957dd6..56ac7ebb215aa 100644 --- a/data/hatseq/hatseqbioschemas.jsonld +++ b/data/hatseq/hatseqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Increased specificity for analysis of tiling-array data in comparison with alternative methods, and that it accurately detected regions-of-interest in different applications of tiling-arrays.", "sc:name": "HATSEQ", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://hema13.erasmusmc.nl/index.php/Hypergeometric_Analysis_of_Tiling-arrays" diff --git a/data/hawkdock/hawkdockbioschemas.jsonld b/data/hawkdock/hawkdockbioschemas.jsonld index 3d728747ee174..431232fda1bcd 100644 --- a/data/hawkdock/hawkdockbioschemas.jsonld +++ b/data/hawkdock/hawkdockbioschemas.jsonld @@ -17,8 +17,8 @@ "Gaoqi Weng" ], "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": [ "pubmed:31106357", @@ -29,22 +29,22 @@ ], "sc:description": "Web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.", "sc:featureList": [ - { - "@id": "edam:operation_2492" - }, { "@id": "edam:operation_0482" }, { "@id": "edam:operation_3899" + }, + { + "@id": "edam:operation_2492" } ], "sc:license": "Unlicense", "sc:name": "HawkDock", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://cadd.zju.edu.cn/hawkdock/" }, diff --git a/data/hawkeye/hawkeyebioschemas.jsonld b/data/hawkeye/hawkeyebioschemas.jsonld index 688b6ceaa3e38..0a597af4d5a51 100644 --- a/data/hawkeye/hawkeyebioschemas.jsonld +++ b/data/hawkeye/hawkeyebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Artistic-2.0", "sc:name": "HawkEye", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://amos.sourceforge.net/wiki/index.php?title=Hawkeye" } \ No newline at end of file diff --git a/data/hayai-annotation_plants/hayai-annotation_plantsbioschemas.jsonld b/data/hayai-annotation_plants/hayai-annotation_plantsbioschemas.jsonld index 8043d3ee81d40..8402d7de5b154 100644 --- a/data/hayai-annotation_plants/hayai-annotation_plantsbioschemas.jsonld +++ b/data/hayai-annotation_plants/hayai-annotation_plantsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Hayai-Annotation Plants", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/kdri-genomics/Hayai-Annotation-Plants" diff --git a/data/haystack/haystackbioschemas.jsonld b/data/haystack/haystackbioschemas.jsonld index 00d3d3461ee8d..8ea49c05b1f15 100644 --- a/data/haystack/haystackbioschemas.jsonld +++ b/data/haystack/haystackbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "AGPL-3.0", "sc:name": "Haystack", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/pinellolab/haystack_bio", "sc:version": "0.5.3" diff --git a/data/hbayesdm/hbayesdmbioschemas.jsonld b/data/hbayesdm/hbayesdmbioschemas.jsonld index a84317a992e7f..01dcfa39cf642 100644 --- a/data/hbayesdm/hbayesdmbioschemas.jsonld +++ b/data/hbayesdm/hbayesdmbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1162/CPSY_a_00002", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/hbayesdm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Woo-Young Ahn", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:29601060", { "@id": "https://doi.org/10.1162/CPSY_a_00002" }, - "pmcid:PMC5869013" + "pmcid:PMC5869013", + "pubmed:29601060" ], "sc:description": "hBayesDM (hierarchical Bayesian modeling of Decision-Making tasks), which offers computational modeling of an array of reinforcement learning and decision-making tasks and social exchange games.", "sc:featureList": { @@ -28,16 +32,12 @@ "sc:license": "Other", "sc:name": "hBayesDM", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/CCS-Lab/hBayesDM", "sc:version": "0.6.0" - }, - { - "@id": "https://doi.org/10.1162/CPSY_a_00002", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hca/hcabioschemas.jsonld b/data/hca/hcabioschemas.jsonld index cf7a0437cd8ae..8e3041352a5d1 100644 --- a/data/hca/hcabioschemas.jsonld +++ b/data/hca/hcabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures.", "sc:name": "HCA (hydrophobic cluster analysis)", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=HCA#forms::HCA" } \ No newline at end of file diff --git a/data/hcsnip/hcsnipbioschemas.jsonld b/data/hcsnip/hcsnipbioschemas.jsonld index 5f15715a7ea62..6b88cf8a17836 100644 --- a/data/hcsnip/hcsnipbioschemas.jsonld +++ b/data/hcsnip/hcsnipbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "HCsnip", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HCsnip.html", diff --git a/data/hdam/hdambioschemas.jsonld b/data/hdam/hdambioschemas.jsonld index 2c9addb985520..a2da5418f4b54 100644 --- a/data/hdam/hdambioschemas.jsonld +++ b/data/hdam/hdambioschemas.jsonld @@ -27,9 +27,9 @@ }, "sc:name": "HDAM", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.megabionet.org/HDAM/" }, diff --git a/data/hdf5array/bioconda_hdf5array.yaml b/data/hdf5array/bioconda_hdf5array.yaml index f494ec763a1a3..934ef5e1c2608 100644 --- a/data/hdf5array/bioconda_hdf5array.yaml +++ b/data/hdf5array/bioconda_hdf5array.yaml @@ -9,7 +9,6 @@ description: Implements the HDF5Array and TENxMatrix classes, 2 convenient and m home: https://bioconductor.org/packages/3.10/bioc/html/HDF5Array.html identifiers: - biotools:hdf5array -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-hdf5array summary: HDF5 backend for DelayedArray objects diff --git a/data/hdock/hdockbioschemas.jsonld b/data/hdock/hdockbioschemas.jsonld index 967794e870303..6a0c137879696 100644 --- a/data/hdock/hdockbioschemas.jsonld +++ b/data/hdock/hdockbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5793843", "pubmed:28521030", { "@id": "https://doi.org/10.1093/nar/gkx407" - } + }, + "pmcid:PMC5793843" ], "sc:description": "Protein-protein and protein-DNA/RNA docking based on a hybrid algorithm of template-based modeling and ab initio free docking.", "sc:featureList": [ diff --git a/data/hdtd/hdtdbioschemas.jsonld b/data/hdtd/hdtdbioschemas.jsonld index c01242a155250..dde100b1c2385 100644 --- a/data/hdtd/hdtdbioschemas.jsonld +++ b/data/hdtd/hdtdbioschemas.jsonld @@ -22,26 +22,26 @@ "@id": "edam:data_1669" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0203" + "@id": "edam:topic_3053" }, { - "@id": "edam:topic_3308" + "@id": "edam:topic_0203" }, { - "@id": "edam:topic_3053" + "@id": "edam:topic_3308" } ], "sc:citation": [ + "pmcid:PMC4937203", "pubmed:27266441", { "@id": "https://doi.org/10.1093/bioinformatics/btw224" - }, - "pmcid:PMC4937203" + } ], "sc:description": "Characterization of intra-individual variability generates physiology-measurement data that can be written as a matrix with the different subsamples in the columns and the different phenotypic units in the rows. These datasets are called high-dimensional transposable data. The package provides functions for conducting statistical inference for the mean relationship between the row and column variables and for the covariance structure within and between the row and column variables.", "sc:featureList": { @@ -50,9 +50,9 @@ "sc:license": "GPL-3.0", "sc:name": "HDTD", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HDTD.html", "sc:version": "1.8.0" diff --git a/data/heap/heapbioschemas.jsonld b/data/heap/heapbioschemas.jsonld index 3deacef052122..6e9e3f9ca1573 100644 --- a/data/heap/heapbioschemas.jsonld +++ b/data/heap/heapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data.", "sc:name": "Heap", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/meiji-bioinf/heap", "sc:version": "0.8.0" diff --git a/data/heat_plus/heat_plusbioschemas.jsonld b/data/heat_plus/heat_plusbioschemas.jsonld index 2bd2ead094abc..a9d2ef1b444e1 100644 --- a/data/heat_plus/heat_plusbioschemas.jsonld +++ b/data/heat_plus/heat_plusbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1080/16549716.2018.1440783", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/heat_plus", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ahmad Reza Hosseinpoor", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6041818", { "@id": "https://doi.org/10.1080/16549716.2018.1440783" }, + "pmcid:PMC6041818", "pubmed:29974823" ], "sc:description": "Health Equity Assessment Toolkit Plus.", @@ -32,12 +28,16 @@ "sc:license": "GPL-2.0", "sc:name": "HEAT Plus", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/WHOequity/HEATPlus-1.0", "sc:version": "1.0" + }, + { + "@id": "https://doi.org/10.1080/16549716.2018.1440783", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/heat_seq/heat_seqbioschemas.jsonld b/data/heat_seq/heat_seqbioschemas.jsonld index 7e1b9f31821af..db699b4ddc552 100644 --- a/data/heat_seq/heat_seqbioschemas.jsonld +++ b/data/heat_seq/heat_seqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain.", "sc:name": "Heat seq", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.heatstarseq.roslin.ed.ac.uk/" diff --git a/data/heatmaps/heatmapsbioschemas.jsonld b/data/heatmaps/heatmapsbioschemas.jsonld index 2c4aeef98147b..eb0920ad0730c 100644 --- a/data/heatmaps/heatmapsbioschemas.jsonld +++ b/data/heatmaps/heatmapsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "heatmaps", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/heatmaps.html", "sc:version": "1.4.0" diff --git a/data/heatplus/bioconda_heatplus.yaml b/data/heatplus/bioconda_heatplus.yaml index 56e6546e4a00c..3ab7c08739483 100644 --- a/data/heatplus/bioconda_heatplus.yaml +++ b/data/heatplus/bioconda_heatplus.yaml @@ -7,7 +7,6 @@ description: Display a rectangular heatmap (intensity plot) of a data matrix. By home: https://bioconductor.org/packages/3.10/bioc/html/Heatplus.html identifiers: - biotools:heatplus -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-heatplus diff --git a/data/heatplus/heatplusbioschemas.jsonld b/data/heatplus/heatplusbioschemas.jsonld index e36944ae74f13..078777e92f2b2 100644 --- a/data/heatplus/heatplusbioschemas.jsonld +++ b/data/heatplus/heatplusbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alexander Ploner", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.", "sc:license": "GPL-2.0", diff --git a/data/hec/hecbioschemas.jsonld b/data/hec/hecbioschemas.jsonld index 1166ce4371fff..813f4a0a2d289 100644 --- a/data/hec/hecbioschemas.jsonld +++ b/data/hec/hecbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for simulation of bacterial (more exactly prokaryotic) communities. It is based on the original modeling approach investigated in the Laboratory of molecular-genetic systems at the Institute of Cytology and Genetics (Novosibirsk, Russia).", "sc:name": "HEC", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://evol-constructor.bionet.nsc.ru/?cat=5&lang=en" } \ No newline at end of file diff --git a/data/heliquest/heliquestbioschemas.jsonld b/data/heliquest/heliquestbioschemas.jsonld index f97b9c722e79d..36ea0db03dd55 100644 --- a/data/heliquest/heliquestbioschemas.jsonld +++ b/data/heliquest/heliquestbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "HELIQUEST calculates the physicochemical properties and amino acid composition of an ��-helix and screens databank to identify protein segments possessing similar features. This server is also dedicated to mutating helices manually or automatically by genetic algorithm to design analogues of defined features.", "sc:name": "HELIQUEST", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://heliquest.ipmc.cnrs.fr" } \ No newline at end of file diff --git a/data/helixturnhelix/helixturnhelixbioschemas.jsonld b/data/helixturnhelix/helixturnhelixbioschemas.jsonld index 3456bd7b3c449..197b019ebc40e 100644 --- a/data/helixturnhelix/helixturnhelixbioschemas.jsonld +++ b/data/helixturnhelix/helixturnhelixbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK MRC", + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Identify nucleic acid-binding motifs in protein sequences.", "sc:funder": [ @@ -27,12 +27,12 @@ "sc:name": "helixturnhelix", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/helixturnhelix.html", "sc:version": "r6" diff --git a/data/helloranges/bioconda_helloranges.yaml b/data/helloranges/bioconda_helloranges.yaml index edd5522abe8e5..a01a63d248652 100644 --- a/data/helloranges/bioconda_helloranges.yaml +++ b/data/helloranges/bioconda_helloranges.yaml @@ -5,7 +5,6 @@ description: Translates bedtools command-line invocations to R code calling func home: https://bioconductor.org/packages/3.10/bioc/html/HelloRanges.html identifiers: - biotools:helloranges -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-helloranges diff --git a/data/helloranges/hellorangesbioschemas.jsonld b/data/helloranges/hellorangesbioschemas.jsonld index 72fb913c871ad..1aab2b42e3489 100644 --- a/data/helloranges/hellorangesbioschemas.jsonld +++ b/data/helloranges/hellorangesbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Lawrence", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Translates bedtools command-line invocations to R code calling functions from the BioConductor *Ranges infrastructure. This is intended to educate novice BioConductor users and to compare the syntax and semantics of the two frameworks.", "sc:license": "GPL-2.0", "sc:name": "HelloRanges", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HelloRanges.html", "sc:version": "1.0.0" diff --git a/data/help/bioconda_help.yaml b/data/help/bioconda_help.yaml index ba11a2bbc7e76..7bc3ecc9550a1 100644 --- a/data/help/bioconda_help.yaml +++ b/data/help/bioconda_help.yaml @@ -4,7 +4,6 @@ description: The package contains a modular pipeline for analysis of HELP microa home: https://bioconductor.org/packages/3.10/bioc/html/HELP.html identifiers: - biotools:help -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-help diff --git a/data/hem/hembioschemas.jsonld b/data/hem/hembioschemas.jsonld index 46eb80efe67fc..3510eed95b3be 100644 --- a/data/hem/hembioschemas.jsonld +++ b/data/hem/hembioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "HyungJun Cho", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package fits heterogeneous error models for analysis of microarray data.", "sc:license": "GPL-2.0", "sc:name": "HEM", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HEM.html", "sc:version": "1.46.0" diff --git a/data/hemaexplorer/hemaexplorerbioschemas.jsonld b/data/hemaexplorer/hemaexplorerbioschemas.jsonld index 3a19c4c760df0..3d99c8f7e7166 100644 --- a/data/hemaexplorer/hemaexplorerbioschemas.jsonld +++ b/data/hemaexplorer/hemaexplorerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool provides a plot of gene expression in hematopoietic cells at different maturation stages based on curated microarray data.", "sc:name": "HemaExplorer", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "binf.ku.dk", "sc:url": "http://servers.binf.ku.dk/hemaexplorer/", diff --git a/data/hemi/hemibioschemas.jsonld b/data/hemi/hemibioschemas.jsonld index dfabd6ab9f04b..6fd46bdec8377 100644 --- a/data/hemi/hemibioschemas.jsonld +++ b/data/hemi/hemibioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0111988", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/hemi", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr. Yu Xue", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:25372567", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0111988" }, - "pubmed:25372567", "pmcid:PMC4221433" ], "sc:description": "Toolkit for illustrating heatmaps.", @@ -27,15 +31,11 @@ }, "sc:name": "HemI", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://hemi.biocuckoo.org/down.php" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0111988", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hemolytik/hemolytikbioschemas.jsonld b/data/hemolytik/hemolytikbioschemas.jsonld index 40729c78bcad9..83b64ea4ce7b3 100644 --- a/data/hemolytik/hemolytikbioschemas.jsonld +++ b/data/hemolytik/hemolytikbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKT1008", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/hemolytik", "@type": "sc:SoftwareApplication", @@ -32,10 +36,6 @@ "Linux" ], "sc:url": "http://crdd.osdd.net/raghava/hemolytik/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKT1008", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hemopi/hemopibioschemas.jsonld b/data/hemopi/hemopibioschemas.jsonld index c34f32ca4eb8b..117c7390000ab 100644 --- a/data/hemopi/hemopibioschemas.jsonld +++ b/data/hemopi/hemopibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Allows user to predict predict hemolytic or hemotoxic or RBC lysing potential of a peptide. It allow users to perform various functions that includes virtual screening of peptides, analog-based peptide design.", "sc:name": "HemoPI", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://crdd.osdd.net/raghava/hemopi/" diff --git a/data/hermes_medical_imaging/hermes_medical_imagingbioschemas.jsonld b/data/hermes_medical_imaging/hermes_medical_imagingbioschemas.jsonld index 1635abba039f3..9329f520d674d 100644 --- a/data/hermes_medical_imaging/hermes_medical_imagingbioschemas.jsonld +++ b/data/hermes_medical_imaging/hermes_medical_imagingbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/HERMES_medical_imaging", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:description": "Aims to bring together geographically dispersed medical personnel in order to share a common workspace where they can collaborate over medical images in real-time.", "sc:license": "Unlicense", diff --git a/data/hervd/hervdbioschemas.jsonld b/data/hervd/hervdbioschemas.jsonld index d4c00c1532b5b..6f9d21256492d 100644 --- a/data/hervd/hervdbioschemas.jsonld +++ b/data/hervd/hervdbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/hervd", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:author": [ - "Ondřej Moravčík", - "Jan Pačes" + "Jan Pačes", + "Ondřej Moravčík" ], "sc:contributor": [ - "Radek Zí­ka", "Lucie Studená", "Adam Pavlí­ček", "Eva Prysiazhniuk", - "Mirka Famfulí­ková" + "Mirka Famfulí­ková", + "Radek Zí­ka" ], "sc:description": "Human endogenous retroviruses database.", "sc:license": "CC-BY-4.0", diff --git a/data/heuraa/heuraabioschemas.jsonld b/data/heuraa/heuraabioschemas.jsonld index 66ea190353ace..12f78c439e28f 100644 --- a/data/heuraa/heuraabioschemas.jsonld +++ b/data/heuraa/heuraabioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0054294", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/heuraa", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "István Peták", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:23349847", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0054294" }, - "pmcid:PMC3548894", - "pubmed:23349847" + "pmcid:PMC3548894" ], "sc:description": "Accurate and Fast Detection of Genetic Variations with a Novel Heuristic Amplicon Aligner Program for Next Generation Sequencing.", "sc:featureList": { @@ -28,10 +32,6 @@ "sc:name": "HeurAA", "sc:operatingSystem": "Linux", "sc:url": "https://sourceforge.net/projects/heuraa/" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0054294", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hexpochem/hexpochembioschemas.jsonld b/data/hexpochem/hexpochembioschemas.jsonld index d1ca69c4b5fe5..240595fb29dfd 100644 --- a/data/hexpochem/hexpochembioschemas.jsonld +++ b/data/hexpochem/hexpochembioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "HExpoChem", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/HExpoChem-1.0/", diff --git a/data/hexserver/hexserverbioschemas.jsonld b/data/hexserver/hexserverbioschemas.jsonld index 33e85c0e81343..44ed2cec1ce1d 100644 --- a/data/hexserver/hexserverbioschemas.jsonld +++ b/data/hexserver/hexserverbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A FFT-based protein docking server powered by graphics processors, HexServer rapidly produces a ranked list of docking predictions for input PDB protein structures.", "sc:name": "HexServer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://hexserver.loria.fr/" } \ No newline at end of file diff --git a/data/hfaim/hfaimbioschemas.jsonld b/data/hfaim/hfaimbioschemas.jsonld index 26463085bee39..392ac933616c9 100644 --- a/data/hfaim/hfaimbioschemas.jsonld +++ b/data/hfaim/hfaimbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1080/15548627.2016.1147668", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/hfaim", "@type": "sc:SoftwareApplication", @@ -18,29 +22,29 @@ }, "edam:has_output": [ { - "@id": "edam:data_1361" + "@id": "edam:data_3479" }, { "@id": "edam:data_1384" }, { - "@id": "edam:data_3479" + "@id": "edam:data_1361" } ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:applicationSubCategory": { "@id": "edam:topic_3510" }, "sc:author": "Oren Tzfadia", "sc:citation": [ - "pmcid:PMC4854547", { "@id": "https://doi.org/10.1080/15548627.2016.1147668" }, - "pubmed:27071037" + "pubmed:27071037", + "pmcid:PMC4854547" ], "sc:description": "A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated atg8-interacting motifs in various organisms.", "sc:featureList": [ @@ -53,17 +57,13 @@ ], "sc:name": "hfAIM", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "PSB", "sc:url": "http://bioinformatics.psb.ugent.be/hfAIM/", "sc:version": "1" - }, - { - "@id": "https://doi.org/10.1080/15548627.2016.1147668", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hgca/hgcabioschemas.jsonld b/data/hgca/hgcabioschemas.jsonld index f8ce753a8c6b3..ad64f3f80d8a2 100644 --- a/data/hgca/hgcabioschemas.jsonld +++ b/data/hgca/hgcabioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-8991-8712", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/1756-0500-5-265", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/hgca", "@type": "sc:SoftwareApplication", @@ -35,10 +27,10 @@ }, "sc:citation": [ "pmcid:PMC3441226", - "pubmed:22672625", { "@id": "https://doi.org/10.1186/1756-0500-5-265" - } + }, + "pubmed:22672625" ], "sc:description": "Tool based on the Pearson Correlation Coefficient (r-value) between the calculated and normalised by MAS 5.0 signal values of the 54613 Probe Sets of Affymetrix Human Genome U133 Plus 2.0 Array Chip from 1959 microarray data sets. Statistical Significance is estimated with Student's t-test and Bonferroni correction is used for multiple testing.", "sc:featureList": { @@ -46,11 +38,19 @@ }, "sc:name": "Human Gene Correlation Analysis (HGCA)", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://biobank-informatics.bioacademy.gr/coexpression/" + }, + { + "@id": "http://orcid.org/0000-0001-8991-8712", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/1756-0500-5-265", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hgcs/hgcsbioschemas.jsonld b/data/hgcs/hgcsbioschemas.jsonld index dfd2e0faf4ae3..ea883c23e0701 100644 --- a/data/hgcs/hgcsbioschemas.jsonld +++ b/data/hgcs/hgcsbioschemas.jsonld @@ -28,17 +28,17 @@ "sc:description": "Prioritizing disease-causing gene variants by biological distance.", "sc:featureList": [ { - "@id": "edam:operation_3226" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_3197" + "@id": "edam:operation_3226" } ], "sc:name": "HGCS", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://hgc.rockefeller.edu/" } diff --git a/data/hgd/hgdbioschemas.jsonld b/data/hgd/hgdbioschemas.jsonld index f4b1799746b82..8e3866e7ddde7 100644 --- a/data/hgd/hgdbioschemas.jsonld +++ b/data/hgd/hgdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Hymenoptera Genome Database is a comprehensive model organism database for insect species of the order Hymenoptera. HGD contains data from 9 different species across 200 million years in the phylogeny of Hymenoptera. Curated data at HGD includes predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains.", "sc:name": "The Hymenoptera Genome Database (HGD)", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://HymenopteraGenome.org" } \ No newline at end of file diff --git a/data/hgmd/hgmdbioschemas.jsonld b/data/hgmd/hgmdbioschemas.jsonld index 227216155d71c..8b91db1814b07 100644 --- a/data/hgmd/hgmdbioschemas.jsonld +++ b/data/hgmd/hgmdbioschemas.jsonld @@ -14,26 +14,26 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact Form", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ - "pmcid:PMC3898141", { "@id": "https://doi.org/10.1007/s00439-013-1358-4" }, + "pmcid:PMC3898141", "pubmed:24077912" ], "sc:description": "The Human Gene Mutation Database (HGMD) - comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. It is a flexible resource that can be adapted to a broad range of applications including searching for an overview of known mutations associated with a particular disease, interpreting clinical test results or looking for the likely causal mutation in a list of variants.", "sc:featureList": [ { - "@id": "edam:operation_3197" + "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3224" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_3224" }, { "@id": "edam:operation_3196" diff --git a/data/hgnc/hgncbioschemas.jsonld b/data/hgnc/hgncbioschemas.jsonld index 33468c8c979f1..92c2f94f8bda2 100644 --- a/data/hgnc/hgncbioschemas.jsonld +++ b/data/hgnc/hgncbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gku1071", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/hgnc", "@type": "sc:SoftwareApplication", @@ -24,18 +28,18 @@ "@id": "edam:topic_2815" }, { - "@id": "edam:topic_0089" + "@id": "edam:topic_0622" }, { - "@id": "edam:topic_0622" + "@id": "edam:topic_0089" } ], "sc:citation": [ - "pubmed:25361968", - "pmcid:PMC4383909", { "@id": "https://doi.org/10.1093/nar/gku1071" - } + }, + "pmcid:PMC4383909", + "pubmed:25361968" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-8380-5247" @@ -46,16 +50,12 @@ }, "sc:name": "Human gene nomenclature database (HGNC)", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.genenames.org/" }, - { - "@id": "https://doi.org/10.1093/nar/gku1071", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-8380-5247", "@type": "schema:Person" diff --git a/data/hgv_add_scores/hgv_add_scoresbioschemas.jsonld b/data/hgv_add_scores/hgv_add_scoresbioschemas.jsonld index 483c231d80088..de8edcaf58b3c 100644 --- a/data/hgv_add_scores/hgv_add_scoresbioschemas.jsonld +++ b/data/hgv_add_scores/hgv_add_scoresbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "hgv_add_scores", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", "sc:version": "1.0.0" diff --git a/data/hgv_codingsnps/hgv_codingsnpsbioschemas.jsonld b/data/hgv_codingsnps/hgv_codingsnpsbioschemas.jsonld index ea35c6cf91e6a..b86956be2725c 100644 --- a/data/hgv_codingsnps/hgv_codingsnpsbioschemas.jsonld +++ b/data/hgv_codingsnps/hgv_codingsnpsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "hgv_codingsnps", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", "sc:version": "1.0.0" diff --git a/data/hgv_david/hgv_davidbioschemas.jsonld b/data/hgv_david/hgv_davidbioschemas.jsonld index 78a4f46cc82a2..9220e724099e6 100644 --- a/data/hgv_david/hgv_davidbioschemas.jsonld +++ b/data/hgv_david/hgv_davidbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool provides functional annotation for a list of genes by connecting with DAVID database.", "sc:name": "hgv_david", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", diff --git a/data/hgv_gpass/hgv_gpassbioschemas.jsonld b/data/hgv_gpass/hgv_gpassbioschemas.jsonld index af1fb8c69a56a..6c3b5a03eed79 100644 --- a/data/hgv_gpass/hgv_gpassbioschemas.jsonld +++ b/data/hgv_gpass/hgv_gpassbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool detects significant single-SNP associations in case-control studies at a user-specified FDR.", "sc:name": "hgv_gpass", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", diff --git a/data/hgv_ldtools/hgv_ldtoolsbioschemas.jsonld b/data/hgv_ldtools/hgv_ldtoolsbioschemas.jsonld index 37f2c575f05d2..c07a9d6eadc90 100644 --- a/data/hgv_ldtools/hgv_ldtoolsbioschemas.jsonld +++ b/data/hgv_ldtools/hgv_ldtoolsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool can be used to analyze the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus.", "sc:name": "hgv_ldtools", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", "sc:version": "1.0.0" diff --git a/data/hgv_linktogprofile/hgv_linktogprofilebioschemas.jsonld b/data/hgv_linktogprofile/hgv_linktogprofilebioschemas.jsonld index 6563e46c1bd1f..a0c75558d31ca 100644 --- a/data/hgv_linktogprofile/hgv_linktogprofilebioschemas.jsonld +++ b/data/hgv_linktogprofile/hgv_linktogprofilebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "hgv_linktogprofile", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", "sc:version": "1.0.0" diff --git a/data/hgv_lps/hgv_lpsbioschemas.jsonld b/data/hgv_lps/hgv_lpsbioschemas.jsonld index 6e65ad4acd59c..d136d515e8eea 100644 --- a/data/hgv_lps/hgv_lpsbioschemas.jsonld +++ b/data/hgv_lps/hgv_lpsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool for LASSO-Patternsearch algorithm. The LASSO-Patternsearch algorithm fits your dataset to an L1-regularized logistic regression model.", "sc:name": "hgv_lps", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", "sc:version": "1.0.0" diff --git a/data/hgv_pass/hgv_passbioschemas.jsonld b/data/hgv_pass/hgv_passbioschemas.jsonld index a2e2879d32b91..829f2a030415a 100644 --- a/data/hgv_pass/hgv_passbioschemas.jsonld +++ b/data/hgv_pass/hgv_passbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "hgv_pass", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", "sc:version": "1.0.0" diff --git a/data/hh-motif/hh-motifbioschemas.jsonld b/data/hh-motif/hh-motifbioschemas.jsonld index 9f571e4efa60c..0691e1a3f05c6 100644 --- a/data/hh-motif/hh-motifbioschemas.jsonld +++ b/data/hh-motif/hh-motifbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1093/NAR/GKX341", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0002-2457-7504", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/hh-motif", "@type": "sc:SoftwareApplication", @@ -30,10 +26,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC5570144", + "pubmed:28460141", { "@id": "https://doi.org/10.1093/NAR/GKX341" - }, - "pubmed:28460141" + } ], "sc:description": "Protein motif discovery method that combines hidden Markov model (HH-) comparisons with a hierarchical representation of identified SLiMs in motif trees.", "sc:featureList": { @@ -41,11 +37,15 @@ }, "sc:name": "HH-MOTiF", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://hh-motif.ibdm.univ-mrs.fr/" + }, + { + "@id": "http://orcid.org/0000-0002-2457-7504", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/hh-suite/hh-suitebioschemas.jsonld b/data/hh-suite/hh-suitebioschemas.jsonld index 80279dd1be423..eb75ad4b7f5d5 100644 --- a/data/hh-suite/hh-suitebioschemas.jsonld +++ b/data/hh-suite/hh-suitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "HH-suite", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/soedinglab/hh-suite" } \ No newline at end of file diff --git a/data/hhalign-kbest/hhalign-kbestbioschemas.jsonld b/data/hhalign-kbest/hhalign-kbestbioschemas.jsonld index a763a3f1db5be..17e93b1da6689 100644 --- a/data/hhalign-kbest/hhalign-kbestbioschemas.jsonld +++ b/data/hhalign-kbest/hhalign-kbestbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Useful to automatically obtain optimized alignments and models in case of low sequence identity (<35%) between a query and a template protein. It can generate k suboptimal (e.g. top-k scoring) alignments rather than only the optimal one which may contain small to large errors.", "sc:name": "HHalign-Kbest", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioserv.rpbs.univ-paris-diderot.fr/services/HHalign-Kbest/", "sc:version": "1.0" diff --git a/data/hhblits/hhblitsbioschemas.jsonld b/data/hhblits/hhblitsbioschemas.jsonld index 59b9eb7b193f6..d505328b2b824 100644 --- a/data/hhblits/hhblitsbioschemas.jsonld +++ b/data/hhblits/hhblitsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The first iterative method based on the pairwise comparison of profile Hidden Markov Models. In benchmarks it achieves better runtimes than other iterative sequence search methods such as PSI-BLAST or HMMER3 by using a fast prefilter based on profile-profile comparison. Furthermore, it greatly improves upon PSI-BLAST and HMMER3 in terms of sensitivity/selectivity and alignment quality.", "sc:name": "HHblits", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://toolkit.tuebingen.mpg.de/#/tools/hhblits" } \ No newline at end of file diff --git a/data/hhmd/hhmdbioschemas.jsonld b/data/hhmd/hhmdbioschemas.jsonld index 427d2a46a2ccb..a468eb440c59a 100644 --- a/data/hhmd/hhmdbioschemas.jsonld +++ b/data/hhmd/hhmdbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/hhmd", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lv Jie", + "Zhang Yan", "Developers", - "Zhang Yan" + "Lv Jie" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:19892823", "sc:description": "Database which focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. It incorporates 43 location-specific histone modifications in human. The database can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. Database also includes a user-friendly visualization tool named HisModView, by which genome-wide histone modification map can be shown.", "sc:name": "HHMD", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinfo.hrbmu.edu.cn/hhmd" } \ No newline at end of file diff --git a/data/hhpred/hhpredbioschemas.jsonld b/data/hhpred/hhpredbioschemas.jsonld index 38fcfe5581f3a..4bdaf163abfd5 100644 --- a/data/hhpred/hhpredbioschemas.jsonld +++ b/data/hhpred/hhpredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.", "sc:name": "HHpred", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://toolkit.tuebingen.mpg.de/#/tools/hhpred" diff --git a/data/hhrep/hhrepbioschemas.jsonld b/data/hhrep/hhrepbioschemas.jsonld index b22d89196ce13..19b375043a96e 100644 --- a/data/hhrep/hhrepbioschemas.jsonld +++ b/data/hhrep/hhrepbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "HHrep", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://toolkit.tuebingen.mpg.de/#/tools/hhpred" } \ No newline at end of file diff --git a/data/hi-jack/hi-jackbioschemas.jsonld b/data/hi-jack/hi-jackbioschemas.jsonld index 8f0b736548482..b575a2623d5ae 100644 --- a/data/hi-jack/hi-jackbioschemas.jsonld +++ b/data/hi-jack/hi-jackbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Novel computational framework, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking.", "sc:name": "Hi-Jack", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cloud.kaust.edu.sa/Pages/Hi-Jack.aspx" } \ No newline at end of file diff --git a/data/hiannotator/bioconda_hiannotator.yaml b/data/hiannotator/bioconda_hiannotator.yaml index a41ad5a70b954..127a0b766c749 100644 --- a/data/hiannotator/bioconda_hiannotator.yaml +++ b/data/hiannotator/bioconda_hiannotator.yaml @@ -12,7 +12,6 @@ description: 'hiAnnotator contains set of functions which allow users to annotat home: https://bioconductor.org/packages/3.10/bioc/html/hiAnnotator.html identifiers: - biotools:hiannotator -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hiannotator diff --git a/data/hiannotator/hiannotatorbioschemas.jsonld b/data/hiannotator/hiannotatorbioschemas.jsonld index 9a872f5277453..8725457f99755 100644 --- a/data/hiannotator/hiannotatorbioschemas.jsonld +++ b/data/hiannotator/hiannotatorbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nirav V Malani", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Set of functions to annotate a GRanges object with custom set of annotations. This package takes two GRanges objects (query & subject) with a common set of seqnames (i.e. chromosomes) and returns associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands).", "sc:license": "GPL-2.0", "sc:name": "hiAnnotator", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hiAnnotator.html", "sc:version": "1.8.0" diff --git a/data/hibag/hibagbioschemas.jsonld b/data/hibag/hibagbioschemas.jsonld index e1d9de5e96398..a743e0c2e951c 100644 --- a/data/hibag/hibagbioschemas.jsonld +++ b/data/hibag/hibagbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1038/tpj.2013.18", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0002-1390-0708", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/hibag", "@type": "sc:SoftwareApplication", @@ -28,11 +24,11 @@ "Command-line tool" ], "sc:citation": [ + "pmcid:PMC3772955", + "pubmed:23712092", { "@id": "https://doi.org/10.1038/tpj.2013.18" - }, - "pubmed:23712092", - "pmcid:PMC3772955" + } ], "sc:description": "It is a software package for imputing HLA types using SNP data, and relies on a training set of HLA and SNP genotypes. It can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging (improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection), an ensemble classifier method, with haplotype inference for SNPs and HLA types.", "sc:featureList": { @@ -41,11 +37,15 @@ "sc:license": "GPL-3.0", "sc:name": "HIBAG", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HIBAG.html", "sc:version": "1.10.0" + }, + { + "@id": "http://orcid.org/0000-0002-1390-0708", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/hic-pro/hic-probioschemas.jsonld b/data/hic-pro/hic-probioschemas.jsonld index ea5d5ed222001..7dc6de19571c3 100644 --- a/data/hic-pro/hic-probioschemas.jsonld +++ b/data/hic-pro/hic-probioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-1678-7410", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/hic-pro", "@type": "sc:SoftwareApplication", @@ -23,11 +27,11 @@ "@id": "http://orcid.org/0000-0003-1678-7410" }, "sc:citation": [ - "pubmed:26619908", + "pmcid:PMC4665391", { "@id": "https://doi.org/10.1186/s13059-015-0831-x" }, - "pmcid:PMC4665391" + "pubmed:26619908" ], "sc:description": "This tool was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, it can analyze data from digestion protocols as well as data from protocols that do not require restriction enzyme such as DNase Hi-C. The pipeline is flexible, scalable and optimized. It can operate either on a single laptop or on a computational cluster using the PBS-Torque scheduler.", "sc:featureList": { @@ -35,8 +39,8 @@ }, "sc:name": "HiC-Pro", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "Institut Curie", @@ -45,10 +49,6 @@ "sc:url": "https://github.com/nservant/HiC-Pro", "sc:version": "2.7.8" }, - { - "@id": "http://orcid.org/0000-0003-1678-7410", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s13059-015-0831-x", "@type": "sc:CreativeWork" diff --git a/data/hicat/hicatbioschemas.jsonld b/data/hicat/hicatbioschemas.jsonld index 8b0fd9625aa2a..d1a3f13c0eb7c 100644 --- a/data/hicat/hicatbioschemas.jsonld +++ b/data/hicat/hicatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Hi-C data analysis tool. Importantly, HiCat is focussed on analysis of larger structural features of chromosomes and on comparative studies.", "sc:name": "HiCat", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.botinst.uzh.ch/research/development/grossnik/HiCat.html" } \ No newline at end of file diff --git a/data/hicnn/hicnnbioschemas.jsonld b/data/hicnn/hicnnbioschemas.jsonld index bca7115be519b..d818f5a27a6d3 100644 --- a/data/hicnn/hicnnbioschemas.jsonld +++ b/data/hicnn/hicnnbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Unlicense", "sc:name": "HiCNN", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://dna.cs.miami.edu/HiCNN/" } \ No newline at end of file diff --git a/data/hicplotter/hicplotterbioschemas.jsonld b/data/hicplotter/hicplotterbioschemas.jsonld index 8de658e7c3e60..378b3348b0ef4 100644 --- a/data/hicplotter/hicplotterbioschemas.jsonld +++ b/data/hicplotter/hicplotterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Python data visualization tool for integrating different data types with interaction matrixes.", "sc:name": "HiCPlotter Beta", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/kcakdemir/HiCPlotter" diff --git a/data/hicrep/hicrepbioschemas.jsonld b/data/hicrep/hicrepbioschemas.jsonld index d01dfc0d3f08c..c9adb15467719 100644 --- a/data/hicrep/hicrepbioschemas.jsonld +++ b/data/hicrep/hicrepbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "hicrep", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hicrep.html", diff --git a/data/hicup/hicupbioschemas.jsonld b/data/hicup/hicupbioschemas.jsonld index 4a0102531e779..a75b9a2bf3e9f 100644 --- a/data/hicup/hicupbioschemas.jsonld +++ b/data/hicup/hicupbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "HiCUP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bioinformatics.babraham.ac.uk/projects/hicup/" } \ No newline at end of file diff --git a/data/hide/hidebioschemas.jsonld b/data/hide/hidebioschemas.jsonld index ba2b93f40f4b2..a498ba038eef1 100644 --- a/data/hide/hidebioschemas.jsonld +++ b/data/hide/hidebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/hide", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Guy Banay", - "Mukul Bansal" + "Mukul Bansal", + "Guy Banay" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:23335015", "sc:description": "Software package for inferring highways of horizontal gene transfer in the evolutionary history of a set of species. It takes as input a collection of unrooted gene trees along with a rooted species tree.", "sc:name": "HiDe", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://acgt.cs.tau.ac.il/hide/" } \ No newline at end of file diff --git a/data/hierarchical_feature_engineering/hierarchical_feature_engineeringbioschemas.jsonld b/data/hierarchical_feature_engineering/hierarchical_feature_engineeringbioschemas.jsonld index 7cd0021da3006..ecbc6dd8c1bc8 100644 --- a/data/hierarchical_feature_engineering/hierarchical_feature_engineeringbioschemas.jsonld +++ b/data/hierarchical_feature_engineering/hierarchical_feature_engineeringbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Hierarchical Feature Engineering", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/HenschelLab/HierarchicalFeatureEngineering" diff --git a/data/hierarchy_web_services/hierarchy_web_servicesbioschemas.jsonld b/data/hierarchy_web_services/hierarchy_web_servicesbioschemas.jsonld index b506f1b2064d8..08bc0f672daa5 100644 --- a/data/hierarchy_web_services/hierarchy_web_servicesbioschemas.jsonld +++ b/data/hierarchy_web_services/hierarchy_web_servicesbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Hierarchy Web services", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://data.bioontology.org/documentation", "sc:version": "1" diff --git a/data/hiergwas/hiergwasbioschemas.jsonld b/data/hiergwas/hiergwasbioschemas.jsonld index c5334c5650405..9d4c5238e3903 100644 --- a/data/hiergwas/hiergwasbioschemas.jsonld +++ b/data/hiergwas/hiergwasbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laura Buzdugan", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.", "sc:license": "GPL-3.0", "sc:name": "hierGWAS", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hierGWAS.html", "sc:version": "1.4.0" diff --git a/data/hifix/hifixbioschemas.jsonld b/data/hifix/hifixbioschemas.jsonld index 2f5b486ec2e0b..27b34fefb0fdd 100644 --- a/data/hifix/hifixbioschemas.jsonld +++ b/data/hifix/hifixbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "The software package HiFiX implements the novel algorithm for HIgh FIdelity Clustering of Sequences.", "sc:name": "HiFiX", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://lbbe.univ-lyon1.fr/-HiFiX-.html", "sc:version": "1.0.5" diff --git a/data/higdb/higdbbioschemas.jsonld b/data/higdb/higdbbioschemas.jsonld index 091258ada1338..1568b0a0bd38d 100644 --- a/data/higdb/higdbbioschemas.jsonld +++ b/data/higdb/higdbbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/higdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Anand Anbarasu", - "Dr. K. Sekar" + "Dr. K. Sekar", + "Dr. Anand Anbarasu" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:25450223", @@ -20,8 +20,8 @@ "sc:name": "HIGDB", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioserver1.physics.iisc.ernet.in/HIGDB/" } \ No newline at end of file diff --git a/data/highmap/highmapbioschemas.jsonld b/data/highmap/highmapbioschemas.jsonld index 3931c5c42fe0d..32f060e176020 100644 --- a/data/highmap/highmapbioschemas.jsonld +++ b/data/highmap/highmapbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Software suitable for genetic map. This software utilized maximum likelihood and smooth algorithm, and could deal with ten thousand markers that make map distance more stably.", "sc:name": "HighMap", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://highmap.biomarker.com.cn/" } \ No newline at end of file diff --git a/data/highresnps/highresnpsbioschemas.jsonld b/data/highresnps/highresnpsbioschemas.jsonld index 7859ce4b11398..cc807e76248a5 100644 --- a/data/highresnps/highresnpsbioschemas.jsonld +++ b/data/highresnps/highresnpsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "HighResNPS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://HighResNPS.com" } \ No newline at end of file diff --git a/data/hiite/hiitebioschemas.jsonld b/data/hiite/hiitebioschemas.jsonld index af574253e06ef..58602fb62fbc1 100644 --- a/data/hiite/hiitebioschemas.jsonld +++ b/data/hiite/hiitebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact form", "sc:additionalType": [ - "Script", - "Web application" + "Web application", + "Script" ], "sc:description": "HIV-1 incidence and infection time estimator, which processes envelope gene sequences using hierarchical clustering algorithms and informs the stage of infection, along with time since infection for incident cases.", "sc:name": "HIITE", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://p512.usc.edu/request/" } \ No newline at end of file diff --git a/data/hilbertcurve/hilbertcurvebioschemas.jsonld b/data/hilbertcurve/hilbertcurvebioschemas.jsonld index 601bbfb4e8e4f..630779a04bcc6 100644 --- a/data/hilbertcurve/hilbertcurvebioschemas.jsonld +++ b/data/hilbertcurve/hilbertcurvebioschemas.jsonld @@ -32,8 +32,8 @@ "sc:name": "HilbertCurve", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HilbertCurve.html", "sc:version": "1.12.0" diff --git a/data/hilbertvis/hilbertvisbioschemas.jsonld b/data/hilbertvis/hilbertvisbioschemas.jsonld index 42add0e3d3587..6053cf2fc9788 100644 --- a/data/hilbertvis/hilbertvisbioschemas.jsonld +++ b/data/hilbertvis/hilbertvisbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "HilbertVis", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HilbertVis.html", "sc:version": "1.32.0" diff --git a/data/hilbertvisgui/hilbertvisguibioschemas.jsonld b/data/hilbertvisgui/hilbertvisguibioschemas.jsonld index 08f9fc7862f19..2ff187141e3e5 100644 --- a/data/hilbertvisgui/hilbertvisguibioschemas.jsonld +++ b/data/hilbertvisgui/hilbertvisguibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "HilbertVisGUI", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HilbertVisGUI.html", "sc:version": "1.32.0" diff --git a/data/hingeprot/hingeprotbioschemas.jsonld b/data/hingeprot/hingeprotbioschemas.jsonld index 0ea24439ab0ea..62b61088e4595 100644 --- a/data/hingeprot/hingeprotbioschemas.jsonld +++ b/data/hingeprot/hingeprotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for predicting rigid protein parts and the flexible hinge regions connecting them in the native topology of protein chains by employing elastic network (EN) models.", "sc:name": "HingeProt", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.prc.boun.edu.tr/appserv/prc/hingeprot/" } \ No newline at end of file diff --git a/data/hipathdb/hipathdbbioschemas.jsonld b/data/hipathdb/hipathdbbioschemas.jsonld index 80a85eae2cf22..da9dafd6cdf40 100644 --- a/data/hipathdb/hipathdbbioschemas.jsonld +++ b/data/hipathdb/hipathdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "human integrated Pathway DataBase with facile visualiztion: an integrated pathway databasethat combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta, and KEGG.", "sc:name": "hiPathDB", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://hipathdb.kobic.re.kr/" } \ No newline at end of file diff --git a/data/hipathia/hipathiabioschemas.jsonld b/data/hipathia/hipathiabioschemas.jsonld index cc3ec4136b23a..1d0cfc355311e 100644 --- a/data/hipathia/hipathiabioschemas.jsonld +++ b/data/hipathia/hipathiabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.18632/oncotarget.14107", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/hipathia", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:28042959", - "pmcid:PMC5354899", { "@id": "https://doi.org/10.18632/oncotarget.14107" - } + }, + "pmcid:PMC5354899" ], "sc:description": "Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway.", "sc:featureList": { @@ -28,16 +32,12 @@ "sc:license": "GPL-2.0", "sc:name": "hipathia", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hipathia.html", "sc:version": "1.0.0" - }, - { - "@id": "https://doi.org/10.18632/oncotarget.14107", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hipfsta/hipfstabioschemas.jsonld b/data/hipfsta/hipfstabioschemas.jsonld index a72c020288611..43377a093c41e 100644 --- a/data/hipfsta/hipfstabioschemas.jsonld +++ b/data/hipfsta/hipfstabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "HiPFSTA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/michaelmell/hipfsta" } \ No newline at end of file diff --git a/data/hireadsprocessor/hireadsprocessorbioschemas.jsonld b/data/hireadsprocessor/hireadsprocessorbioschemas.jsonld index 81f7cf421bdb0..cd6800bde8773 100644 --- a/data/hireadsprocessor/hireadsprocessorbioschemas.jsonld +++ b/data/hireadsprocessor/hireadsprocessorbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nirav V Malani", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.", "sc:license": "GPL-3.0", diff --git a/data/hisat2/hisat2bioschemas.jsonld b/data/hisat2/hisat2bioschemas.jsonld index 249d458432bf2..129ced11768ce 100644 --- a/data/hisat2/hisat2bioschemas.jsonld +++ b/data/hisat2/hisat2bioschemas.jsonld @@ -13,34 +13,26 @@ "@id": "https://doi.org/10.1038/nmeth.4106", "@type": "sc:CreativeWork" }, - { - "@id": "https://doi.org/10.1038/nmeth.3317", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1038/nprot.2016.095", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/hisat2", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5792058", + "pmcid:PMC4655817", + { + "@id": "https://doi.org/10.1038/nmeth.4106" + }, + "pubmed:27941783", "pubmed:27560171", "pubmed:25751142", { "@id": "https://doi.org/10.1038/nmeth.3317" }, "pmcid:PMC5032908", - "pmcid:PMC4655817", - "pubmed:27941783", - { - "@id": "https://doi.org/10.1038/nmeth.4106" - }, { "@id": "https://doi.org/10.1038/nprot.2016.095" - } + }, + "pmcid:PMC5792058" ], "sc:description": "Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).", "sc:featureList": { @@ -50,10 +42,18 @@ "sc:name": "HISAT2", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://ccb.jhu.edu/software/hisat2/index.shtml" + }, + { + "@id": "https://doi.org/10.1038/nprot.2016.095", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://doi.org/10.1038/nmeth.3317", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/histome/histomebioschemas.jsonld b/data/histome/histomebioschemas.jsonld index 3f3c5942d9787..6115631723780 100644 --- a/data/histome/histomebioschemas.jsonld +++ b/data/histome/histomebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A browsable, manually curated, and relational database of human histone proteins and histone modifying enzymes. It contains 55 human histone proteins, 106 distinct sites of their post-translational modifications (PTMs) and 152 histone-modifying enzymes. Entries have been grouped into 5 types of histones, 8 types of post-translational modifications and 14 types of enzymes that catalyze addition and removal of these modifications.", "sc:name": "HIstome", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.iiserpune.ac.in/~coee/histome/" diff --git a/data/histone_coder/histone_coderbioschemas.jsonld b/data/histone_coder/histone_coderbioschemas.jsonld index d76a180d73944..e9610d2a3d026 100644 --- a/data/histone_coder/histone_coderbioschemas.jsonld +++ b/data/histone_coder/histone_coderbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Count the number of MS/MS ions in a given spectrum to determine the unambiguous localization of a post-translational modification (PTM). The software lists number and type of site determining ions found between the assigned PTM localization by Mascot (Matrix Science) and the closest other amino acids which can host the modification. The PTMs included in the script are phosphorylation (S,T,Y), acetylation (K), mono- and dimethylation (K,R) and trimethylation (K).", "sc:name": "Histone Coder", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "bmb.sdu.dk", "sc:url": "https://github.com/middle-down/Software", diff --git a/data/histone_tails/histone_tailsbioschemas.jsonld b/data/histone_tails/histone_tailsbioschemas.jsonld index 48333a9b4754b..a438b439e7584 100644 --- a/data/histone_tails/histone_tailsbioschemas.jsonld +++ b/data/histone_tails/histone_tailsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Structural Genomics of Histone Tail Recognition", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://apps.thesgc.org/resources/histone_tails/" } \ No newline at end of file diff --git a/data/histonehmm/histonehmmbioschemas.jsonld b/data/histonehmm/histonehmmbioschemas.jsonld index 2104508ce668a..8ada1c780bc31 100644 --- a/data/histonehmm/histonehmmbioschemas.jsonld +++ b/data/histonehmm/histonehmmbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Matthias Heinig", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC4347972", { "@id": "https://doi.org/10.1186/s12859-015-0491-6" }, - "pmcid:PMC4347972", "pubmed:25884684" ], "sc:description": "Analyse ChIP-seq data of histone modifications with broad genomic footprints like H3K27me3. It allows for calling modified regions in single samples as well as for calling differentially modified regions in a comparison of two samples.", diff --git a/data/historian/historianbioschemas.jsonld b/data/historian/historianbioschemas.jsonld index 1fc7c8087a005..2fd6393baa6cb 100644 --- a/data/historian/historianbioschemas.jsonld +++ b/data/historian/historianbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Historian", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/evoldoers/historian" } \ No newline at end of file diff --git a/data/hit/hitbioschemas.jsonld b/data/hit/hitbioschemas.jsonld index d3c84a4958d59..d3d46c96e1a64 100644 --- a/data/hit/hitbioschemas.jsonld +++ b/data/hit/hitbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A comprehensive and fully curated database for Herb Ingredients’ Targets. Molecular target information involves those proteins being directly/indirectly activated/inhibited, protein binders and enzymes whose substrates or products are those compounds. Those up/down regulated genes are included under the treatment of individual ingredients. The experimental condition, observed bioactivity and various references are provided. The database can be queried via keyword or similarity search.", "sc:name": "HIT", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://lifecenter.sgst.cn/hit/" } \ No newline at end of file diff --git a/data/hitc/hitcbioschemas.jsonld b/data/hitc/hitcbioschemas.jsonld index 9f81c4b9c71a1..7cf28ba6669d1 100644 --- a/data/hitc/hitcbioschemas.jsonld +++ b/data/hitc/hitcbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-1678-7410", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/hitc", "@type": "sc:SoftwareApplication", @@ -20,22 +24,22 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:22923296", { "@id": "https://doi.org/10.1093/bioinformatics/bts521" }, - "pubmed:22923296", "pmcid:PMC3476334" ], "sc:description": "This package was developed to explore high-throughput 'C' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_3435" }, { "@id": "edam:operation_2428" }, { - "@id": "edam:operation_3435" + "@id": "edam:operation_0337" } ], "sc:license": "Artistic-2.0", @@ -48,10 +52,6 @@ "sc:url": "http://bioconductor.org/packages/release/bioc/html/HiTC.html", "sc:version": "1.18.0" }, - { - "@id": "http://orcid.org/0000-0003-1678-7410", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1093/bioinformatics/bts521", "@type": "sc:CreativeWork" diff --git a/data/hitpredict/hitpredictbioschemas.jsonld b/data/hitpredict/hitpredictbioschemas.jsonld index 7ebe08f73eb92..941e183a34f16 100644 --- a/data/hitpredict/hitpredictbioschemas.jsonld +++ b/data/hitpredict/hitpredictbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "HitPredict is a database with quality assessed PPIs in nine species. HitPredict assigns a confidence level to interactions based on a reliability score that is computed using evidence from sequence, structure and functional annotations of the interacting proteins.", "sc:name": "HitPredict", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://hintdb.hgc.jp/htp/" } \ No newline at end of file diff --git a/data/hitrace-web/hitrace-webbioschemas.jsonld b/data/hitrace-web/hitrace-webbioschemas.jsonld index 9840f000d7572..1fc460093bb14 100644 --- a/data/hitrace-web/hitrace-webbioschemas.jsonld +++ b/data/hitrace-web/hitrace-webbioschemas.jsonld @@ -13,17 +13,17 @@ "biotools:primaryContact": [ "Pablo Cordero (Site admin)", "Rhiju Das (PI)", - "Site admins: Hanjoo Kim (Site admin)", - "Sungroh Yoon (PI)" + "Sungroh Yoon (PI)", + "Site admins: Hanjoo Kim (Site admin)" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:23761448", "sc:description": "HiTRACE (High Throughput Robust Analysis of Capillary Electrophoresis) web server uses command line MATLAB scripts to analyze input high throughput capillary electrophoresis data.", "sc:name": "HiTRACE-Web", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://hitrace.org" } \ No newline at end of file diff --git a/data/hitselect/hitselectbioschemas.jsonld b/data/hitselect/hitselectbioschemas.jsonld index 5efe65da8e9ef..da3c3961a6335 100644 --- a/data/hitselect/hitselectbioschemas.jsonld +++ b/data/hitselect/hitselectbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. It provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis.", "sc:name": "HiTSelect", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/diazlab/HiTSelect" } \ No newline at end of file diff --git a/data/hivcleave/hivcleavebioschemas.jsonld b/data/hivcleave/hivcleavebioschemas.jsonld index 3a5b74f90caf8..2f94b2f90246b 100644 --- a/data/hivcleave/hivcleavebioschemas.jsonld +++ b/data/hivcleave/hivcleavebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-server for predicting HIV protease cleavage sites in proteins.", "sc:name": "HIVcleave", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/HIV/" } \ No newline at end of file diff --git a/data/hive/hivebioschemas.jsonld b/data/hive/hivebioschemas.jsonld index 330348b3c176e..aad932badf43b 100644 --- a/data/hive/hivebioschemas.jsonld +++ b/data/hive/hivebioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Contact form", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:26989153", + "pmcid:PMC4795927", { "@id": "https://doi.org/10.1093/DATABASE/BAW022" - }, - "pubmed:26989153", - "pmcid:PMC4795927" + } ], "sc:description": "High-performance integrated virtual environment: a robust infrastructure for next-generation sequence data analysis.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "HIVE", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://hive.biochemistry.gwu.edu/home" } diff --git a/data/hivproti/hivprotibioschemas.jsonld b/data/hivproti/hivprotibioschemas.jsonld index e15f5a23d5aad..d9c827691556f 100644 --- a/data/hivproti/hivprotibioschemas.jsonld +++ b/data/hivproti/hivprotibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "HIVprotI", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioinfo.imtech.res.in/manojk/hivproti/" } \ No newline at end of file diff --git a/data/hla_bind/hla_bindbioschemas.jsonld b/data/hla_bind/hla_bindbioschemas.jsonld index 4b6f1b85f6955..8f7a78bb821e4 100644 --- a/data/hla_bind/hla_bindbioschemas.jsonld +++ b/data/hla_bind/hla_bindbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Function: Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature.", "sc:name": "Bimas HLA Peptide Binding Predictions", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www-bimas.cit.nih.gov/molbio/hla_bind/" } \ No newline at end of file diff --git a/data/hlarestrictor/hlarestrictorbioschemas.jsonld b/data/hlarestrictor/hlarestrictorbioschemas.jsonld index 6f7655173ffb9..e879cf19c9af9 100644 --- a/data/hlarestrictor/hlarestrictorbioschemas.jsonld +++ b/data/hlarestrictor/hlarestrictorbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7885-4311", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/hlarestrictor", "@type": "sc:SoftwareApplication", @@ -21,17 +25,13 @@ "sc:license": "Other", "sc:name": "HLArestrictor", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/HLArestrictor/", "sc:version": "1.2" - }, - { - "@id": "http://orcid.org/0000-0001-7885-4311", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/hmdad/hmdadbioschemas.jsonld b/data/hmdad/hmdadbioschemas.jsonld index a49a7bb7eb886..6a246d34662cf 100644 --- a/data/hmdad/hmdadbioschemas.jsonld +++ b/data/hmdad/hmdadbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Human microbe-disease association prediction using network consistency projection.", "sc:name": "Human Microbe-Disease Association Database (HMDAD)", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cuilab.cn/hmdad" } \ No newline at end of file diff --git a/data/hmdb/hmdbbioschemas.jsonld b/data/hmdb/hmdbbioschemas.jsonld index 5cfd429f64c75..82514311790bf 100644 --- a/data/hmdb/hmdbbioschemas.jsonld +++ b/data/hmdb/hmdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.", "sc:name": "HMDB", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.hmdb.ca/" diff --git a/data/hmdbquery/hmdbquerybioschemas.jsonld b/data/hmdbquery/hmdbquerybioschemas.jsonld index d67a7d9c54c0c..d04cb8427425d 100644 --- a/data/hmdbquery/hmdbquerybioschemas.jsonld +++ b/data/hmdbquery/hmdbquerybioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "hmdbQuery", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hmdbQuery.html", "sc:version": "1.0.1" diff --git a/data/hml/hmlbioschemas.jsonld b/data/hml/hmlbioschemas.jsonld index 079f60e9cb2c9..958e8fb244c1a 100644 --- a/data/hml/hmlbioschemas.jsonld +++ b/data/hml/hmlbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "HML", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://emu.src.riken.jp/HML/" } \ No newline at end of file diff --git a/data/hmm-tm/hmm-tmbioschemas.jsonld b/data/hmm-tm/hmm-tmbioschemas.jsonld index d330bbf821ea9..ef262ab64f3d3 100644 --- a/data/hmm-tm/hmm-tmbioschemas.jsonld +++ b/data/hmm-tm/hmm-tmbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-7-189", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0003-4935-2325", "@type": "schema:Person" @@ -28,18 +32,18 @@ "sc:additionalType": "Web application", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0078" + "@id": "edam:topic_0820" }, { - "@id": "edam:topic_0820" + "@id": "edam:topic_0078" } ], "sc:citation": [ - "pmcid:PMC1523218", { "@id": "https://doi.org/10.1186/1471-2105-7-189" }, - "pubmed:16597327" + "pubmed:16597327", + "pmcid:PMC1523218" ], "sc:description": "HMM-TM is a tool that takes a protein sequence as input and predicts the transmembrane regions of alpha-helical", "sc:featureList": [ @@ -47,24 +51,20 @@ "@id": "edam:operation_2423" }, { - "@id": "edam:operation_0270" + "@id": "edam:operation_0269" }, { - "@id": "edam:operation_0269" + "@id": "edam:operation_0270" } ], "sc:name": "HMM-TM", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.compgen.org/tools/HMM-TM", "sc:version": "1.1" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-7-189", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hmmcopy/bioconda_hmmcopy.yaml b/data/hmmcopy/bioconda_hmmcopy.yaml index 7ecbc62913150..238f6d709b04f 100644 --- a/data/hmmcopy/bioconda_hmmcopy.yaml +++ b/data/hmmcopy/bioconda_hmmcopy.yaml @@ -6,7 +6,6 @@ description: Corrects GC and mappability biases for readcounts (i.e. coverage) i home: https://bioconductor.org/packages/3.10/bioc/html/HMMcopy.html identifiers: - biotools:hmmcopy -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hmmcopy diff --git a/data/hmmcopy/hmmcopybioschemas.jsonld b/data/hmmcopy/hmmcopybioschemas.jsonld index 9fa50344a24bd..ab46a3127ee75 100644 --- a/data/hmmcopy/hmmcopybioschemas.jsonld +++ b/data/hmmcopy/hmmcopybioschemas.jsonld @@ -15,16 +15,16 @@ "Daniel Lai" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for further analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.", "sc:license": "GPL-3.0", "sc:name": "HMMcopy", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HMMcopy.html", "sc:version": "1.16.0" diff --git a/data/hmmer2/hmmer2bioschemas.jsonld b/data/hmmer2/hmmer2bioschemas.jsonld index a81115eec8f74..4e5f212fff551 100644 --- a/data/hmmer2/hmmer2bioschemas.jsonld +++ b/data/hmmer2/hmmer2bioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/HMMER2", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", - "Web application" + "Web application", + "Library" ], "sc:description": "Older version of the HMMER3 program (https://bio.tools/hmmer3) used for searching sequence databases for sequence homologs, and for making sequence alignments.", "sc:license": "BSD-3-Clause", "sc:name": "HMMER2", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://hmmer.org/", "sc:version": "2.1.1 - 2.4i" diff --git a/data/hmmer3/hmmer3bioschemas.jsonld b/data/hmmer3/hmmer3bioschemas.jsonld index 912d0a0d40ddd..19fa151da7f3e 100644 --- a/data/hmmer3/hmmer3bioschemas.jsonld +++ b/data/hmmer3/hmmer3bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-6676-4706", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/hmmer3", "@type": "sc:SoftwareApplication", @@ -23,16 +27,12 @@ "sc:license": "Other", "sc:name": "HMMER3", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://hmmer.org/", "sc:version": "3.1b1" - }, - { - "@id": "http://orcid.org/0000-0001-6676-4706", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/hmmerctter/hmmerctterbioschemas.jsonld b/data/hmmerctter/hmmerctterbioschemas.jsonld index 52d02eea0e051..2c06bb81cbdf3 100644 --- a/data/hmmerctter/hmmerctterbioschemas.jsonld +++ b/data/hmmerctter/hmmerctterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Supervised classification of superfamily protein sequences with a reliable cut-off threshold.", "sc:name": "HMMERCTTER", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/BBCMdP/HMMERCTTER" diff --git a/data/hmmgene/hmmgenebioschemas.jsonld b/data/hmmgene/hmmgenebioschemas.jsonld index f2aa10ed93e77..b30fc13b4dc0d 100644 --- a/data/hmmgene/hmmgenebioschemas.jsonld +++ b/data/hmmgene/hmmgenebioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "Other", "sc:name": "HMMgene", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/HMMgene/", diff --git a/data/hmmibd/hmmibdbioschemas.jsonld b/data/hmmibd/hmmibdbioschemas.jsonld index bb1bf4875b035..16713beae2aed 100644 --- a/data/hmmibd/hmmibdbioschemas.jsonld +++ b/data/hmmibd/hmmibdbioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Stephen F. Schaffner", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:29764422", { "@id": "https://doi.org/10.1186/s12936-018-2349-7" }, - "pubmed:29764422", "pmcid:PMC5952413" ], "sc:description": "A hidden Markov model for detecting segments of shared ancestry (identity by descent) in genetic sequence data.", diff --git a/data/hmmptm/hmmptmbioschemas.jsonld b/data/hmmptm/hmmptmbioschemas.jsonld index 44219da553ebf..cc25d3a3cde06 100644 --- a/data/hmmptm/hmmptmbioschemas.jsonld +++ b/data/hmmptm/hmmptmbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "HMMpTM", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://aias.biol.uoa.gr/HMMpTM/" } \ No newline at end of file diff --git a/data/hmmscan_ebi/hmmscan_ebibioschemas.jsonld b/data/hmmscan_ebi/hmmscan_ebibioschemas.jsonld index 867dfb72edb0d..11ee217e4b28d 100644 --- a/data/hmmscan_ebi/hmmscan_ebibioschemas.jsonld +++ b/data/hmmscan_ebi/hmmscan_ebibioschemas.jsonld @@ -20,12 +20,12 @@ "sc:name": "hmmscan (EBI)", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ - "EMBL-EBI", - "HHMI" + "HHMI", + "EMBL-EBI" ], "sc:url": "http://www.ebi.ac.uk/Tools/pfa/hmmer_hmmscan/", "sc:version": "1" diff --git a/data/hmmsplicer/hmmsplicerbioschemas.jsonld b/data/hmmsplicer/hmmsplicerbioschemas.jsonld index 33e4d981f3019..bb89566c750e9 100644 --- a/data/hmmsplicer/hmmsplicerbioschemas.jsonld +++ b/data/hmmsplicer/hmmsplicerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Splice junction discovery in RNA-Seq data", "sc:name": "HMMSplicer", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://derisilab.ucsf.edu/software/hmmsplicer" } \ No newline at end of file diff --git a/data/hmmtop/hmmtopbioschemas.jsonld b/data/hmmtop/hmmtopbioschemas.jsonld index 9653ac6e1116e..1a587c2d45dbb 100644 --- a/data/hmmtop/hmmtopbioschemas.jsonld +++ b/data/hmmtop/hmmtopbioschemas.jsonld @@ -25,8 +25,8 @@ "sc:name": "HMMTOP", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.enzim.hu/hmmtop/" } diff --git a/data/hmmufotu/hmmufotubioschemas.jsonld b/data/hmmufotu/hmmufotubioschemas.jsonld index 44acea1b233c2..84a3ae3b3e19e 100644 --- a/data/hmmufotu/hmmufotubioschemas.jsonld +++ b/data/hmmufotu/hmmufotubioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies.", "sc:name": "HmmUFOtu", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/Grice-Lab/HmmUFOtu/releases" } \ No newline at end of file diff --git a/data/hmoment/hmomentbioschemas.jsonld b/data/hmoment/hmomentbioschemas.jsonld index 9c5f1a015a883..91d3b090b5858 100644 --- a/data/hmoment/hmomentbioschemas.jsonld +++ b/data/hmoment/hmomentbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "Wellcome Trust", "UK BBSRC", "UK MRC", - "Wellcome Trust", "EMBOSS Contributors" ], "sc:description": "Calculate and plot hydrophobic moment for protein sequence(s).", @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "hmoment", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/hmp2/hmp2bioschemas.jsonld b/data/hmp2/hmp2bioschemas.jsonld index 85a888b168c69..7a3834885d59e 100644 --- a/data/hmp2/hmp2bioschemas.jsonld +++ b/data/hmp2/hmp2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/S41586-019-1237-9", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/HMP2", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ ], "sc:additionalType": "Workflow", "sc:citation": [ + "pubmed:31142855", "pmcid:PMC6650278", { "@id": "https://doi.org/10.1038/S41586-019-1237-9" - }, - "pubmed:31142855" + } ], "sc:description": "Collection of workflows that handle processing several different data types assocaited with the IBDMDB (Inflammatory Bowel Disease Multi’omics Database) project.", "sc:featureList": [ @@ -44,10 +48,6 @@ "Mac" ], "sc:url": "https://bitbucket.org/biobakery/hmp2_workflows" - }, - { - "@id": "https://doi.org/10.1038/S41586-019-1237-9", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hmrfbayeshic/hmrfbayeshicbioschemas.jsonld b/data/hmrfbayeshic/hmrfbayeshicbioschemas.jsonld index 7dc6179f75bf2..656b4ab6e6e18 100644 --- a/data/hmrfbayeshic/hmrfbayeshicbioschemas.jsonld +++ b/data/hmrfbayeshic/hmrfbayeshicbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Ming Hu", - "Zheng Xu", - "Yun Li" + "Yun Li", + "Zheng Xu" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:26543175", diff --git a/data/hms-ics/hms-icsbioschemas.jsonld b/data/hms-ics/hms-icsbioschemas.jsonld index 7e6f927cef188..e3368f712a91a 100644 --- a/data/hms-ics/hms-icsbioschemas.jsonld +++ b/data/hms-ics/hms-icsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The Hyperlink Management System (HMS) automatically updates and maintains hyperlinks among major databases using various data IDs (e.g. HUGO Gene Symbols, IDs from PDB, UniProt). The ID Converter System (ICS) supports the conversion of data IDs using the corresponding tables in HMS.", "sc:name": "HMS-ICS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://biodb.jp/" diff --git a/data/hmtdb/hmtdbbioschemas.jsonld b/data/hmtdb/hmtdbbioschemas.jsonld index d71033a6d7568..149c98689babb 100644 --- a/data/hmtdb/hmtdbbioschemas.jsonld +++ b/data/hmtdb/hmtdbbioschemas.jsonld @@ -13,14 +13,6 @@ "@id": "https://doi.org/10.1186/1471-2105-6-S4-S4", "@type": "sc:CreativeWork" }, - { - "@id": "https://doi.org/10.1093/nar/gkr1086", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1093/nar/gkw1066", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/hmtdb", "@type": "sc:SoftwareApplication", @@ -30,21 +22,21 @@ "Web API" ], "sc:citation": [ - "pmcid:PMC1866381", - "pubmed:22139932", + "pubmed:27899581", { - "@id": "https://doi.org/10.1093/nar/gkw1066" + "@id": "https://doi.org/10.1186/1471-2105-6-S4-S4" }, + "pubmed:22139932", + "pmcid:PMC3245114", "pubmed:16351753", + "pmcid:PMC1866381", { - "@id": "https://doi.org/10.1186/1471-2105-6-S4-S4" + "@id": "https://doi.org/10.1093/nar/gkw1066" }, "pmcid:PMC5210550", { "@id": "https://doi.org/10.1093/nar/gkr1086" - }, - "pubmed:27899581", - "pmcid:PMC3245114" + } ], "sc:description": "Database of human mitochondrial genomes from primary INSDC databases, personal submissions and application of MtoolBox to NGS data.", "sc:featureList": { @@ -53,11 +45,19 @@ "sc:name": "HmtDB", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ELIXIR-ITA-BARI", "sc:url": "http://www.hmtdb.uniba.it/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkw1066", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://doi.org/10.1093/nar/gkr1086", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hnadock/hnadockbioschemas.jsonld b/data/hnadock/hnadockbioschemas.jsonld index 8fbedb6484e39..bb84a3b2b17fe 100644 --- a/data/hnadock/hnadockbioschemas.jsonld +++ b/data/hnadock/hnadockbioschemas.jsonld @@ -17,17 +17,17 @@ "@id": "https://bio.tools/HNADOCK", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sheng-You Huang", + "Yi Xiao", "Lab of Bioinformatics and Molecular Modeling", - "Yi Xiao" + "Sheng-You Huang" ], "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC6602492", { "@id": "https://doi.org/10.1093/NAR/GKZ412" }, - "pubmed:31114906", - "pmcid:PMC6602492" + "pubmed:31114906" ], "sc:description": "Nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures.", "sc:featureList": [ @@ -44,9 +44,9 @@ "sc:license": "Unlicense", "sc:name": "HNADOCK", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://huanglab.phys.hust.edu.cn/hnadock/" } diff --git a/data/hncdb/hncdbbioschemas.jsonld b/data/hncdb/hncdbbioschemas.jsonld index 00a9a1c0e734f..c59e1b7564787 100644 --- a/data/hncdb/hncdbbioschemas.jsonld +++ b/data/hncdb/hncdbbioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3389/FONC.2019.00371", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/HNCDB", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ankui Yang", "Zhixiang Zuo", - "Xiaoqing Pei" + "Xiaoqing Pei", + "Ankui Yang" ], "sc:additionalType": [ "Database portal", @@ -35,23 +31,27 @@ "sc:description": "Integrated Gene and Drug Database for Head and Neck Cancer.", "sc:featureList": [ { - "@id": "edam:operation_3223" + "@id": "edam:operation_0306" }, { "@id": "edam:operation_3463" }, { - "@id": "edam:operation_0306" + "@id": "edam:operation_3223" } ], "sc:license": "Unlicense", "sc:name": "HNCDB", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://hncdb.cancerbio.info" + }, + { + "@id": "https://doi.org/10.3389/FONC.2019.00371", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hogenom/hogenombioschemas.jsonld b/data/hogenom/hogenombioschemas.jsonld index 3a1b64ab7283c..37450376d7703 100644 --- a/data/hogenom/hogenombioschemas.jsonld +++ b/data/hogenom/hogenombioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/hogenom", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web service" + "Web service", + "Database portal" ], "sc:description": "It allows selection of sets of homologous genes among species, and visualisation of multiple alignments and phylogenetic trees. It is useful for comparative sequence analysis, phylogeny, molecular evolution studies and to get a view of what is known about a peculiar gene family.", "sc:name": "HOGENOM", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://pbil.univ-lyon1.fr/databases/hogenom3.html" } \ No newline at end of file diff --git a/data/holmes/holmesbioschemas.jsonld b/data/holmes/holmesbioschemas.jsonld index 38c1b643137c5..4656d2a078b4c 100644 --- a/data/holmes/holmesbioschemas.jsonld +++ b/data/holmes/holmesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "Holmes", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html" } \ No newline at end of file diff --git a/data/homa/homabioschemas.jsonld b/data/homa/homabioschemas.jsonld index 918ebc74fac07..d1d936ba7001e 100644 --- a/data/homa/homabioschemas.jsonld +++ b/data/homa/homabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "HOMA", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www-nmr.cabm.rutgers.edu/HOMA/" } \ No newline at end of file diff --git a/data/home/homebioschemas.jsonld b/data/home/homebioschemas.jsonld index bac21b6fde5dc..a7edc682c61c2 100644 --- a/data/home/homebioschemas.jsonld +++ b/data/home/homebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-019-2845-Y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/HOME", "@type": "sc:SoftwareApplication", @@ -21,22 +17,22 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6521357", { "@id": "https://doi.org/10.1186/S12859-019-2845-Y" }, - "pubmed:31096906" + "pubmed:31096906", + "pmcid:PMC6521357" ], "sc:description": "HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification.", "sc:featureList": [ - { - "@id": "edam:operation_3206" - }, { "@id": "edam:operation_3186" }, { "@id": "edam:operation_3207" + }, + { + "@id": "edam:operation_3206" } ], "sc:name": "HOME", @@ -46,6 +42,10 @@ { "@id": "https://orcid.org/0000-0001-6637-7239", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/S12859-019-2845-Y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/homer-a/homer-abioschemas.jsonld b/data/homer-a/homer-abioschemas.jsonld index d58f03dcb0ce2..08f5a3819f143 100644 --- a/data/homer-a/homer-abioschemas.jsonld +++ b/data/homer-a/homer-abioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A comparative modelling server for protein structure prediction. Automatic template selection.", "sc:name": "HOMER-A", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "ELIXIR-ITA-PADOVA", diff --git a/data/homer-m/homer-mbioschemas.jsonld b/data/homer-m/homer-mbioschemas.jsonld index 3e8bcee7b80dc..8f9f8962d08c8 100644 --- a/data/homer-m/homer-mbioschemas.jsonld +++ b/data/homer-m/homer-mbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "HOMER-M", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/homer/", diff --git a/data/homolens/homolensbioschemas.jsonld b/data/homolens/homolensbioschemas.jsonld index eb01eea5433ac..41a1c4d58a3a0 100644 --- a/data/homolens/homolensbioschemas.jsonld +++ b/data/homolens/homolensbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system.", "sc:name": "HOMOLENS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://pbil.univ-lyon1.fr/databases/homolens.php" } \ No newline at end of file diff --git a/data/homologous_series_detection/homologous_series_detectionbioschemas.jsonld b/data/homologous_series_detection/homologous_series_detectionbioschemas.jsonld index e5da2c9508e28..ea727f145fec2 100644 --- a/data/homologous_series_detection/homologous_series_detectionbioschemas.jsonld +++ b/data/homologous_series_detection/homologous_series_detectionbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Homologous Series Detection", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.envihomolog.eawag.ch/" } \ No newline at end of file diff --git a/data/homozygositymapper/homozygositymapperbioschemas.jsonld b/data/homozygositymapper/homozygositymapperbioschemas.jsonld index 736a9aa1e2d63..4a5c0fd973d25 100644 --- a/data/homozygositymapper/homozygositymapperbioschemas.jsonld +++ b/data/homozygositymapper/homozygositymapperbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A web base approach to homozygosity mapping. Users upload SNP genotype or sequencing files for analysis and detection of long homozygous stretches between affected individuals. Human, rodent and other mammals are mappable.", "sc:name": "HomozygosityMapper", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.homozygositymapper.org" } \ No newline at end of file diff --git a/data/homsi/homsibioschemas.jsonld b/data/homsi/homsibioschemas.jsonld index 045fdd085d4e0..9d80d876fab42 100644 --- a/data/homsi/homsibioschemas.jsonld +++ b/data/homsi/homsibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Homozygous stretch identifier from next-generation sequencing data.", "sc:name": "HomSI", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI/" } \ No newline at end of file diff --git a/data/hopach/bioconda_hopach.yaml b/data/hopach/bioconda_hopach.yaml index eb70ce664cd53..e2f580bdd9e70 100644 --- a/data/hopach/bioconda_hopach.yaml +++ b/data/hopach/bioconda_hopach.yaml @@ -9,7 +9,6 @@ description: The HOPACH clustering algorithm builds a hierarchical tree of clust home: https://bioconductor.org/packages/3.10/bioc/html/hopach.html identifiers: - biotools:hopach -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hopach diff --git a/data/hopach/hopachbioschemas.jsonld b/data/hopach/hopachbioschemas.jsonld index 942acc4146604..4d956b43e2561 100644 --- a/data/hopach/hopachbioschemas.jsonld +++ b/data/hopach/hopachbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "hopach", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hopach.html", "sc:version": "2.34.0" diff --git a/data/hora/horabioschemas.jsonld b/data/hora/horabioschemas.jsonld index 89c063249e2a2..4222563059991 100644 --- a/data/hora/horabioschemas.jsonld +++ b/data/hora/horabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "HorA (Homology or Analogy) is a web server that identifies likely homologs for a given query protein structure. HorA combines sequence information with structure information from spatial similarity measures.", "sc:name": "HorA", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://prodata.swmed.edu/horaserver/" diff --git a/data/hot/hotbioschemas.jsonld b/data/hot/hotbioschemas.jsonld index 6f306fa73e2e3..931dac8131a24 100644 --- a/data/hot/hotbioschemas.jsonld +++ b/data/hot/hotbioschemas.jsonld @@ -17,10 +17,10 @@ "@id": "https://bio.tools/HOT", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Verdan Franske", { "@id": "https://orcid.org/0000-0002-0468-0117" - } + }, + "Verdan Franske" ], "sc:additionalType": "Script", "sc:citation": [ @@ -32,14 +32,14 @@ ], "sc:description": "Examining the basis of high-occupancy target regions.", "sc:featureList": [ - { - "@id": "edam:operation_0445" - }, { "@id": "edam:operation_3207" }, { "@id": "edam:operation_0417" + }, + { + "@id": "edam:operation_0445" } ], "sc:license": "Unlicense", diff --git a/data/hotnet2/hotnet2bioschemas.jsonld b/data/hotnet2/hotnet2bioschemas.jsonld index 6da15e2b8df92..889ff00f64169 100644 --- a/data/hotnet2/hotnet2bioschemas.jsonld +++ b/data/hotnet2/hotnet2bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "HotNet2", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "imada.sdu.dk", "sc:url": "https://github.com/raphael-group/hotnet2", diff --git a/data/hotregion/hotregionbioschemas.jsonld b/data/hotregion/hotregionbioschemas.jsonld index 533db67ebb79b..0d47d11ffc819 100644 --- a/data/hotregion/hotregionbioschemas.jsonld +++ b/data/hotregion/hotregionbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of predicted hot spot clusters. Hot spots are energetically important residues at protein interfaces, clustered across the interface. HotRegion provides the hot region information of the interfaces by using predicted hot spot resides, and structural properties.", "sc:name": "HotRegion", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://prism.ccbb.ku.edu.tr/hotregion/" } \ No newline at end of file diff --git a/data/hotspot/hotspotbioschemas.jsonld b/data/hotspot/hotspotbioschemas.jsonld index 7c5a80d105e7c..586c07d1315af 100644 --- a/data/hotspot/hotspotbioschemas.jsonld +++ b/data/hotspot/hotspotbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "HotSpot is a software of prediction of hot spot residues through physicochemical characteristics of amino acid sequences", "sc:name": "HotSpot", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sfb.kaust.edu.sa/Pages/Software.aspx" } \ No newline at end of file diff --git a/data/hotspot_wizard/hotspot_wizardbioschemas.jsonld b/data/hotspot_wizard/hotspot_wizardbioschemas.jsonld index 137a7ee7ec65f..707f5debd75d6 100644 --- a/data/hotspot_wizard/hotspot_wizardbioschemas.jsonld +++ b/data/hotspot_wizard/hotspot_wizardbioschemas.jsonld @@ -12,43 +12,43 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:author": [ - "Jan Brezovsky", - "Jiri Damborsky", + "Jan Stourac", "Jaroslav Bendl", - "Jan Stourac" + "Jiri Damborsky", + "Jan Brezovsky" ], "sc:contributor": [ - "Ondrej Vavra", - "Ministry of Education of the Czech Republic [LO1214, LQ1605, LM2015055 and LM2015047]", + "Antonin Pavelka", "Milos Musil", - "Brno University of Technology [FIT-S-14-2299 to M.M.]", - "CESNET and the CERIT Scientific Cloud [LM2015042 and LM2015085]", - "Horizon 2020 Research Infrastructure ELIXIR-EXCELERATE [676559]", "Eva Sebestova", "European Commission REGPOT [316345]", + "Horizon 2020 Research Infrastructure ELIXIR-EXCELERATE [676559]", + "Brno University of Technology [FIT-S-14-2299 to M.M.]", + "CESNET and the CERIT Scientific Cloud [LM2015042 and LM2015085]", "Grant Agency of the Czech Republic [GA16-06096S]", - "Antonin Pavelka" + "Ministry of Education of the Czech Republic [LO1214, LQ1605, LM2015055 and LM2015047]", + "Ondrej Vavra" ], "sc:description": "An automated design of mutations and smart libraries for engineering of protein function and stability and annotation of protein structures.", "sc:funder": [ - "Horizon 2020 Research Infrastructure ELIXIR-EXCELERATE [676559]", - "European Commission REGPOT [316345]", + "CESNET and the CERIT Scientific Cloud [LM2015042 and LM2015085]", "Grant Agency of the Czech Republic [GA16-06096S]", "Ministry of Education of the Czech Republic [LO1214, LQ1605, LM2015055 and LM2015047]", "Brno University of Technology [FIT-S-14-2299 to M.M.]", - "CESNET and the CERIT Scientific Cloud [LM2015042 and LM2015085]" + "Horizon 2020 Research Infrastructure ELIXIR-EXCELERATE [676559]", + "European Commission REGPOT [316345]" ], "sc:name": "HotSpot Wizard", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ - "Loschmidt Laboratories", - "Masaryk University, Brno, Czech Republic", "International Centre for Clinical Research, Brno, Czech Republic", - "Brno University of Technology, Brno, Czech Republic" + "Masaryk University, Brno, Czech Republic", + "Brno University of Technology, Brno, Czech Republic", + "Loschmidt Laboratories" ], "sc:url": "http://loschmidt.chemi.muni.cz/hotspotwizard", "sc:version": "2.0" diff --git a/data/hotspring/hotspringbioschemas.jsonld b/data/hotspring/hotspringbioschemas.jsonld index 5d7944c4a932b..a96f50fc628c9 100644 --- a/data/hotspring/hotspringbioschemas.jsonld +++ b/data/hotspring/hotspringbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web server to predict the host spots in RNA binding proteins (RBPs)", "sc:name": "HotSPRing", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.csb.iitkgp.ernet.in/applications/HotSPRing/main.php" diff --git a/data/hovergen/hovergenbioschemas.jsonld b/data/hovergen/hovergenbioschemas.jsonld index 4fbb60693c1ca..d92acad029e90 100644 --- a/data/hovergen/hovergenbioschemas.jsonld +++ b/data/hovergen/hovergenbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This database allows selection of sets of homologous genes among vertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family.", "sc:name": "Homologous vertebrate genes database (HOVERGEN)", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://pbil.univ-lyon1.fr/databases/hovergen.html" } \ No newline at end of file diff --git a/data/hpar/bioconda_hpar.yaml b/data/hpar/bioconda_hpar.yaml index e7d591756fba9..fe6aaebe15ee9 100644 --- a/data/hpar/bioconda_hpar.yaml +++ b/data/hpar/bioconda_hpar.yaml @@ -4,7 +4,6 @@ description: The hpar package provides a simple R interface to and data from the home: https://bioconductor.org/packages/3.10/bioc/html/hpar.html identifiers: - biotools:hpar -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-hpar summary: Human Protein Atlas in R diff --git a/data/hpar/hparbioschemas.jsonld b/data/hpar/hparbioschemas.jsonld index ac5a781964cc4..3784518ce1623 100644 --- a/data/hpar/hparbioschemas.jsonld +++ b/data/hpar/hparbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "hpar", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hpar.html", "sc:version": "1.16.0" diff --git a/data/hpeak/hpeakbioschemas.jsonld b/data/hpeak/hpeakbioschemas.jsonld index 78d501b23fdaf..99a7da4cfd717 100644 --- a/data/hpeak/hpeakbioschemas.jsonld +++ b/data/hpeak/hpeakbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Hidden Markov model (HMM)-based Peak-finding algorithm for analyzing ChIP-seq data to identify protein-interacting genomic regions.", "sc:name": "HPeak", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/cauyrd/HPeak" diff --git a/data/hpg_aligner/hpg_alignerbioschemas.jsonld b/data/hpg_aligner/hpg_alignerbioschemas.jsonld index 96cf0d7bf3aff..6068b4a77206d 100644 --- a/data/hpg_aligner/hpg_alignerbioschemas.jsonld +++ b/data/hpg_aligner/hpg_alignerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/hpg_aligner", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ignacio Medina", - "Joaquín Dopazo" + "Joaquín Dopazo", + "Ignacio Medina" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:25143289", diff --git a/data/hplcsimulator/hplcsimulatorbioschemas.jsonld b/data/hplcsimulator/hplcsimulatorbioschemas.jsonld index 84a34c2f2158b..3cc34422ae1dc 100644 --- a/data/hplcsimulator/hplcsimulatorbioschemas.jsonld +++ b/data/hplcsimulator/hplcsimulatorbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A general tool for simulating and optimizing HPLC gradients.", "sc:name": "hplcsimulator", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.hplcsimulator.org/" } \ No newline at end of file diff --git a/data/hpm/hpmbioschemas.jsonld b/data/hpm/hpmbioschemas.jsonld index 1fb0d33f1eecc..16190a19f78f3 100644 --- a/data/hpm/hpmbioschemas.jsonld +++ b/data/hpm/hpmbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-1974-0271", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/hpm", "@type": "sc:SoftwareApplication", @@ -24,11 +20,15 @@ "sc:description": "HPM (Haplotype Pattern Mining) is a program for gene mapping in case-control haplotype data.", "sc:name": "HPM", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cs.helsinki.fi/group/genetics/hpm.html" + }, + { + "@id": "https://orcid.org/0000-0003-1974-0271", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/hpo/hpobioschemas.jsonld b/data/hpo/hpobioschemas.jsonld index 8d1b09cc13dc1..55fae1680321a 100644 --- a/data/hpo/hpobioschemas.jsonld +++ b/data/hpo/hpobioschemas.jsonld @@ -9,28 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkt1026", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/hpo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Melissa Haendel", + "Peter Robinson", "Sebastian Köhler", - "Peter Robinson" + "Melissa Haendel" ], "sc:additionalType": [ "Ontology", "Web application" ], "sc:citation": [ - "pubmed:24217912", "pmcid:PMC3965098", { "@id": "https://doi.org/10.1093/nar/gkt1026" - } + }, + "pubmed:24217912" ], "sc:description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. It can be used for clinical diagnostics in human genetics, bioinformatics research on the relationships between human phenotypic abnormalities and cellular and biochemical networks, for mapping between human and model organism phenotypes and for providing a standardized vocabulary for clinical databases. All the data is available for download and can be browsed online.", "sc:featureList": [ @@ -46,11 +42,15 @@ ], "sc:name": "HPO", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://hpo.jax.org/app/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkt1026", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/hprd/hprdbioschemas.jsonld b/data/hprd/hprdbioschemas.jsonld index fa064be2e24af..4fb2c09c7e85d 100644 --- a/data/hprd/hprdbioschemas.jsonld +++ b/data/hprd/hprdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in it is curated by experts, who manually extract it from published literature.", "sc:name": "The Human Protein Reference Database (HPRD)", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.hprd.org/" } \ No newline at end of file diff --git a/data/hrm/hrmbioschemas.jsonld b/data/hrm/hrmbioschemas.jsonld index 3132cbbae8788..89f70f80638a7 100644 --- a/data/hrm/hrmbioschemas.jsonld +++ b/data/hrm/hrmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "General statistical inference framework for stochastic transcription-translation networks.", "sc:name": "HRM", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://homepages.inf.ed.ac.uk/gsanguin/software.html" diff --git a/data/hrtbldb/hrtbldbbioschemas.jsonld b/data/hrtbldb/hrtbldbbioschemas.jsonld index 2bc6562f84132..c5b8b07b008a2 100644 --- a/data/hrtbldb/hrtbldbbioschemas.jsonld +++ b/data/hrtbldb/hrtbldbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Hormone Receptor Target Binding Loci, HRTBLDb database contains hormone receptor binding regions (binding loci) from in vivo ChIP-based high-throughput experiments as well as in silico, computationally predicted, binding motifs and cis-regulatory modules for the co-occurring transcription factor binding motifs, which are within a binding locus. It also contains individual binding sites whose regulatory action has been verified by in vitro experiments.", "sc:name": "HRTBLDb", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://compbio.uthscsa.edu/hrtbldb/" } \ No newline at end of file diff --git a/data/hrvanalysis/hrvanalysisbioschemas.jsonld b/data/hrvanalysis/hrvanalysisbioschemas.jsonld index 7c37cf4a338f5..103e69a29a83b 100644 --- a/data/hrvanalysis/hrvanalysisbioschemas.jsonld +++ b/data/hrvanalysis/hrvanalysisbioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5118625", - "pubmed:27920726", { "@id": "https://doi.org/10.3389/fphys.2016.00557" - } + }, + "pmcid:PMC5118625", + "pubmed:27920726" ], "sc:description": "HRVanalysis is a free software that can be used to analyze cardiac autonomic activity.", "sc:featureList": { diff --git a/data/hsa/hsabioschemas.jsonld b/data/hsa/hsabioschemas.jsonld index 2fa2b6349b255..5fe19e4e95e91 100644 --- a/data/hsa/hsabioschemas.jsonld +++ b/data/hsa/hsabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "HSA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ouyanglab.jax.org/hsa/" } \ No newline at end of file diff --git a/data/hslpred/hslpredbioschemas.jsonld b/data/hslpred/hslpredbioschemas.jsonld index 61f8e499b7db9..0621114077938 100644 --- a/data/hslpred/hslpredbioschemas.jsonld +++ b/data/hslpred/hslpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Allows predicting the subcellular localization of human proteins. This is based on various type of residue composition of proteins using SVM technique.", "sc:name": "HSLpred", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/hslpred/" } \ No newline at end of file diff --git a/data/hsymdock/hsymdockbioschemas.jsonld b/data/hsymdock/hsymdockbioschemas.jsonld index db063be33940e..71dca6317cb21 100644 --- a/data/hsymdock/hsymdockbioschemas.jsonld +++ b/data/hsymdock/hsymdockbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Symmetric protein docking for oligomers with Cn or Dn symmetry from the structure or sequence of a subunit molecule.", "sc:name": "HSYMDOCK", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://huanglab.phys.hust.edu.cn/hsymdock/", "sc:version": "2018-06-02" diff --git a/data/htm-one/htm-onebioschemas.jsonld b/data/htm-one/htm-onebioschemas.jsonld index d4ca157c8b56b..00032c01042f7 100644 --- a/data/htm-one/htm-onebioschemas.jsonld +++ b/data/htm-one/htm-onebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "HTM-ONE takes single amino acid sequence as input and returns residue-wise prediction of several one-dimensional structural properties of helical transmembrane regions.", "sc:name": "HTM-ONE", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://mizuguchilab.org/netasa/htmone/" } \ No newline at end of file diff --git a/data/html4blast/html4blastbioschemas.jsonld b/data/html4blast/html4blastbioschemas.jsonld index d85ca67ad27b4..74c21d02fcdfe 100644 --- a/data/html4blast/html4blastbioschemas.jsonld +++ b/data/html4blast/html4blastbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Create a html report from a blast result.", "sc:name": "html4blast", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://bioweb.pasteur.fr/packages/pack@html4blast@1.7a", "sc:version": "1.7a" diff --git a/data/htp-oligodesigner/htp-oligodesignerbioschemas.jsonld b/data/htp-oligodesigner/htp-oligodesignerbioschemas.jsonld index 103a72d600f87..49ea9e0fcc85a 100644 --- a/data/htp-oligodesigner/htp-oligodesignerbioschemas.jsonld +++ b/data/htp-oligodesigner/htp-oligodesignerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Created to provide the scientific community with a simple and intuitive online primer design tool for both laboratory-scale and high-throughput projects of sequence-independent gene cloning and site-directed mutagenesis and a Tm calculator for quick queries.", "sc:name": "HTP-OligoDesigner", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.ifsc.usp.br/htpoligo/" diff --git a/data/htpheno/htphenobioschemas.jsonld b/data/htpheno/htphenobioschemas.jsonld index f9de71e713635..6a32d2e226088 100644 --- a/data/htpheno/htphenobioschemas.jsonld +++ b/data/htpheno/htphenobioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "HTPheno is a software for high-throughput plant phenotyping is presented. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening.", "sc:name": "HTPheno", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://htpheno.ipk-gatersleben.de/" diff --git a/data/htqpcr/htqpcrbioschemas.jsonld b/data/htqpcr/htqpcrbioschemas.jsonld index c7eccf3ae1f04..9ed8d5104a1c0 100644 --- a/data/htqpcr/htqpcrbioschemas.jsonld +++ b/data/htqpcr/htqpcrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btp578", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/htqpcr", "@type": "sc:SoftwareApplication", @@ -16,14 +20,14 @@ "@id": "http://orcid.org/0000-0003-1741-0738" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pubmed:19808880", { "@id": "https://doi.org/10.1093/bioinformatics/btp578" }, - "pubmed:19808880", "pmcid:PMC2788924" ], "sc:description": "Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science, etc. It handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features.", @@ -33,8 +37,8 @@ "sc:license": "Artistic-2.0", "sc:name": "HTqPCR", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HTqPCR.html", @@ -43,10 +47,6 @@ { "@id": "http://orcid.org/0000-0003-1741-0738", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btp578", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/htr/htrbioschemas.jsonld b/data/htr/htrbioschemas.jsonld index 2722be0eab7c0..c88f21565cdc7 100644 --- a/data/htr/htrbioschemas.jsonld +++ b/data/htr/htrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Haplotype/Trait Association Software.", "sc:name": "HTR", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://statgen.ncsu.edu/zaykin/htr.html" } \ No newline at end of file diff --git a/data/htsanalyzer/htsanalyzerbioschemas.jsonld b/data/htsanalyzer/htsanalyzerbioschemas.jsonld index e2137a4a58cb7..7a070acf8ea8c 100644 --- a/data/htsanalyzer/htsanalyzerbioschemas.jsonld +++ b/data/htsanalyzer/htsanalyzerbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-5122-2418", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btr028", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/htsanalyzer", "@type": "sc:SoftwareApplication", @@ -25,10 +17,10 @@ }, "edam:has_input": [ { - "@id": "edam:data_2600" + "@id": "edam:data_2872" }, { - "@id": "edam:data_2872" + "@id": "edam:data_2600" }, { "@id": "edam:data_2603" @@ -39,41 +31,41 @@ "@id": "edam:data_2048" }, { - "@id": "edam:data_1669" + "@id": "edam:data_2884" }, { - "@id": "edam:data_2884" + "@id": "edam:data_1669" } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3523" + "@id": "edam:topic_0085" }, { "@id": "edam:topic_0602" }, { - "@id": "edam:topic_0085" + "@id": "edam:topic_3523" } ], "sc:citation": [ + "pubmed:21258062", + "pmcid:PMC3051329", { "@id": "https://doi.org/10.1093/bioinformatics/btr028" - }, - "pmcid:PMC3051329", - "pubmed:21258062" + } ], "sc:description": "This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package.", "sc:featureList": [ { - "@id": "edam:operation_0533" + "@id": "edam:operation_2436" }, { - "@id": "edam:operation_2436" + "@id": "edam:operation_0533" }, { "@id": "edam:operation_3224" @@ -82,12 +74,20 @@ "sc:license": "Artistic-2.0", "sc:name": "HTSanalyzeR", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HTSanalyzeR.html", "sc:version": "2.26.0" + }, + { + "@id": "http://orcid.org/0000-0002-5122-2418", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btr028", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/htscluster/htsclusterbioschemas.jsonld b/data/htscluster/htsclusterbioschemas.jsonld index 42ea6833a3ed2..2c4ae5c08542f 100644 --- a/data/htscluster/htsclusterbioschemas.jsonld +++ b/data/htscluster/htsclusterbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "HTSCluster", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cran.r-project.org/web/packages/HTSCluster/index.html" } \ No newline at end of file diff --git a/data/htseq/htseqbioschemas.jsonld b/data/htseq/htseqbioschemas.jsonld index d2ef70bac98e1..ed98c285a1d40 100644 --- a/data/htseq/htseqbioschemas.jsonld +++ b/data/htseq/htseqbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "HTSeq", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://htseq.readthedocs.io/en/release_0.9.1/" } \ No newline at end of file diff --git a/data/htseqcount/htseqcountbioschemas.jsonld b/data/htseqcount/htseqcountbioschemas.jsonld index 73734436ddde9..2cbe1fd09c75a 100644 --- a/data/htseqcount/htseqcountbioschemas.jsonld +++ b/data/htseqcount/htseqcountbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This script takes an alignment file in SAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it.", "sc:name": "htseqcount", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://htseq.readthedocs.io/en/release_0.9.1/", diff --git a/data/htseqgenie/htseqgeniebioschemas.jsonld b/data/htseqgenie/htseqgeniebioschemas.jsonld index 392242ba96011..bdf64fac09f7e 100644 --- a/data/htseqgenie/htseqgeniebioschemas.jsonld +++ b/data/htseqgenie/htseqgeniebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "HTSeqGenie", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HTSeqGenie.html", diff --git a/data/htseqtools/htseqtoolsbioschemas.jsonld b/data/htseqtools/htseqtoolsbioschemas.jsonld index f991a8ffa9d1c..2c5276c157893 100644 --- a/data/htseqtools/htseqtoolsbioschemas.jsonld +++ b/data/htseqtools/htseqtoolsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Oscar Reina", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.", "sc:license": "GPL-2.0", "sc:name": "htSeqTools", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/htSeqTools.html", "sc:version": "1.22.0" diff --git a/data/htsfilter/htsfilterbioschemas.jsonld b/data/htsfilter/htsfilterbioschemas.jsonld index 2e9ab6507cda1..490992d300905 100644 --- a/data/htsfilter/htsfilterbioschemas.jsonld +++ b/data/htsfilter/htsfilterbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Andrea Rau", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC3740625", "pubmed:23821648", { "@id": "https://doi.org/10.1093/bioinformatics/btt350" - }, - "pmcid:PMC3740625" + } ], "sc:description": "This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.", "sc:featureList": { @@ -35,9 +35,9 @@ "sc:license": "Artistic-2.0", "sc:name": "HTSFilter", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HTSFilter.html", "sc:version": "1.14.1" diff --git a/data/htsint/htsintbioschemas.jsonld b/data/htsint/htsintbioschemas.jsonld index 39ad4609f1250..5f1acfc522e1c 100644 --- a/data/htsint/htsintbioschemas.jsonld +++ b/data/htsint/htsintbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Python package used to create gene sets for the study of high-throughput sequencing data.", "sc:name": "htsint", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ajrichards.github.io/htsint/" } \ No newline at end of file diff --git a/data/htslib/htslibbioschemas.jsonld b/data/htslib/htslibbioschemas.jsonld index e6b3615cf9ef7..462303bb56106 100644 --- a/data/htslib/htslibbioschemas.jsonld +++ b/data/htslib/htslibbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "HTSlib", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.htslib.org/" } \ No newline at end of file diff --git a/data/htssip/htssipbioschemas.jsonld b/data/htssip/htssipbioschemas.jsonld index 1554e2fc3e167..66badb80106d0 100644 --- a/data/htssip/htssipbioschemas.jsonld +++ b/data/htssip/htssipbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) data. Analyses include high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP).", "sc:name": "HTSSIP", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/HTSSIP/index.html" } \ No newline at end of file diff --git a/data/htsvi/htsvibioschemas.jsonld b/data/htsvi/htsvibioschemas.jsonld index 61a7188c9b730..b7e642459fd9f 100644 --- a/data/htsvi/htsvibioschemas.jsonld +++ b/data/htsvi/htsvibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Exploratory data analysis and visualization of arrayed high-throughput screens.", "sc:name": "HTSvi", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/boutroslab/HTSvis" } \ No newline at end of file diff --git a/data/htsvis/htsvisbioschemas.jsonld b/data/htsvis/htsvisbioschemas.jsonld index d036417abad3a..42050ab3ae927 100644 --- a/data/htsvis/htsvisbioschemas.jsonld +++ b/data/htsvis/htsvisbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Exploratory data analysis and visualization of arrayed high-throughput screens.", "sc:name": "HTSvis", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://htsvis.dkfz.de/HTSvis/" } \ No newline at end of file diff --git a/data/httmm/httmmbioschemas.jsonld b/data/httmm/httmmbioschemas.jsonld index 80d294937f67a..92020a4f9227b 100644 --- a/data/httmm/httmmbioschemas.jsonld +++ b/data/httmm/httmmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Package designed for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree.", "sc:name": "HTTMM", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://page.amss.ac.cn/shihua.zhang/software.html" } \ No newline at end of file diff --git a/data/hubba/hubbabioschemas.jsonld b/data/hubba/hubbabioschemas.jsonld index 0de5198a5a853..b1a9a79ab6e75 100644 --- a/data/hubba/hubbabioschemas.jsonld +++ b/data/hubba/hubbabioschemas.jsonld @@ -13,18 +13,18 @@ "biotools:primaryContact": [ "Hsin-Hung Wu", "Chia-Hao Chin", + "Chung-Yen Lin", "Shu-Hwa Chen", - "Chin-Wen Ho", - "Chung-Yen Lin" + "Chin-Wen Ho" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:18503085", "sc:description": "Hub Objects Analyzer or Hubba is a web-based service for characterizing nodes of importance within a protein interactome data set.", "sc:name": "Hubba", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://hub.iis.sinica.edu.tw/Hubba" } \ No newline at end of file diff --git a/data/hubmed/hubmedbioschemas.jsonld b/data/hubmed/hubmedbioschemas.jsonld index e5f6c65b4e3ad..5c25106985fef 100644 --- a/data/hubmed/hubmedbioschemas.jsonld +++ b/data/hubmed/hubmedbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organising and gathering information from the biomedical literature.", "sc:name": "HubMed", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.hubmed.org/" } \ No newline at end of file diff --git a/data/hudsen/hudsenbioschemas.jsonld b/data/hudsen/hudsenbioschemas.jsonld index 76051b9a640ec..c1198d25b9629 100644 --- a/data/hudsen/hudsenbioschemas.jsonld +++ b/data/hudsen/hudsenbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC2967454", - "pubmed:20979583", { "@id": "https://doi.org/10.1111/j.1469-7580.2010.01290.x" - } + }, + "pubmed:20979583", + "pmcid:PMC2967454" ], "sc:description": "Atlas pages that are unique in containing digital 3D models of human developmental stages, organ specific gene expression datasets as well as annotated histology sections.", "sc:featureList": { @@ -31,8 +31,8 @@ "sc:name": "HuDSeN atlas and spatial gene expression database", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.hudsen.org/" } diff --git a/data/huf-zinc/huf-zincbioschemas.jsonld b/data/huf-zinc/huf-zincbioschemas.jsonld index 9e321b7f6421f..31b01d93a5f26 100644 --- a/data/huf-zinc/huf-zincbioschemas.jsonld +++ b/data/huf-zinc/huf-zincbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "HMM-based web server for prediction of the novel, as well as conventional, zinc finger motifs in protein sequences.", "sc:name": "HUF-ZINC", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://mendel.bii.a-star.edu.sg/METHODS/hufzinc/" } \ No newline at end of file diff --git a/data/hulk/hulkbioschemas.jsonld b/data/hulk/hulkbioschemas.jsonld index 563a76d6a59a3..b71bcafaab860 100644 --- a/data/hulk/hulkbioschemas.jsonld +++ b/data/hulk/hulkbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s40168-019-0653-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/HULK", "@type": "sc:SoftwareApplication", @@ -28,23 +24,27 @@ "sc:description": "Histosketching Using Little Kmers (HULK) - tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.", "sc:featureList": [ { - "@id": "edam:operation_3472" + "@id": "edam:operation_3435" }, { - "@id": "edam:operation_3798" + "@id": "edam:operation_3472" }, { - "@id": "edam:operation_3435" + "@id": "edam:operation_3798" } ], "sc:license": "Other", "sc:name": "HULK", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/will-rowe/hulk" + }, + { + "@id": "https://doi.org/10.1186/s40168-019-0653-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/human_splicing_finder/human_splicing_finderbioschemas.jsonld b/data/human_splicing_finder/human_splicing_finderbioschemas.jsonld index d5dc11c374f1e..0572e288f3a42 100644 --- a/data/human_splicing_finder/human_splicing_finderbioschemas.jsonld +++ b/data/human_splicing_finder/human_splicing_finderbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The Human Splicing Finder (HSF) system combines 12 different algorithms to identify and predict mutations’ effect on splicing motifs including the acceptor and donor splice sites, the branch point and auxiliary sequences known to either enhance or repress splicing: Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS).", "sc:name": "Human Splicing Finder", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.umd.be/HSF3/" } \ No newline at end of file diff --git a/data/humcfs/humcfsbioschemas.jsonld b/data/humcfs/humcfsbioschemas.jsonld index a06fdf1b5ea4d..8dbf11689a1b8 100644 --- a/data/humcfs/humcfsbioschemas.jsonld +++ b/data/humcfs/humcfsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Manually curated database of human chromosomal fragile sites. HumCFS provides useful information on fragile sites such as coordinates on the chromosome, cytoband, their chemical inducers and frequency of fragile site (rare or common), genes and miRNAs lying in fragile sites.", "sc:name": "HumCFS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://webs.iiitd.edu.in/raghava/humcfs/index.html" } \ No newline at end of file diff --git a/data/hupho/huphobioschemas.jsonld b/data/hupho/huphobioschemas.jsonld index 7679b02e0a00d..352ec1cbd1ca1 100644 --- a/data/hupho/huphobioschemas.jsonld +++ b/data/hupho/huphobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-9528-6018", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/hupho", "@type": "sc:SoftwareApplication", @@ -29,9 +33,9 @@ "sc:description": "Online web resource for recovering information about human phosphatases.", "sc:name": "Hupho", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy", @@ -39,10 +43,6 @@ ], "sc:url": "http://hupho.uniroma2.it", "sc:version": "1" - }, - { - "@id": "https://orcid.org/0000-0002-9528-6018", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/hx-express/hx-expressbioschemas.jsonld b/data/hx-express/hx-expressbioschemas.jsonld index 3b5cbece30b4c..fdc8765d659b6 100644 --- a/data/hx-express/hx-expressbioschemas.jsonld +++ b/data/hx-express/hx-expressbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "GPL-2.0", "sc:name": "HX-Express", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.hxms.com/HXExpress/", "sc:version": "v2" diff --git a/data/hybridcheck/hybridcheckbioschemas.jsonld b/data/hybridcheck/hybridcheckbioschemas.jsonld index 93f711ca2841f..233783212fbe7 100644 --- a/data/hybridcheck/hybridcheckbioschemas.jsonld +++ b/data/hybridcheck/hybridcheckbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Software package to visualise the recombination signal in large DNA sequence dataset, and it can be used to analyse recombination, genetic introgression, hybridisation and horizontal gene transfer.", "sc:name": "HybridCheck", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/BenJWard/HybridCheck" diff --git a/data/hybridmtest/bioconda_hybridmtest.yaml b/data/hybridmtest/bioconda_hybridmtest.yaml index 0c851c92e07b3..72d6385938ed4 100644 --- a/data/hybridmtest/bioconda_hybridmtest.yaml +++ b/data/hybridmtest/bioconda_hybridmtest.yaml @@ -10,7 +10,6 @@ description: Performs hybrid multiple testing that incorporates method selection home: https://bioconductor.org/packages/3.10/bioc/html/HybridMTest.html identifiers: - biotools:hybridmtest -- doi:10.1038/nmeth.3252 license: GPL Version 2 or later license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hybridmtest diff --git a/data/hybridmtest/hybridmtestbioschemas.jsonld b/data/hybridmtest/hybridmtestbioschemas.jsonld index 8f809db7b373e..29987bff7ca8b 100644 --- a/data/hybridmtest/hybridmtestbioschemas.jsonld +++ b/data/hybridmtest/hybridmtestbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "HybridMTest", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/HybridMTest.html", "sc:version": "1.18.0" diff --git a/data/hybtrack/hybtrackbioschemas.jsonld b/data/hybtrack/hybtrackbioschemas.jsonld index ebd6cf88c8151..8ce2e8583468d 100644 --- a/data/hybtrack/hybtrackbioschemas.jsonld +++ b/data/hybtrack/hybtrackbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A hybrid single particle tracking software using manual and automatic detection of dim signals.", "sc:name": "HybTrack", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/bhlee1117/HybTrack" } \ No newline at end of file diff --git a/data/hyddb/hyddbbioschemas.jsonld b/data/hyddb/hyddbbioschemas.jsonld index 06b65816b86f7..fb317157ac1f7 100644 --- a/data/hyddb/hyddbbioschemas.jsonld +++ b/data/hyddb/hyddbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Provides access to an accurate classifier for hydrogenase sequences and a curated database of hydrogenases by known type.", "sc:name": "HydDB", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://services.birc.au.dk/hyddb", diff --git a/data/hyden/hydenbioschemas.jsonld b/data/hyden/hydenbioschemas.jsonld index 8fe8388cec6ac..d54486da98a7c 100644 --- a/data/hyden/hydenbioschemas.jsonld +++ b/data/hyden/hydenbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/hyden", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Chaim Linhart", - "Ron Shamir" + "Ron Shamir", + "Chaim Linhart" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:17951798", diff --git a/data/hydpred/hydpredbioschemas.jsonld b/data/hydpred/hydpredbioschemas.jsonld index 7048447ab5ac3..7e81d0807c28c 100644 --- a/data/hydpred/hydpredbioschemas.jsonld +++ b/data/hydpred/hydpredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease.", "sc:name": "HydPred", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://lishuyan.lzu.edu.cn/hydpred/" diff --git a/data/hydrogen_bondifier/hydrogen_bondifierbioschemas.jsonld b/data/hydrogen_bondifier/hydrogen_bondifierbioschemas.jsonld index 61021f434954d..a3177c0c7d14e 100644 --- a/data/hydrogen_bondifier/hydrogen_bondifierbioschemas.jsonld +++ b/data/hydrogen_bondifier/hydrogen_bondifierbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "hydrogen_bondifier", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/jtprince/hydrogen_bondifier" } \ No newline at end of file diff --git a/data/hydrophobicity/hydrophobicitybioschemas.jsonld b/data/hydrophobicity/hydrophobicitybioschemas.jsonld index c758d7ee61623..336a2f695c5a0 100644 --- a/data/hydrophobicity/hydrophobicitybioschemas.jsonld +++ b/data/hydrophobicity/hydrophobicitybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Hydrophobicity", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://athena.bioc.uvic.ca/virology-ca-tools/hydrophobicity/" } \ No newline at end of file diff --git a/data/hyfi/hyfibioschemas.jsonld b/data/hyfi/hyfibioschemas.jsonld index 6feb4256d4fb3..2e2268400c96c 100644 --- a/data/hyfi/hyfibioschemas.jsonld +++ b/data/hyfi/hyfibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Identifies primer and microarray probe binding sites in genomic DNA.", "sc:name": "hyfi", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://hyfi.sourceforge.net/" } \ No newline at end of file diff --git a/data/hype/hypebioschemas.jsonld b/data/hype/hypebioschemas.jsonld index 8ed181a21769f..386c8442136f3 100644 --- a/data/hype/hypebioschemas.jsonld +++ b/data/hype/hypebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Helps in the identification and classification of novel peptidoglycan hydrolases from complete genomic or metagenomic ORFs.", "sc:name": "HyPe", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://metabiosys.iiserb.ac.in/hype/" diff --git a/data/hypercldb/hypercldbbioschemas.jsonld b/data/hypercldb/hypercldbbioschemas.jsonld index d056aee8c14f9..6a468205b186b 100644 --- a/data/hypercldb/hypercldbbioschemas.jsonld +++ b/data/hypercldb/hypercldbbioschemas.jsonld @@ -9,38 +9,34 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-4694-3883", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/hypercldb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Maria Assunta Manniello", { "@id": "http://orcid.org/0000-0003-4694-3883" - } + }, + "Maria Assunta Manniello" ], "sc:additionalType": "Web application", "sc:author": [ - "Paolo Romano", "Massimiliano Armento", - "Beatrice Iannotta", - "Domenico Marra" + "Domenico Marra", + "Paolo Romano", + "Beatrice Iannotta" ], "sc:citation": [ - "pubmed:18927105", - "pmcid:PMC2686526", - "pubmed:7763741", { "@id": "https://doi.org/10.1093/nar/gkn730" - } + }, + "pubmed:18927105", + "pubmed:7763741", + "pmcid:PMC2686526" ], "sc:contributor": [ "Leonardo Santi", - "Barbara Parodi", "Tiziana Ruzzon", + "Barbara Parodi", "Ottavia Aresu" ], "sc:description": "The hypertextual version of the Cell Line Database (CLDB), which is not directly accessible, a collection of information on human and animal cell lines available from some of the main European cell banks and many Italian research laboratories", @@ -50,6 +46,10 @@ "sc:url": "http://bioinformatics.hsanmartino.it/hypercldb/", "sc:version": "4.0.201503" }, + { + "@id": "http://orcid.org/0000-0003-4694-3883", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/nar/gkn730", "@type": "sc:CreativeWork" diff --git a/data/hyperdraw/bioconda_hyperdraw.yaml b/data/hyperdraw/bioconda_hyperdraw.yaml index 889c54b76c336..7e6890de9356e 100644 --- a/data/hyperdraw/bioconda_hyperdraw.yaml +++ b/data/hyperdraw/bioconda_hyperdraw.yaml @@ -3,7 +3,6 @@ description: Functions for visualizing hypergraphs. home: https://bioconductor.org/packages/3.10/bioc/html/hyperdraw.html identifiers: - biotools:hyperdraw -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hyperdraw diff --git a/data/hyperdraw/hyperdrawbioschemas.jsonld b/data/hyperdraw/hyperdrawbioschemas.jsonld index 88929d22a55c9..e0fe965206005 100644 --- a/data/hyperdraw/hyperdrawbioschemas.jsonld +++ b/data/hyperdraw/hyperdrawbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "hyperdraw", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hyperdraw.html", "sc:version": "1.26.0" diff --git a/data/hypergeny/hypergenybioschemas.jsonld b/data/hypergeny/hypergenybioschemas.jsonld index 69070ff6ddadf..1d36bd0e6c13c 100644 --- a/data/hypergeny/hypergenybioschemas.jsonld +++ b/data/hypergeny/hypergenybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/hypergeny", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", "Desktop application", + "Command-line tool", "Web application" ], "sc:description": "HYPERbolic phyloGENY viewer allows hyperbolic visualisation of very large tree structures.", diff --git a/data/hypergraph/bioconda_hypergraph.yaml b/data/hypergraph/bioconda_hypergraph.yaml index c7391147bc4bf..b384e73094f09 100644 --- a/data/hypergraph/bioconda_hypergraph.yaml +++ b/data/hypergraph/bioconda_hypergraph.yaml @@ -4,7 +4,6 @@ description: A package that implements some simple capabilities for representing home: https://bioconductor.org/packages/3.10/bioc/html/hypergraph.html identifiers: - biotools:hypergraph -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-hypergraph summary: A package providing hypergraph data structures diff --git a/data/hypergraph/hypergraphbioschemas.jsonld b/data/hypergraph/hypergraphbioschemas.jsonld index 89b43c156e3e4..fe9388b254bad 100644 --- a/data/hypergraph/hypergraphbioschemas.jsonld +++ b/data/hypergraph/hypergraphbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "hypergraph", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/hypergraph.html", "sc:version": "1.46.0" diff --git a/data/hypergraph_dynamic_correlation/hypergraph_dynamic_correlationbioschemas.jsonld b/data/hypergraph_dynamic_correlation/hypergraph_dynamic_correlationbioschemas.jsonld index ab4119f5f78e6..7d971c2fdff68 100644 --- a/data/hypergraph_dynamic_correlation/hypergraph_dynamic_correlationbioschemas.jsonld +++ b/data/hypergraph_dynamic_correlation/hypergraph_dynamic_correlationbioschemas.jsonld @@ -21,30 +21,30 @@ }, "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC6530038", - "pubmed:31117943", { "@id": "https://doi.org/10.1186/S12864-019-5787-X" - } + }, + "pubmed:31117943", + "pmcid:PMC6530038" ], "sc:description": "Method to construct module-level three-way interaction networks. The method is able to present integrative uniform hypergraphs to reflect the global dynamic correlation pattern in the biological system, providing guidance to down-stream gene triplet-level analyses.", "sc:featureList": [ { - "@id": "edam:operation_3766" + "@id": "edam:operation_3501" }, { "@id": "edam:operation_3463" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_3766" } ], "sc:license": "MIT", "sc:name": "Hypergraph Dynamic Correlation", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/yunchuankong/HypergraphDynamicCorrelation" }, diff --git a/data/hyperlasso/hyperlassobioschemas.jsonld b/data/hyperlasso/hyperlassobioschemas.jsonld index cf6e526c95048..f7d8f4c5205a7 100644 --- a/data/hyperlasso/hyperlassobioschemas.jsonld +++ b/data/hyperlasso/hyperlassobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software of simultaneous analysis of many SNPs and covariates.", "sc:name": "HyperLasso", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.ebi.ac.uk/projects/BARGEN/" } \ No newline at end of file diff --git a/data/hyperprior/hyperpriorbioschemas.jsonld b/data/hyperprior/hyperpriorbioschemas.jsonld index 9e56249ad9e40..bb1625e2fff3e 100644 --- a/data/hyperprior/hyperpriorbioschemas.jsonld +++ b/data/hyperprior/hyperpriorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "HyperPrior", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://compbio.cs.umn.edu/HyperPrior/" } \ No newline at end of file diff --git a/data/hypertree/hypertreebioschemas.jsonld b/data/hypertree/hypertreebioschemas.jsonld index eedcf8604ba4d..60a4f2741f3b4 100644 --- a/data/hypertree/hypertreebioschemas.jsonld +++ b/data/hypertree/hypertreebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "HYPERTREE is a Java phylogenetic tree viewer, with a hyperbolic (‘fish-eye’) view and editing abilities that help in managing very large trees.", "sc:name": "HyperTree", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://kinase.com/tools/HyperTree.html", "sc:version": "1.2.2" diff --git a/data/hyphy/hyphybioschemas.jsonld b/data/hyphy/hyphybioschemas.jsonld index f76e9f72c80f3..06d6cc044f0c4 100644 --- a/data/hyphy/hyphybioschemas.jsonld +++ b/data/hyphy/hyphybioschemas.jsonld @@ -11,12 +11,12 @@ "@id": "https://bio.tools/HyPhy", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:author": [ - "Steven Weaver", "Sergei L Kosakovsky Pond", + "Steven Weaver", "Art FY Poon" ], "sc:citation": "pubmed:30298394", @@ -24,9 +24,9 @@ "sc:license": "Unlicense", "sc:name": "HyPhy", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://hyphy.org" } \ No newline at end of file diff --git a/data/hypocotyl-unet/hypocotyl-unetbioschemas.jsonld b/data/hypocotyl-unet/hypocotyl-unetbioschemas.jsonld index 22f66f7f9acee..14309df0d5690 100644 --- a/data/hypocotyl-unet/hypocotyl-unetbioschemas.jsonld +++ b/data/hypocotyl-unet/hypocotyl-unetbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Unlicense", "sc:name": "hypocotyl-UNet", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/biomag-lab/hypocotyl-UNet" } \ No newline at end of file diff --git a/data/hypoxiadb/hypoxiadbbioschemas.jsonld b/data/hypoxiadb/hypoxiadbbioschemas.jsonld index 29e84cf9edc20..e32a1878a3610 100644 --- a/data/hypoxiadb/hypoxiadbbioschemas.jsonld +++ b/data/hypoxiadb/hypoxiadbbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Pankaj Khurana", "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:24178989", { "@id": "https://doi.org/10.1093/database/bat074" }, - "pmcid:PMC3813937", - "pubmed:24178989" + "pmcid:PMC3813937" ], "sc:description": "Manually-curated non-redundant catalogue of human hypoxia-regulated proteins with a goal of collecting proteins whose expression patterns are altered in hypoxic conditions.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "HypoxiaDB", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.hypoxiadb.com/hypoxiadb.html" diff --git a/data/hysp/hyspbioschemas.jsonld b/data/hysp/hyspbioschemas.jsonld index 7ee1c3e96be7f..604ad139924b7 100644 --- a/data/hysp/hyspbioschemas.jsonld +++ b/data/hysp/hyspbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Other", "sc:name": "Hyper-Spectral Phasors (HySP)", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioimaging.usc.edu/software.html" } \ No newline at end of file diff --git a/data/hzanalyzer/hzanalyzerbioschemas.jsonld b/data/hzanalyzer/hzanalyzerbioschemas.jsonld index 324574a651b41..b547eceecf04b 100644 --- a/data/hzanalyzer/hzanalyzerbioschemas.jsonld +++ b/data/hzanalyzer/hzanalyzerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "hzAnalyzer", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://emu.src.riken.jp/hzAnalyzer/" } \ No newline at end of file diff --git a/data/i-gsea4gwas/i-gsea4gwasbioschemas.jsonld b/data/i-gsea4gwas/i-gsea4gwasbioschemas.jsonld index 2ec3f8153a6f8..596eae112e704 100644 --- a/data/i-gsea4gwas/i-gsea4gwasbioschemas.jsonld +++ b/data/i-gsea4gwas/i-gsea4gwasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web server for identification of pathways and gene sets associated with traits. An improved gene set enrichment analysis (i-GSEA) is applied to genome wide association studies (GWAS).", "sc:name": "i-GSEA4GWAS", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://gsea4gwas.psych.ac.cn" diff --git a/data/i-mutant/i-mutantbioschemas.jsonld b/data/i-mutant/i-mutantbioschemas.jsonld index 31f2b6239cf76..ff04589bc1e8f 100644 --- a/data/i-mutant/i-mutantbioschemas.jsonld +++ b/data/i-mutant/i-mutantbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Neural Network based Predictor of Protein stability Changes upon Single Point Mutation from the Protein Structure.", "sc:name": "I-MUTANT", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "http://folding.biofold.org/i-mutant/i-mutant2.0.html", diff --git a/data/i-mutant_suite/i-mutant_suitebioschemas.jsonld b/data/i-mutant_suite/i-mutant_suitebioschemas.jsonld index 79fa15a813345..217afafd25a55 100644 --- a/data/i-mutant_suite/i-mutant_suitebioschemas.jsonld +++ b/data/i-mutant_suite/i-mutant_suitebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Predictor of effects of single point protein mutation on its stability from protein sequences or structures.", "sc:name": "I-MUTANT Suite", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant3.0/I-Mutant3.0.cgi", diff --git a/data/i-pv/i-pvbioschemas.jsonld b/data/i-pv/i-pvbioschemas.jsonld index 7e4306a5ddbeb..b4bf0da364d62 100644 --- a/data/i-pv/i-pvbioschemas.jsonld +++ b/data/i-pv/i-pvbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software that uses Circos to render interactive images for protein sequence visualization.", "sc:name": "I-PV", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.i-pv.org/" } \ No newline at end of file diff --git a/data/i-tasser-mr/i-tasser-mrbioschemas.jsonld b/data/i-tasser-mr/i-tasser-mrbioschemas.jsonld index 2e4f9b9135ad2..f602075c4dfbc 100644 --- a/data/i-tasser-mr/i-tasser-mrbioschemas.jsonld +++ b/data/i-tasser-mr/i-tasser-mrbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkx349", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/i-tasser-mr", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28472524", { "@id": "https://doi.org/10.1093/nar/gkx349" }, - "pmcid:PMC5793832" + "pmcid:PMC5793832", + "pubmed:28472524" ], "sc:description": "Automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation", "sc:featureList": { @@ -26,10 +30,6 @@ }, "sc:name": "I-TASSER-MR", "sc:url": "http://zhanglab.ccmb.med.umich.edu/I-TASSER-MR" - }, - { - "@id": "https://doi.org/10.1093/nar/gkx349", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/i-tasser/i-tasserbioschemas.jsonld b/data/i-tasser/i-tasserbioschemas.jsonld index f8ce9073b6932..a5aac56653294 100644 --- a/data/i-tasser/i-tasserbioschemas.jsonld +++ b/data/i-tasser/i-tasserbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Best in tertiary structure prediction (as ‘Zhang-Server’) in the community-wide blind benchmarks CASP7 and CASP8. It uses mainly profile-profile comparison to identify templates and alignments for deriving distance constraints. Its power lies in how it combines the distance constraints from up to the 50 best-ranked templates. It performs some knowledge-based free modelling in regions without any template-based information.", "sc:name": "I-TASSER", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://zhanglab.ccmb.med.umich.edu/I-TASSER/" } \ No newline at end of file diff --git a/data/i-tracker/i-trackerbioschemas.jsonld b/data/i-tracker/i-trackerbioschemas.jsonld index 982bd438803e9..b595b085b98ad 100644 --- a/data/i-tracker/i-trackerbioschemas.jsonld +++ b/data/i-tracker/i-trackerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-1.0", "sc:name": "i-Tracker", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://bessantlab.org/software/i-tracker/" } \ No newline at end of file diff --git a/data/i2d/i2dbioschemas.jsonld b/data/i2d/i2dbioschemas.jsonld index 61f12910d4747..cfc0075014634 100644 --- a/data/i2d/i2dbioschemas.jsonld +++ b/data/i2d/i2dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "To faciliate experimentation and integrated computational analysis with model organism PPI networks, we have integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database.", "sc:name": "I2D", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://ophid.utoronto.ca/ophidv2.204/" } \ No newline at end of file diff --git a/data/i2i-siteengine/i2i-siteenginebioschemas.jsonld b/data/i2i-siteengine/i2i-siteenginebioschemas.jsonld index 1502815c737f4..59ac9b2a5afd7 100644 --- a/data/i2i-siteengine/i2i-siteenginebioschemas.jsonld +++ b/data/i2i-siteengine/i2i-siteenginebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.", "sc:name": "I2I-SiteEngine", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/" } \ No newline at end of file diff --git a/data/iacp/iacpbioschemas.jsonld b/data/iacp/iacpbioschemas.jsonld index edebfb68a1003..67b0413d12714 100644 --- a/data/iacp/iacpbioschemas.jsonld +++ b/data/iacp/iacpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This web-server was developed to identify the anticancer peptides based on the sequence information.", "sc:name": "iACP", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://lin.uestc.edu.cn/server/iACP" } \ No newline at end of file diff --git a/data/iadmix/iadmixbioschemas.jsonld b/data/iadmix/iadmixbioschemas.jsonld index 4c3bab21da6b9..b7091b8db3eae 100644 --- a/data/iadmix/iadmixbioschemas.jsonld +++ b/data/iadmix/iadmixbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Program to estimate individual admixture proportions from DNA sequencing experiments (exome sequencing, targeted sequencing, low coverage whole-genome sequencing or genotyping)", "sc:name": "iAdmix", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://bansal-lab.github.io/software/iadmix.html", "sc:version": "0.2" diff --git a/data/iambee/iambeebioschemas.jsonld b/data/iambee/iambeebioschemas.jsonld index 1d29c0892d974..0bae4b8614795 100644 --- a/data/iambee/iambeebioschemas.jsonld +++ b/data/iambee/iambeebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-9998-2408", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/IAMBEE", "@type": "sc:SoftwareApplication", @@ -24,22 +20,22 @@ "Web service" ], "sc:citation": [ + "pmcid:PMC6602435", + "pubmed:31127271", { "@id": "https://doi.org/10.1093/NAR/GKZ451" - }, - "pubmed:31127271", - "pmcid:PMC6602435" + } ], "sc:description": "Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE) - web server designed for network-based genotype-phenotype mapping of clonal populations that display the same focal phenotype.", "sc:featureList": [ - { - "@id": "edam:operation_3196" - }, { "@id": "edam:operation_3280" }, { "@id": "edam:operation_3216" + }, + { + "@id": "edam:operation_3196" } ], "sc:license": "Unlicense", @@ -54,6 +50,10 @@ { "@id": "https://doi.org/10.1093/NAR/GKZ451", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-9998-2408", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/iamp-2l/iamp-2lbioschemas.jsonld b/data/iamp-2l/iamp-2lbioschemas.jsonld index 0b9c44fbabdc3..35a52c4aaf0ae 100644 --- a/data/iamp-2l/iamp-2lbioschemas.jsonld +++ b/data/iamp-2l/iamp-2lbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This web-server is a two-level multi-label predictor. It can be used to identify an uncharacterized peptide as antimicrobial peptide (AMP) or non-AMP according to its sequences information alone.", "sc:name": "iAMP-2L", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.jci-bioinfo.cn/iAMP-2L" diff --git a/data/iamxt/iamxtbioschemas.jsonld b/data/iamxt/iamxtbioschemas.jsonld index c2c908c905aff..4de0bec500cfb 100644 --- a/data/iamxt/iamxtbioschemas.jsonld +++ b/data/iamxt/iamxtbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "BSD-2-Clause", "sc:name": "iamxt", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/ElsevierSoftwareX/SOFTX-D-15-00049", "sc:version": "v0.1" diff --git a/data/iaseq/iaseqbioschemas.jsonld b/data/iaseq/iaseqbioschemas.jsonld index 2d83fb8d48b73..a4454a281122b 100644 --- a/data/iaseq/iaseqbioschemas.jsonld +++ b/data/iaseq/iaseqbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "iASeq", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iASeq.html", "sc:version": "1.18.0" diff --git a/data/ibbig/ibbigbioschemas.jsonld b/data/ibbig/ibbigbioschemas.jsonld index e3c63c079875a..8cf7d92dac877 100644 --- a/data/ibbig/ibbigbioschemas.jsonld +++ b/data/ibbig/ibbigbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "iBBiG", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iBBiG.html", "sc:version": "1.18.0" diff --git a/data/ibdmap/ibdmapbioschemas.jsonld b/data/ibdmap/ibdmapbioschemas.jsonld index 87e9a7f079e9e..e55c5ae8ede1b 100644 --- a/data/ibdmap/ibdmapbioschemas.jsonld +++ b/data/ibdmap/ibdmapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Factorial HMM based algorithm. Several models are supported in this implementation, including both the standard model and the 4-track model which uses a first order Markovian model for the LD process in a subset of the founders.", "sc:name": "IBDmap", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo.cs.technion.ac.il/IBDmap/" } \ No newline at end of file diff --git a/data/ibdsim/ibdsimbioschemas.jsonld b/data/ibdsim/ibdsimbioschemas.jsonld index 14cbab099ce1a..2c863bed3f8ba 100644 --- a/data/ibdsim/ibdsimbioschemas.jsonld +++ b/data/ibdsim/ibdsimbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Computer package for the simulation of genotypic data under general isolation by distance models.", "sc:name": "IBDSim", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://raphael.leblois.free.fr/#softwares" } \ No newline at end of file diff --git a/data/ibh/bioconda_ibh.yaml b/data/ibh/bioconda_ibh.yaml index 449cfdca17ce2..b4b4ecc8e2c16 100644 --- a/data/ibh/bioconda_ibh.yaml +++ b/data/ibh/bioconda_ibh.yaml @@ -6,7 +6,6 @@ description: This package contains methods for calculating Interaction Based Hom home: https://bioconductor.org/packages/3.10/bioc/html/ibh.html identifiers: - biotools:ibh -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-ibh diff --git a/data/ibh/ibhbioschemas.jsonld b/data/ibh/ibhbioschemas.jsonld index 489a45c7c5dca..5f4c6bd8a071f 100644 --- a/data/ibh/ibhbioschemas.jsonld +++ b/data/ibh/ibhbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "ibh", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ibh.html", "sc:version": "1.22.0" diff --git a/data/ibig/ibigbioschemas.jsonld b/data/ibig/ibigbioschemas.jsonld index a0447f89a2eae..3bcd337d74790 100644 --- a/data/ibig/ibigbioschemas.jsonld +++ b/data/ibig/ibigbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-based tool for building and visualizing interaction network of gene and gene set.", "sc:name": "iBIG", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://lei.big.ac.cn/ibig" } \ No newline at end of file diff --git a/data/ibis/ibisbioschemas.jsonld b/data/ibis/ibisbioschemas.jsonld index 444afe6fe04d8..cd1863f224dae 100644 --- a/data/ibis/ibisbioschemas.jsonld +++ b/data/ibis/ibisbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Ibis (Improved base identification system), is an accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. Ibis is faster and makes fewer assumptions about chemistry and technology", "sc:name": "Ibis", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioinf.eva.mpg.de/Ibis/" } \ No newline at end of file diff --git a/data/ibis_ncbi/ibis_ncbibioschemas.jsonld b/data/ibis_ncbi/ibis_ncbibioschemas.jsonld index 88c813cfea15e..e9bd849871c44 100644 --- a/data/ibis_ncbi/ibis_ncbibioschemas.jsonld +++ b/data/ibis_ncbi/ibis_ncbibioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins. It provides annotations for different types of binding partners (protein, chemical, nucleic acid and peptides), and facilitates the mapping of a comprehensive biomolecular interaction network for a given protein query.", "sc:name": "IBIS", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi" } \ No newline at end of file diff --git a/data/ibiss/ibissbioschemas.jsonld b/data/ibiss/ibissbioschemas.jsonld index aec53c7afc88a..dc3e3f88f7f95 100644 --- a/data/ibiss/ibissbioschemas.jsonld +++ b/data/ibiss/ibissbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "IBiSS", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://ibiss.igbmc.fr/" diff --git a/data/ibmq/ibmqbioschemas.jsonld b/data/ibmq/ibmqbioschemas.jsonld index 9bd55e8d4ce6a..27fa25d432bd6 100644 --- a/data/ibmq/ibmqbioschemas.jsonld +++ b/data/ibmq/ibmqbioschemas.jsonld @@ -9,27 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-2626-4584", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1515/1544-6115.1760", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ibmq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Greg Imholte", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:22850063", { "@id": "https://doi.org/10.1515/1544-6115.1760" }, + "pubmed:22850063", "pmcid:PMC4627701" ], "sc:contributor": { @@ -42,12 +34,20 @@ "sc:license": "Artistic-2.0", "sc:name": "iBMQ", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iBMQ.html", "sc:version": "1.14.0" + }, + { + "@id": "http://orcid.org/0000-0003-2626-4584", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1515/1544-6115.1760", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ibs/ibsbioschemas.jsonld b/data/ibs/ibsbioschemas.jsonld index 35497cb95b0e1..996aaa516f94d 100644 --- a/data/ibs/ibsbioschemas.jsonld +++ b/data/ibs/ibsbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/ibs", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jian Ren", - "Yu Xue" + "Yu Xue", + "Jian Ren" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:26069263", "sc:description": "Software package that can be used for representing the organization of either protein or nucleotide sequences, in a convenient, efficient and precise manner.", "sc:name": "IBS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://ibs.biocuckoo.org/" diff --git a/data/ibws_ws/ibws_wsbioschemas.jsonld b/data/ibws_ws/ibws_wsbioschemas.jsonld index 5543e97865951..fb87e1d50040d 100644 --- a/data/ibws_ws/ibws_wsbioschemas.jsonld +++ b/data/ibws_ws/ibws_wsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa compiled a suite of free web services IBWS.", "sc:name": "IBWS: IST Bioinformatics Web Services", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioinformatics.hsanmartino.it/ibws/" } \ No newline at end of file diff --git a/data/icarus/icarusbioschemas.jsonld b/data/icarus/icarusbioschemas.jsonld index 9e256411e6735..abd7e41f213d9 100644 --- a/data/icarus/icarusbioschemas.jsonld +++ b/data/icarus/icarusbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "GPL-2.0", "sc:name": "Icarus", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://quast.sourceforge.net/icarus.html" } \ No newline at end of file diff --git a/data/icataly-pseaac/icataly-pseaacbioschemas.jsonld b/data/icataly-pseaac/icataly-pseaacbioschemas.jsonld index df1c56ca2e49b..13fa9229b6450 100644 --- a/data/icataly-pseaac/icataly-pseaacbioschemas.jsonld +++ b/data/icataly-pseaac/icataly-pseaacbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server that could predict methylation sites in proteins. With the assistance of FKNN, the highlight of this tool is to employ amino acid sequence features extracted by incorporating the sequence evolution information into PseAAC via a grey system model (Grey-PSSM).", "sc:name": "iCataly-PseAAC", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.jci-bioinfo.cn/iCataly-PseAAC" } \ No newline at end of file diff --git a/data/icbn/icbnbioschemas.jsonld b/data/icbn/icbnbioschemas.jsonld index a15fa7db54e34..a0156d78d9b67 100644 --- a/data/icbn/icbnbioschemas.jsonld +++ b/data/icbn/icbnbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "icbn", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.bsse.ethz.ch/cbg/software/icbn" } \ No newline at end of file diff --git a/data/icc/iccbioschemas.jsonld b/data/icc/iccbioschemas.jsonld index 11cda681360b0..1b866e00e2fcb 100644 --- a/data/icc/iccbioschemas.jsonld +++ b/data/icc/iccbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "ICC (Indel and Carryforward Correction) is a software pipeline to analyze 454 pyrosequencing data, including read quality filtering and alignment, indel and carryforward error correction, single nucleotide variant calling, and calculation of nucleotide variant and hyplotype frequencies.", "sc:name": "ICC", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://indra.mullins.microbiol.washington.edu/ICC/", "sc:version": "2.0.1" diff --git a/data/iccare/iccarebioschemas.jsonld b/data/iccare/iccarebioschemas.jsonld index 6b2ae8995552f..cd2ca4718a5c3 100644 --- a/data/iccare/iccarebioschemas.jsonld +++ b/data/iccare/iccarebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Iccare", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genoweb.toulouse.inra.fr/iccare/index.php" } \ No newline at end of file diff --git a/data/icd-10/icd-10bioschemas.jsonld b/data/icd-10/icd-10bioschemas.jsonld index 0f856dbe52127..fa68e25b5e973 100644 --- a/data/icd-10/icd-10bioschemas.jsonld +++ b/data/icd-10/icd-10bioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "ICD-10", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.icd10data.com" } \ No newline at end of file diff --git a/data/icdi-psefpt/icdi-psefptbioschemas.jsonld b/data/icdi-psefpt/icdi-psefptbioschemas.jsonld index a1d28c204cc58..84f820b13a9c2 100644 --- a/data/icdi-psefpt/icdi-psefptbioschemas.jsonld +++ b/data/icdi-psefpt/icdi-psefptbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Independent predictor using Fuzzy K-Nearest Neighbor algorithm, used to predict ion channel-drug interactions. It can be used to identify a pair as Ion channel-drug pair or non-Ion channel drug pair according to the sequence of protein and the molecular fingerprint of drug.", "sc:name": "iCDI-PseFpt", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.jci-bioinfo.cn/iCDI-PseFpt/" } \ No newline at end of file diff --git a/data/ice/icebioschemas.jsonld b/data/ice/icebioschemas.jsonld index 982dff9408dd3..4310681bd487f 100644 --- a/data/ice/icebioschemas.jsonld +++ b/data/ice/icebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Cloud-based freely open-source DNA part, plasmid, microbial strain, and Arabidopsis seed repository with physical sample tracking capabilities.", "sc:name": "ICE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/JBEI/ice" } \ No newline at end of file diff --git a/data/iceberg/icebergbioschemas.jsonld b/data/iceberg/icebergbioschemas.jsonld index c8a42082c7f7c..63aa5cbac300a 100644 --- a/data/iceberg/icebergbioschemas.jsonld +++ b/data/iceberg/icebergbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-based resource for integrative and conjugative elements (ICEs) found in bacteria.", "sc:name": "ICEberg", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://db-mml.sjtu.edu.cn/ICEberg/" } \ No newline at end of file diff --git a/data/icens/bioconda_icens.yaml b/data/icens/bioconda_icens.yaml index 65e6d79dc446e..1df61685a9eea 100644 --- a/data/icens/bioconda_icens.yaml +++ b/data/icens/bioconda_icens.yaml @@ -3,7 +3,6 @@ description: Many functions for computing the NPMLE for censored and truncated d home: https://bioconductor.org/packages/3.10/bioc/html/Icens.html identifiers: - biotools:icens -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-icens summary: NPMLE for Censored and Truncated Data diff --git a/data/icens/icensbioschemas.jsonld b/data/icens/icensbioschemas.jsonld index d3c0a1a1cb512..9f4a7dc0419fd 100644 --- a/data/icens/icensbioschemas.jsonld +++ b/data/icens/icensbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Many functions for computing the NPMLE for censored and truncated data.", "sc:license": "Artistic-2.0", "sc:name": "Icens", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Icens.html", "sc:version": "1.46.0" diff --git a/data/icgc_data_portal/icgc_data_portalbioschemas.jsonld b/data/icgc_data_portal/icgc_data_portalbioschemas.jsonld index e66b2770ab67b..0bbcbb57f945e 100644 --- a/data/icgc_data_portal/icgc_data_portalbioschemas.jsonld +++ b/data/icgc_data_portal/icgc_data_portalbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. Currently has data from 24 cancer projects. Open access data (eg. Somatic mutations, copy number alterations, structural rearrangements, gene expression, miRNAs). Easy to search and analyze data, construct queries across multiple data sets.", "sc:name": "ICGC Data Portal", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://dcc.icgc.org/" diff --git a/data/icheck/icheckbioschemas.jsonld b/data/icheck/icheckbioschemas.jsonld index 500225a128ec1..90d4392e79f26 100644 --- a/data/icheck/icheckbioschemas.jsonld +++ b/data/icheck/icheckbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Weiliang Qiu", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.", "sc:license": "GPL-2.0", "sc:name": "iCheck", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iCheck.html", "sc:version": "1.4.0" diff --git a/data/ichem/ichembioschemas.jsonld b/data/ichem/ichembioschemas.jsonld index 51efb1deae0ad..1becbd970dd51 100644 --- a/data/ichem/ichembioschemas.jsonld +++ b/data/ichem/ichembioschemas.jsonld @@ -15,8 +15,8 @@ "biotools:primaryContact": "Dr. Didier Rognan", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:29024463", "pmcid:PMC5901026", + "pubmed:29024463", { "@id": "https://doi.org/10.1002/cmdc.201700505" } diff --git a/data/ichet/ichetbioschemas.jsonld b/data/ichet/ichetbioschemas.jsonld index 76f2a5cece093..9c465c55f7062 100644 --- a/data/ichet/ichetbioschemas.jsonld +++ b/data/ichet/ichetbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "icHET", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/vtphan/HeteroplasmyWorkflow" } \ No newline at end of file diff --git a/data/ichip/ichipbioschemas.jsonld b/data/ichip/ichipbioschemas.jsonld index fb9d4ec5922e4..ba99740e80a30 100644 --- a/data/ichip/ichipbioschemas.jsonld +++ b/data/ichip/ichipbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Qianxing Mo", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. It can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.", "sc:license": "GPL-2.0", "sc:name": "iChip", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iChip.html", "sc:version": "1.28.0" diff --git a/data/ichseg/ichsegbioschemas.jsonld b/data/ichseg/ichsegbioschemas.jsonld index 7819286466fe3..5f2648b51cb74 100644 --- a/data/ichseg/ichsegbioschemas.jsonld +++ b/data/ichseg/ichsegbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1016/j.nicl.2017.02.007", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ichseg", "@type": "sc:SoftwareApplication", @@ -31,10 +35,6 @@ "Mac" ], "sc:url": "https://github.com/muschellij2/ichseg" - }, - { - "@id": "https://doi.org/10.1016/j.nicl.2017.02.007", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/iclabel/iclabelbioschemas.jsonld b/data/iclabel/iclabelbioschemas.jsonld index 439936854314e..384310472ba56 100644 --- a/data/iclabel/iclabelbioschemas.jsonld +++ b/data/iclabel/iclabelbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:31103785", + "pmcid:PMC6592775", { "@id": "https://doi.org/10.1016/J.NEUROIMAGE.2019.05.026" - }, - "pmcid:PMC6592775" + } ], "sc:description": "Automated electroencephalographic independent component classifier, dataset, and website.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "Unlicense", "sc:name": "ICLabel", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://iclabel.ucsd.edu/" } diff --git a/data/iclc/iclcbioschemas.jsonld b/data/iclc/iclcbioschemas.jsonld index 028b56c838362..7aea84d194bbf 100644 --- a/data/iclc/iclcbioschemas.jsonld +++ b/data/iclc/iclcbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/iclc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Maria Assunta Manniello", - "Paolo Romano" + "Paolo Romano", + "Maria Assunta Manniello" ], "sc:additionalType": "Database portal", "sc:author": "Paolo Romano", diff --git a/data/iclusterplus/iclusterplusbioschemas.jsonld b/data/iclusterplus/iclusterplusbioschemas.jsonld index 81dd09201f429..d555cc68f5d48 100644 --- a/data/iclusterplus/iclusterplusbioschemas.jsonld +++ b/data/iclusterplus/iclusterplusbioschemas.jsonld @@ -15,16 +15,16 @@ "Ronglai Shen" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Integrative clustering of multiple genomic data using a joint latent variable model.", "sc:license": "GPL-2.0", "sc:name": "iClusterPlus", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iClusterPlus.html", "sc:version": "1.10.0" diff --git a/data/icm_web/icm_webbioschemas.jsonld b/data/icm_web/icm_webbioschemas.jsonld index 67dfbab2b80fb..7eaf27268c991 100644 --- a/data/icm_web/icm_webbioschemas.jsonld +++ b/data/icm_web/icm_webbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Interactive Chromatin Modeling (ICM) web server is an interactive tool that allows users to rapidly assess nucleosome stability and fold sequences of DNA into putative chromatin templates.", "sc:name": "ICM Web", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://dna.ccs.tulane.edu/icm" } \ No newline at end of file diff --git a/data/icobra/icobrabioschemas.jsonld b/data/icobra/icobrabioschemas.jsonld index 5f2af1e0d8a34..3d081e0152600 100644 --- a/data/icobra/icobrabioschemas.jsonld +++ b/data/icobra/icobrabioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "iCOBRA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iCOBRA.html", "sc:version": "1.2.0" diff --git a/data/iconvert/iconvertbioschemas.jsonld b/data/iconvert/iconvertbioschemas.jsonld index a2986df011004..35302760d13dd 100644 --- a/data/iconvert/iconvertbioschemas.jsonld +++ b/data/iconvert/iconvertbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool).", "sc:name": "iConvert", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioinformatics.tecnoparco.org/SNPchimp/index.php/links" } \ No newline at end of file diff --git a/data/icover/icoverbioschemas.jsonld b/data/icover/icoverbioschemas.jsonld index 0b8261fbbbf03..f46b0e3d95c67 100644 --- a/data/icover/icoverbioschemas.jsonld +++ b/data/icover/icoverbioschemas.jsonld @@ -31,8 +31,8 @@ }, "sc:name": "ICoVeR", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://git.list.lu/eScience/ICoVeR" diff --git a/data/icplquant/icplquantbioschemas.jsonld b/data/icplquant/icplquantbioschemas.jsonld index ab707727bcae3..22c2ae1a350fd 100644 --- a/data/icplquant/icplquantbioschemas.jsonld +++ b/data/icplquant/icplquantbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool for processing and analyzing ICPL LC-MALDI data.", "sc:name": "ICPLQuant", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://www.biochem.mpg.de/en/rg/lottspeich/technologies/ICPLQuant" diff --git a/data/icsf/icsfbioschemas.jsonld b/data/icsf/icsfbioschemas.jsonld index 7f2fa024d471e..81cd82cadb366 100644 --- a/data/icsf/icsfbioschemas.jsonld +++ b/data/icsf/icsfbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Identify conserved structural features at sequentially degenerate locations in transcription factor binding sites. ICSF uses base-pair step parameters obtained from a collection of high-resolution DNA crystal structures to discover structural conservation that exists in the sequentially degenerate areas within a binding site and produce profiles of the structural features along the entire site.", "sc:name": "ICSF", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://zlab.bu.edu/ICSF/" } \ No newline at end of file diff --git a/data/icsnpathway/icsnpathwaybioschemas.jsonld b/data/icsnpathway/icsnpathwaybioschemas.jsonld index b4d042f2939dd..990bdea2bd451 100644 --- a/data/icsnpathway/icsnpathwaybioschemas.jsonld +++ b/data/icsnpathway/icsnpathwaybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ICSNPathway is a web tool for the identification of candidate causal SNPs and their corresponding candidate causal pathways from genome wide association studies. ISCNPathway integrates linkage disequilibrium analysis, functional SNP annotation and pathway based analysis to identify these SNPs and pathways.", "sc:name": "ICSNPathway", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://icsnpathway.psych.ac.cn/" } \ No newline at end of file diff --git a/data/ictnet2/ictnet2bioschemas.jsonld b/data/ictnet2/ictnet2bioschemas.jsonld index ad67cec1707b7..9e69b18d6130b 100644 --- a/data/ictnet2/ictnet2bioschemas.jsonld +++ b/data/ictnet2/ictnet2bioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.6836.2", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ictnet2", "@type": "sc:SoftwareApplication", "sc:additionalType": "Plug-in", "sc:citation": [ + "pmcid:PMC4706053", { "@id": "https://doi.org/10.12688/F1000RESEARCH.6836.2" }, - "pubmed:26834985", - "pmcid:PMC4706053" + "pubmed:26834985" ], "sc:description": "Integrated Complex Traits Networks. Database that allows researchers to build heterogeneous networks by integrating a variety of biological interactions, thus offering a systems-level view of human complex traits.", "sc:featureList": [ @@ -35,15 +39,11 @@ "sc:license": "MIT", "sc:name": "iCTNet2", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://apps.cytoscape.org/apps/ictnet2" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.6836.2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/icy/icybioschemas.jsonld b/data/icy/icybioschemas.jsonld index 433c144471892..ad880e923cf13 100644 --- a/data/icy/icybioschemas.jsonld +++ b/data/icy/icybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Icy", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.icy.bioimageanalysis.org/", "sc:version": "1.6.1.1" diff --git a/data/icytree/icytreebioschemas.jsonld b/data/icytree/icytreebioschemas.jsonld index 9fcb0a4ba8fa8..58d508fc7d325 100644 --- a/data/icytree/icytreebioschemas.jsonld +++ b/data/icytree/icytreebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Rapid browser-based visualization for phylogenetic trees and networks.", "sc:name": "IcyTree", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://icytree.org/" } \ No newline at end of file diff --git a/data/id-align/id-alignbioschemas.jsonld b/data/id-align/id-alignbioschemas.jsonld index 1f79057a7ca73..2114a7c94a71d 100644 --- a/data/id-align/id-alignbioschemas.jsonld +++ b/data/id-align/id-alignbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Aligns metabolite data from multiple files to single spreadsheet.", "sc:name": "ID-Align", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.ce4csb.org/applications/idalign/idalign.html" } \ No newline at end of file diff --git a/data/id_history_converter/id_history_converterbioschemas.jsonld b/data/id_history_converter/id_history_converterbioschemas.jsonld index 9788ad36f9673..4b3e375a184ac 100644 --- a/data/id_history_converter/id_history_converterbioschemas.jsonld +++ b/data/id_history_converter/id_history_converterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Convert a set of Ensembl IDs from a previous release into their current equivalents.", "sc:name": "ID History converter", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": [ diff --git a/data/idade2/idade2bioschemas.jsonld b/data/idade2/idade2bioschemas.jsonld index 87357ff5d614a..ce72950b45482 100644 --- a/data/idade2/idade2bioschemas.jsonld +++ b/data/idade2/idade2bioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/IDADE2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Carme Rissech Badallo", "Marta San-Millán", + "Carme Rissech Badallo", "Allysha Winburn" ], "sc:additionalType": [ @@ -25,8 +25,8 @@ "sc:name": "IDADE2", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bass.uib.es/~jaume/IDADE2/https/index.html" } \ No newline at end of file diff --git a/data/idbases/idbasesbioschemas.jsonld b/data/idbases/idbasesbioschemas.jsonld index ffccb5f5400dd..7b7ca2deb7755 100644 --- a/data/idbases/idbasesbioschemas.jsonld +++ b/data/idbases/idbasesbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Locus-specific databases for immunodeficiency-causing mutations.", "sc:name": "Immunodeficiency mutation databases (IDbases)", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://structure.bmc.lu.se/idbase/" } \ No newline at end of file diff --git a/data/idbps/idbpsbioschemas.jsonld b/data/idbps/idbpsbioschemas.jsonld index 889057601d9e0..62a38b94391ae 100644 --- a/data/idbps/idbpsbioschemas.jsonld +++ b/data/idbps/idbpsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool was developed for the identification of DNA binding proteins (DBPs) for proteins with known three-dimensional structure", "sc:name": "iDBPs", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://idbps.tau.ac.il/" } \ No newline at end of file diff --git a/data/idconvert/idconvertbioschemas.jsonld b/data/idconvert/idconvertbioschemas.jsonld index fd7f2037d0fdc..8a8545d27f86e 100644 --- a/data/idconvert/idconvertbioschemas.jsonld +++ b/data/idconvert/idconvertbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "idconvert", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "lumc.nl", diff --git a/data/ideal/idealbioschemas.jsonld b/data/ideal/idealbioschemas.jsonld index 68bf3134ee2f0..d6fe8429a4ec3 100644 --- a/data/ideal/idealbioschemas.jsonld +++ b/data/ideal/idealbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Collection of experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). Manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites.", "sc:name": "IDEAL", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/" } \ No newline at end of file diff --git a/data/ideal_expression/ideal_expressionbioschemas.jsonld b/data/ideal_expression/ideal_expressionbioschemas.jsonld index 199d169c61614..36921a09c4671 100644 --- a/data/ideal_expression/ideal_expressionbioschemas.jsonld +++ b/data/ideal_expression/ideal_expressionbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ideal", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ideal.html", "sc:version": "1.4.0" diff --git a/data/ideal_rna/ideal_rnabioschemas.jsonld b/data/ideal_rna/ideal_rnabioschemas.jsonld index b033a899586fb..872950ad53bd7 100644 --- a/data/ideal_rna/ideal_rnabioschemas.jsonld +++ b/data/ideal_rna/ideal_rnabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "ideal", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ideal.html", "sc:version": "1.4.0" diff --git a/data/ideoviz/bioconda_ideoviz.yaml b/data/ideoviz/bioconda_ideoviz.yaml index 5aad3108f3439..0694ba63a1d22 100644 --- a/data/ideoviz/bioconda_ideoviz.yaml +++ b/data/ideoviz/bioconda_ideoviz.yaml @@ -4,7 +4,6 @@ description: Plots data associated with arbitrary genomic intervals along chromo home: https://bioconductor.org/packages/3.10/bioc/html/IdeoViz.html identifiers: - biotools:ideoviz -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-ideoviz diff --git a/data/ideoviz/ideovizbioschemas.jsonld b/data/ideoviz/ideovizbioschemas.jsonld index d5a294e377fb2..94a95efb894fb 100644 --- a/data/ideoviz/ideovizbioschemas.jsonld +++ b/data/ideoviz/ideovizbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Shraddha Pai", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Plots data associated with arbitrary genomic intervals along chromosomal ideogram.", "sc:license": "GPL-2.0", "sc:name": "IdeoViz", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IdeoViz.html", "sc:version": "1.8.0" diff --git a/data/idep/idepbioschemas.jsonld b/data/idep/idepbioschemas.jsonld index 2655331408cf1..61c00f5d8fcf6 100644 --- a/data/idep/idepbioschemas.jsonld +++ b/data/idep/idepbioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:30567491", - "pmcid:PMC6299935", { "@id": "https://doi.org/10.1186/s12859-018-2486-6" - } + }, + "pmcid:PMC6299935" ], "sc:description": "Integrated web application for differential expression and pathway analysis of RNA-Seq.", "sc:featureList": [ @@ -27,17 +27,17 @@ "@id": "edam:operation_3680" }, { - "@id": "edam:operation_3766" + "@id": "edam:operation_3223" }, { - "@id": "edam:operation_3223" + "@id": "edam:operation_3766" } ], "sc:license": "Unlicense", "sc:name": "iDEP", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioinformatics.sdstate.edu/idep/" diff --git a/data/idepi/idepibioschemas.jsonld b/data/idepi/idepibioschemas.jsonld index 4c4f93d778cc7..57c49621c04b3 100644 --- a/data/idepi/idepibioschemas.jsonld +++ b/data/idepi/idepibioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003842", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/idepi", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC4177671", + "pubmed:25254639", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003842" - }, - "pubmed:25254639" + } ], "sc:description": "Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "GPL-3.0", "sc:name": "IDEPI", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/veg/idepi" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003842", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/idhs-dmcac/idhs-dmcacbioschemas.jsonld b/data/idhs-dmcac/idhs-dmcacbioschemas.jsonld index a6789ed45ea7e..16d144d4f0ff5 100644 --- a/data/idhs-dmcac/idhs-dmcacbioschemas.jsonld +++ b/data/idhs-dmcac/idhs-dmcacbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "iDHS-DMCAC", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/shengli0201/Datasets" } \ No newline at end of file diff --git a/data/idiogram/bioconda_idiogram.yaml b/data/idiogram/bioconda_idiogram.yaml index 8f53602b0f437..b9cb451c91f9a 100644 --- a/data/idiogram/bioconda_idiogram.yaml +++ b/data/idiogram/bioconda_idiogram.yaml @@ -3,7 +3,6 @@ description: A package for plotting genomic data by chromosomal location home: https://bioconductor.org/packages/3.10/bioc/html/idiogram.html identifiers: - biotools:idiogram -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-idiogram diff --git a/data/idiogram/idiogrambioschemas.jsonld b/data/idiogram/idiogrambioschemas.jsonld index 0388c7f4ad8be..8a131ff7ab721 100644 --- a/data/idiogram/idiogrambioschemas.jsonld +++ b/data/idiogram/idiogrambioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Karl J. Dykema", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A package for plotting genomic data by chromosomal location.", "sc:license": "GPL-2.0", "sc:name": "idiogram", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/idiogram.html", "sc:version": "1.50.0" diff --git a/data/idiographica/idiographicabioschemas.jsonld b/data/idiographica/idiographicabioschemas.jsonld index 3b9cf5967bd5f..65b721adf601f 100644 --- a/data/idiographica/idiographicabioschemas.jsonld +++ b/data/idiographica/idiographicabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Idiographica is a general-purpose web application to build idiograms on-demand for human, mouse and rat. It allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/annotation data through an easy-to-use interface.", "sc:name": "Idiographica", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://rtools.cbrc.jp/idiographica/" diff --git a/data/idmappinganalysis/idmappinganalysisbioschemas.jsonld b/data/idmappinganalysis/idmappinganalysisbioschemas.jsonld index 4f1b0c6c62918..56ebc129029bc 100644 --- a/data/idmappinganalysis/idmappinganalysisbioschemas.jsonld +++ b/data/idmappinganalysis/idmappinganalysisbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/idmappinganalysis", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Roger Day", - "Alex Lisovich" + "Alex Lisovich", + "Roger Day" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Identifier mapping performance analysis.", "sc:license": "GPL-2.0", "sc:name": "IdMappingAnalysis", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IdMappingAnalysis.html", diff --git a/data/idna-methyl/idna-methylbioschemas.jsonld b/data/idna-methyl/idna-methylbioschemas.jsonld index 2ff44bf704b5b..03569cb2cff45 100644 --- a/data/idna-methyl/idna-methylbioschemas.jsonld +++ b/data/idna-methyl/idna-methylbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This web-server is according to its genetic codes by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample. And by means of the approach of optimizing training datasets for predicting DNA methylation sites. Rigorous cross-validations on a set of experiment-confirmed datasets have indicated that these new predictors remarkably outperformed their counterparts in the existing prediction methods.", "sc:name": "iDNA-Methyl", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.jci-bioinfo.cn/iDNA-Methyl" } \ No newline at end of file diff --git a/data/idna4mc/idna4mcbioschemas.jsonld b/data/idna4mc/idna4mcbioschemas.jsonld index 4fce02cf135d9..01668700e8d0c 100644 --- a/data/idna4mc/idna4mcbioschemas.jsonld +++ b/data/idna4mc/idna4mcbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Identifying DNA 4-methylcytosine sites.", "sc:name": "iDNA4mC", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://lin.uestc.edu.cn/server/iDNA4mC" diff --git a/data/idna6ma-pseknc/idna6ma-psekncbioschemas.jsonld b/data/idna6ma-pseknc/idna6ma-psekncbioschemas.jsonld index 4bd06074753f6..0c9bdf0192ff9 100644 --- a/data/idna6ma-pseknc/idna6ma-psekncbioschemas.jsonld +++ b/data/idna6ma-pseknc/idna6ma-psekncbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "iDNA6mA-PseKNC", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://lin-group.cn/server/iDNA6mA-PseKNC" } \ No newline at end of file diff --git a/data/idrem/idrembioschemas.jsonld b/data/idrem/idrembioschemas.jsonld index c6267794a5378..400d3c7baf111 100644 --- a/data/idrem/idrembioschemas.jsonld +++ b/data/idrem/idrembioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "iDREM", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/phoenixding/idrem" } \ No newline at end of file diff --git a/data/idrug-target/idrug-targetbioschemas.jsonld b/data/idrug-target/idrug-targetbioschemas.jsonld index abe2179bd9632..65f7dba1c190d 100644 --- a/data/idrug-target/idrug-targetbioschemas.jsonld +++ b/data/idrug-target/idrug-targetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "iDrug-Target", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.jci-bioinfo.cn/iDrug-Target/" } \ No newline at end of file diff --git a/data/idt_scitools/idt_scitoolsbioschemas.jsonld b/data/idt_scitools/idt_scitoolsbioschemas.jsonld index fe2fc38a25597..773cd4511d507 100644 --- a/data/idt_scitools/idt_scitoolsbioschemas.jsonld +++ b/data/idt_scitools/idt_scitoolsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "IDT SciTools", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.idtdna.com/SciTools/SciTools.aspx" } \ No newline at end of file diff --git a/data/idtarget/idtargetbioschemas.jsonld b/data/idtarget/idtargetbioschemas.jsonld index b25223f6b56cb..62fd17e878c35 100644 --- a/data/idtarget/idtargetbioschemas.jsonld +++ b/data/idtarget/idtargetbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "idTarget is a web server for identifying biomolecular targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. idTarget screens against protein structures in PDB.", "sc:name": "idTarget", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://idtarget.rcas.sinica.edu.tw" } \ No newline at end of file diff --git a/data/iedb-3d/iedb-3dbioschemas.jsonld b/data/iedb-3d/iedb-3dbioschemas.jsonld index 8732588084337..4413cc753cd33 100644 --- a/data/iedb-3d/iedb-3dbioschemas.jsonld +++ b/data/iedb-3d/iedb-3dbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The 3D structural component of the Immune Epitope Database (IEDB). It catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-cell receptors or MHC molecules are available in the Protein Data Bank (PDB).", "sc:name": "IEDB-3D", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.iedb.org" diff --git a/data/iedb-ar/iedb-arbioschemas.jsonld b/data/iedb-ar/iedb-arbioschemas.jsonld index eb6160f34cf1e..9f34d49da6837 100644 --- a/data/iedb-ar/iedb-arbioschemas.jsonld +++ b/data/iedb-ar/iedb-arbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools. peptide:MHC-I binding and T-cell epitope tools have been added, mapping of discontinuous epitopes onto 3D structures was also added.", "sc:name": "IEDB-AR", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://tools.immuneepitope.org" } \ No newline at end of file diff --git a/data/iedb/iedbbioschemas.jsonld b/data/iedb/iedbbioschemas.jsonld index dc8126f5663fd..747b6f9f6e177 100644 --- a/data/iedb/iedbbioschemas.jsonld +++ b/data/iedb/iedbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Immune Epitope Database provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes.", "sc:name": "The Immune Epitope Database (IEDB)", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://tools.immuneepitope.org/" } \ No newline at end of file diff --git a/data/ielm/ielmbioschemas.jsonld b/data/ielm/ielmbioschemas.jsonld index 081f9cd177206..36b9e3e2585bb 100644 --- a/data/ielm/ielmbioschemas.jsonld +++ b/data/ielm/ielmbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Peter Jehl", - "Toby J. Gibson", - "Robert J. Weatheritt" + "Robert J. Weatheritt", + "Toby J. Gibson" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:22638578", @@ -21,8 +21,8 @@ "sc:name": "iELM", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://i.elm.eu.org" } \ No newline at end of file diff --git a/data/ielu/ielubioschemas.jsonld b/data/ielu/ielubioschemas.jsonld index aa2bb05922ee4..bf33f82a23cc8 100644 --- a/data/ielu/ielubioschemas.jsonld +++ b/data/ielu/ielubioschemas.jsonld @@ -22,10 +22,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pubmed:27915398", - "pmcid:PMC5777932", { "@id": "https://doi.org/10.1007/s11548-016-1504-2" - } + }, + "pmcid:PMC5777932" ], "sc:description": "Interactive electrode localization utility (ielu) is a software package that provides a full pipeline for the registration, localization, and labeling of iEEG electrodes from CT and MR images.", "sc:featureList": { @@ -34,9 +34,9 @@ "sc:license": "GPL-3.0", "sc:name": "ielu", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/aestrivex/ielu" }, diff --git a/data/iembase/iembasebioschemas.jsonld b/data/iembase/iembasebioschemas.jsonld index c005a3e135db3..6710e25dc23cd 100644 --- a/data/iembase/iembasebioschemas.jsonld +++ b/data/iembase/iembasebioschemas.jsonld @@ -9,34 +9,26 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1007/s10545-017-0125-4", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1038/gim.2017.108", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/iembase", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Prof. Dr. Nenad Blau", "sc:additionalType": [ "Database portal", - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:citation": [ - "pmcid:PMC5959948", "pubmed:28726811", + "pmcid:PMC5959948", + "pmcid:PMC5763153", { "@id": "https://doi.org/10.1007/s10545-017-0125-4" }, { "@id": "https://doi.org/10.1038/gim.2017.108" }, - "pubmed:29340838", - "pmcid:PMC5763153" + "pubmed:29340838" ], "sc:description": "Inborn Errors of Metabolism Knowledgebase (IEMbase) accepts an array of biochemical and clinical symptoms from a user and returns a ranked list of possible IEM disorders that match the input profile. In addition, the system can explain the rationale of its results, suggest possible tests that would assist in narrowing down the differential diagnosis, and provide access to its database of biochemical, molecular, and clinical information if more evidence is desired.", "sc:featureList": { @@ -44,11 +36,19 @@ }, "sc:name": "IEMbase", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://iembase.org/" + }, + { + "@id": "https://doi.org/10.1007/s10545-017-0125-4", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://doi.org/10.1038/gim.2017.108", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/iep/iepbioschemas.jsonld b/data/iep/iepbioschemas.jsonld index 9bde64e7cd9aa..a32f1142ed42f 100644 --- a/data/iep/iepbioschemas.jsonld +++ b/data/iep/iepbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "UK BBSRC", + "UK MRC", "EMBOSS Contributors", "Wellcome Trust" ], "sc:description": "Calculate the isoelectric point of proteins.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "iep", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/iep.html", "sc:version": "r6" diff --git a/data/ifeature/ifeaturebioschemas.jsonld b/data/ifeature/ifeaturebioschemas.jsonld index 0c34ea225019a..88b74ac8c3e98 100644 --- a/data/ifeature/ifeaturebioschemas.jsonld +++ b/data/ifeature/ifeaturebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/ifeature", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Zhen Chen", - "Jiangning Song" + "Jiangning Song", + "Zhen Chen" ], "sc:additionalType": [ "Web application", @@ -21,9 +21,9 @@ "sc:description": "Python Toolkit and Web Server for Calculating a Wide Range of Structural and Physicochemical Feature Descriptors from Protein and Peptide Sequences.", "sc:name": "iFeature", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://ifeature.erc.monash.edu/" } \ No newline at end of file diff --git a/data/iform/iformbioschemas.jsonld b/data/iform/iformbioschemas.jsonld index 6fac9dfecae83..a142b40fdac5f 100644 --- a/data/iform/iformbioschemas.jsonld +++ b/data/iform/iformbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Wenjie Shu", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5167396", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0168607" }, - "pmcid:PMC5167396", "pubmed:27992540" ], "sc:description": "Incorporating Find Occurrence of Regulatory Motifs.", @@ -27,8 +27,8 @@ }, "sc:name": "iFORM", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/wenjiegroup/iFORM" }, diff --git a/data/ifuse/ifusebioschemas.jsonld b/data/ifuse/ifusebioschemas.jsonld index 402b41b7f6a15..716879ec18dd1 100644 --- a/data/ifuse/ifusebioschemas.jsonld +++ b/data/ifuse/ifusebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Integrated fusion gene explorer.", "sc:name": "iFUSE", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ifuse.erasmusmc.nl/" } \ No newline at end of file diff --git a/data/igc/igcbioschemas.jsonld b/data/igc/igcbioschemas.jsonld index 777aca385ea60..cbff7fb94f1dd 100644 --- a/data/igc/igcbioschemas.jsonld +++ b/data/igc/igcbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-016-1438-2", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-3697-0386", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/igc", "@type": "sc:SoftwareApplication", @@ -32,11 +40,11 @@ } ], "sc:citation": [ - "pubmed:28088185", "pmcid:PMC5237550", { "@id": "https://doi.org/10.1186/s12859-016-1438-2" - } + }, + "pubmed:28088185" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-3697-0386" @@ -48,20 +56,12 @@ "sc:license": "GPL-2.0", "sc:name": "iGC", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iGC.html", "sc:version": "1.4.0" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1438-2", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-3697-0386", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/igdd/igddbioschemas.jsonld b/data/igdd/igddbioschemas.jsonld index 09af1ca1bf99d..66e337f8083bc 100644 --- a/data/igdd/igddbioschemas.jsonld +++ b/data/igdd/igddbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Integrated and curated repository of mutation data on common genetic diseases afflicting the Indian populations. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers.", "sc:name": "IGDD", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.igdd.iicb.res.in" } \ No newline at end of file diff --git a/data/igdiscover/igdiscoverbioschemas.jsonld b/data/igdiscover/igdiscoverbioschemas.jsonld index 7ca63226bf3f4..7b02b50262a8d 100644 --- a/data/igdiscover/igdiscoverbioschemas.jsonld +++ b/data/igdiscover/igdiscoverbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "IgDiscover", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://igdiscover.se/", "sc:version": "0.6.0" diff --git a/data/iges/igesbioschemas.jsonld b/data/iges/igesbioschemas.jsonld index 187c77ff86112..48c7cafef1466 100644 --- a/data/iges/igesbioschemas.jsonld +++ b/data/iges/igesbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/iges", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Can Yang", "Xiang Wan", + "Can Yang", "Zongben X" ], "sc:additionalType": "Desktop application", diff --git a/data/igipt/igiptbioschemas.jsonld b/data/igipt/igiptbioschemas.jsonld index af280bdfc8a3a..2acae08fbf073 100644 --- a/data/igipt/igiptbioschemas.jsonld +++ b/data/igipt/igiptbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Web-based integrated platform for the identification of genomic islands (GIs). It incorporates thirteen parametric measures based on anomalous nucleotide composition on a single platform, thus improving the predictive power of a horizontally acquired region, since it is known that no single measure can absolutely predict a horizontally transferred region.", "sc:name": "IGIPT", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinf.iiit.ac.in/IGIPT/" } \ No newline at end of file diff --git a/data/igpred/igpredbioschemas.jsonld b/data/igpred/igpredbioschemas.jsonld index beff3c9ef7b85..a54e854bd9655 100644 --- a/data/igpred/igpredbioschemas.jsonld +++ b/data/igpred/igpredbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "IGPred", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://lin.uestc.edu.cn/server/IGPred" } \ No newline at end of file diff --git a/data/iguide/iguidebioschemas.jsonld b/data/iguide/iguidebioschemas.jsonld index e269812b7a6f6..82d878f64ab8b 100644 --- a/data/iguide/iguidebioschemas.jsonld +++ b/data/iguide/iguidebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13059-019-1625-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/iGUIDE", "@type": "sc:SoftwareApplication", @@ -20,31 +16,35 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC6337799", + "pubmed:30654827", { "@id": "https://doi.org/10.1186/s13059-019-1625-3" - }, - "pubmed:30654827" + } ], "sc:description": "Improved pipeline for analyzing CRISPR cleavage specificity.", "sc:featureList": [ { - "@id": "edam:operation_0308" + "@id": "edam:operation_3501" }, { "@id": "edam:operation_3216" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_0308" } ], "sc:license": "GPL-3.0", "sc:name": "iGUIDE", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/cnobles/iGUIDE" + }, + { + "@id": "https://doi.org/10.1186/s13059-019-1625-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/igv/igvbioschemas.jsonld b/data/igv/igvbioschemas.jsonld index 4f294a5d98866..2f817f3cca57f 100644 --- a/data/igv/igvbioschemas.jsonld +++ b/data/igv/igvbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/igv", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "IGV help group", "IGV GitHub issues", - "IGV support" + "IGV support", + "IGV help group" ], "sc:additionalType": "Desktop application", "sc:description": "High-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http.", diff --git a/data/igvtools/igvtoolsbioschemas.jsonld b/data/igvtools/igvtoolsbioschemas.jsonld index 8ee465fe56de0..a96f771f241ce 100644 --- a/data/igvtools/igvtoolsbioschemas.jsonld +++ b/data/igvtools/igvtoolsbioschemas.jsonld @@ -20,24 +20,24 @@ { "@id": "https://doi.org/10.1093/bib/bbs017" }, - "pubmed:22517427", - "pmcid:PMC3603213" + "pmcid:PMC3603213", + "pubmed:22517427" ], "sc:description": "The igvtools utility provides a set of tools for pre-processing data files.", "sc:featureList": [ { - "@id": "edam:operation_0256" + "@id": "edam:operation_0335" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_0256" } ], "sc:license": "MIT", "sc:name": "IGVtools", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://software.broadinstitute.org/software/igv/igvtools" }, diff --git a/data/ihop_ws/ihop_wsbioschemas.jsonld b/data/ihop_ws/ihop_wsbioschemas.jsonld index 9751892c1b645..e7be9506a0c5e 100644 --- a/data/ihop_ws/ihop_wsbioschemas.jsonld +++ b/data/ihop_ws/ihop_wsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "iHOP WS", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ws.bioinfo.cnio.es/iHOP/", "sc:version": "1" diff --git a/data/ihsp-pseraaac/ihsp-pseraaacbioschemas.jsonld b/data/ihsp-pseraaac/ihsp-pseraaacbioschemas.jsonld index ab9ca02195341..3863b8e4db21e 100644 --- a/data/ihsp-pseraaac/ihsp-pseraaacbioschemas.jsonld +++ b/data/ihsp-pseraaac/ihsp-pseraaacbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This web-server was developed to identify the family of heat shock proteins by using reduced amino acid alphabet.", "sc:name": "iHSP-PseRAAAC", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://lin.uestc.edu.cn/server/iHSP-PseRAAAC" } \ No newline at end of file diff --git a/data/ihw/ihwbioschemas.jsonld b/data/ihw/ihwbioschemas.jsonld index b3e20793f6602..c4621c339b457 100644 --- a/data/ihw/ihwbioschemas.jsonld +++ b/data/ihw/ihwbioschemas.jsonld @@ -20,8 +20,8 @@ { "@id": "https://doi.org/10.1038/nmeth.3885" }, - "pmcid:PMC4930141", - "pubmed:27240256" + "pubmed:27240256", + "pmcid:PMC4930141" ], "sc:description": "Multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.", "sc:featureList": { diff --git a/data/ihyd-pseaac/ihyd-pseaacbioschemas.jsonld b/data/ihyd-pseaac/ihyd-pseaacbioschemas.jsonld index 25268ad77ffa3..40439c0eb6407 100644 --- a/data/ihyd-pseaac/ihyd-pseaacbioschemas.jsonld +++ b/data/ihyd-pseaac/ihyd-pseaacbioschemas.jsonld @@ -15,17 +15,17 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:24857907", - "pmcid:PMC4057693", { "@id": "https://doi.org/10.3390/ijms15057594" - } + }, + "pmcid:PMC4057693" ], "sc:description": "New predictor which was proposed by incorporating the dipeptide position-specific propensity into the general form of pseudo amino acid composition.", "sc:name": "iHyd-PseAAC", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://app.aporc.org/iHyd-PseAAC/" }, diff --git a/data/iis/iisbioschemas.jsonld b/data/iis/iisbioschemas.jsonld index 1ce862fc361a9..5f557cc48a266 100644 --- a/data/iis/iisbioschemas.jsonld +++ b/data/iis/iisbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC4065059", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0100385" }, - "pubmed:24949626", - "pmcid:PMC4065059" + "pubmed:24949626" ], "sc:description": "Integrated Interactome System: A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a Variety of Data Sources and Tools.", "sc:featureList": [ @@ -31,17 +31,17 @@ "@id": "edam:operation_3083" }, { - "@id": "edam:operation_3672" + "@id": "edam:operation_2497" }, { - "@id": "edam:operation_2497" + "@id": "edam:operation_3672" } ], "sc:name": "IIS", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioinfo03.ibi.unicamp.br/lnbio/IIS2/" } diff --git a/data/ikap/ikapbioschemas.jsonld b/data/ikap/ikapbioschemas.jsonld index e87bb839cbfa5..94cf083c85e0e 100644 --- a/data/ikap/ikapbioschemas.jsonld +++ b/data/ikap/ikapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Heuristic framework for inference of kinase activities from Phosphoproteomics data.", "sc:name": "IKAP", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/marcel-mischnik/IKAP" } \ No newline at end of file diff --git a/data/ikmc/ikmcbioschemas.jsonld b/data/ikmc/ikmcbioschemas.jsonld index e09befc9c510e..fa88cc0df51b6 100644 --- a/data/ikmc/ikmcbioschemas.jsonld +++ b/data/ikmc/ikmcbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "IKMC", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.knockoutmouse.org" } \ No newline at end of file diff --git a/data/ilastik/ilastikbioschemas.jsonld b/data/ilastik/ilastikbioschemas.jsonld index 8e158fea73d06..4ab7e33275189 100644 --- a/data/ilastik/ilastikbioschemas.jsonld +++ b/data/ilastik/ilastikbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "ilastik", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://www.ilastik.org/index.html" } \ No newline at end of file diff --git a/data/ilbind/ilbindbioschemas.jsonld b/data/ilbind/ilbindbioschemas.jsonld index 22b74663608e7..663f034f53682 100644 --- a/data/ilbind/ilbindbioschemas.jsonld +++ b/data/ilbind/ilbindbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Consensus predictor that combines the two complementary inverse ligand binding predictors implemented using FINDSITE and SMAP and Support Vector Machines.", "sc:name": "ILbind", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://biomine.cs.vcu.edu/servers/ILbind/" diff --git a/data/ilearn/ilearnbioschemas.jsonld b/data/ilearn/ilearnbioschemas.jsonld index aaf2aa25ed02b..bfa6cc6241d06 100644 --- a/data/ilearn/ilearnbioschemas.jsonld +++ b/data/ilearn/ilearnbioschemas.jsonld @@ -11,21 +11,21 @@ "@id": "https://bio.tools/iLearn", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jiangning Song", - "Zhen Chen" + "Zhen Chen", + "Jiangning Song" ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:31067315", "sc:description": "Integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.", "sc:license": "Unlicense", "sc:name": "iLearn", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://ilearn.erc.monash.edu/" } \ No newline at end of file diff --git a/data/illumina/illuminabioschemas.jsonld b/data/illumina/illuminabioschemas.jsonld index 6028c32ab7108..951074d20ee65 100644 --- a/data/illumina/illuminabioschemas.jsonld +++ b/data/illumina/illuminabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R Library for preprocessing Illumina Whole Genome Expression BeadChips.", "sc:name": "illumina", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioinf.wehi.edu.au/illumina/index.html" } \ No newline at end of file diff --git a/data/illuminaio/illuminaiobioschemas.jsonld b/data/illuminaio/illuminaiobioschemas.jsonld index a979f85ba7d1d..58849b56339f4 100644 --- a/data/illuminaio/illuminaiobioschemas.jsonld +++ b/data/illuminaio/illuminaiobioschemas.jsonld @@ -16,12 +16,12 @@ "@id": "http://orcid.org/0000-0003-0086-0687" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:24701342", "pmcid:PMC3968891", + "pubmed:24701342", { "@id": "https://doi.org/10.12688/f1000research.2-264.v1" } @@ -33,20 +33,20 @@ "sc:license": "GPL-2.0", "sc:name": "illuminaio", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/illuminaio.html", "sc:version": "0.16.0" }, - { - "@id": "http://orcid.org/0000-0003-0086-0687", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.12688/f1000research.2-264.v1", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-0086-0687", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/iloc-cell/iloc-cellbioschemas.jsonld b/data/iloc-cell/iloc-cellbioschemas.jsonld index d4117491e20a8..c70dad4ded7f2 100644 --- a/data/iloc-cell/iloc-cellbioschemas.jsonld +++ b/data/iloc-cell/iloc-cellbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "iLoc-Cell", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.jci-bioinfo.cn/iLoc-Hum" } \ No newline at end of file diff --git a/data/iloops/iloopsbioschemas.jsonld b/data/iloops/iloopsbioschemas.jsonld index 0e6eb71439f80..9d0250d7a5033 100644 --- a/data/iloops/iloopsbioschemas.jsonld +++ b/data/iloops/iloopsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6279-2483", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/iloops", "@type": "sc:SoftwareApplication", @@ -27,10 +31,6 @@ "sc:provider": "upf.edu", "sc:url": "http://sbi.imim.es/iLoopsServer", "sc:version": "1" - }, - { - "@id": "http://orcid.org/0000-0002-6279-2483", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/imaaagine/imaaaginebioschemas.jsonld b/data/imaaagine/imaaaginebioschemas.jsonld index cd6fcd8f581b1..d1fdf6cff91b6 100644 --- a/data/imaaagine/imaaaginebioschemas.jsonld +++ b/data/imaaagine/imaaaginebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The IMAAAGINE server is a protein structural motif database searching program. Users can define an amino acid arrangment of 3 to 8 residues which will be converted into a search pattern. The search using the query is carried out against the PDB. 3D arrangements of amino acids in PDB structures that conform to the query will be returned to the user.", "sc:name": "IMAAAGINE", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://mfrlab.org/grafss/imaaagine/" diff --git a/data/imagehts/bioconda_imagehts.yaml b/data/imagehts/bioconda_imagehts.yaml index 11cb687c69dc1..33a14f0906a35 100644 --- a/data/imagehts/bioconda_imagehts.yaml +++ b/data/imagehts/bioconda_imagehts.yaml @@ -8,7 +8,6 @@ description: imageHTS is an R package dedicated to the analysis of high-throughp home: https://bioconductor.org/packages/3.10/bioc/html/imageHTS.html identifiers: - biotools:imagehts -- doi:10.1038/nmeth.3252 license: LGPL-2.1 license_file: /lib/R/share/licenses/LGPL-2.1 name: bioconductor-imagehts diff --git a/data/imagehts/imagehtsbioschemas.jsonld b/data/imagehts/imagehtsbioschemas.jsonld index 5f1f32531c645..7f8950acbacbe 100644 --- a/data/imagehts/imagehtsbioschemas.jsonld +++ b/data/imagehts/imagehtsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "imageHTS", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/imageHTS.html", diff --git a/data/imagej/imagejbioschemas.jsonld b/data/imagej/imagejbioschemas.jsonld index 1629c92accad3..97588c95202e6 100644 --- a/data/imagej/imagejbioschemas.jsonld +++ b/data/imagej/imagejbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.", "sc:name": "ImageJ2", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://imagej.net/" } \ No newline at end of file diff --git a/data/imagej_nih/imagej_nihbioschemas.jsonld b/data/imagej_nih/imagej_nihbioschemas.jsonld index a5a9c5b6810e0..49e8fbc5d56db 100644 --- a/data/imagej_nih/imagej_nihbioschemas.jsonld +++ b/data/imagej_nih/imagej_nihbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "ImageJ (NIH)", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "IFB ELIXIR-FR", "sc:url": "http://rsb.info.nih.gov/ij/index.html", diff --git a/data/imageo/imageobioschemas.jsonld b/data/imageo/imageobioschemas.jsonld index 3db25a510e747..5e200ea27a845 100644 --- a/data/imageo/imageobioschemas.jsonld +++ b/data/imageo/imageobioschemas.jsonld @@ -25,8 +25,8 @@ "sc:name": "ImaGEO", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo.genyo.es/imageo/" }, diff --git a/data/imagepy/imagepybioschemas.jsonld b/data/imagepy/imagepybioschemas.jsonld index ab5883fa0a2b4..ee55853030b08 100644 --- a/data/imagepy/imagepybioschemas.jsonld +++ b/data/imagepy/imagepybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "BSD-2-Clause", "sc:name": "ImagePy", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/Image-Py/imagepy" } \ No newline at end of file diff --git a/data/imagic/imagicbioschemas.jsonld b/data/imagic/imagicbioschemas.jsonld index 78786900d55a9..3a55c8fa7289b 100644 --- a/data/imagic/imagicbioschemas.jsonld +++ b/data/imagic/imagicbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Image analysis software package for electron microscopy, which is also used to process images from other devices, spectra and other multi-dimensional data-sets.", "sc:name": "Imagic", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "Instruct", "sc:url": "http://imagescience.de/imagic/", diff --git a/data/imaginr/imaginrbioschemas.jsonld b/data/imaginr/imaginrbioschemas.jsonld index 79883d2a2ce09..01440f196223e 100644 --- a/data/imaginr/imaginrbioschemas.jsonld +++ b/data/imaginr/imaginrbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Chin-Long Ky", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:31101851", "pmcid:PMC6525208", { "@id": "https://doi.org/10.1038/S41598-019-43777-4" - }, - "pubmed:31101851" + } ], "sc:description": "Characterization of inner shell colour variations in Pinctada margaritifera assessed by HSV colour quantification.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "GPL-2.0", "sc:name": "ImaginR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/ImaginR/index.html" }, diff --git a/data/imas/imasbioschemas.jsonld b/data/imas/imasbioschemas.jsonld index 87144fee2ec88..7218c19445d84 100644 --- a/data/imas/imasbioschemas.jsonld +++ b/data/imas/imasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "IMAS", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IMAS.html", "sc:version": "1.4.0" diff --git a/data/imeges/imegesbioschemas.jsonld b/data/imeges/imegesbioschemas.jsonld index 2b549c969362d..84d51d58b11e4 100644 --- a/data/imeges/imegesbioschemas.jsonld +++ b/data/imeges/imegesbioschemas.jsonld @@ -22,11 +22,11 @@ ], "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC6309067", { "@id": "https://doi.org/10.1186/s12859-018-2469-7" }, - "pubmed:30591030" + "pubmed:30591030", + "pmcid:PMC6309067" ], "sc:description": "Integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes.", "sc:featureList": [ @@ -43,8 +43,8 @@ "sc:license": "Unlicense", "sc:name": "iMEGES", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/WGLab/iMEGES" } diff --git a/data/imem-seq/imem-seqbioschemas.jsonld b/data/imem-seq/imem-seqbioschemas.jsonld index b1da444ffb9a2..fe2e8f0a3e286 100644 --- a/data/imem-seq/imem-seqbioschemas.jsonld +++ b/data/imem-seq/imem-seqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Multi-label classifier for identifying membrane proteins with single and multiple types via physical-chemical property matrix and grey-PSSM.", "sc:name": "iMem-Seq", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.jci-bioinfo.cn/iMem-Seq" diff --git a/data/imembrane/imembranebioschemas.jsonld b/data/imembrane/imembranebioschemas.jsonld index 17676b5cb4bc5..71d33a6e93930 100644 --- a/data/imembrane/imembranebioschemas.jsonld +++ b/data/imembrane/imembranebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Homology-based method, which predicts a membrane protein’s position within a lipid bilayer. It projects the results of coarse-grained molecular dynamics simulations onto any membrane protein structure or sequence provided by the user.", "sc:name": "iMembrane", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://opig.stats.ox.ac.uk/webapps/medeller/home.pl?app=iMembrane" } \ No newline at end of file diff --git a/data/imet-q/imet-qbioschemas.jsonld b/data/imet-q/imet-qbioschemas.jsonld index 840bcc025761a..6448e5cfb111b 100644 --- a/data/imet-q/imet-qbioschemas.jsonld +++ b/data/imet-q/imet-qbioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Ting-Yi Sung", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC4718670", { "@id": "https://doi.org/10.1371/journal.pone.0146112" }, + "pmcid:PMC4718670", "pubmed:26784691" ], "sc:description": "iMet-Q (intelligent Metabolomic Quantitation) is a software that quantifies metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data.", diff --git a/data/imetagene/imetagenebioschemas.jsonld b/data/imetagene/imetagenebioschemas.jsonld index c033eb1a9a77c..60512ca797da3 100644 --- a/data/imetagene/imetagenebioschemas.jsonld +++ b/data/imetagene/imetagenebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "Imetagene", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Imetagene.html", "sc:version": "1.4.0" diff --git a/data/imeter/imeterbioschemas.jsonld b/data/imeter/imeterbioschemas.jsonld index 854aef3aec698..b71d6c61c401e 100644 --- a/data/imeter/imeterbioschemas.jsonld +++ b/data/imeter/imeterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Not licensed", "sc:name": "IMEter", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://korflab.ucdavis.edu/cgi-bin/web-imeter.pl", diff --git a/data/imex/imexbioschemas.jsonld b/data/imex/imexbioschemas.jsonld index 34e8c85caba59..36c408c66c657 100644 --- a/data/imex/imexbioschemas.jsonld +++ b/data/imex/imexbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This consortium is an international collaboration between a group of major public interaction data providers.", "sc:name": "IMEx", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.imexconsortium.org/" } \ No newline at end of file diff --git a/data/img2net/img2netbioschemas.jsonld b/data/img2net/img2netbioschemas.jsonld index 72cabba3c48e9..759b2df091830 100644 --- a/data/img2net/img2netbioschemas.jsonld +++ b/data/img2net/img2netbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software to automatedly analyze structures by reconstructing the underlying network, computing relevant network properties, and statistically comparing networks of different types or under different conditions.", "sc:name": "img2net", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mathbiol.mpimp-golm.mpg.de/img2net/" } \ No newline at end of file diff --git a/data/img_m/img_mbioschemas.jsonld b/data/img_m/img_mbioschemas.jsonld index ff6974e31bc19..a5d91322a6e34 100644 --- a/data/img_m/img_mbioschemas.jsonld +++ b/data/img_m/img_mbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "IMG M", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://img.jgi.doe.gov/cgi-bin/m/main.cgi" } \ No newline at end of file diff --git a/data/imgt/imgtbioschemas.jsonld b/data/imgt/imgtbioschemas.jsonld index e59726ed796ea..1d7c49af52ee3 100644 --- a/data/imgt/imgtbioschemas.jsonld +++ b/data/imgt/imgtbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/imgt", "@type": "sc:SoftwareApplication", "sc:additionalType": [ + "Ontology", "Web application", "Bioinformatics portal", - "Database portal", - "Ontology" + "Database portal" ], "sc:citation": "pubmed:25378316", "sc:description": "IMGT®, the international ImMunoGeneTics information system® is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS). IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates. IMGT® provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT® works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT® consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.", "sc:name": "IMGT, the international ImMunoGeneTics information system", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.imgt.org/" } \ No newline at end of file diff --git a/data/imgt_3dstructure/imgt_3dstructurebioschemas.jsonld b/data/imgt_3dstructure/imgt_3dstructurebioschemas.jsonld index f74b51fb7609e..d779783792f1b 100644 --- a/data/imgt_3dstructure/imgt_3dstructurebioschemas.jsonld +++ b/data/imgt_3dstructure/imgt_3dstructurebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "IMGT/3Dstructure-DB is the IMGT® database for 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins, related proteins of the immune system (RPI) and fusion proteins for immune applications (FPIA).\nAnnotation is based on the IMGT-ONTOLOGY concepts.", "sc:name": "IMGT 3Dstructure-DB", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.imgt.org/3Dstructure-DB/" diff --git a/data/imgt_hla-sequence_alignment/imgt_hla-sequence_alignmentbioschemas.jsonld b/data/imgt_hla-sequence_alignment/imgt_hla-sequence_alignmentbioschemas.jsonld index a3b1b0bb0dc65..2c75a47b51a62 100644 --- a/data/imgt_hla-sequence_alignment/imgt_hla-sequence_alignmentbioschemas.jsonld +++ b/data/imgt_hla-sequence_alignment/imgt_hla-sequence_alignmentbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Interactive sequence alignment tool with help page available.", "sc:name": "IMGT HLA Sequence Alignment", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/ipd/imgt/hla/align.html", diff --git a/data/imgt_hla/imgt_hlabioschemas.jsonld b/data/imgt_hla/imgt_hlabioschemas.jsonld index a96f0dff6faae..17e6d1f3f4847 100644 --- a/data/imgt_hla/imgt_hlabioschemas.jsonld +++ b/data/imgt_hla/imgt_hlabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data.", "sc:name": "IMGT database of human MHC", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.ebi.ac.uk/imgt/hla/" } \ No newline at end of file diff --git a/data/imgt_v-quest/imgt_v-questbioschemas.jsonld b/data/imgt_v-quest/imgt_v-questbioschemas.jsonld index c19c4659f61c6..d57ee4ca9d279 100644 --- a/data/imgt_v-quest/imgt_v-questbioschemas.jsonld +++ b/data/imgt_v-quest/imgt_v-questbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "IMGT/V-QUEST is the IMGT® tool for nucleotide sequence alignment and analysis of immunoglobulin (IG) or antibody and T cell receptor (TR) variable domains, integrates IMGT/JunctionAnalysis, IMGT/Automat and IMGT/Collier-de-Perles.\nAnalysis is based on the IMGT-ONTOLOGY concepts.", "sc:name": "IMGT V-QUEST", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.imgt.org/IMGT_vquest" } \ No newline at end of file diff --git a/data/imir/imirbioschemas.jsonld b/data/imir/imirbioschemas.jsonld index 1f63138708746..06205150a8daa 100644 --- a/data/imir/imirbioschemas.jsonld +++ b/data/imir/imirbioschemas.jsonld @@ -9,15 +9,27 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-0455-2083", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-362", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-0538-8978", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/imir", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "http://orcid.org/0000-0003-0455-2083" + "@id": "http://orcid.org/0000-0002-0538-8978" }, { - "@id": "http://orcid.org/0000-0002-0538-8978" + "@id": "http://orcid.org/0000-0003-0455-2083" } ], "sc:additionalType": "Command-line tool", @@ -26,8 +38,8 @@ { "@id": "https://doi.org/10.1186/1471-2105-14-362" }, - "pmcid:PMC3878829", - "pubmed:24330401" + "pubmed:24330401", + "pmcid:PMC3878829" ], "sc:description": "Modular pipeline for comprehensive analysis of small RNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow.", "sc:featureList": { @@ -41,18 +53,6 @@ "sc:provider": "ELIXIR-ITA-SALERNO", "sc:url": "http://www.labmedmolge.unisa.it/italiano/home/imir", "sc:version": "1" - }, - { - "@id": "http://orcid.org/0000-0002-0538-8978", - "@type": "schema:Person" - }, - { - "@id": "http://orcid.org/0000-0003-0455-2083", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-14-362", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/imirp/imirpbioschemas.jsonld b/data/imirp/imirpbioschemas.jsonld index fbe74ef2e88a7..a64eb7542dc04 100644 --- a/data/imirp/imirpbioschemas.jsonld +++ b/data/imirp/imirpbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Robert L. Chow", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:27122020", "pmcid:PMC4848830", { "@id": "https://doi.org/10.1186/S12859-016-1057-Y" - } + }, + "pubmed:27122020" ], "sc:description": "Web application designed to selectively mutate predicted miRNA target sites while ensuring that predicted target sites for other miRNAs, termed illegitimate target sites, are not created in the process.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "ImiRP", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://imirp.org/" diff --git a/data/imkt/imktbioschemas.jsonld b/data/imkt/imktbioschemas.jsonld index 0c867b44c191b..b0a5765e3f16f 100644 --- a/data/imkt/imktbioschemas.jsonld +++ b/data/imkt/imktbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-0374-1475", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/NAR/GKZ372", "@type": "sc:CreativeWork" @@ -27,36 +31,32 @@ "Web application" ], "sc:citation": [ - "pubmed:31081014", - "pmcid:PMC6602517", { "@id": "https://doi.org/10.1093/NAR/GKZ372" - } + }, + "pmcid:PMC6602517", + "pubmed:31081014" ], "sc:description": "integrative McDonald and Kreitman test.", "sc:featureList": [ - { - "@id": "edam:operation_2495" - }, { "@id": "edam:operation_0451" }, { "@id": "edam:operation_0310" + }, + { + "@id": "edam:operation_2495" } ], "sc:license": "GPL-3.0", "sc:name": "iMKT", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://imkt.uab.cat" - }, - { - "@id": "https://orcid.org/0000-0002-0374-1475", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/imman/immanbioschemas.jsonld b/data/imman/immanbioschemas.jsonld index 99b5ce261f009..2e02ab697ed63 100644 --- a/data/imman/immanbioschemas.jsonld +++ b/data/imman/immanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "IMMAN", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IMMAN.html", "sc:version": "1.0.0" diff --git a/data/immclass2019/immclass2019bioschemas.jsonld b/data/immclass2019/immclass2019bioschemas.jsonld index 82bcccea0e133..4544747f15599 100644 --- a/data/immclass2019/immclass2019bioschemas.jsonld +++ b/data/immclass2019/immclass2019bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "ImmClass2019", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/KlinkeLab/ImmClass2019" } \ No newline at end of file diff --git a/data/immport/immportbioschemas.jsonld b/data/immport/immportbioschemas.jsonld index bff90b22a7593..6f52688f22b89 100644 --- a/data/immport/immportbioschemas.jsonld +++ b/data/immport/immportbioschemas.jsonld @@ -17,31 +17,31 @@ "@id": "https://bio.tools/ImmPort", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ + "pubmed:29485622", { "@id": "https://doi.org/10.1038/sdata.2018.15" }, - "pubmed:29485622", "pmcid:PMC5827693" ], "sc:description": "Data repository with analysis tools that is mainly focused on cytometry and immunology.", "sc:featureList": [ { - "@id": "edam:operation_0224" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_0224" } ], "sc:license": "Unlicense", "sc:name": "ImmPort", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.immport.org" } diff --git a/data/immquant/immquantbioschemas.jsonld b/data/immquant/immquantbioschemas.jsonld index 2d21cad4479ed..1b2a8984d9935 100644 --- a/data/immquant/immquantbioschemas.jsonld +++ b/data/immquant/immquantbioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Irit Gat-Viks", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5167062", { "@id": "https://doi.org/10.1093/bioinformatics/btw535" }, + "pmcid:PMC5167062", "pubmed:27531105" ], "sc:description": "ImmQuant is a software tool allowing immunologists to upload transcription profiles of multiple tissue samples, apply deconvolution methodology to predict differences in cell-type quantities between the samples, and then inspect the inferred cell-type alterations using convenient visualization tools.", @@ -32,8 +32,8 @@ "sc:license": "Other", "sc:name": "ImmQuant", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://csgi.tau.ac.il/ImmQuant/" } diff --git a/data/immuneregulation/immuneregulationbioschemas.jsonld b/data/immuneregulation/immuneregulationbioschemas.jsonld index 26fa765f443b6..8f805e5a41d4d 100644 --- a/data/immuneregulation/immuneregulationbioschemas.jsonld +++ b/data/immuneregulation/immuneregulationbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKZ450", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ImmuneRegulation", "@type": "sc:SoftwareApplication", @@ -17,11 +21,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC6602512", { "@id": "https://doi.org/10.1093/NAR/GKZ450" }, - "pubmed:31114925", - "pmcid:PMC6602512" + "pubmed:31114925" ], "sc:description": "Web-based tool for identifying human immune regulatory elements.", "sc:featureList": [ @@ -47,10 +51,6 @@ { "@id": "https://orcid.org/0000-0002-7364-2202", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ450", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/immunespacer/immunespacerbioschemas.jsonld b/data/immunespacer/immunespacerbioschemas.jsonld index d286555b5ac4b..8cb0730118b61 100644 --- a/data/immunespacer/immunespacerbioschemas.jsonld +++ b/data/immunespacer/immunespacerbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "ImmuneSpaceR", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ImmuneSpaceR.html", "sc:version": "1.2.0" diff --git a/data/immunoclust/immunoclustbioschemas.jsonld b/data/immunoclust/immunoclustbioschemas.jsonld index 08582877635e0..727fe559fe05c 100644 --- a/data/immunoclust/immunoclustbioschemas.jsonld +++ b/data/immunoclust/immunoclustbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Till Soerensen", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Model based clustering and meta-clustering of Flow Cytometry Data.", "sc:license": "Artistic-2.0", diff --git a/data/immunodb/immunodbbioschemas.jsonld b/data/immunodb/immunodbbioschemas.jsonld index d25f185dacfa2..d503d1e105ed3 100644 --- a/data/immunodb/immunodbbioschemas.jsonld +++ b/data/immunodb/immunodbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.", "sc:name": "ImmunoDB", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://cegg.unige.ch/Insecta/immunodb" diff --git a/data/immunomebrowser/immunomebrowserbioschemas.jsonld b/data/immunomebrowser/immunomebrowserbioschemas.jsonld index 0b48a33fa9484..df2fb02928ef6 100644 --- a/data/immunomebrowser/immunomebrowserbioschemas.jsonld +++ b/data/immunomebrowser/immunomebrowserbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Unlicense", "sc:name": "ImmunomeBrowser", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://tools.iedb.org/immunomebrowser/" diff --git a/data/imod/imodbioschemas.jsonld b/data/imod/imodbioschemas.jsonld index ed922dafed828..25b4a23428029 100644 --- a/data/imod/imodbioschemas.jsonld +++ b/data/imod/imodbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Set of image processing, modelling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.", "sc:name": "IMOD", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://bio3d.colorado.edu/imod/", diff --git a/data/imos/imosbioschemas.jsonld b/data/imos/imosbioschemas.jsonld index 159f909a08a86..b3a6ef828ed6e 100644 --- a/data/imos/imosbioschemas.jsonld +++ b/data/imos/imosbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Hadadian Nejad Youesfi", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6345043", + "pubmed:30678641", { "@id": "https://doi.org/10.1186/s12859-018-2592-5" }, - "pubmed:30678641" + "pmcid:PMC6345043" ], "sc:description": "Aligner for mapping noisy long reads to the reference genome.", "sc:featureList": [ @@ -33,9 +33,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "IMOS", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/Mosjava/IMOS" }, diff --git a/data/imp/impbioschemas.jsonld b/data/imp/impbioschemas.jsonld index 2a87c9e9c24ab..8687b6d752fde 100644 --- a/data/imp/impbioschemas.jsonld +++ b/data/imp/impbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Integrative Multi-species Prediction (IMP) is a webserver that enables biologists to analyze their experimental results in the functional context of gene networks from multiple organisms.", "sc:name": "IMP", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://imp.princeton.edu" } \ No newline at end of file diff --git a/data/imp_biomolecules/imp_biomoleculesbioschemas.jsonld b/data/imp_biomolecules/imp_biomoleculesbioschemas.jsonld index 8210469f1422b..ecdfe7cb3d813 100644 --- a/data/imp_biomolecules/imp_biomoleculesbioschemas.jsonld +++ b/data/imp_biomolecules/imp_biomoleculesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Integrative Modeling Platform broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies. Detailed structural characterization of assemblies is generally impossible by any single existing experimental or computational method. This barrier can be overcome by hybrid approaches that integrate data from diverse biochemical and biophysical experiments.", "sc:name": "IMP", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.salilab.org/imp/" } \ No newline at end of file diff --git a/data/imp_omic/imp_omicbioschemas.jsonld b/data/imp_omic/imp_omicbioschemas.jsonld index 42fb480aef112..e2272b1393453 100644 --- a/data/imp_omic/imp_omicbioschemas.jsonld +++ b/data/imp_omic/imp_omicbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13059-016-1116-8", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/imp_omic", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ "Command-line tool" ], "sc:citation": [ - "pubmed:7986083", - "pmcid:PMC5159968", { "@id": "https://doi.org/10.1186/s13059-016-1116-8" - } + }, + "pmcid:PMC5159968", + "pubmed:7986083" ], "sc:description": "Integrated Meta-omic Pipeline. Large-scale standardized integrated analysis of coupled metagenomic and metatranscriptomic data. Incorporates robust read preprocessing, iterative co-assembly of metagenomic and metatranscriptomic data, analyses of microbial community structure and function as well as genomic signature-based visualizations.", "sc:featureList": { @@ -32,10 +36,6 @@ "sc:name": "IMP", "sc:url": "http://r3lab.uni.lu/web/imp/", "sc:version": "1.4" - }, - { - "@id": "https://doi.org/10.1186/s13059-016-1116-8", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/impact_framework/impact_frameworkbioschemas.jsonld b/data/impact_framework/impact_frameworkbioschemas.jsonld index 1615217af3288..b2e908b89ca1d 100644 --- a/data/impact_framework/impact_frameworkbioschemas.jsonld +++ b/data/impact_framework/impact_frameworkbioschemas.jsonld @@ -20,26 +20,26 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:31011536", + "pmcid:PMC6462781", { "@id": "https://doi.org/10.1016/j.mec.2019.e00089" - }, - "pmcid:PMC6462781" + } ], "sc:description": "Python package for writing data analysis workflows to interpret microbial physiology.", "sc:featureList": [ { - "@id": "edam:operation_1812" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_1812" } ], "sc:license": "GPL-3.0", "sc:name": "Impact framework", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/lmse/impact", "sc:version": "0.5.0" diff --git a/data/impact_s/impact_sbioschemas.jsonld b/data/impact_s/impact_sbioschemas.jsonld index 0a4e042a22bd7..fc087f282f353 100644 --- a/data/impact_s/impact_sbioschemas.jsonld +++ b/data/impact_s/impact_sbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/impact_s", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Emanuel Maldonado", - "Agostinho Antunes" + "Agostinho Antunes", + "Emanuel Maldonado" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:25329307", "sc:description": "Java swing based Graphical User Interface program for analyzing and/or combining several selection results from programs like, PAML (codeml), Datamonkey, TreeSAAP. Provides 3D homology modeling through Swiss Model and 3D mapping of selection results through Jmol.", "sc:name": "IMPACT_S", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://impact-s.sourceforge.net/" diff --git a/data/impala/impalabioschemas.jsonld b/data/impala/impalabioschemas.jsonld index 2d317f40ca24f..3c65c0414bb53 100644 --- a/data/impala/impalabioschemas.jsonld +++ b/data/impala/impalabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "IMPaLA is a web tool for the joint pathway analysis of transcriptomics or proteomics and metabolomics data.", "sc:name": "IMPaLA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://impala.molgen.mpg.de/", "sc:version": "9" diff --git a/data/impc/impcbioschemas.jsonld b/data/impc/impcbioschemas.jsonld index 6835515ebc274..c299a3d2496e4 100644 --- a/data/impc/impcbioschemas.jsonld +++ b/data/impc/impcbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Genotype-phenotype annotations from knockout mouse strain for every protein coding gene in the mouse genome.", "sc:name": "IMPC", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.mousephenotype.org", "sc:version": "1" diff --git a/data/impcdata/impcdatabioschemas.jsonld b/data/impcdata/impcdatabioschemas.jsonld index 961aad1648161..c4fac0cbf5c02 100644 --- a/data/impcdata/impcdatabioschemas.jsonld +++ b/data/impcdata/impcdatabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "IMPCdata", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IMPCdata.html", "sc:version": "1.16.0" diff --git a/data/impre/imprebioschemas.jsonld b/data/impre/imprebioschemas.jsonld index 032c6565b7cf9..3e60c044569e6 100644 --- a/data/impre/imprebioschemas.jsonld +++ b/data/impre/imprebioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3389/fimmu.2016.00457", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/impre", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xiao Liu", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27867380", { "@id": "https://doi.org/10.3389/fimmu.2016.00457" }, + "pubmed:27867380", "pmcid:PMC5095119" ], "sc:description": "Immune Germline Prediction (IMPre), a tool for predicting germline Variable/Joining genes and alleles using deep-sequencing data derived from T-cell receptor/B-cell receptor repertoires.", @@ -33,6 +29,10 @@ "sc:name": "IMPre", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/zhangwei2015/IMPre" + }, + { + "@id": "https://doi.org/10.3389/fimmu.2016.00457", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/impulsede/impulsedebioschemas.jsonld b/data/impulsede/impulsedebioschemas.jsonld index ef135f8e14e9c..600bf010c63e7 100644 --- a/data/impulsede/impulsedebioschemas.jsonld +++ b/data/impulsede/impulsedebioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/impulsede", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jil Sander", - "Nir Yosef" + "Nir Yosef", + "Jil Sander" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This tool captures single impulse-like patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes whether across time points in a single experiment or between two time courses from two experiments. To optimize the running time, the code makes use of clustering steps and multi-threading.", "sc:license": "GPL-3.0", "sc:name": "ImpulseDE", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ImpulseDE.html", "sc:version": "1.0.0" diff --git a/data/impulsede2/impulsede2bioschemas.jsonld b/data/impulsede2/impulsede2bioschemas.jsonld index 5232437a8959e..7addd95c8b7b1 100644 --- a/data/impulsede2/impulsede2bioschemas.jsonld +++ b/data/impulsede2/impulsede2bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "ImpulseDE2", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ImpulseDE2.html", "sc:version": "1.4.0" diff --git a/data/impute/imputebioschemas.jsonld b/data/impute/imputebioschemas.jsonld index 91c959c934cc7..d19e93bf511ec 100644 --- a/data/impute/imputebioschemas.jsonld +++ b/data/impute/imputebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "impute", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/impute.html", "sc:version": "1.48.0" diff --git a/data/imsdb/imsdbbioschemas.jsonld b/data/imsdb/imsdbbioschemas.jsonld index 658966c829a8a..15d718fa89551 100644 --- a/data/imsdb/imsdbbioschemas.jsonld +++ b/data/imsdb/imsdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Comprehensive database application and analysis platform that is capable of combining metabolic data, like IMS chromatograms, and heterogeneous biomedical data, like patient records, into a centralized data structure.", "sc:name": "IMSDB", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "bmb.sdu.dk", diff --git a/data/imtrbm/imtrbmbioschemas.jsonld b/data/imtrbm/imtrbmbioschemas.jsonld index ec7fb5698d5b0..82b59f53af512 100644 --- a/data/imtrbm/imtrbmbioschemas.jsonld +++ b/data/imtrbm/imtrbmbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "IMTRBM", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/liuying201705/IMTRBM" } \ No newline at end of file diff --git a/data/imtrdb/imtrdbbioschemas.jsonld b/data/imtrdb/imtrdbbioschemas.jsonld index 0a12e66230ad4..9d2d312d4f279 100644 --- a/data/imtrdb/imtrdbbioschemas.jsonld +++ b/data/imtrdb/imtrdbbioschemas.jsonld @@ -21,8 +21,8 @@ "Desktop application" ], "sc:citation": [ - "pubmed:31284879", "pmcid:PMC6614062", + "pubmed:31284879", { "@id": "https://doi.org/10.1186/s12864-019-5536-1" } @@ -39,9 +39,9 @@ "sc:license": "Unlicense", "sc:name": "ImtRDB", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioinfodbs.kantiana.ru/ImtRDB/" }, diff --git a/data/incarnafbinv/incarnafbinvbioschemas.jsonld b/data/incarnafbinv/incarnafbinvbioschemas.jsonld index 1be47573a7170..c069b5634a34e 100644 --- a/data/incarnafbinv/incarnafbinvbioschemas.jsonld +++ b/data/incarnafbinv/incarnafbinvbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Fragment-based design of RNA sequences.", "sc:name": "incaRNAfbinv", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://www.cs.bgu.ac.il/incaRNAfbinv/" } \ No newline at end of file diff --git a/data/incgraph/incgraphbioschemas.jsonld b/data/incgraph/incgraphbioschemas.jsonld index c0c7bb424c655..7dc5d2d154bff 100644 --- a/data/incgraph/incgraphbioschemas.jsonld +++ b/data/incgraph/incgraphbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An efficient and incremental approach for calculating the differences in orbit counts when performing single edge modifications in a network. Calculating the differences in orbit counts is much more efficient than recalculating all orbit counts from scratch for each time point.", "sc:name": "IncGraph", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/incgraph/index.html" } \ No newline at end of file diff --git a/data/inchi/inchibioschemas.jsonld b/data/inchi/inchibioschemas.jsonld index 150093f160594..11f1047301051 100644 --- a/data/inchi/inchibioschemas.jsonld +++ b/data/inchi/inchibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A set of algorithms for the standard representation of chemical structures that will be readily accessible to chemists in all countries at no cost. The standard chemical representation could be used as input into existing and newly developed computer programs to generate a IUPAC name and a unique IUPAC identifier.", "sc:name": "InChI", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.chemspider.com/InChI.asmx", "sc:version": "1" diff --git a/data/incidence/incidencebioschemas.jsonld b/data/incidence/incidencebioschemas.jsonld index d350405de17ce..035added88e19 100644 --- a/data/incidence/incidencebioschemas.jsonld +++ b/data/incidence/incidencebioschemas.jsonld @@ -19,29 +19,29 @@ "biotools:primaryContact": "Zhian N. Kamvar", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:31119031", { "@id": "https://doi.org/10.12688/f1000research.18002.1" }, + "pubmed:31119031", "pmcid:PMC6509961" ], "sc:description": "R package for computation and visualization of epicurves from unaggregated linelist data.", "sc:featureList": [ { - "@id": "edam:operation_3503" + "@id": "edam:operation_3798" }, { "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3798" + "@id": "edam:operation_3503" } ], "sc:license": "MIT", "sc:name": "incidence", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://www.repidemicsconsortium.org/incidence", diff --git a/data/incromap/incromapbioschemas.jsonld b/data/incromap/incromapbioschemas.jsonld index 6937e2499765f..40334f32470df 100644 --- a/data/incromap/incromapbioschemas.jsonld +++ b/data/incromap/incromapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Powerful tool for pathway-based analysis or visualization of heterogeneous cross-platform microarray datasets (mRNA, miRNA, DNA methylation and protein).", "sc:name": "InCroMAP", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ra.cs.uni-tuebingen.de/software/InCroMAP/index.htm" } \ No newline at end of file diff --git a/data/incucytedrc/incucytedrcbioschemas.jsonld b/data/incucytedrc/incucytedrcbioschemas.jsonld index 6af7d40d17d8c..232e704ca86ac 100644 --- a/data/incucytedrc/incucytedrcbioschemas.jsonld +++ b/data/incucytedrc/incucytedrcbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/f1000research.8694.1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/incucytedrc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Phil J. Chapman", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5031130", { "@id": "https://doi.org/10.12688/f1000research.8694.1" }, - "pubmed:27703665" + "pubmed:27703665", + "pmcid:PMC5031130" ], "sc:description": "IncucyteDRC is an R package for the analysis of data from live cell imaging cell proliferation experiments carried out on the Essen Biosciences IncuCyte ZOOM instrument.", "sc:featureList": { @@ -33,10 +37,6 @@ ], "sc:url": "https://cran.r-project.org/web/packages/IncucyteDRC/index.html", "sc:version": "0.5.4" - }, - { - "@id": "https://doi.org/10.12688/f1000research.8694.1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/indcaps/indcapsbioschemas.jsonld b/data/indcaps/indcapsbioschemas.jsonld index 73e1fb0d9f252..544e7b2c85d78 100644 --- a/data/indcaps/indcapsbioschemas.jsonld +++ b/data/indcaps/indcapsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool for generating primers suitable for CAPS or dCAPS analyses of sites with insertions or deletions as well as SNPs.", "sc:name": "indCAPS", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://indcaps.kieber.cloudapps.unc.edu/" } \ No newline at end of file diff --git a/data/indecut/indecutbioschemas.jsonld b/data/indecut/indecutbioschemas.jsonld index cdf4f474ff433..21d4c8ac94d4a 100644 --- a/data/indecut/indecutbioschemas.jsonld +++ b/data/indecut/indecutbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/indecut", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Molly Megraw", - "David Koslicki" + "David Koslicki", + "Molly Megraw" ], "sc:additionalType": "Command-line tool", "sc:description": "A first method to evaluate uniform/independent graph sampling.", diff --git a/data/indeed/indeedbioschemas.jsonld b/data/indeed/indeedbioschemas.jsonld index 4bece8c8df8cf..99566ce22ed57 100644 --- a/data/indeed/indeedbioschemas.jsonld +++ b/data/indeed/indeedbioschemas.jsonld @@ -17,36 +17,36 @@ "@id": "https://bio.tools/INDEED", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yiming Zuo", - "Zhenzhi Li" + "Zhenzhi Li", + "Yiming Zuo" ], "sc:additionalType": "Library", "sc:author": "Zhenzhi Li", "sc:citation": [ + "pubmed:31179159", "pmcid:PMC6549230", { "@id": "https://doi.org/10.1109/BIBM.2018.8621426" - }, - "pubmed:31179159" + } ], "sc:description": "R package for network based differential expression analysis.", "sc:featureList": [ - { - "@id": "edam:operation_3741" - }, { "@id": "edam:operation_3463" }, { "@id": "edam:operation_3766" + }, + { + "@id": "edam:operation_3741" } ], "sc:license": "Artistic-2.0", "sc:name": "INDEED", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://bioconductor.org/packages/release/bioc/html/INDEED.html", "sc:version": "1.2.0" diff --git a/data/indelfr/indelfrbioschemas.jsonld b/data/indelfr/indelfrbioschemas.jsonld index 75834860273c6..69daf7048dc05 100644 --- a/data/indelfr/indelfrbioschemas.jsonld +++ b/data/indelfr/indelfrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of indels in protein structures and their flanking regions. Contains indels with flanking regions extracted from structural alignment pairs of non-redundant domains from superfamilies. Provides access to information about indels and their flanking regions.", "sc:name": "IndelFR", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://indel.bioinfo.sdu.edu.cn/gridsphere/gridsphere" } \ No newline at end of file diff --git a/data/indices_diversity/indices_diversitybioschemas.jsonld b/data/indices_diversity/indices_diversitybioschemas.jsonld index c7af1f4bf2fde..83e5edcdd1756 100644 --- a/data/indices_diversity/indices_diversitybioschemas.jsonld +++ b/data/indices_diversity/indices_diversitybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Compute Chao, Simpson and Shannon values from Sabund and Rabund files.", "sc:name": "indices_diversity", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/Indices_diversity/0.1%20beta", diff --git a/data/indigo/indigobioschemas.jsonld b/data/indigo/indigobioschemas.jsonld index 7bd94c2200064..bee499858d615 100644 --- a/data/indigo/indigobioschemas.jsonld +++ b/data/indigo/indigobioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:24324765", - "pmcid:PMC3855842", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0082210" - } + }, + "pubmed:24324765", + "pmcid:PMC3855842" ], "sc:description": "INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles.", "sc:featureList": [ @@ -36,9 +36,9 @@ ], "sc:name": "INDIGO", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.cbrc.kaust.edu.sa/indigo/begin.do" } diff --git a/data/indra-ipm/indra-ipmbioschemas.jsonld b/data/indra-ipm/indra-ipmbioschemas.jsonld index fb4707576176b..3a22a4d6a907e 100644 --- a/data/indra-ipm/indra-ipmbioschemas.jsonld +++ b/data/indra-ipm/indra-ipmbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "BSD-2-Clause", "sc:name": "INDRA-IPM", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://pathwaymap.indra.bio/" } \ No newline at end of file diff --git a/data/infernal_cmscan/infernal_cmscanbioschemas.jsonld b/data/infernal_cmscan/infernal_cmscanbioschemas.jsonld index e9ea9662a1aef..666f35e96d7da 100644 --- a/data/infernal_cmscan/infernal_cmscanbioschemas.jsonld +++ b/data/infernal_cmscan/infernal_cmscanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Infernal cmscan", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/rna/infernal_cmscan_rest", "sc:version": "1" diff --git a/data/infiniumpurify/infiniumpurifybioschemas.jsonld b/data/infiniumpurify/infiniumpurifybioschemas.jsonld index a08b7f1046613..b560352e11df8 100644 --- a/data/infiniumpurify/infiniumpurifybioschemas.jsonld +++ b/data/infiniumpurify/infiniumpurifybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/infiniumpurify", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Naiqian Zhang", - "Xiaoqi Zheng" + "Xiaoqi Zheng", + "Naiqian Zhang" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:26112293", diff --git a/data/infmod3dgen/infmod3dgenbioschemas.jsonld b/data/infmod3dgen/infmod3dgenbioschemas.jsonld index c53c5fd21ea62..02001eeac9403 100644 --- a/data/infmod3dgen/infmod3dgenbioschemas.jsonld +++ b/data/infmod3dgen/infmod3dgenbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "New Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data.", "sc:name": "InfMod3DGen", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/wangsy11/InfMod3DGen" } \ No newline at end of file diff --git a/data/info-rna/info-rnabioschemas.jsonld b/data/info-rna/info-rnabioschemas.jsonld index b50ddc12907ca..9f22036d58adf 100644 --- a/data/info-rna/info-rnabioschemas.jsonld +++ b/data/info-rna/info-rnabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.", "sc:name": "INFO-RNA", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.bioinf.uni-freiburg.de/Software/INFO-RNA/start.html" } \ No newline at end of file diff --git a/data/infoalign/infoalignbioschemas.jsonld b/data/infoalign/infoalignbioschemas.jsonld index feff0dfd216e9..715111f7f1adc 100644 --- a/data/infoalign/infoalignbioschemas.jsonld +++ b/data/infoalign/infoalignbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK BBSRC", + "EMBOSS Contributors", "UK MRC", "Wellcome Trust" ], "sc:description": "Display basic information about a multiple sequence alignment.", "sc:funder": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "infoalign", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/infoalign.html", "sc:version": "r6" diff --git a/data/infoassembly/infoassemblybioschemas.jsonld b/data/infoassembly/infoassemblybioschemas.jsonld index 46809e447944f..bb30f9922eb9e 100644 --- a/data/infoassembly/infoassemblybioschemas.jsonld +++ b/data/infoassembly/infoassemblybioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK MRC", "UK BBSRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK MRC", + "Wellcome Trust" ], "sc:description": "An Emboss tool that writes statistics for a sequence assembly", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "infoassembly", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/infobase/infobasebioschemas.jsonld b/data/infobase/infobasebioschemas.jsonld index 2cd3abd1eca3f..fc0484cbcd1d8 100644 --- a/data/infobase/infobasebioschemas.jsonld +++ b/data/infobase/infobasebioschemas.jsonld @@ -27,8 +27,8 @@ "sc:name": "infobase", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/infocalc/infocalcbioschemas.jsonld b/data/infocalc/infocalcbioschemas.jsonld index 2b14be8dd2f2c..f79dd867bec3d 100644 --- a/data/infocalc/infocalcbioschemas.jsonld +++ b/data/infocalc/infocalcbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Small script for calculating statistics that measure the ancestry information content of genetic markers.", "sc:name": "infocalc", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.stanford.edu/group/rosenberglab/infocalc.html" } \ No newline at end of file diff --git a/data/inforesidue/inforesiduebioschemas.jsonld b/data/inforesidue/inforesiduebioschemas.jsonld index d8326ea48b489..03ddc9e51d9ea 100644 --- a/data/inforesidue/inforesiduebioschemas.jsonld +++ b/data/inforesidue/inforesiduebioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", "Wellcome Trust", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK MRC", + "UK BBSRC" ], "sc:description": "Return information on a given amino acid residue.", "sc:funder": [ - "UK BBSRC", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "inforesidue", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/inforna/infornabioschemas.jsonld b/data/inforna/infornabioschemas.jsonld index 9ba240f74cc1e..15e7c1ad2f365 100644 --- a/data/inforna/infornabioschemas.jsonld +++ b/data/inforna/infornabioschemas.jsonld @@ -13,14 +13,18 @@ "@id": "http://orcid.org/0000-0001-8231-3323", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1093/nar/gkm218", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/inforna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Anke Busch", { "@id": "http://orcid.org/0000-0001-8231-3323" - } + }, + "Anke Busch" ], "edam:has_input": { "@id": "edam:data_0880" @@ -57,9 +61,9 @@ "sc:isAccessibleForFree": true, "sc:name": "INFORNA Sequence Design", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": [ "University Freiburg", @@ -70,10 +74,6 @@ }, "sc:url": "http://rna.informatik.uni-freiburg.de/INFORNA/", "sc:version": "2.2.0" - }, - { - "@id": "https://doi.org/10.1093/nar/gkm218", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/infoseq/infoseqbioschemas.jsonld b/data/infoseq/infoseqbioschemas.jsonld index 2295f08fb7ef1..2bf8f4bddb7cd 100644 --- a/data/infoseq/infoseqbioschemas.jsonld +++ b/data/infoseq/infoseqbioschemas.jsonld @@ -13,21 +13,21 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "UK BBSRC", + "EMBOSS Contributors", "UK MRC", - "EMBOSS Contributors" + "UK BBSRC" ], "sc:description": "Display basic information about sequences.", "sc:funder": [ "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "infoseq", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ diff --git a/data/inga/ingabioschemas.jsonld b/data/inga/ingabioschemas.jsonld index 0d4925cb8b61f..2db53ea28f0d4 100644 --- a/data/inga/ingabioschemas.jsonld +++ b/data/inga/ingabioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1093/nar/gkv523", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0003-4525-7793", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/inga", "@type": "sc:SoftwareApplication", @@ -25,18 +21,18 @@ }, "edam:has_input": [ { - "@id": "edam:data_3021" + "@id": "edam:data_2976" }, { - "@id": "edam:data_2976" + "@id": "edam:data_3021" } ], "edam:has_output": { "@id": "edam:data_2858" }, "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:applicationSubCategory": { "@id": "edam:topic_1775" @@ -54,16 +50,20 @@ }, "sc:name": "INGA", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", - "ELIXIR-ITA-PADOVA" + "ELIXIR-ITA-PADOVA", + "University of Padua, Department of Biomedical Sciences, BioComputing UP lab" ], "sc:url": "http://protein.bio.unipd.it/inga", "sc:version": "1.1" + }, + { + "@id": "http://orcid.org/0000-0003-4525-7793", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/ingap-sv/ingap-svbioschemas.jsonld b/data/ingap-sv/ingap-svbioschemas.jsonld index 05a55151efb6b..bcdbadbe834fa 100644 --- a/data/ingap-sv/ingap-svbioschemas.jsonld +++ b/data/ingap-sv/ingap-svbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/ingap-sv", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ji Qi", - "Fangqing Zhao" + "Fangqing Zhao", + "Ji Qi" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:21715388", @@ -20,8 +20,8 @@ "sc:name": "inGAP-sv", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://ingap.sourceforge.net" } \ No newline at end of file diff --git a/data/ingap/ingapbioschemas.jsonld b/data/ingap/ingapbioschemas.jsonld index 1dfcc8512f40f..a4f3ff0db025b 100644 --- a/data/ingap/ingapbioschemas.jsonld +++ b/data/ingap/ingapbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/ingap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ji Qi", - "F Zhao" + "F Zhao", + "Ji Qi" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:19880367", @@ -20,8 +20,8 @@ "sc:name": "inGAP", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ingap.sourceforge.net/" } \ No newline at end of file diff --git a/data/ingeneue/ingeneuebioschemas.jsonld b/data/ingeneue/ingeneuebioschemas.jsonld index c826418ad69e4..8f0f742383695 100644 --- a/data/ingeneue/ingeneuebioschemas.jsonld +++ b/data/ingeneue/ingeneuebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Ingeneue", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://rusty.fhl.washington.edu/ingeneue/index.html" } \ No newline at end of file diff --git a/data/ingenuity_variant_analysis/ingenuity_variant_analysisbioschemas.jsonld b/data/ingenuity_variant_analysis/ingenuity_variant_analysisbioschemas.jsonld index 7df4e690c288f..d924491bae4f5 100644 --- a/data/ingenuity_variant_analysis/ingenuity_variant_analysisbioschemas.jsonld +++ b/data/ingenuity_variant_analysis/ingenuity_variant_analysisbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web application that helps researchers studying human disease to identify causal variants.", "sc:name": "Ingenuity Variant Analysis", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.ingenuity.com/products/ingenuity_variant_analysis.html" } \ No newline at end of file diff --git a/data/initro-tyr/initro-tyrbioschemas.jsonld b/data/initro-tyr/initro-tyrbioschemas.jsonld index 396719e5354c2..c5d15e8c31609 100644 --- a/data/initro-tyr/initro-tyrbioschemas.jsonld +++ b/data/initro-tyr/initro-tyrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "iNitro-Tyr", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://app.aporc.org/iNitro-Tyr/" } \ No newline at end of file diff --git a/data/inmex/inmexbioschemas.jsonld b/data/inmex/inmexbioschemas.jsonld index 4954e1e027573..c3a196e5d53b0 100644 --- a/data/inmex/inmexbioschemas.jsonld +++ b/data/inmex/inmexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web based tool designed to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments.", "sc:name": "INMEX", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.inmex.ca" diff --git a/data/innatedb/innatedbbioschemas.jsonld b/data/innatedb/innatedbbioschemas.jsonld index 7866db9c735a7..312d214ee54f0 100644 --- a/data/innatedb/innatedbbioschemas.jsonld +++ b/data/innatedb/innatedbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource.", "sc:name": "InnateDB", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.innatedb.com/", "sc:version": "1" diff --git a/data/inparanoid/inparanoidbioschemas.jsonld b/data/inparanoid/inparanoidbioschemas.jsonld index 18a2d2ce780b8..b3fe054121767 100644 --- a/data/inparanoid/inparanoidbioschemas.jsonld +++ b/data/inparanoid/inparanoidbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A database of orthologs in eukaryotes.", "sc:name": "Inparanoid", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "bils.se", "sc:url": "http://inparanoid.sbc.su.se/" diff --git a/data/inpas/inpasbioschemas.jsonld b/data/inpas/inpasbioschemas.jsonld index 831b3ee3aae9d..bf2b11a0e31dd 100644 --- a/data/inpas/inpasbioschemas.jsonld +++ b/data/inpas/inpasbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "InPAS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/InPAS.html", "sc:version": "1.6.0" diff --git a/data/inpower/bioconda_inpower.yaml b/data/inpower/bioconda_inpower.yaml index 6cf3575b673ff..ded11eaf49273 100644 --- a/data/inpower/bioconda_inpower.yaml +++ b/data/inpower/bioconda_inpower.yaml @@ -4,7 +4,6 @@ description: An R package for computing the number of susceptibility SNPs and po home: https://bioconductor.org/packages/3.10/bioc/html/INPower.html identifiers: - biotools:inpower -- doi:10.1038/nmeth.3252 license: GPL-2 + file LICENSE license_file: LICENSE name: bioconductor-inpower diff --git a/data/inpower/inpowerbioschemas.jsonld b/data/inpower/inpowerbioschemas.jsonld index 209dc20014c45..58db04b45e335 100644 --- a/data/inpower/inpowerbioschemas.jsonld +++ b/data/inpower/inpowerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "INPower", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/INPower.html", "sc:version": "1.10.0" diff --git a/data/inps/inpsbioschemas.jsonld b/data/inps/inpsbioschemas.jsonld index 4403d3d39b526..9a6ebf1477579 100644 --- a/data/inps/inpsbioschemas.jsonld +++ b/data/inps/inpsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Predicting the impact of mutations on protein stability from sequence", "sc:name": "INPS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "http://inps.biocomp.unibo.it", diff --git a/data/inr-physchem/inr-physchembioschemas.jsonld b/data/inr-physchem/inr-physchembioschemas.jsonld index 263c3d25ef332..ef66e6a4d9d02 100644 --- a/data/inr-physchem/inr-physchembioschemas.jsonld +++ b/data/inr-physchem/inr-physchembioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "iNR-PhysChem", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.jci-bioinfo.cn/iNR-PhysChem" } \ No newline at end of file diff --git a/data/insdc/insdcbioschemas.jsonld b/data/insdc/insdcbioschemas.jsonld index eddc4b638c530..078cc28dfc3b4 100644 --- a/data/insdc/insdcbioschemas.jsonld +++ b/data/insdc/insdcbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This database consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. It is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. It covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations.", "sc:name": "Nucleotide Sequence Database Collaboration", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "Identifiers.org", "sc:url": "http://identifiers.org/insdc/" diff --git a/data/insect/insectbioschemas.jsonld b/data/insect/insectbioschemas.jsonld index 8c1fb294132cd..0b0559e067f1e 100644 --- a/data/insect/insectbioschemas.jsonld +++ b/data/insect/insectbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Easy-to-use and powerful web server for biologists analysing genomic sequence data for in silico cis-regulatory modules prediction and analysis.", "sc:name": "INSECT", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT2/" diff --git a/data/insectbase/insectbasebioschemas.jsonld b/data/insectbase/insectbasebioschemas.jsonld index 00f75f3d13715..15760ce373202 100644 --- a/data/insectbase/insectbasebioschemas.jsonld +++ b/data/insectbase/insectbasebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "InsectBase", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.insect-genome.com/" } \ No newline at end of file diff --git a/data/inserm-remap/inserm-remapbioschemas.jsonld b/data/inserm-remap/inserm-remapbioschemas.jsonld index 3d4073e45f89c..98309c76f426d 100644 --- a/data/inserm-remap/inserm-remapbioschemas.jsonld +++ b/data/inserm-remap/inserm-remapbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:description": "Integrative analysis of transcription factor ChIP-seq experiments publicly available merged with the Encode dataset. We propose an extensive regulatory catalogue of 8 million transcription factor binding sites from 237 transcription factors (TFs). Among those factors 50 TFs are common with Encode, 82 TFs are Public specific and 105 Encode specific. The results of this analysis are available to browse or download either for a given transcription factor or for the entire dataset.", "sc:name": "ReMap", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://tagc.univ-mrs.fr/remap/index.php", diff --git a/data/insertionmapper/insertionmapperbioschemas.jsonld b/data/insertionmapper/insertionmapperbioschemas.jsonld index 259187e39c6ce..58ab884a4e6b7 100644 --- a/data/insertionmapper/insertionmapperbioschemas.jsonld +++ b/data/insertionmapper/insertionmapperbioschemas.jsonld @@ -27,8 +27,8 @@ }, "sc:name": "InsertionMapper", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://sourceforge.net/projects/insertionmapper/" diff --git a/data/insilicosimmolbioexpt/insilicosimmolbioexptbioschemas.jsonld b/data/insilicosimmolbioexpt/insilicosimmolbioexptbioschemas.jsonld index 7de2f5c74fd6e..6a6d9657e8548 100644 --- a/data/insilicosimmolbioexpt/insilicosimmolbioexptbioschemas.jsonld +++ b/data/insilicosimmolbioexpt/insilicosimmolbioexptbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "In silico simulation of molbio experiments", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://insilico.ehu.es/" } \ No newline at end of file diff --git a/data/insilicospectro/insilicospectrobioschemas.jsonld b/data/insilicospectro/insilicospectrobioschemas.jsonld index ac6911557af5d..ad347be48e838 100644 --- a/data/insilicospectro/insilicospectrobioschemas.jsonld +++ b/data/insilicospectro/insilicospectrobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "InSilicoSpectro", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://search.cpan.org/~alexmass/InSilicoSpectro/" } \ No newline at end of file diff --git a/data/inspiired/inspiiredbioschemas.jsonld b/data/inspiired/inspiiredbioschemas.jsonld index ad9738269339f..855fd9d45fb49 100644 --- a/data/inspiired/inspiiredbioschemas.jsonld +++ b/data/inspiired/inspiiredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "INSPIIRED", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/BushmanLab/INSPIIRED" } \ No newline at end of file diff --git a/data/institute_of_enzymology_servers/institute_of_enzymology_serversbioschemas.jsonld b/data/institute_of_enzymology_servers/institute_of_enzymology_serversbioschemas.jsonld index bd3a2513b5bbf..6bb3b0da962c2 100644 --- a/data/institute_of_enzymology_servers/institute_of_enzymology_serversbioschemas.jsonld +++ b/data/institute_of_enzymology_servers/institute_of_enzymology_serversbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.", "sc:name": "Institute of Enzymology Servers", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.ttk.mta.hu/en/szolgaltatas/adatbazisok/" } \ No newline at end of file diff --git a/data/insyght/insyghtbioschemas.jsonld b/data/insyght/insyghtbioschemas.jsonld index 1c52c4b4b1270..93a15a1039723 100644 --- a/data/insyght/insyghtbioschemas.jsonld +++ b/data/insyght/insyghtbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Browser that helps navigate among abundant homologies, syntenies and genes annotations.", "sc:name": "Insyght", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://genome.jouy.inra.fr/Insyght" } \ No newline at end of file diff --git a/data/intaa/intaabioschemas.jsonld b/data/intaa/intaabioschemas.jsonld index 69c099c27fe0d..6ed626819678f 100644 --- a/data/intaa/intaabioschemas.jsonld +++ b/data/intaa/intaabioschemas.jsonld @@ -17,16 +17,16 @@ "Jakub Galgonek" ], "sc:contributor": [ - "Jiří Vymětal", - "David Jakubec" + "David Jakubec", + "Jiří Vymětal" ], "sc:description": "Calculates the residue Interaction Energy Matrix for any protein structure and offers comprehensive analysis of the interfaces in protein–DNA complexes.", "sc:license": "Other", "sc:name": "Amino Acids Interactions Web Server", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioinfo.uochb.cas.cz/INTAA/", "sc:version": "1.0" diff --git a/data/intact/intactbioschemas.jsonld b/data/intact/intactbioschemas.jsonld index 03f6c39ad898e..2a87d22b62707 100644 --- a/data/intact/intactbioschemas.jsonld +++ b/data/intact/intactbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Protein interaction database and analysis system.", "sc:name": "IntAct", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI Databases", "sc:url": "http://www.ebi.ac.uk/intact/" diff --git a/data/intad/intadbioschemas.jsonld b/data/intad/intadbioschemas.jsonld index 30ad905d14162..1b613f74d00f4 100644 --- a/data/intad/intadbioschemas.jsonld +++ b/data/intad/intadbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "InTAD", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/InTAD.html", "sc:version": "1.0.0" diff --git a/data/intansv/intansvbioschemas.jsonld b/data/intansv/intansvbioschemas.jsonld index 644830a6788f2..5a7f25112382b 100644 --- a/data/intansv/intansvbioschemas.jsonld +++ b/data/intansv/intansvbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Wen Yao", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.", "sc:license": "Artistic-2.0", "sc:name": "intansv", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/intansv.html", diff --git a/data/intarna/intarnabioschemas.jsonld b/data/intarna/intarnabioschemas.jsonld index 113970ea9434a..f06c0463e0cdb 100644 --- a/data/intarna/intarnabioschemas.jsonld +++ b/data/intarna/intarnabioschemas.jsonld @@ -9,32 +9,32 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-8231-3323", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1093/nar/gku359", "@type": "sc:CreativeWork" }, + { + "@id": "http://orcid.org/0000-0001-8231-3323", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/intarna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Patrick Wright", { "@id": "http://orcid.org/0000-0001-8231-3323" - } + }, + "Patrick Wright" ], "edam:has_input": { "@id": "edam:data_3495" }, "edam:has_output": [ { - "@id": "edam:data_1270" + "@id": "edam:data_2968" }, { - "@id": "edam:data_2968" + "@id": "edam:data_1270" } ], "sc:additionalType": "Web application", @@ -43,11 +43,11 @@ }, "sc:author": "Patrick Wright", "sc:citation": [ - "pmcid:PMC4086077", - "pubmed:24838564", { "@id": "https://doi.org/10.1093/nar/gku359" - } + }, + "pmcid:PMC4086077", + "pubmed:24838564" ], "sc:description": "sRNA target prediction.", "sc:featureList": { diff --git a/data/intb/intbbioschemas.jsonld b/data/intb/intbbioschemas.jsonld index 4aea7186da255..9669acfe251c0 100644 --- a/data/intb/intbbioschemas.jsonld +++ b/data/intb/intbbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-14-264", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/intb", "@type": "sc:SoftwareApplication", @@ -22,31 +18,35 @@ "Web application" ], "sc:citation": [ + "pubmed:24001185", { "@id": "https://doi.org/10.1186/1471-2105-14-264" }, - "pmcid:PMC3847221", - "pubmed:24001185" + "pmcid:PMC3847221" ], "sc:description": "Data integration platform for molecular and clinical epidemiological analysis of tuberculosis.", "sc:featureList": [ - { - "@id": "edam:operation_3461" - }, { "@id": "edam:operation_2421" }, { "@id": "edam:operation_3197" + }, + { + "@id": "edam:operation_3461" } ], "sc:name": "inTB", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.evocell.org/inTB" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-264", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/intcomp/intcompbioschemas.jsonld b/data/intcomp/intcompbioschemas.jsonld index c973638318f97..ffa4d0a642daf 100644 --- a/data/intcomp/intcompbioschemas.jsonld +++ b/data/intcomp/intcompbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This R package provides a benchmarking tools for quantitative comparison of cancer gene detection algorithms based on integrative analysis of DNA copy number and gene expression data.", "sc:name": "intcomp", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://intcomp.r-forge.r-project.org/" } \ No newline at end of file diff --git a/data/integrall/integrallbioschemas.jsonld b/data/integrall/integrallbioschemas.jsonld index 03827b82c305e..84883f5ad0e3b 100644 --- a/data/integrall/integrallbioschemas.jsonld +++ b/data/integrall/integrallbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/integrall", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Thomas Jové (Curation and In numbering attributions)", "General Support", + "Thomas Jové (Curation and In numbering attributions)", "Alexandra Moura (Website and database related issues)" ], "sc:additionalType": "Web application", @@ -20,9 +20,9 @@ "sc:description": "INTEGRALL is a freely available, text-based search system developed to collect and organize information on integrons. There are more than 4800 integron sequences in the database.", "sc:name": "INTEGRALL", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://integrall.bio.ua.pt/" } \ No newline at end of file diff --git a/data/integrate-vis/integrate-visbioschemas.jsonld b/data/integrate-vis/integrate-visbioschemas.jsonld index 479b373c05cfb..b193660ca58e3 100644 --- a/data/integrate-vis/integrate-visbioschemas.jsonld +++ b/data/integrate-vis/integrate-visbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "INTEGRATE-Vis", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ChrisMaherLab/INTEGRATE-Vis" } \ No newline at end of file diff --git a/data/integrative_somatic_mutation_analysis/integrative_somatic_mutation_analysisbioschemas.jsonld b/data/integrative_somatic_mutation_analysis/integrative_somatic_mutation_analysisbioschemas.jsonld index 4aefe6533c80c..e7cbb3f40c509 100644 --- a/data/integrative_somatic_mutation_analysis/integrative_somatic_mutation_analysisbioschemas.jsonld +++ b/data/integrative_somatic_mutation_analysis/integrative_somatic_mutation_analysisbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2701-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/integrative_somatic_mutation_analysis", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC6394085", - "pubmed:30819096", { "@id": "https://doi.org/10.1186/s12859-019-2701-0" - } + }, + "pubmed:30819096" ], "sc:description": "isma (integrative somatic mutation analysis) - R package for the integrative analysis of mutations detected by multiple pipelines.", "sc:featureList": [ @@ -38,10 +42,6 @@ ], "sc:url": "https://www.itb.cnr.it/web/bioinformatics/isma", "sc:version": "0.1.3" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2701-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/integrative_somatic_mutation_analysis_isma/integrative_somatic_mutation_analysis_ismabioschemas.jsonld b/data/integrative_somatic_mutation_analysis_isma/integrative_somatic_mutation_analysis_ismabioschemas.jsonld index 809c78019a10e..2a8ccce46ae8a 100644 --- a/data/integrative_somatic_mutation_analysis_isma/integrative_somatic_mutation_analysis_ismabioschemas.jsonld +++ b/data/integrative_somatic_mutation_analysis_isma/integrative_somatic_mutation_analysis_ismabioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2701-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/integrative_somatic_mutation_analysis_isma", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Noemi Di Nanni", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:30819096", "pmcid:PMC6394085", { "@id": "https://doi.org/10.1186/s12859-019-2701-0" - }, - "pubmed:30819096" + } ], "sc:description": "R package for the integrative analysis of mutations detected by multiple pipelines.", "sc:featureList": [ @@ -33,15 +37,11 @@ "sc:name": "integrative somatic mutation analysis (isma)", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.itb.cnr.it/web/bioinformatics/isma", "sc:version": "0.1.3" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2701-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/integron_finder/integron_finderbioschemas.jsonld b/data/integron_finder/integron_finderbioschemas.jsonld index b2285f5083c81..9dd450e26b0a6 100644 --- a/data/integron_finder/integron_finderbioschemas.jsonld +++ b/data/integron_finder/integron_finderbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "Integron Finder", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Institut Pasteur", "sc:url": "https://github.com/gem-pasteur/Integron_Finder", diff --git a/data/interactionset/interactionsetbioschemas.jsonld b/data/interactionset/interactionsetbioschemas.jsonld index 8351e1ff2fd9d..c12de63fac1a7 100644 --- a/data/interactionset/interactionsetbioschemas.jsonld +++ b/data/interactionset/interactionsetbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://doi.org/10.12688/f1000research.8759.2", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0002-3564-4813", + "@type": "schema:Person" }, { "@id": "https://bio.tools/interactionset", @@ -20,14 +20,14 @@ "@id": "http://orcid.org/0000-0002-3564-4813" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:27303634", { "@id": "https://doi.org/10.12688/f1000research.8759.2" }, + "pubmed:27303634", "pmcid:PMC4890298" ], "sc:description": "This tool provides objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.", @@ -37,16 +37,16 @@ "sc:license": "GPL-3.0", "sc:name": "InteractionSet", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/InteractionSet.html", "sc:version": "1.2.0" }, { - "@id": "http://orcid.org/0000-0002-3564-4813", - "@type": "schema:Person" + "@id": "https://doi.org/10.12688/f1000research.8759.2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/interactivedisplay/bioconda_interactivedisplay.yaml b/data/interactivedisplay/bioconda_interactivedisplay.yaml index 5e36697abc908..240ac885bb9ac 100644 --- a/data/interactivedisplay/bioconda_interactivedisplay.yaml +++ b/data/interactivedisplay/bioconda_interactivedisplay.yaml @@ -4,7 +4,6 @@ description: The interactiveDisplay package contains the methods needed to gener home: https://bioconductor.org/packages/3.10/bioc/html/interactiveDisplay.html identifiers: - biotools:interactivedisplay -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-interactivedisplay summary: Package for enabling powerful shiny web displays of Bioconductor objects diff --git a/data/interactivedisplay/interactivedisplaybioschemas.jsonld b/data/interactivedisplay/interactivedisplaybioschemas.jsonld index 375e6b070c289..b8fb69a52f044 100644 --- a/data/interactivedisplay/interactivedisplaybioschemas.jsonld +++ b/data/interactivedisplay/interactivedisplaybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "interactiveDisplay", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/interactiveDisplay.html", "sc:version": "1.12.0" diff --git a/data/interactivedisplaybase/bioconda_interactivedisplaybase.yaml b/data/interactivedisplaybase/bioconda_interactivedisplaybase.yaml index 248b3285b9a0d..89083fd4cbe07 100644 --- a/data/interactivedisplaybase/bioconda_interactivedisplaybase.yaml +++ b/data/interactivedisplaybase/bioconda_interactivedisplaybase.yaml @@ -4,7 +4,6 @@ description: The interactiveDisplayBase package contains the the basic methods n home: https://bioconductor.org/packages/3.10/bioc/html/interactiveDisplayBase.html identifiers: - biotools:interactivedisplaybase -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-interactivedisplaybase summary: Base package for enabling powerful shiny web displays of Bioconductor objects diff --git a/data/interactivedisplaybase/interactivedisplaybasebioschemas.jsonld b/data/interactivedisplaybase/interactivedisplaybasebioschemas.jsonld index 7d101d7ff2b15..91d061dc06f05 100644 --- a/data/interactivedisplaybase/interactivedisplaybasebioschemas.jsonld +++ b/data/interactivedisplaybase/interactivedisplaybasebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Shawn Balcome", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package contains the basic methods needed to generate interactive Shiny-based display methods for BioConductor objects.", "sc:license": "Artistic-2.0", "sc:name": "interactiveDisplayBase", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/interactiveDisplayBase.html", "sc:version": "1.12.0" diff --git a/data/interactivenn/interactivennbioschemas.jsonld b/data/interactivenn/interactivennbioschemas.jsonld index 57bdf4c505ebb..0d5ada5ad6eb6 100644 --- a/data/interactivenn/interactivennbioschemas.jsonld +++ b/data/interactivenn/interactivennbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Henry Heberle", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4455604", { "@id": "https://doi.org/10.1186/S12859-015-0611-3" }, - "pubmed:25994840" + "pubmed:25994840", + "pmcid:PMC4455604" ], "sc:description": "A web-based tool for the analysis of sets through Venn diagrams.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "InteractiVenn", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.interactivenn.net/" } diff --git a/data/interactiverosetta/interactiverosettabioschemas.jsonld b/data/interactiverosetta/interactiverosettabioschemas.jsonld index 7b206631a3fa3..d9072bd740537 100644 --- a/data/interactiverosetta/interactiverosettabioschemas.jsonld +++ b/data/interactiverosetta/interactiverosettabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A wxPython graphical interface for the PyRosetta and Rosetta protein modeling suites.", "sc:name": "InteractiveROSETTA", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/schenc3/InteractiveROSETTA" } \ No newline at end of file diff --git a/data/interactome_insider/interactome_insiderbioschemas.jsonld b/data/interactome_insider/interactome_insiderbioschemas.jsonld index 9b80e6ff01a90..ae221076a3cb0 100644 --- a/data/interactome_insider/interactome_insiderbioschemas.jsonld +++ b/data/interactome_insider/interactome_insiderbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Freeware", "sc:name": "Interactome INSIDER", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://interactomeinsider.yulab.org/" diff --git a/data/interest/interestbioschemas.jsonld b/data/interest/interestbioschemas.jsonld index 8c208cb51d4c3..708978b65ed55 100644 --- a/data/interest/interestbioschemas.jsonld +++ b/data/interest/interestbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "IntEREst", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IntEREst.html", "sc:version": "1.4.1" diff --git a/data/interevol/interevolbioschemas.jsonld b/data/interevol/interevolbioschemas.jsonld index 20b80bda65491..c9f2d2a7eafd4 100644 --- a/data/interevol/interevolbioschemas.jsonld +++ b/data/interevol/interevolbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database designed to explore 3D structures of homologous interfaces of protein complexes. Provides tools to retrieve and visualize these structures, including downloadable pre-computed multiple sequence alignments.", "sc:name": "InterEvol", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://biodev.cea.fr/interevol/" } \ No newline at end of file diff --git a/data/interferome/interferomebioschemas.jsonld b/data/interferome/interferomebioschemas.jsonld index cc1a416174ad1..7666b931aee70 100644 --- a/data/interferome/interferomebioschemas.jsonld +++ b/data/interferome/interferomebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Open access database of types I, II and III Interferon regulated genes collected from analysing expression data sets of cells treated with IFNs. This database integrates expression information with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and gene regulatory information.", "sc:name": "INTERFEROME", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.interferome.org/" } \ No newline at end of file diff --git a/data/intergr8/intergr8bioschemas.jsonld b/data/intergr8/intergr8bioschemas.jsonld index df0494a0afe0e..bc03f2aace716 100644 --- a/data/intergr8/intergr8bioschemas.jsonld +++ b/data/intergr8/intergr8bioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Browser for information relating to completed genomes and proteomes. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO.", "sc:name": "Intergr8", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.ebi.ac.uk/integr8/" diff --git a/data/intermap3d/intermap3dbioschemas.jsonld b/data/intermap3d/intermap3dbioschemas.jsonld index 81368c89e2776..5ba8f47e0b7b0 100644 --- a/data/intermap3d/intermap3dbioschemas.jsonld +++ b/data/intermap3d/intermap3dbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "InterMap3D", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "CBS", diff --git a/data/intermine/interminebioschemas.jsonld b/data/intermine/interminebioschemas.jsonld index eee483b2886d0..c7b25480652d8 100644 --- a/data/intermine/interminebioschemas.jsonld +++ b/data/intermine/interminebioschemas.jsonld @@ -9,50 +9,50 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/bts577", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/intermine", "@type": "sc:SoftwareApplication", "sc:additionalType": [ + "Database portal", "Web API", - "Command-line tool", "Web application", - "Database portal" + "Command-line tool" ], "sc:citation": [ - "pubmed:23023984", + "pmcid:PMC3516146", { "@id": "https://doi.org/10.1093/bioinformatics/bts577" }, - "pmcid:PMC3516146", - "pubmed:24753429" + "pubmed:24753429", + "pubmed:23023984" ], "sc:contributor": [ - "NIH", "Wellcome Trust", + "NIH", "BBSRC" ], "sc:description": "Open source data warehouse built specifically for the integration and analysis of complex biological data. It enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data.", "sc:funder": [ "BBSRC", - "Wellcome Trust", - "NIH" + "NIH", + "Wellcome Trust" ], "sc:license": "LGPL-2.1", "sc:name": "InterMine", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "University of Cambridge", - "gen.cam.ac.uk" + "gen.cam.ac.uk", + "University of Cambridge" ], "sc:url": "http://www.intermine.org", "sc:version": "4.1.1" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/bts577", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/interminer/interminerbioschemas.jsonld b/data/interminer/interminerbioschemas.jsonld index d952a098d848e..b3827ee87fb34 100644 --- a/data/interminer/interminerbioschemas.jsonld +++ b/data/interminer/interminerbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "InterMine Team", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:23023984", - "pmcid:PMC3516146", { "@id": "https://doi.org/10.1093/bioinformatics/bts577" - } + }, + "pmcid:PMC3516146", + "pubmed:23023984" ], "sc:description": "Databases based on the InterMine platform such as FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine and TargetMine are integrated databases of genomic, expression and protein data for various organisms. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:license": "LGPL-2.0", "sc:name": "InterMineR", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/InterMineR.html", diff --git a/data/interolog/interologbioschemas.jsonld b/data/interolog/interologbioschemas.jsonld index 2f4dd432bc541..152edbf793c53 100644 --- a/data/interolog/interologbioschemas.jsonld +++ b/data/interolog/interologbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/interolog", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Xiaowei Zhu", - "Haiyuan Yu" + "Haiyuan Yu", + "Xiaowei Zhu" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:15173116", "sc:description": "Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.", "sc:name": "Interolog Regulog Database", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://interolog.gersteinlab.org/" } \ No newline at end of file diff --git a/data/interolog_regulog_db/interolog_regulog_dbbioschemas.jsonld b/data/interolog_regulog_db/interolog_regulog_dbbioschemas.jsonld index 9abb14cbdcc80..2a525b13838b8 100644 --- a/data/interolog_regulog_db/interolog_regulog_dbbioschemas.jsonld +++ b/data/interolog_regulog_db/interolog_regulog_dbbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.", "sc:name": "Interolog Regulog Database", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://interolog.gersteinlab.org/" } \ No newline at end of file diff --git a/data/interoporc/interoporcbioschemas.jsonld b/data/interoporc/interoporcbioschemas.jsonld index 04193d5032fc5..c4a0dd9c96851 100644 --- a/data/interoporc/interoporcbioschemas.jsonld +++ b/data/interoporc/interoporcbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Automatic prediction tool to infer protein-protein interaction networks. It is applicable for any species present in the Integr8 database (more than 1500 organisms). The method combines known interactions and clusters of orthologous proteins. The tool can be downloaded or used through the web application.", "sc:name": "InteroPORC", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://biodev.extra.cea.fr/interoporc/" } \ No newline at end of file diff --git a/data/interpol/interpolbioschemas.jsonld b/data/interpol/interpolbioschemas.jsonld index d64fd0fa64270..65f1e025d3a60 100644 --- a/data/interpol/interpolbioschemas.jsonld +++ b/data/interpol/interpolbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "This software encodes amino acid sequences as numerical descriptor vectors using a database of currently 532 descriptors (mainly from AAindex), and normalizes sequences to uniform length with one of five linear or non-linear interpolation algorithms.", "sc:name": "Interpol", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.uni-due.de/~hy0546/Interpol/", diff --git a/data/interpopula/interpopulabioschemas.jsonld b/data/interpopula/interpopulabioschemas.jsonld index 329b35f6d85cb..1f75732b38bd7 100644 --- a/data/interpopula/interpopulabioschemas.jsonld +++ b/data/interpopula/interpopulabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Python API to access the HapMap dataset. It provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relavant human population datasets (e.g. Ensembl and UCSC Known Genes)", "sc:name": "interPopula", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://popgen.net/soft/interPop/" diff --git a/data/interpred/interpredbioschemas.jsonld b/data/interpred/interpredbioschemas.jsonld index 46cf3de060aea..46279258e5d7c 100644 --- a/data/interpred/interpredbioschemas.jsonld +++ b/data/interpred/interpredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A pipeline to identify and model protein–protein interactions.", "sc:name": "InterPred", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioinfo.ifm.liu.se/inter/interpred/" diff --git a/data/interproscan_4/interproscan_4bioschemas.jsonld b/data/interproscan_4/interproscan_4bioschemas.jsonld index c2ab6fffed904..c0ee63d8b7199 100644 --- a/data/interproscan_4/interproscan_4bioschemas.jsonld +++ b/data/interproscan_4/interproscan_4bioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "InterPro team", - "Web Production" + "Web Production", + "InterPro team" ], "sc:description": "Scan sequences against the InterPro protein signature databases.", "sc:name": "InterProScan (EBI)", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/pfa/iprscan/", diff --git a/data/interproscan_ws/interproscan_wsbioschemas.jsonld b/data/interproscan_ws/interproscan_wsbioschemas.jsonld index dbc98632bb921..16ddfda0bc61c 100644 --- a/data/interproscan_ws/interproscan_wsbioschemas.jsonld +++ b/data/interproscan_ws/interproscan_wsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Tool that combines different protein signature recognition methods into one resource. It is a reimplementation of the traditional InterProScan 4.x series and adds features such as pathway annotations and signal peptide and transmembrane prediction using Phobius.", "sc:name": "InterProScan WS (EBI)", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan5_rest", "sc:version": "1" diff --git a/data/intersim/intersimbioschemas.jsonld b/data/intersim/intersimbioschemas.jsonld index b630caef46445..aa8953bb2419c 100644 --- a/data/intersim/intersimbioschemas.jsonld +++ b/data/intersim/intersimbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1016/j.cmpb.2016.02.011", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/intersim", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Prabhakar Chalise", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27040832", + "pmcid:PMC4833453", { "@id": "https://doi.org/10.1016/j.cmpb.2016.02.011" - }, - "pubmed:27040832", - "pmcid:PMC4833453" + } ], "sc:description": "InterSIM is a software application tool for simulating multiple interrelated data types with realistic intra- and inter-relationships based on the DNA methylation, mRNA gene expression, and protein expression from the TCGA ovarian cancer study.", "sc:featureList": { @@ -33,10 +37,6 @@ ], "sc:url": "https://cran.r-project.org/web/packages/InterSIM/index.html", "sc:version": "2.2.0" - }, - { - "@id": "https://doi.org/10.1016/j.cmpb.2016.02.011", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/interspia/interspiabioschemas.jsonld b/data/interspia/interspiabioschemas.jsonld index c72d3c081d5dd..71c726d319431 100644 --- a/data/interspia/interspiabioschemas.jsonld +++ b/data/interspia/interspiabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "INTER-Species Protein Interaction Analysis. Given a set of proteins of user's interest, it first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface.", "sc:name": "INTERSPIA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioinfo.konkuk.ac.kr/INTERSPIA/" } \ No newline at end of file diff --git a/data/intervar/intervarbioschemas.jsonld b/data/intervar/intervarbioschemas.jsonld index 613b45128c06a..4d6ef4061993a 100644 --- a/data/intervar/intervarbioschemas.jsonld +++ b/data/intervar/intervarbioschemas.jsonld @@ -20,18 +20,18 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5294755", + "pubmed:28132688", { "@id": "https://doi.org/10.1016/j.ajhg.2017.01.004" - }, - "pubmed:28132688" + } ], "sc:description": "Helps human reviewers interpret the clinical significance of variants. InterVar can take a pre-annotated or VCF file as input and generate automated interpretation on 18 criteria.", "sc:featureList": [ { - "@id": "edam:operation_0338" + "@id": "edam:operation_2451" }, { - "@id": "edam:operation_2451" + "@id": "edam:operation_0338" } ], "sc:license": "Other", diff --git a/data/intervene/intervenebioschemas.jsonld b/data/intervene/intervenebioschemas.jsonld index bd3326d5abdf7..fefb6fffade1b 100644 --- a/data/intervene/intervenebioschemas.jsonld +++ b/data/intervene/intervenebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-6459-6224", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/intervene", "@type": "sc:SoftwareApplication", @@ -16,15 +20,15 @@ "@id": "https://orcid.org/0000-0002-6459-6224" }, "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.", "sc:license": "MIT", "sc:name": "Intervene", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://bitbucket.org/CBGR/intervene", @@ -32,10 +36,6 @@ "0.5.8", "0.6.4" ] - }, - { - "@id": "https://orcid.org/0000-0002-6459-6224", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/intfold/intfoldbioschemas.jsonld b/data/intfold/intfoldbioschemas.jsonld index 772c3ad54ffc6..341be053b15eb 100644 --- a/data/intfold/intfoldbioschemas.jsonld +++ b/data/intfold/intfoldbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.", "sc:name": "IntFOLD", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.reading.ac.uk/bioinf/IntFOLD/" diff --git a/data/intogen/intogenbioschemas.jsonld b/data/intogen/intogenbioschemas.jsonld index f748aa81b5389..754c845ae1602 100644 --- a/data/intogen/intogenbioschemas.jsonld +++ b/data/intogen/intogenbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Collect and analyse somatic mutations in thousands of tumor genomes to identify cancer driver genes.", "sc:name": "Intogen", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "upf.edu", "sc:url": "http://www.intogen.org/" diff --git a/data/intramirexplorer/intramirexplorerbioschemas.jsonld b/data/intramirexplorer/intramirexplorerbioschemas.jsonld index 693db7b65efba..1850d6bd54517 100644 --- a/data/intramirexplorer/intramirexplorerbioschemas.jsonld +++ b/data/intramirexplorer/intramirexplorerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "IntramiRExploreR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IntramiRExploreR.html", "sc:version": "1.2.0" diff --git a/data/intreped/intrepedbioschemas.jsonld b/data/intreped/intrepedbioschemas.jsonld index 017f10ccab03f..7cd3a4752190b 100644 --- a/data/intreped/intrepedbioschemas.jsonld +++ b/data/intreped/intrepedbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "INTeractive dna REPair prEDiction is a collection of services for predicting properties relating to DNA repair. DNA repair is thought to exist in all organisms that have an active metabolism, and repair systems are crucial for repairing many types of DNA damage. External damage includes (but is not limited to) ionizing (UV) radiation, tobacco smoke, and chemical alteration. Examples of internal damage are DNA copying errors, oxygen byproducts resulting from metabolism, and hydrolysis.", "sc:name": "INTREPED", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sunflower.kuicr.kyoto-u.ac.jp/~jbbrown/dnaRepairPrediction/v2/index.py", "sc:version": "2.0" diff --git a/data/intrepid/intrepidbioschemas.jsonld b/data/intrepid/intrepidbioschemas.jsonld index 23af9dc97ce60..dc007dccf0447 100644 --- a/data/intrepid/intrepidbioschemas.jsonld +++ b/data/intrepid/intrepidbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.", "sc:name": "INTREPID", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/berkeleyphylogenomics/intrepid" } \ No newline at end of file diff --git a/data/intsplice/intsplicebioschemas.jsonld b/data/intsplice/intsplicebioschemas.jsonld index 49571d3011d76..e43a6da4174e8 100644 --- a/data/intsplice/intsplicebioschemas.jsonld +++ b/data/intsplice/intsplicebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool to predict a splicing consequence of an SNV at intron positions -50 to -3 close the 3’ end of an intron of the human genome.", "sc:name": "IntSplice", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice/" diff --git a/data/inuc-pseknc/inuc-psekncbioschemas.jsonld b/data/inuc-pseknc/inuc-psekncbioschemas.jsonld index 3333ebab0d7e1..73f6838ba759d 100644 --- a/data/inuc-pseknc/inuc-psekncbioschemas.jsonld +++ b/data/inuc-pseknc/inuc-psekncbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This web-server was developed to predict nucleosome occupancy of H. sapiens, C. elegan and D. melanogaster.", "sc:name": "iNuc-PseKNC", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://lin.uestc.edu.cn/server/iNuc-PseKNC" } \ No newline at end of file diff --git a/data/invfest/invfestbioschemas.jsonld b/data/invfest/invfestbioschemas.jsonld index 82ce1135dd17c..c8b34a5f13eac 100644 --- a/data/invfest/invfestbioschemas.jsonld +++ b/data/invfest/invfestbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkt1122", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/invfest", "@type": "sc:SoftwareApplication", @@ -30,10 +26,10 @@ "sc:description": "Database that stores inversion predictions from healthy individuals and enables to search inversions by gene symbol, genomic position and inversion name.", "sc:featureList": [ { - "@id": "edam:operation_3436" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_3197" + "@id": "edam:operation_3436" }, { "@id": "edam:operation_3431" @@ -42,11 +38,15 @@ "sc:license": "CC-BY-4.0", "sc:name": "InvFEST", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://invfestdb.uab.cat/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkt1122", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/iobio/iobiobioschemas.jsonld b/data/iobio/iobiobioschemas.jsonld index ac4bb8569683a..5e94d10e680b1 100644 --- a/data/iobio/iobiobioschemas.jsonld +++ b/data/iobio/iobiobioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "iobio Support", "sc:additionalType": "Suite", "sc:citation": [ + "pubmed:25423016", + "pmcid:PMC4282680", { "@id": "https://doi.org/10.1038/nmeth.3174" - }, - "pmcid:PMC4282680", - "pubmed:25423016" + } ], "sc:description": "Real-time Genomic Analysis\niobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "Iobio", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://iobio.io/" }, diff --git a/data/iocbio/iocbiobioschemas.jsonld b/data/iocbio/iocbiobioschemas.jsonld index 162d2176ef79e..698921eb1ad99 100644 --- a/data/iocbio/iocbiobioschemas.jsonld +++ b/data/iocbio/iocbiobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "IOCBio", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/pearu/iocbio" } \ No newline at end of file diff --git a/data/iom/iombioschemas.jsonld b/data/iom/iombioschemas.jsonld index d84c3852863f1..5b94283bd9157 100644 --- a/data/iom/iombioschemas.jsonld +++ b/data/iom/iombioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/iom", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:contributor": "Marie Doležalová", "sc:description": "Dedicated for MS data measured in high resolution mode and their interpretation. Primarily oriented on devices developed by the Thermo-Fisher Scientific company.", diff --git a/data/iomics/iomicsbioschemas.jsonld b/data/iomics/iomicsbioschemas.jsonld index f6c5c438379e0..4cd759196544e 100644 --- a/data/iomics/iomicsbioschemas.jsonld +++ b/data/iomics/iomicsbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Cloud based workflow analysis framework for managing, analyzing and visualizing NGS data.", "sc:name": "IOmics", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://interpretomics.co/iomics" } \ No newline at end of file diff --git a/data/iongap/iongapbioschemas.jsonld b/data/iongap/iongapbioschemas.jsonld index 6c906ad716028..b7905beedcfc2 100644 --- a/data/iongap/iongapbioschemas.jsonld +++ b/data/iongap/iongapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Publicly available integrated pipeline designed for the assembly and subsequent analysis of Ion Torrent bacterial sequence data. Both its components and their configuration are based on a research process aimed to discover the optimal combination of tools for obtaining good results from single-end reads generated by the Ion Torrent PGM sequencer.", "sc:name": "IonGAP", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://iongap.hpc.iter.es/" } \ No newline at end of file diff --git a/data/ioniser/bioconda_ioniser.yaml b/data/ioniser/bioconda_ioniser.yaml index be6d8a5010cef..df8f661767911 100644 --- a/data/ioniser/bioconda_ioniser.yaml +++ b/data/ioniser/bioconda_ioniser.yaml @@ -7,7 +7,6 @@ description: IONiseR provides tools for the quality assessment of Oxford Nanopor home: https://bioconductor.org/packages/3.10/bioc/html/IONiseR.html identifiers: - biotools:ioniser -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-ioniser diff --git a/data/ioniser/ioniserbioschemas.jsonld b/data/ioniser/ioniserbioschemas.jsonld index f01dc8fc846be..1f0fde018a008 100644 --- a/data/ioniser/ioniserbioschemas.jsonld +++ b/data/ioniser/ioniserbioschemas.jsonld @@ -17,13 +17,13 @@ "sc:license": "MIT", "sc:name": "IONiseR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": [ - "hdhub", - "EMBL Heidelberg" + "EMBL Heidelberg", + "hdhub" ], "sc:url": "http://bioconductor.org/packages/IONiseR/" } \ No newline at end of file diff --git a/data/iontree/iontreebioschemas.jsonld b/data/iontree/iontreebioschemas.jsonld index a9990e4937b48..f666b7a279110 100644 --- a/data/iontree/iontreebioschemas.jsonld +++ b/data/iontree/iontreebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mingshu Cao", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry.", "sc:license": "GPL-2.0", "sc:name": "iontree", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iontree.html", "sc:version": "1.20.0" diff --git a/data/ipac/ipacbioschemas.jsonld b/data/ipac/ipacbioschemas.jsonld index 60a376076ce22..22dfc1cd8b5bf 100644 --- a/data/ipac/ipacbioschemas.jsonld +++ b/data/ipac/ipacbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "iPAC", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iPAC.html", "sc:version": "1.18.0" diff --git a/data/ipage/ipagebioschemas.jsonld b/data/ipage/ipagebioschemas.jsonld index c4cd5ed06d463..4010dfd29aea4 100644 --- a/data/ipage/ipagebioschemas.jsonld +++ b/data/ipage/ipagebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Powerful package which in conjunction with FIRE provides a complete meta-analysis of whole-genome datasets.", "sc:name": "iPAGE", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://tavazoielab.c2b2.columbia.edu/iPAGE/", "sc:version": "1.2a" diff --git a/data/iparts/ipartsbioschemas.jsonld b/data/iparts/ipartsbioschemas.jsonld index 71f9e8d567288..611fc963ac39c 100644 --- a/data/iparts/ipartsbioschemas.jsonld +++ b/data/iparts/ipartsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach.", "sc:name": "iPARTS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://genome.cs.nthu.edu.tw/iPARTS/" } \ No newline at end of file diff --git a/data/ipat/ipatbioschemas.jsonld b/data/ipat/ipatbioschemas.jsonld index ff5dfece2162f..3049d9341cf29 100644 --- a/data/ipat/ipatbioschemas.jsonld +++ b/data/ipat/ipatbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Intelligent prediction and association tool for genomic research.", "sc:name": "iPat", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://zzlab.net/iPat/" } \ No newline at end of file diff --git a/data/ipath/ipathbioschemas.jsonld b/data/ipath/ipathbioschemas.jsonld index 87ea9fe3d5e74..8a276abc3d40c 100644 --- a/data/ipath/ipathbioschemas.jsonld +++ b/data/ipath/ipathbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://orcid.org/0000-0003-1429-7485", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/nar/gkr313", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/ipath", @@ -21,31 +21,31 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC3125749", + "pubmed:21546551", + "pubmed:18276143", { "@id": "https://doi.org/10.1093/nar/gkr313" }, - "pubmed:21546551", - "pubmed:18276143" + "pmcid:PMC3125749" ], "sc:description": "Web-based tool for the visualization and analysis of cellular pathways. Based on functional annotations (such as KEGG), it provides pathway maps for primary cellular metabolism as well as for some additional secondary metabolite synthesis and regulatory pathways. Users can map their own data onto these pathway maps. Due to its navigation and customization functions, it thus allows users to easily explore and analyze the functional and metabolic capabilities of their (meta-)genomic data sets.", "sc:license": "GPL-3.0", "sc:name": "iPATH", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "European Molecular Biology Laboratory (EMBL)", - "HD-HuB" + "HD-HuB", + "European Molecular Biology Laboratory (EMBL)" ], "sc:url": "http://pathways.embl.de/iPath2.cgi", "sc:version": "2.0" }, { - "@id": "https://doi.org/10.1093/nar/gkr313", - "@type": "sc:CreativeWork" + "@id": "https://orcid.org/0000-0003-1429-7485", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/ipavs/ipavsbioschemas.jsonld b/data/ipavs/ipavsbioschemas.jsonld index bf64f65b8d3b0..44c0d66f99391 100644 --- a/data/ipavs/ipavsbioschemas.jsonld +++ b/data/ipavs/ipavsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "integrated Pathway Resources, Analysis and Visualization System: provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate,filter, browse, search, analyze, visualize and compare the integrated pathway resources.", "sc:name": "iPAVS", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://ipavs.cidms.org/" diff --git a/data/ipba/ipbabioschemas.jsonld b/data/ipba/ipbabioschemas.jsonld index 6d8f364cd130d..01ae602f5ae2e 100644 --- a/data/ipba/ipbabioschemas.jsonld +++ b/data/ipba/ipbabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "iPBA", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.dsimb.inserm.fr/dsimb_tools/ipba/" } \ No newline at end of file diff --git a/data/ipc/ipcbioschemas.jsonld b/data/ipc/ipcbioschemas.jsonld index f04a9cce29ddc..f2c8d06dfb11b 100644 --- a/data/ipc/ipcbioschemas.jsonld +++ b/data/ipc/ipcbioschemas.jsonld @@ -34,7 +34,7 @@ "@id": "edam:topic_3047" }, { - "@id": "edam:topic_0121" + "@id": "edam:topic_3520" }, { "@id": "edam:topic_0123" @@ -43,15 +43,15 @@ "@id": "edam:topic_3292" }, { - "@id": "edam:topic_3520" + "@id": "edam:topic_0121" } ], "sc:citation": [ { "@id": "https://doi.org/10.1186/s13062-016-0159-9" }, - "pmcid:PMC5075173", - "pubmed:27769290" + "pubmed:27769290", + "pmcid:PMC5075173" ], "sc:description": "Web service and standalone program for the estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including computationally optimized pKa sets. According to the benchmarks, the newly developed pKa sets outperform previous algorithms by at least 14.9 % for proteins and 0.9 % for peptides (on average, 22.1 % and 59.6 %, respectively), which corresponds to an average error of the pI estimation of 0.87 and 0.25 pH units, respectively.", "sc:featureList": { @@ -61,9 +61,9 @@ "sc:license": "Other", "sc:name": "IPC", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:softwareHelp": { "@id": "http://isoelectric.org/algorithms.html" diff --git a/data/ipcaps/ipcapsbioschemas.jsonld b/data/ipcaps/ipcapsbioschemas.jsonld index c575d01c2ca60..4f4046fe81dcf 100644 --- a/data/ipcaps/ipcapsbioschemas.jsonld +++ b/data/ipcaps/ipcapsbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Kridsadakorn Chaichoompu", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6427891", + "pubmed:30936940", { "@id": "https://doi.org/10.1186/s13029-019-0072-6" - }, - "pmcid:PMC6427891", - "pubmed:30936940" + } ], "sc:description": "R package for iterative pruning to capture population structure.", "sc:featureList": [ @@ -40,9 +40,9 @@ "sc:license": "GPL-3.0", "sc:name": "IPCAPS", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://cran.r-project.org/package=IPCAPS", "sc:version": "1.1.5" diff --git a/data/ipd-imgt_hla/ipd-imgt_hlabioschemas.jsonld b/data/ipd-imgt_hla/ipd-imgt_hlabioschemas.jsonld index 6bec0c058818e..918180033571e 100644 --- a/data/ipd-imgt_hla/ipd-imgt_hlabioschemas.jsonld +++ b/data/ipd-imgt_hla/ipd-imgt_hlabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database that provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data.", "sc:name": "IMGT HLA database", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/imgt/hla/" } \ No newline at end of file diff --git a/data/ipd/ipdbioschemas.jsonld b/data/ipd/ipdbioschemas.jsonld index 01780e1023e40..61eb32b5934d7 100644 --- a/data/ipd/ipdbioschemas.jsonld +++ b/data/ipd/ipdbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Set of specialist databases related to the study of polymorphic genes in the immune system. The project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted for online publication. It consists of four databases: KIR, MHC, human platelet antigens and ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines.", "sc:name": "IPD", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.ebi.ac.uk/ipd/" diff --git a/data/ipgwas/ipgwasbioschemas.jsonld b/data/ipgwas/ipgwasbioschemas.jsonld index 318c01c461373..d36818683cd35 100644 --- a/data/ipgwas/ipgwasbioschemas.jsonld +++ b/data/ipgwas/ipgwasbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Integrated pipeline for rational quality control and association analysis of genome-wide genetic studies.", "sc:name": "IPGWAS", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://sourceforge.net/projects/ipgwas/" } \ No newline at end of file diff --git a/data/ipig/ipigbioschemas.jsonld b/data/ipig/ipigbioschemas.jsonld index e6f297d35908d..a51665223aa41 100644 --- a/data/ipig/ipigbioschemas.jsonld +++ b/data/ipig/ipigbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser", "sc:name": "iPiG", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sourceforge.net/projects/ipig/", "sc:version": "r5" diff --git a/data/ipk_blast/ipk_blastbioschemas.jsonld b/data/ipk_blast/ipk_blastbioschemas.jsonld index 7fe288b2cbb63..2498c9a477d8f 100644 --- a/data/ipk_blast/ipk_blastbioschemas.jsonld +++ b/data/ipk_blast/ipk_blastbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "IPK BLAST Server", "sc:operatingSystem": "Linux", "sc:provider": [ - "ipk", - "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben" + "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben", + "ipk" ], "sc:url": "http://webblast.ipk-gatersleben.de", "sc:version": "1" diff --git a/data/ipknot/ipknotbioschemas.jsonld b/data/ipknot/ipknotbioschemas.jsonld index 5931f4de27edc..16f0bc3cd02ca 100644 --- a/data/ipknot/ipknotbioschemas.jsonld +++ b/data/ipknot/ipknotbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "IPknot provides services for predicting RNA secondary structures including a wide class of pseudoknots. IPknot can also predict the consensus secondary structure when a multiple alignment of RNA sequences is given. IPknot runs fast and predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut.", "sc:name": "IPknot", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://rtips.dna.bio.keio.ac.jp/ipknot/", "sc:version": "1.3.1" diff --git a/data/ipo/ipobioschemas.jsonld b/data/ipo/ipobioschemas.jsonld index dc81956684596..c18e0f78972cb 100644 --- a/data/ipo/ipobioschemas.jsonld +++ b/data/ipo/ipobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-015-0562-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ipo", "@type": "sc:SoftwareApplication", @@ -22,8 +18,8 @@ "Command-line tool" ], "sc:citation": [ - "pubmed:25888443", "pmcid:PMC4404568", + "pubmed:25888443", { "@id": "https://doi.org/10.1186/s12859-015-0562-8" } @@ -35,12 +31,16 @@ "sc:license": "GPL-2.0", "sc:name": "IPO", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IPO.html", "sc:version": "1.0.0" + }, + { + "@id": "https://doi.org/10.1186/s12859-015-0562-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ippbs-opt/ippbs-optbioschemas.jsonld b/data/ippbs-opt/ippbs-optbioschemas.jsonld index cd277221354e5..5400b40353580 100644 --- a/data/ippbs-opt/ippbs-optbioschemas.jsonld +++ b/data/ippbs-opt/ippbs-optbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This web-server used to predict the Protein-Protein Binding Sites(PPBS).", "sc:name": "iPPBS-Opt", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.jci-bioinfo.cn/iPPBS-Opt" } \ No newline at end of file diff --git a/data/ippbs-pseaac/ippbs-pseaacbioschemas.jsonld b/data/ippbs-pseaac/ippbs-pseaacbioschemas.jsonld index 32bfbaa5f8985..eaca048a2ad95 100644 --- a/data/ippbs-pseaac/ippbs-pseaacbioschemas.jsonld +++ b/data/ippbs-pseaac/ippbs-pseaacbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This web-server is used to predict the Protein-Protein Binding Sites(PPBS).", "sc:name": "iPPBS-PseAAC", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.jci-bioinfo.cn/iPPBS-PseAAC" } \ No newline at end of file diff --git a/data/ippd/ippdbioschemas.jsonld b/data/ippd/ippdbioschemas.jsonld index bb4d22973a027..598f0c54c7c10 100644 --- a/data/ippd/ippdbioschemas.jsonld +++ b/data/ippd/ippdbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "IPPD", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IPPD.html", "sc:version": "1.22.0" diff --git a/data/ippi-esml/ippi-esmlbioschemas.jsonld b/data/ippi-esml/ippi-esmlbioschemas.jsonld index a1cd3e30e796a..be4cfad55d69f 100644 --- a/data/ippi-esml/ippi-esmlbioschemas.jsonld +++ b/data/ippi-esml/ippi-esmlbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC.", "sc:name": "iPPI-Esml", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.jci-bioinfo.cn/iPPI-Esml" } \ No newline at end of file diff --git a/data/ippi/ippibioschemas.jsonld b/data/ippi/ippibioschemas.jsonld index fb1f298664079..5b98cec863364 100644 --- a/data/ippi/ippibioschemas.jsonld +++ b/data/ippi/ippibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "IPPI is a web server of inferring protein-protein interactions", "sc:name": "IPPI", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://sunflower.kuicr.kyoto-u.ac.jp/~morihiro/protint/ppi-form.html" } \ No newline at end of file diff --git a/data/ipro54-pseknc/ipro54-psekncbioschemas.jsonld b/data/ipro54-pseknc/ipro54-psekncbioschemas.jsonld index 5518dabaa9406..7f4ccebf73130 100644 --- a/data/ipro54-pseknc/ipro54-psekncbioschemas.jsonld +++ b/data/ipro54-pseknc/ipro54-psekncbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Hao Lin", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4245931", { "@id": "https://doi.org/10.1093/nar/gku1019" }, - "pubmed:25361964" + "pubmed:25361964", + "pmcid:PMC4245931" ], "sc:description": "Sequence-based predictor for identifying\nσ54 promoters with pseudo k-tuple nucleotide composition.", "sc:featureList": { diff --git a/data/ipromoter-2l/ipromoter-2lbioschemas.jsonld b/data/ipromoter-2l/ipromoter-2lbioschemas.jsonld index 942a469c7350d..f3d2ce4725235 100644 --- a/data/ipromoter-2l/ipromoter-2lbioschemas.jsonld +++ b/data/ipromoter-2l/ipromoter-2lbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "iPromoter-2L", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioinformatics.hitsz.edu.cn/iPromoter-2L/" } \ No newline at end of file diff --git a/data/iprot-sub/iprot-subbioschemas.jsonld b/data/iprot-sub/iprot-subbioschemas.jsonld index ff0e4ebc04a0b..de0a731564d1d 100644 --- a/data/iprot-sub/iprot-subbioschemas.jsonld +++ b/data/iprot-sub/iprot-subbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bib/bby028", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/iProt-Sub", "@type": "sc:SoftwareApplication", @@ -21,19 +17,19 @@ "Web application" ], "sc:citation": [ - "pubmed:29897410", - "pmcid:PMC6556904", { "@id": "https://doi.org/10.1093/bib/bby028" - } + }, + "pmcid:PMC6556904", + "pubmed:29897410" ], "sc:description": "Integrated feature-based webserver in silico prediction of protease substrates and their cleavage sites for 38 different protease types, covering four major protease families: Aspartic (A), Cysteine (C), Metallo (M) and Serine (S).", "sc:featureList": [ { - "@id": "edam:operation_0267" + "@id": "edam:operation_0418" }, { - "@id": "edam:operation_0418" + "@id": "edam:operation_0267" }, { "@id": "edam:operation_0422" @@ -41,6 +37,10 @@ ], "sc:name": "iProt-Sub", "sc:url": "http://iprot-sub.erc.monash.edu.au/" + }, + { + "@id": "https://doi.org/10.1093/bib/bby028", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/iprstats/iprstatsbioschemas.jsonld b/data/iprstats/iprstatsbioschemas.jsonld index 470eb4a30ea84..80b21ce680744 100644 --- a/data/iprstats/iprstatsbioschemas.jsonld +++ b/data/iprstats/iprstatsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A tool for the visualization of Interproscan results. Interproscan results are parsed from the Interproscan XML or EBIXML file into an SQLite or MySQL database. The results for each signature database scan are read and displayed as pie-charts or bar charts as summary statistics.", "sc:name": "IPRStats", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/devrkel/IPRStats", "sc:version": "0.4.2" diff --git a/data/ipsa/ipsabioschemas.jsonld b/data/ipsa/ipsabioschemas.jsonld index a4ddbf98e8a88..65a3829453191 100644 --- a/data/ipsa/ipsabioschemas.jsonld +++ b/data/ipsa/ipsabioschemas.jsonld @@ -20,8 +20,8 @@ "Mac" ], "sc:provider": [ - "crg.eu", - "Lab Roderic Guigo Group" + "Lab Roderic Guigo Group", + "crg.eu" ], "sc:url": "https://github.com/pervouchine/ipsa-full", "sc:version": "3.3" diff --git a/data/iq-tree/iq-treebioschemas.jsonld b/data/iq-tree/iq-treebioschemas.jsonld index 676e13d21d729..296125aee6ef7 100644 --- a/data/iq-tree/iq-treebioschemas.jsonld +++ b/data/iq-tree/iq-treebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Very efficient phylogenetic software for reconstructing maximum-likelihood trees and assessing branch supports with the ultrafast bootstrap approximation. It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features.", "sc:name": "IQ-TREE", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.cibiv.at/software/iqtree/" diff --git a/data/iquant/iquantbioschemas.jsonld b/data/iquant/iquantbioschemas.jsonld index b9172608edfcf..d35de04b5de8b 100644 --- a/data/iquant/iquantbioschemas.jsonld +++ b/data/iquant/iquantbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification.", "sc:name": "IQuant", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sourceforge.net/projects/iquant/" } \ No newline at end of file diff --git a/data/iranges/irangesbioschemas.jsonld b/data/iranges/irangesbioschemas.jsonld index 1c135d0c9c723..6e0893713f76c 100644 --- a/data/iranges/irangesbioschemas.jsonld +++ b/data/iranges/irangesbioschemas.jsonld @@ -14,34 +14,34 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC3738458", - "pubmed:23950696", { "@id": "https://doi.org/10.1371/journal.pcbi.1003118" - } + }, + "pubmed:23950696" ], "sc:description": "Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_3436" }, { "@id": "edam:operation_3438" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_3431" } ], "sc:license": "Artistic-2.0", "sc:name": "IRanges", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IRanges.html", "sc:version": "2.8.1" diff --git a/data/irbis/irbisbioschemas.jsonld b/data/irbis/irbisbioschemas.jsonld index 02b90b0934af2..c9ad1ea49e8a7 100644 --- a/data/irbis/irbisbioschemas.jsonld +++ b/data/irbis/irbisbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "AGPL-3.0", "sc:name": "IRBIS", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "Lab Roderic Guigo Group", diff --git a/data/irefindex/irefindexbioschemas.jsonld b/data/irefindex/irefindexbioschemas.jsonld index ec819944ec9ec..04e842bacddb1 100644 --- a/data/irefindex/irefindexbioschemas.jsonld +++ b/data/irefindex/irefindexbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB and MPPI.", "sc:name": "iRefIndex", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "UiO", "sc:url": "http://irefindex.org/" diff --git a/data/irefr/irefrbioschemas.jsonld b/data/irefr/irefrbioschemas.jsonld index 257b9616f0b08..d5f4d44f6cefd 100644 --- a/data/irefr/irefrbioschemas.jsonld +++ b/data/irefr/irefrbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Antonio Mora", - "Ian Donaldson" + "Ian Donaldson", + "Antonio Mora" ], "sc:description": "This tool allows the user to load any version of the consolidated protein interaction database \"iRefIndex\" and perform tasks such as: selecting databases, pmids, experimental methods, searching for specific proteins, separate binary interactions from complexes and polymers, generate complexes according to an algorithm that looks after possible binary-represented complexes, make general database statistics and create network graphs, among others.", "sc:license": "GPL-3.0", diff --git a/data/irefscape/irefscapebioschemas.jsonld b/data/irefscape/irefscapebioschemas.jsonld index 2ed1cc8b1c3d1..9255bb602fb7a 100644 --- a/data/irefscape/irefscapebioschemas.jsonld +++ b/data/irefscape/irefscapebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:author": [ - "Ian Donaldson", - "Sabry Razick" + "Sabry Razick", + "Ian Donaldson" ], "sc:description": "Plugin for Cytoscape that exposes iRefIndex data as a navigable graphical network.", "sc:license": "GPL-3.0", "sc:name": "iRefScape", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "UiO", "sc:url": "http://irefindex.org/wiki/index.php?title=iRefScape", diff --git a/data/iresite/iresitebioschemas.jsonld b/data/iresite/iresitebioschemas.jsonld index 15d2fcc5651e8..f839057460902 100644 --- a/data/iresite/iresitebioschemas.jsonld +++ b/data/iresite/iresitebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Our database presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.", "sc:name": "IRESite", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "ELIXIR-CZ", diff --git a/data/irespred/irespredbioschemas.jsonld b/data/irespred/irespredbioschemas.jsonld index 39fab134e3dff..1166537306440 100644 --- a/data/irespred/irespredbioschemas.jsonld +++ b/data/irespred/irespredbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Support Vector Machine (SVM) based computational tool to predict the presence of Internal Ribosome Entry Site (IRES) in viral and cellular sequences.", "sc:name": "IRESPred", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioinfo.net.in/IRESPred/" diff --git a/data/irisspatialfeatures/irisspatialfeaturesbioschemas.jsonld b/data/irisspatialfeatures/irisspatialfeaturesbioschemas.jsonld index 5ae125804a3dd..4de8dd1f48575 100644 --- a/data/irisspatialfeatures/irisspatialfeaturesbioschemas.jsonld +++ b/data/irisspatialfeatures/irisspatialfeaturesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "IrisSpatialFeatures", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IrisSpatialFeatures.html", "sc:version": "1.3.0" diff --git a/data/irma/irmabioschemas.jsonld b/data/irma/irmabioschemas.jsonld index 7960a4b0a4df6..9493fc73f8acc 100644 --- a/data/irma/irmabioschemas.jsonld +++ b/data/irma/irmabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "IRMa ( Interprétation des Résultats Mascot)  toolbox provides an interactive application to assist in the validation of Mascot® search results. IRMa reads MASCOT® result (using Matrix Science® Parser distributed free of charge) and automatically filters identified peptides. All relevant information is displayed in a structured manner, showing “proteins hits” details. User can then manually or automatically confirm or reject individual peptide spectrum matches.", "sc:name": "IRMa", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://biodev.extra.cea.fr/docs/irma/doku.php", "sc:version": "1.31.1" diff --git a/data/irnad/irnadbioschemas.jsonld b/data/irnad/irnadbioschemas.jsonld index 9ee9d3c705b5b..5fada9391c9d0 100644 --- a/data/irnad/irnadbioschemas.jsonld +++ b/data/irnad/irnadbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Computational tool for identifying D modification sites in RNA sequence.", "sc:name": "iRNAD", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://lin-group.cn/server/iRNAD" } \ No newline at end of file diff --git a/data/iro-3wpseknc/iro-3wpsekncbioschemas.jsonld b/data/iro-3wpseknc/iro-3wpsekncbioschemas.jsonld index d9a9f63d275f5..bfb99fc090e7c 100644 --- a/data/iro-3wpseknc/iro-3wpsekncbioschemas.jsonld +++ b/data/iro-3wpseknc/iro-3wpsekncbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Identify DNA replication origins by three-window-based PseKNC.", "sc:name": "iRO-3wPseKNC", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioinformatics.hitsz.edu.cn/iRO-3wPseKNC/" diff --git a/data/irods/irodsbioschemas.jsonld b/data/irods/irodsbioschemas.jsonld index a0de4e867ee08..7433e81ad832c 100644 --- a/data/irods/irodsbioschemas.jsonld +++ b/data/irods/irodsbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "iRODS Consortium Team", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6334444", { "@id": "https://doi.org/10.1186/s12859-018-2576-5" }, - "pubmed:30646845", - "pmcid:PMC6334444" + "pubmed:30646845" ], "sc:description": "Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow.", "sc:featureList": [ @@ -36,8 +36,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "iRODS", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://irods.org/", "sc:version": "4.2.5" diff --git a/data/irootlab/irootlabbioschemas.jsonld b/data/irootlab/irootlabbioschemas.jsonld index bd04d90c00f8e..260e2bd4c640c 100644 --- a/data/irootlab/irootlabbioschemas.jsonld +++ b/data/irootlab/irootlabbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Open-source project dedicated to providing a MATLAB framework for vibrational spectroscopy. The goal of the project is to provide a comprehensive and user-friendly environment for analysis, whilst facilitating development and validation of algorithms for computational biology using vibrational spectroscopy.", "sc:name": "irootlab", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://trevisanj.github.io/irootlab/" } \ No newline at end of file diff --git a/data/irprofiler/irprofilerbioschemas.jsonld b/data/irprofiler/irprofilerbioschemas.jsonld index b75cbeff587cb..5d3fdfb872fd2 100644 --- a/data/irprofiler/irprofilerbioschemas.jsonld +++ b/data/irprofiler/irprofilerbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2144-z", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/irprofiler", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christos Maramis", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5907363", + "pubmed:29669518", { "@id": "https://doi.org/10.1186/s12859-018-2144-z" }, - "pubmed:29669518" + "pmcid:PMC5907363" ], "sc:description": "High throughput immune receptor profiling.", "sc:featureList": { @@ -37,6 +33,10 @@ "Linux" ], "sc:url": "http://irprofiler.med.auth.gr:8080/" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2144-z", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/irscope/irscopebioschemas.jsonld b/data/irscope/irscopebioschemas.jsonld index b89bf5e5d3d52..37d5356521a8f 100644 --- a/data/irscope/irscopebioschemas.jsonld +++ b/data/irscope/irscopebioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Visualize the junction sites of chloroplast genomes.", "sc:name": "IRscope", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://irscope.shinyapps.io/irapp/" diff --git a/data/irspot-psednc/irspot-psedncbioschemas.jsonld b/data/irspot-psednc/irspot-psedncbioschemas.jsonld index f603bca8562fd..ea413d1f4fece 100644 --- a/data/irspot-psednc/irspot-psedncbioschemas.jsonld +++ b/data/irspot-psednc/irspot-psedncbioschemas.jsonld @@ -31,9 +31,9 @@ }, "sc:name": "iRSpot-PseDNC", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://lin-group.cn/server/iRSpot-PseDNC" } diff --git a/data/irspot-tncpseaac/irspot-tncpseaacbioschemas.jsonld b/data/irspot-tncpseaac/irspot-tncpseaacbioschemas.jsonld index 5ae43f8b42538..7062521438118 100644 --- a/data/irspot-tncpseaac/irspot-tncpseaacbioschemas.jsonld +++ b/data/irspot-tncpseaac/irspot-tncpseaacbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3390/IJMS15021746", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/irspot-tncpseaac", "@type": "sc:SoftwareApplication", @@ -27,15 +31,11 @@ }, "sc:name": "iRSpot-TNCPseAAC", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.jci-bioinfo.cn/iRSpot-TNCPseAAC" - }, - { - "@id": "https://doi.org/10.3390/IJMS15021746", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/isa_tools/isa_toolsbioschemas.jsonld b/data/isa_tools/isa_toolsbioschemas.jsonld index 185384fc6cbe3..d04525ae5ae94 100644 --- a/data/isa_tools/isa_toolsbioschemas.jsonld +++ b/data/isa_tools/isa_toolsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Framework and tools that help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies.", "sc:name": "ISA tools", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://isa-tools.org/" } \ No newline at end of file diff --git a/data/isambard/isambardbioschemas.jsonld b/data/isambard/isambardbioschemas.jsonld index 06339eadf0901..9435fd4d6cefb 100644 --- a/data/isambard/isambardbioschemas.jsonld +++ b/data/isambard/isambardbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Intelligent System for Analysis, Model Building And Rational Design.", "sc:name": "ISAMBARD", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://pypi.org/project/ISAMBARD/" } \ No newline at end of file diff --git a/data/isarst/isarstbioschemas.jsonld b/data/isarst/isarstbioschemas.jsonld index d9be4fbb5dc38..b1e2ed2ce533b 100644 --- a/data/isarst/isarstbioschemas.jsonld +++ b/data/isarst/isarstbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.", "sc:name": "iSARST", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://sarst.life.nthu.edu.tw/iSARST/" diff --git a/data/iseq/iseqbioschemas.jsonld b/data/iseq/iseqbioschemas.jsonld index 2028a11732b41..36a50f8596f18 100644 --- a/data/iseq/iseqbioschemas.jsonld +++ b/data/iseq/iseqbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "iSeq", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iSeq.html", diff --git a/data/isescan/isescanbioschemas.jsonld b/data/isescan/isescanbioschemas.jsonld index 1f8a0d1f42430..3dcb193ab1494 100644 --- a/data/isescan/isescanbioschemas.jsonld +++ b/data/isescan/isescanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Automated identification of insertion sequence elements in prokaryotic genomes.", "sc:name": "ISEScan", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/xiezhq/ISEScan" } \ No newline at end of file diff --git a/data/isetbio/isetbiobioschemas.jsonld b/data/isetbio/isetbiobioschemas.jsonld index 4012e6fe3995c..c68312c7f8cca 100644 --- a/data/isetbio/isetbiobioschemas.jsonld +++ b/data/isetbio/isetbiobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1007063", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ISETBIO", "@type": "sc:SoftwareApplication", @@ -17,11 +21,11 @@ }, "sc:additionalType": "Suite", "sc:citation": [ - "pmcid:PMC6553792", + "pubmed:31125331", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1007063" }, - "pubmed:31125331" + "pmcid:PMC6553792" ], "sc:description": "Image System Engineering Toolbox for Biology (ISETBIO) is a Matlab toolbox designed for calculating the properties of the front end of biological visual systems.", "sc:featureList": { @@ -30,19 +34,15 @@ "sc:license": "MIT", "sc:name": "ISETBIO", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://isetbio.org/" }, { "@id": "https://orcid.org/0000-0002-4972-5307", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1007063", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/islandpath/islandpathbioschemas.jsonld b/data/islandpath/islandpathbioschemas.jsonld index 1775581a4c6de..07b0982e8cde2 100644 --- a/data/islandpath/islandpathbioschemas.jsonld +++ b/data/islandpath/islandpathbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool aids genomic island detection in prokaryotic genome seqeunces, using features such as dinucleotide bias, G+C, location of tRNA genes, annotations of mobility genes, etc. Genomic islands are defined here as genomic regions of potential horizontal origin.", "sc:name": "IslandPath", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.pathogenomics.sfu.ca/islandpath/" diff --git a/data/islandviewer/islandviewerbioschemas.jsonld b/data/islandviewer/islandviewerbioschemas.jsonld index caeaffff7d81d..7a15dfc2bdcf8 100644 --- a/data/islandviewer/islandviewerbioschemas.jsonld +++ b/data/islandviewer/islandviewerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Prediction and analysis of genomic islands in bacterial and archael genomes. It integrates four different genomic island prediction methods: IslandPick, IslandPath-DIMOB, SIGI-HMM, and Islander.", "sc:name": "IslandViewer 4", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.pathogenomics.sfu.ca/islandviewer/" } \ No newline at end of file diff --git a/data/isma/ismabioschemas.jsonld b/data/isma/ismabioschemas.jsonld index 69cb43de7c851..cf4525cd50756 100644 --- a/data/isma/ismabioschemas.jsonld +++ b/data/isma/ismabioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Sofie Demeyer", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:23620730", + "pmcid:PMC3631255", { "@id": "https://doi.org/10.1371/journal.pone.0061183" - }, - "pmcid:PMC3631255", - "pubmed:23620730" + } ], "sc:description": "Index-based Subgraph Matching Algorithm. Fast subgraph enumeration in large networks using optimized search trees.", "sc:featureList": { diff --git a/data/ismara/ismarabioschemas.jsonld b/data/ismara/ismarabioschemas.jsonld index 3ccffa0e22a9f..c961f96a205fc 100644 --- a/data/ismara/ismarabioschemas.jsonld +++ b/data/ismara/ismarabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.", "sc:name": "ISMARA", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", diff --git a/data/ismara_client/ismara_clientbioschemas.jsonld b/data/ismara_client/ismara_clientbioschemas.jsonld index 23a8f4a695d6e..29cc5e02bcceb 100644 --- a/data/ismara_client/ismara_clientbioschemas.jsonld +++ b/data/ismara_client/ismara_clientbioschemas.jsonld @@ -22,8 +22,8 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:28232860", "pmcid:PMC5302150", + "pubmed:28232860", { "@id": "https://doi.org/10.12688/F1000RESEARCH.9794.1" } diff --git a/data/isno-aapair/isno-aapairbioschemas.jsonld b/data/isno-aapair/isno-aapairbioschemas.jsonld index 61125df53d207..1d38bff54f616 100644 --- a/data/isno-aapair/isno-aapairbioschemas.jsonld +++ b/data/isno-aapair/isno-aapairbioschemas.jsonld @@ -15,18 +15,18 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC3792191", + "pubmed:21168420", + "pubmed:24109555", { "@id": "https://doi.org/10.7717/peerj.171" - }, - "pubmed:21168420", - "pubmed:24109555" + } ], "sc:description": "New predictor which was developed by taking into account the coupling effects for all the pairs formed by the nearest residues and the pairs by the next nearest residues along protein chains.", "sc:name": "iSNO-AAPair", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://app.aporc.org/iSNO-AAPair/" }, diff --git a/data/isno-pseaac/isno-pseaacbioschemas.jsonld b/data/isno-pseaac/isno-pseaacbioschemas.jsonld index 221fa888e7f69..bd2e24cbbf144 100644 --- a/data/isno-pseaac/isno-pseaacbioschemas.jsonld +++ b/data/isno-pseaac/isno-pseaacbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "iSNO-PseAAC", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://app.aporc.org/iSNO-PseAAC/" } \ No newline at end of file diff --git a/data/iso2flux/iso2fluxbioschemas.jsonld b/data/iso2flux/iso2fluxbioschemas.jsonld index 24434a2602dd9..d20e445a27ba3 100644 --- a/data/iso2flux/iso2fluxbioschemas.jsonld +++ b/data/iso2flux/iso2fluxbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Iso2Flux", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/cfoguet/iso2flux", "sc:version": "0.6" diff --git a/data/isobar/isobarbioschemas.jsonld b/data/isobar/isobarbioschemas.jsonld index 53a31d1c6fedf..71416449c4e10 100644 --- a/data/isobar/isobarbioschemas.jsonld +++ b/data/isobar/isobarbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-6192-0853", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/isobar", "@type": "sc:SoftwareApplication", @@ -30,10 +34,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/isobar.html", "sc:version": "1.20.0" - }, - { - "@id": "http://orcid.org/0000-0001-6192-0853", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/isoblat/isoblatbioschemas.jsonld b/data/isoblat/isoblatbioschemas.jsonld index 1dac8aace4196..aa6a057c80d36 100644 --- a/data/isoblat/isoblatbioschemas.jsonld +++ b/data/isoblat/isoblatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Isoblat", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/josephryan/isoblat" } \ No newline at end of file diff --git a/data/isochore-ebi/isochore-ebibioschemas.jsonld b/data/isochore-ebi/isochore-ebibioschemas.jsonld index 5ac5a2107fbae..c91070df227f1 100644 --- a/data/isochore-ebi/isochore-ebibioschemas.jsonld +++ b/data/isochore-ebi/isochore-ebibioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Plot potential isochore features.", "sc:name": "isochore (EBI)", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "EMBL-EBI", diff --git a/data/isochore/isochorebioschemas.jsonld b/data/isochore/isochorebioschemas.jsonld index c4a05d5bba185..c998ceefb863c 100644 --- a/data/isochore/isochorebioschemas.jsonld +++ b/data/isochore/isochorebioschemas.jsonld @@ -13,9 +13,9 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "UK BBSRC", "UK MRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Plot isochores in DNA sequences.", "sc:funder": [ diff --git a/data/isoem/isoembioschemas.jsonld b/data/isoem/isoembioschemas.jsonld index 8194900b4f03f..532379867de7a 100644 --- a/data/isoem/isoembioschemas.jsonld +++ b/data/isoem/isoembioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/isoem", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alex Zelikovsky", "Ion Mandoiu", + "Sahar Al Seesi", "Igor Mandric", - "Sahar Al Seesi" + "Alex Zelikovsky" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:21504602", "sc:description": "Expectation maximization algorithm for estimating alternative splicing isoform frequencies", "sc:name": "IsoEM", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://dna.engr.uconn.edu/?page_id=105" diff --git a/data/isoexpresso/isoexpressobioschemas.jsonld b/data/isoexpresso/isoexpressobioschemas.jsonld index e78d4694ca84f..1cd8220fc7eef 100644 --- a/data/isoexpresso/isoexpressobioschemas.jsonld +++ b/data/isoexpresso/isoexpressobioschemas.jsonld @@ -13,16 +13,16 @@ "@id": "https://bio.tools/isoexpresso", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sangwoo Kim", - "In Seok Yang" + "In Seok Yang", + "Sangwoo Kim" ], "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4983006", - "pubmed:27519173", { "@id": "https://doi.org/10.1186/S12864-016-2852-6" - } + }, + "pubmed:27519173", + "pmcid:PMC4983006" ], "sc:description": "Web-based platform for isoform-level expression analysis in human cancer.", "sc:featureList": { @@ -31,8 +31,8 @@ "sc:name": "ISOexpresso", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://wiki.tgilab.org/ISOexpresso/" }, diff --git a/data/isofinder/isofinderbioschemas.jsonld b/data/isofinder/isofinderbioschemas.jsonld index b021dfb10e3cf..2b3753177666d 100644 --- a/data/isofinder/isofinderbioschemas.jsonld +++ b/data/isofinder/isofinderbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "IsoFinder is a tool for the prediction of isochores for a user-supplied sequence.", "sc:name": "IsoFinder", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://isofinder.sourceforge.net/" } \ No newline at end of file diff --git a/data/isoformswitchanalyzer/isoformswitchanalyzerbioschemas.jsonld b/data/isoformswitchanalyzer/isoformswitchanalyzerbioschemas.jsonld index 05ba52ff0e391..13c1ad1630159 100644 --- a/data/isoformswitchanalyzer/isoformswitchanalyzerbioschemas.jsonld +++ b/data/isoformswitchanalyzer/isoformswitchanalyzerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-2.0", "sc:name": "IsoformSwitchAnalyzeR", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/IsoformSwitchAnalyzeR/" } \ No newline at end of file diff --git a/data/isogenegui/isogeneguibioschemas.jsonld b/data/isogenegui/isogeneguibioschemas.jsonld index 531c91b89b243..fc65546276739 100644 --- a/data/isogenegui/isogeneguibioschemas.jsonld +++ b/data/isogenegui/isogeneguibioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Setia Pramana", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This interface of the IsoGene package identifies genes with a monotonic trend in the expression levels with respect to the increasing doses through several test statistics.", "sc:license": "GPL-2.0", "sc:name": "IsoGeneGUI", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IsoGeneGUI.html", "sc:version": "2.10.0" diff --git a/data/isolde/bioconda_isolde.yaml b/data/isolde/bioconda_isolde.yaml index 57afb7e9d37f9..1beeaac689ecc 100644 --- a/data/isolde/bioconda_isolde.yaml +++ b/data/isolde/bioconda_isolde.yaml @@ -6,7 +6,6 @@ description: This package provides ISoLDE a new method for identifying imprinted home: https://bioconductor.org/packages/3.10/bioc/html/ISoLDE.html identifiers: - biotools:isolde -- doi:10.1038/nmeth.3252 license: GPL (>= 2.0) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-isolde diff --git a/data/isolde/isoldebioschemas.jsonld b/data/isolde/isoldebioschemas.jsonld index 4b82787ebb73b..8c3499cfb99dd 100644 --- a/data/isolde/isoldebioschemas.jsonld +++ b/data/isolde/isoldebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christelle Reynès", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies.", "sc:license": "GPL-2.0", "sc:name": "ISoLDE", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ISoLDE.html", "sc:version": "1.2.0" diff --git a/data/isomir-sea/isomir-seabioschemas.jsonld b/data/isomir-sea/isomir-seabioschemas.jsonld index 090600d047d9f..2f7521c829bad 100644 --- a/data/isomir-sea/isomir-seabioschemas.jsonld +++ b/data/isomir-sea/isomir-seabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "isomiR-SEA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://eda.polito.it/isomir-sea" } \ No newline at end of file diff --git a/data/isomirs/isomirsbioschemas.jsonld b/data/isomirs/isomirsbioschemas.jsonld index d3637598cbbb2..d53f93fc3c74a 100644 --- a/data/isomirs/isomirsbioschemas.jsonld +++ b/data/isomirs/isomirsbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lorena Pantano", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Characterization of miRNAs and isomiRs, clustering and differential expression.", "sc:license": "MIT", "sc:name": "isomiRs", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/isomiRs.html", diff --git a/data/isoscale/isoscalebioschemas.jsonld b/data/isoscale/isoscalebioschemas.jsonld index cfeeec781c756..d62804631c073 100644 --- a/data/isoscale/isoscalebioschemas.jsonld +++ b/data/isoscale/isoscalebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Proteomics software to quantify peptides based on the total ion intensity of the MS/MS spectra. The software provides also relative quantification of isobaric peptides co-fragmented in MS/MS spectra which share the same sequence but have distinct localizations of post-translational modifications (PTMs).", "sc:name": "isoScale", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "bmb.sdu.dk", "sc:url": "https://github.com/middle-down/Software", diff --git a/data/isoscm/isoscmbioschemas.jsonld b/data/isoscm/isoscmbioschemas.jsonld index a7d94013450df..3cf475a7038c3 100644 --- a/data/isoscm/isoscmbioschemas.jsonld +++ b/data/isoscm/isoscmbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "New method for transcript assembly  that incorporates change-point analysis to improve the 3′ UTR annotation process.", "sc:name": "IsoSCM", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/shenkers/isoscm" } \ No newline at end of file diff --git a/data/isotop/isotopbioschemas.jsonld b/data/isotop/isotopbioschemas.jsonld index 53205384d07f9..a8d83312e958f 100644 --- a/data/isotop/isotopbioschemas.jsonld +++ b/data/isotop/isotopbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "isotop", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ms-utils.org/isotop.html" } \ No newline at end of file diff --git a/data/isotopica/isotopicabioschemas.jsonld b/data/isotopica/isotopicabioschemas.jsonld index edbf852dc2db9..aaf07a9e96062 100644 --- a/data/isotopica/isotopicabioschemas.jsonld +++ b/data/isotopica/isotopicabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.", "sc:name": "ISOTOPICA", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://coco.protein.osaka-u.ac.jp/isotopica/" } \ No newline at end of file diff --git a/data/isotopident/isotopidentbioschemas.jsonld b/data/isotopident/isotopidentbioschemas.jsonld index 9b00f2069bc01..03cedc69ec35a 100644 --- a/data/isotopident/isotopidentbioschemas.jsonld +++ b/data/isotopident/isotopidentbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Isotopident can estimate the theoretical isotopic distribution of a peptide or protein, a polynucleotide and a chemical compound from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, sequence of nucleotides or its chemical formula). Isotopident can also compute its monoisotopic mass. and predict the most likely isotope combination and the exact mass of the given input.", "sc:name": "IsotopIdent", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://education.expasy.org/student_projects/isotopident/htdocs/" } \ No newline at end of file diff --git a/data/isown/isownbioschemas.jsonld b/data/isown/isownbioschemas.jsonld index cb54ac2108b2c..2fbb0d52715ec 100644 --- a/data/isown/isownbioschemas.jsonld +++ b/data/isown/isownbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Irina Kalatskaya", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5490163", "pubmed:28659176", { "@id": "https://doi.org/10.1186/s13073-017-0446-9" - }, - "pmcid:PMC5490163" + } ], "sc:description": "Accurate somatic mutation identification in the absence of normal tissue controls.", "sc:featureList": { diff --git a/data/ispot/ispotbioschemas.jsonld b/data/ispot/ispotbioschemas.jsonld index ab6387caf24e5..31a3466213524 100644 --- a/data/ispot/ispotbioschemas.jsonld +++ b/data/ispot/ispotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.", "sc:name": "iSPOT", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://cbm.bio.uniroma2.it/ispot/" } \ No newline at end of file diff --git a/data/istable/istablebioschemas.jsonld b/data/istable/istablebioschemas.jsonld index f61d4608a060f..637f630f3a033 100644 --- a/data/istable/istablebioschemas.jsonld +++ b/data/istable/istablebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An integrated predictor constructed by using sequence information and prediction results from different element predictors.", "sc:name": "iStable", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://predictor.nchu.edu.tw/istable/" diff --git a/data/isuc-pseopt/isuc-pseoptbioschemas.jsonld b/data/isuc-pseopt/isuc-pseoptbioschemas.jsonld index 5bc3a604e5c9a..5cbe409ecffa1 100644 --- a/data/isuc-pseopt/isuc-pseoptbioschemas.jsonld +++ b/data/isuc-pseopt/isuc-pseoptbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This web-server used to predict the lysine succinylation in protein.", "sc:name": "iSuc-PseOpt", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.jci-bioinfo.cn/iSuc-PseOpt" } \ No newline at end of file diff --git a/data/isulf-cys/isulf-cysbioschemas.jsonld b/data/isulf-cys/isulf-cysbioschemas.jsonld index 1486d0c206849..6f97ae0c379e4 100644 --- a/data/isulf-cys/isulf-cysbioschemas.jsonld +++ b/data/isulf-cys/isulf-cysbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC4841585", + "pubmed:27104833", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0154237" - }, - "pubmed:27104833" + } ], "sc:description": "Prediction of S-sulfenylation Sites in Proteins with Physicochemical Properties of Amino Acids.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "iSulf-Cys", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://app.aporc.org/iSulf-Cys/" } diff --git a/data/isvase/isvasebioschemas.jsonld b/data/isvase/isvasebioschemas.jsonld index 9edf2d27bba90..930c82e60af30 100644 --- a/data/isvase/isvasebioschemas.jsonld +++ b/data/isvase/isvasebioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:28659141", + "pmcid:PMC5490186", { "@id": "https://doi.org/10.1186/s12859-017-1732-7" - }, - "pmcid:PMC5490186" + } ], "sc:description": "Identification of sequence variant associated with splicing event using RNA-seq data.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:license": "GPL-3.0", "sc:name": "ISVASE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/isvase/" } diff --git a/data/itagplot/itagplotbioschemas.jsonld b/data/itagplot/itagplotbioschemas.jsonld index 3ceea7e73fcce..fac053315be71 100644 --- a/data/itagplot/itagplotbioschemas.jsonld +++ b/data/itagplot/itagplotbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool to accurately compute and interactively visualize tag density (read coverage)from genomic sequencing data.", "sc:name": "iTagPlot", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://sourceforge.net/projects/itagplot/" diff --git a/data/italics/italicsbioschemas.jsonld b/data/italics/italicsbioschemas.jsonld index f15257886d2ce..cee8435517c0e 100644 --- a/data/italics/italicsbioschemas.jsonld +++ b/data/italics/italicsbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "ITALICS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ITALICS.html", "sc:version": "2.34.0" diff --git a/data/itar/itarbioschemas.jsonld b/data/itar/itarbioschemas.jsonld index 0743c832a02b7..beb459315a575 100644 --- a/data/itar/itarbioschemas.jsonld +++ b/data/itar/itarbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12864-016-2963-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/itar", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chao Cheng", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:27519564", "pmcid:PMC4983039", { "@id": "https://doi.org/10.1186/S12864-016-2963-0" - }, - "pubmed:27519564" + } ], "sc:description": "A web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.", "sc:featureList": [ @@ -37,10 +41,6 @@ "Mac" ], "sc:url": "http://syslab3.nchu.edu.tw/iTAR/" - }, - { - "@id": "https://doi.org/10.1186/S12864-016-2963-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/iterativebma/iterativebmabioschemas.jsonld b/data/iterativebma/iterativebmabioschemas.jsonld index 6d41b7ea6c00b..5e2d5ffd19768 100644 --- a/data/iterativebma/iterativebmabioschemas.jsonld +++ b/data/iterativebma/iterativebmabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "iterativeBMA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iterativeBMA.html", "sc:version": "1.32.0" diff --git a/data/iterativebmasurv/iterativebmasurvbioschemas.jsonld b/data/iterativebmasurv/iterativebmasurvbioschemas.jsonld index 8f45391bd252b..26a50268a5840 100644 --- a/data/iterativebmasurv/iterativebmasurvbioschemas.jsonld +++ b/data/iterativebmasurv/iterativebmasurvbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ka Yee Yeung", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Variable selection method for applying survival analysis to microarray data.", "sc:license": "GPL-2.0", diff --git a/data/iteremoval/iteremovalbioschemas.jsonld b/data/iteremoval/iteremovalbioschemas.jsonld index 99b6309d41e16..1a986cbf824ab 100644 --- a/data/iteremoval/iteremovalbioschemas.jsonld +++ b/data/iteremoval/iteremovalbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "iteremoval", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/iteremoval.html", "sc:version": "1.0.0" diff --git a/data/iterm-pseknc/iterm-psekncbioschemas.jsonld b/data/iterm-pseknc/iterm-psekncbioschemas.jsonld index 7c422423a138e..208575ee84e79 100644 --- a/data/iterm-pseknc/iterm-psekncbioschemas.jsonld +++ b/data/iterm-pseknc/iterm-psekncbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hao Lin", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:description": "Sequence-based tool for predicting bacterial transcriptional terminators.", "sc:license": "Unlicense", diff --git a/data/itextmine/itextminebioschemas.jsonld b/data/itextmine/itextminebioschemas.jsonld index f1dc1ee73f823..f4873a1272c25 100644 --- a/data/itextmine/itextminebioschemas.jsonld +++ b/data/itextmine/itextminebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "iTextMine", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://research.bioinformatics.udel.edu/itextmine/integrate" diff --git a/data/itis-psetnc/itis-psetncbioschemas.jsonld b/data/itis-psetnc/itis-psetncbioschemas.jsonld index 4ba589d6321ff..9e9b95ee968d6 100644 --- a/data/itis-psetnc/itis-psetncbioschemas.jsonld +++ b/data/itis-psetnc/itis-psetncbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This web-server was developed to identify Translation initiation site (TIS) by using the physicochemical properties of the pseudo trinucleotide composition.", "sc:name": "iTIS-PseTNC", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://lin.uestc.edu.cn/server/iTIS-PseTNC" } \ No newline at end of file diff --git a/data/its2/its2bioschemas.jsonld b/data/its2/its2bioschemas.jsonld index 2761a89e34399..cf272754476b3 100644 --- a/data/its2/its2bioschemas.jsonld +++ b/data/its2/its2bioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/its2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Prof. Dr. Jörg Schultz", - "Dr. Matthias Wolf" + "Dr. Matthias Wolf", + "Prof. Dr. Jörg Schultz" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:15769870", diff --git a/data/itsonedb/itsonedbbioschemas.jsonld b/data/itsonedb/itsonedbbioschemas.jsonld index 8a174d6f4ecb6..d1dd8a948ecf1 100644 --- a/data/itsonedb/itsonedbbioschemas.jsonld +++ b/data/itsonedb/itsonedbbioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Graziano Pesole", "sc:additionalType": "Database portal", "sc:author": [ - "C.N.R. - IBIOM", - "C.N.R. - ITB, Bari" + "C.N.R. - ITB, Bari", + "C.N.R. - IBIOM" ], "sc:description": "A comprehensive collection of the fungal ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences aimed at supporting metagenomic surveys of fungal environmental communities.", "sc:name": "ITSoneDB", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ELIXIR-ITA-CNR", "sc:url": "http://itsonedb.ba.itb.cnr.it" diff --git a/data/itsxpress/itsxpressbioschemas.jsonld b/data/itsxpress/itsxpressbioschemas.jsonld index d12363722ad1b..2c5ee277eba3f 100644 --- a/data/itsxpress/itsxpressbioschemas.jsonld +++ b/data/itsxpress/itsxpressbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "CC0-1.0", "sc:name": "ITSxpress", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/USDA-ARS-GBRU/itsxpress", "sc:version": "v1.6.0" diff --git a/data/iubiq-lys/iubiq-lysbioschemas.jsonld b/data/iubiq-lys/iubiq-lysbioschemas.jsonld index a798faefd6adf..79a76fce02fb3 100644 --- a/data/iubiq-lys/iubiq-lysbioschemas.jsonld +++ b/data/iubiq-lys/iubiq-lysbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This web-server is a web server that could predict ubiquitination sites in proteins. With the assistance of SVM, the highlight is to employ amino acid sequence features extracted from the sequence evolution information via grey system model (Grey-PSSM).", "sc:name": "iUbiq-Lys", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.jci-bioinfo.cn/iUbiq-Lys" } \ No newline at end of file diff --git a/data/iuphar-db/iuphar-dbbioschemas.jsonld b/data/iuphar-db/iuphar-dbbioschemas.jsonld index db8eaafcdee6f..79f1a7d9c9dd3 100644 --- a/data/iuphar-db/iuphar-dbbioschemas.jsonld +++ b/data/iuphar-db/iuphar-dbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An online reference resource for classes of human drug targets and related proteins. As well as providing recommended nomenclature, the database integrates information on the chemical, genetic, functional and pathophysiological properties of receptors and ion channels, curated and peer-reviewed from the biomedical literature by a network of experts.", "sc:name": "IUPHAR-DB", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.guidetopharmacology.org/" } \ No newline at end of file diff --git a/data/iupred_ws_jabaws/iupred_ws_jabawsbioschemas.jsonld b/data/iupred_ws_jabaws/iupred_ws_jabawsbioschemas.jsonld index 2430681aee7b1..d4d03c85ccb83 100644 --- a/data/iupred_ws_jabaws/iupred_ws_jabawsbioschemas.jsonld +++ b/data/iupred_ws_jabaws/iupred_ws_jabawsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Recognizes unstructured/disordered regions from the amino acid sequence based on the estimated pairwise energy content.", "sc:name": "IUPred WS (jabaws)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.compbio.dundee.ac.uk/jabaws/", "sc:version": "1" diff --git a/data/iuta/iutabioschemas.jsonld b/data/iuta/iutabioschemas.jsonld index 11b5a41a0205b..ac50d9a62a9f3 100644 --- a/data/iuta/iutabioschemas.jsonld +++ b/data/iuta/iutabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2164-15-862", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/iuta", "@type": "sc:SoftwareApplication", @@ -33,10 +29,14 @@ "sc:name": "IUTA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.niehs.nih.gov/research/resources/software/biostatistics/iuta/index.cfm" + }, + { + "@id": "https://doi.org/10.1186/1471-2164-15-862", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ivas/ivasbioschemas.jsonld b/data/ivas/ivasbioschemas.jsonld index b545f764974ca..6bcdef67a6397 100644 --- a/data/ivas/ivasbioschemas.jsonld +++ b/data/ivas/ivasbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Seonggyun Han", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Identification of genetic variants affecting alternative splicing.", "sc:license": "GPL-2.0", "sc:name": "IVAS", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IVAS.html", "sc:version": "1.6.0" diff --git a/data/iview/iviewbioschemas.jsonld b/data/iview/iviewbioschemas.jsonld index bc60b1b5ec7bc..b7a74eb35832b 100644 --- a/data/iview/iviewbioschemas.jsonld +++ b/data/iview/iviewbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Interactive HTML5 visualizer of protein-ligand complex.", "sc:name": "iview", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://istar.cse.cuhk.edu.hk/iview/" diff --git a/data/ivkc-otc/ivkc-otcbioschemas.jsonld b/data/ivkc-otc/ivkc-otcbioschemas.jsonld index 5bb7f4d91fb19..526c32d4d2a9d 100644 --- a/data/ivkc-otc/ivkc-otcbioschemas.jsonld +++ b/data/ivkc-otc/ivkc-otcbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This web-server was developed to predict the subfamilies of votaged-gated potassium channel using tripeptide compositions.", "sc:name": "iVKC-OTC", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://lin.uestc.edu.cn/server/iVKC-OTC" } \ No newline at end of file diff --git a/data/ivygapse/ivygapsebioschemas.jsonld b/data/ivygapse/ivygapsebioschemas.jsonld index d9a7e9e5b5070..c12699140823e 100644 --- a/data/ivygapse/ivygapsebioschemas.jsonld +++ b/data/ivygapse/ivygapsebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "ivygapSE", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ivygapSE.html", "sc:version": "1.2.0" diff --git a/data/iwepoissonpaper/iwepoissonpaperbioschemas.jsonld b/data/iwepoissonpaper/iwepoissonpaperbioschemas.jsonld index a595da078eb2e..173e824666ef8 100644 --- a/data/iwepoissonpaper/iwepoissonpaperbioschemas.jsonld +++ b/data/iwepoissonpaper/iwepoissonpaperbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "IWEPoissonPaper", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com//statgenlmu//IWEPoissonPaper" } \ No newline at end of file diff --git a/data/iwtomics/iwtomicsbioschemas.jsonld b/data/iwtomics/iwtomicsbioschemas.jsonld index caae06f1f1d76..e9d34ceb76a44 100644 --- a/data/iwtomics/iwtomicsbioschemas.jsonld +++ b/data/iwtomics/iwtomicsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "IWTomics", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/IWTomics.html", "sc:version": "1.4.0" diff --git a/data/j-circos/j-circosbioschemas.jsonld b/data/j-circos/j-circosbioschemas.jsonld index 3bb04c16fa5ee..db4277d7b93da 100644 --- a/data/j-circos/j-circosbioschemas.jsonld +++ b/data/j-circos/j-circosbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Circos plot tool that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions.", "sc:name": "J-Circos", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.australianprostatecentre.org/research/software/jcircos" } \ No newline at end of file diff --git a/data/j-express/j-expressbioschemas.jsonld b/data/j-express/j-expressbioschemas.jsonld index 09f06cb3fcc36..5028ac16c8102 100644 --- a/data/j-express/j-expressbioschemas.jsonld +++ b/data/j-express/j-expressbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It is a comprehensive portable software package for analysis and visualization of microarray data. It gives access to methods for unsupervised analysis, supervised analysis and visualisation in an integrated and flexible way. Its efficiency allows interactive clustering of thousands of expression profiles on standard personal computers. Supervised analysis can be performed on samples by simple sample annotation or on genes through tools for metabolic pathway analysis and Gene Ontology mapping.", "sc:name": "J-Express", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://jexpress.bioinfo.no/site/", "sc:version": "2012" diff --git a/data/j/jbioschemas.jsonld b/data/j/jbioschemas.jsonld index bbeeccb8e63dc..201231de70c1f 100644 --- a/data/j/jbioschemas.jsonld +++ b/data/j/jbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Java graphical user interface (GUI) for the popular QTL data analysis software R/qtl.", "sc:name": "J", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://churchill.jax.org/software/jqtl.shtml" } \ No newline at end of file diff --git a/data/jabaws/jabawsbioschemas.jsonld b/data/jabaws/jabawsbioschemas.jsonld index 62e0965a31355..a6ea97a25d6ae 100644 --- a/data/jabaws/jabawsbioschemas.jsonld +++ b/data/jabaws/jabawsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Apache-2.0", "sc:name": "JABAWS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.compbio.dundee.ac.uk/jabaws/" diff --git a/data/jacks/jacksbioschemas.jsonld b/data/jacks/jacksbioschemas.jsonld index 44fd4711851a8..5db4289612b90 100644 --- a/data/jacks/jacksbioschemas.jsonld +++ b/data/jacks/jacksbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "F. Allen", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:30674557", "pmcid:PMC6396427", { "@id": "https://doi.org/10.1101/gr.238923.118" - } + }, + "pubmed:30674557" ], "sc:description": "Analysis package for processing counts from genome-wide CRISPR/Cas9 screens.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:license": "Unlicense", "sc:name": "JACKS", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/felicityallen/JACKS" }, diff --git a/data/jadis/jadisbioschemas.jsonld b/data/jadis/jadisbioschemas.jsonld index 1e92b051a27e7..6185633c807ce 100644 --- a/data/jadis/jadisbioschemas.jsonld +++ b/data/jadis/jadisbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Program for computing distances between nucleic acid sequences. It allows specific comparison of coding sequences, of non-coding sequences, or of coding and non-coding sequences.", "sc:name": "JaDis", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://wwwabi.snv.jussieu.fr/public/Jadis/" } \ No newline at end of file diff --git a/data/jal/jalbioschemas.jsonld b/data/jal/jalbioschemas.jsonld index 9ac7ea9f44e19..138647aef0eb4 100644 --- a/data/jal/jalbioschemas.jsonld +++ b/data/jal/jalbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/JAL", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Chandra S. Verma", - "Minh N. Nguyen" + "Minh N. Nguyen", + "Chandra S. Verma" ], "sc:additionalType": [ "Web service", @@ -25,8 +25,8 @@ "sc:name": "JAL", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mspc.bii.a-star.edu.sg/minhn/jal.html" } \ No newline at end of file diff --git a/data/jali/jalibioschemas.jsonld b/data/jali/jalibioschemas.jsonld index fd24dc503c83b..09cc0ee56c465 100644 --- a/data/jali/jalibioschemas.jsonld +++ b/data/jali/jalibioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/jali", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", "Command-line tool", + "Web application", "Web API" ], "sc:author": "Jens Stoye", @@ -20,13 +20,13 @@ "sc:name": "JAli", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "CeBiTec", - "BiBiServ", - "Bielefeld University" + "Bielefeld University", + "BiBiServ" ], "sc:url": "http://bibiserv.cebitec.uni-bielefeld.de/jali", "sc:version": "1.3" diff --git a/data/jamberoo/jamberoobioschemas.jsonld b/data/jamberoo/jamberoobioschemas.jsonld index fd8f3d314f4ae..31d75e6dffdbf 100644 --- a/data/jamberoo/jamberoobioschemas.jsonld +++ b/data/jamberoo/jamberoobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Jamberoo (former JMolEditor) is a program for displaying, analyzing, editing, converting, and animating molecular systems.", "sc:name": "Jamberoo", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html", "sc:version": "11" diff --git a/data/jamming/jammingbioschemas.jsonld b/data/jamming/jammingbioschemas.jsonld index 39386e94ad0ce..e341813e293f4 100644 --- a/data/jamming/jammingbioschemas.jsonld +++ b/data/jamming/jammingbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "JAMMING is a software for prediction of critical residues for protein function based only on the 3D structure of proteins", "sc:name": "JAMMING", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bis.ifc.unam.mx:8090/JAMMING/" } \ No newline at end of file diff --git a/data/jamss/jamssbioschemas.jsonld b/data/jamss/jamssbioschemas.jsonld index f845e664665b2..3a7f0dcbf14e5 100644 --- a/data/jamss/jamssbioschemas.jsonld +++ b/data/jamss/jamssbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Fast, self-contained in silico simulator capable of generating simulated MS and LC- MS runs while providing meta information on the provenance of each generated signal.", "sc:name": "JAMSS", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://ms.cs.umt.edu/simulation.html" } \ No newline at end of file diff --git a/data/janus/janusbioschemas.jsonld b/data/janus/janusbioschemas.jsonld index 31356d7704efc..adef9fdb9965e 100644 --- a/data/janus/janusbioschemas.jsonld +++ b/data/janus/janusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "Janus", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/CCQC/janus" } \ No newline at end of file diff --git a/data/jar3d/jar3dbioschemas.jsonld b/data/jar3d/jar3dbioschemas.jsonld index 62304d8744c0f..6f0f9665d3fb9 100644 --- a/data/jar3d/jar3dbioschemas.jsonld +++ b/data/jar3d/jar3dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Scores RNA hairpin and internal loop sequences against motif groups from the RNA 3D Motif Atlas, by exact sequence match for sequences already observed in 3D and by probabilistic scoring and edit distance for novel sequences.", "sc:name": "JAR3D", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://rna.bgsu.edu/jar3d" } \ No newline at end of file diff --git a/data/jaspar/jasparbioschemas.jsonld b/data/jaspar/jasparbioschemas.jsonld index bada408725e99..84dc6b79c1f96 100644 --- a/data/jaspar/jasparbioschemas.jsonld +++ b/data/jaspar/jasparbioschemas.jsonld @@ -17,17 +17,17 @@ "@id": "https://bio.tools/jaspar", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wyeth Wasserman", { "@id": "http://orcid.org/0000-0001-5127-5459" }, "Boris Lenhard", + "Wyeth Wasserman", "Albin Sandelin" ], "sc:additionalType": [ "Web application", - "Database portal", - "Web API" + "Web API", + "Database portal" ], "sc:description": "The high-quality transcription factor binding profile database.", "sc:license": "CC-BY-NC-4.0", diff --git a/data/jaspar2018/jaspar2018bioschemas.jsonld b/data/jaspar2018/jaspar2018bioschemas.jsonld index 52d0e3d51ebb6..e40dab82e34a2 100644 --- a/data/jaspar2018/jaspar2018bioschemas.jsonld +++ b/data/jaspar2018/jaspar2018bioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "JASPAR2018", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/data/annotation/html/JASPAR2018.html", "sc:version": "1.1.0" diff --git a/data/jaspar_api/jaspar_apibioschemas.jsonld b/data/jaspar_api/jaspar_apibioschemas.jsonld index 892ab5a53e27d..8ce13985d8cb5 100644 --- a/data/jaspar_api/jaspar_apibioschemas.jsonld +++ b/data/jaspar_api/jaspar_apibioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/jaspar_api", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Anthony Mathelier", - "Aziz Khan" + "Aziz Khan", + "Anthony Mathelier" ], "sc:additionalType": "Web API", "sc:description": "Widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to access JASPAR data using the Representational State Transfer (REST) architecture.", "sc:license": "GPL-3.0", "sc:name": "JASPAR RESTful API", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://jaspar.genereg.net/api/" diff --git a/data/jaspar_ws/jaspar_wsbioschemas.jsonld b/data/jaspar_ws/jaspar_wsbioschemas.jsonld index 52603c77a7070..d6264e78715a6 100644 --- a/data/jaspar_ws/jaspar_wsbioschemas.jsonld +++ b/data/jaspar_ws/jaspar_wsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Jaspar WS", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://api.bioinfo.no/wsdl/Jaspar_webservice_0.2.wsdl", "sc:version": "1" diff --git a/data/jaspardb/jaspardbbioschemas.jsonld b/data/jaspardb/jaspardbbioschemas.jsonld index 43ec75a981817..15d838d213abc 100644 --- a/data/jaspardb/jaspardbbioschemas.jsonld +++ b/data/jaspardb/jaspardbbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Web service interface to the Jaspar database containing profiles of transcription factor binding sites.", "sc:name": "JasparDB", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://api.bioinfo.no/wsdl/JasparDB.wsdl", diff --git a/data/jaspextract/jaspextractbioschemas.jsonld b/data/jaspextract/jaspextractbioschemas.jsonld index a2b5b86528285..0c35f676ea2a8 100644 --- a/data/jaspextract/jaspextractbioschemas.jsonld +++ b/data/jaspextract/jaspextractbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", "EMBOSS Contributors", - "UK BBSRC" + "Wellcome Trust" ], "sc:description": "Extract data from JASPAR.", "sc:funder": [ - "UK MRC", "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", @@ -31,8 +31,8 @@ "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/jaspextract.html", "sc:version": "r6" diff --git a/data/jaspscan/jaspscanbioschemas.jsonld b/data/jaspscan/jaspscanbioschemas.jsonld index 5125302c2c8cd..b1e1d9dcf55ba 100644 --- a/data/jaspscan/jaspscanbioschemas.jsonld +++ b/data/jaspscan/jaspscanbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "EMBOSS Contributors", + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Scan DNA sequences for transcription factors.", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "jaspscan", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/jassa/jassabioschemas.jsonld b/data/jassa/jassabioschemas.jsonld index 0babee791bb5a..66991edfea1f4 100644 --- a/data/jassa/jassabioschemas.jsonld +++ b/data/jassa/jassabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs.", "sc:name": "JASSA", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.jassa.fr/" } \ No newline at end of file diff --git a/data/jbiclustge/jbiclustgebioschemas.jsonld b/data/jbiclustge/jbiclustgebioschemas.jsonld index ce7359ce9bd68..0e2983c67dd16 100644 --- a/data/jbiclustge/jbiclustgebioschemas.jsonld +++ b/data/jbiclustge/jbiclustgebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Rui Mendes", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "A new Java API for biclustering analysis in the context of gene expression data, allowing the use of 21 biclustering algorithms.", "sc:license": "Other", "sc:name": "JBiclustGE", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://jbiclustge.github.io/" } \ No newline at end of file diff --git a/data/jbrowse/jbrowsebioschemas.jsonld b/data/jbrowse/jbrowsebioschemas.jsonld index fc5c7e9ddcc3b..3eb2ddd076cdd 100644 --- a/data/jbrowse/jbrowsebioschemas.jsonld +++ b/data/jbrowse/jbrowsebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.", "sc:name": "JBrowse", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://gmod.org/wiki/JBrowse" } \ No newline at end of file diff --git a/data/jcdsa/jcdsabioschemas.jsonld b/data/jcdsa/jcdsabioschemas.jsonld index 325a84e98e8db..bf387b4d6e494 100644 --- a/data/jcdsa/jcdsabioschemas.jsonld +++ b/data/jcdsa/jcdsabioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://orcid.org/0000-0003-2272-6278", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/s12859-018-2213-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/jcdsa", "@type": "sc:SoftwareApplication", @@ -21,10 +25,10 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5975448", { "@id": "https://doi.org/10.1186/s12859-018-2213-3" }, + "pmcid:PMC5975448", "pubmed:29843599" ], "sc:description": "Joint covariate detection tool for survival analysis on tumor expression profiles.", @@ -38,10 +42,6 @@ "Windows" ], "sc:url": "http://bio-nefu.com/resource/jcdsa" - }, - { - "@id": "https://doi.org/10.1186/s12859-018-2213-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/jchem_for_office/jchem_for_officebioschemas.jsonld b/data/jchem_for_office/jchem_for_officebioschemas.jsonld index 5e0a99bfd649c..28ad6865a2f87 100644 --- a/data/jchem_for_office/jchem_for_officebioschemas.jsonld +++ b/data/jchem_for_office/jchem_for_officebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Integrates structure handling and visualizing capabilities within a Microsoft Office environment. The bundle includes JChem for Excel which is our long-standing Excel integration. With JChem for Office, chemistry is made live in your Office application and structures are fully supported within spreadsheets, documents, slides and e-mails.", "sc:name": "JChem for Office", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://www.chemaxon.com/products/jchem-for-office/", "sc:version": "15.6.1500" diff --git a/data/jd2stat/jd2statbioschemas.jsonld b/data/jd2stat/jd2statbioschemas.jsonld index 80701aaed9ddf..b45806f94dc3e 100644 --- a/data/jd2stat/jd2statbioschemas.jsonld +++ b/data/jd2stat/jd2statbioschemas.jsonld @@ -17,10 +17,10 @@ }, "edam:has_input": [ { - "@id": "edam:data_1245" + "@id": "edam:data_1246" }, { - "@id": "edam:data_1246" + "@id": "edam:data_1245" } ], "edam:has_output": { @@ -31,19 +31,19 @@ "@id": "edam:topic_0080" }, "sc:citation": [ - "pmcid:PMC4179140", "pubmed:25266120", { "@id": "https://doi.org/10.1038/srep06504" - } + }, + "pmcid:PMC4179140" ], "sc:description": "A Java package that utilises a series of D2 statistics to extract k-mers (subsequences at defined k length) from a set of biological sequences, and generate pairwise distances for each possible pair. This distance can be used directly for phylogenetic inference using neighbour-joining.", "sc:featureList": [ { - "@id": "edam:operation_0289" + "@id": "edam:operation_3472" }, { - "@id": "edam:operation_3472" + "@id": "edam:operation_0289" } ], "sc:isAccessibleForFree": true, @@ -55,13 +55,13 @@ }, "sc:url": "http://bioinformatics.org.au/tools/jD2Stat/" }, - { - "@id": "https://doi.org/10.1038/srep06504", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-3729-8176", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1038/srep06504", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/jdftx/jdftxbioschemas.jsonld b/data/jdftx/jdftxbioschemas.jsonld index 8ecdc308c9775..cf09177b4c290 100644 --- a/data/jdftx/jdftxbioschemas.jsonld +++ b/data/jdftx/jdftxbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-0625-4592", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/jdftx", "@type": "sc:SoftwareApplication", @@ -22,10 +18,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5992620", - "pubmed:29892692", { "@id": "https://doi.org/10.1016/j.softx.2017.10.006" - } + }, + "pubmed:29892692" ], "sc:description": "JDFTx is a fully-featured open-source electronic density-functional theory software designed specifically to facilitate rapid development of new theories, models and algorithms.", "sc:featureList": { @@ -35,8 +31,8 @@ "sc:name": "JDFTx", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00063", "sc:version": "1.3.1" @@ -44,6 +40,10 @@ { "@id": "https://doi.org/10.1016/j.softx.2017.10.006", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-0625-4592", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/jdinac/jdinacbioschemas.jsonld b/data/jdinac/jdinacbioschemas.jsonld index 1c738b0208e74..17e241b727227 100644 --- a/data/jdinac/jdinacbioschemas.jsonld +++ b/data/jdinac/jdinacbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data .", "sc:name": "JDINAC", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/jijiadong/JDINAC" } \ No newline at end of file diff --git a/data/jdpd/jdpdbioschemas.jsonld b/data/jdpd/jdpdbioschemas.jsonld index 7126c72a86f12..9fbe4ab015645 100644 --- a/data/jdpd/jdpdbioschemas.jsonld +++ b/data/jdpd/jdpdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Jdpd", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/zielesny/Jdpd" } \ No newline at end of file diff --git a/data/jecho/jechobioschemas.jsonld b/data/jecho/jechobioschemas.jsonld index 4bdab3992a8ba..b6201bba17df9 100644 --- a/data/jecho/jechobioschemas.jsonld +++ b/data/jecho/jechobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.", "sc:name": "jEcho", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.healthinformaticslab.org/supp/" diff --git a/data/jellyfish/jellyfishbioschemas.jsonld b/data/jellyfish/jellyfishbioschemas.jsonld index 9e3db6947ffee..967eae8a77b78 100644 --- a/data/jellyfish/jellyfishbioschemas.jsonld +++ b/data/jellyfish/jellyfishbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "Jellyfish", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.genome.umd.edu/jellyfish.html", "sc:version": "2.0" diff --git a/data/jensemb/jensembbioschemas.jsonld b/data/jensemb/jensembbioschemas.jsonld index 9566619acd4c8..bc7c7846543bd 100644 --- a/data/jensemb/jensembbioschemas.jsonld +++ b/data/jensemb/jensembbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources.", "sc:name": "JEnsemb", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://jensembl.sourceforge.net/" } \ No newline at end of file diff --git a/data/jesam/jesambioschemas.jsonld b/data/jesam/jesambioschemas.jsonld index fea689e68efc5..4f6147f5ea8a9 100644 --- a/data/jesam/jesambioschemas.jsonld +++ b/data/jesam/jesambioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software components to create and publish EST alignments and clusters.", "sc:name": "JESAM", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.littlest.co.uk/software/bioinf/old_packages/jesam/jesam_paper.html" } \ No newline at end of file diff --git a/data/jevtrace/jevtracebioschemas.jsonld b/data/jevtrace/jevtracebioschemas.jsonld index 808109c6492ea..fdbeee43fcfea 100644 --- a/data/jevtrace/jevtracebioschemas.jsonld +++ b/data/jevtrace/jevtracebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.", "sc:name": "JEvTrace", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://compbio.berkeley.edu/people/marcin/jevtrace/" diff --git a/data/jgi_genome_portal/jgi_genome_portalbioschemas.jsonld b/data/jgi_genome_portal/jgi_genome_portalbioschemas.jsonld index 143b8cfeb4e35..adcced0f5ee34 100644 --- a/data/jgi_genome_portal/jgi_genome_portalbioschemas.jsonld +++ b/data/jgi_genome_portal/jgi_genome_portalbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms.", "sc:name": "JGI Genome Portal", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://genome.jgi.doe.gov/" } \ No newline at end of file diff --git a/data/jiffynet/jiffynetbioschemas.jsonld b/data/jiffynet/jiffynetbioschemas.jsonld index d62fa72454cbf..82998e7e704b5 100644 --- a/data/jiffynet/jiffynetbioschemas.jsonld +++ b/data/jiffynet/jiffynetbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a query species with only protein sequences provided.", "sc:name": "JiffyNet", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.jiffynet.org" } \ No newline at end of file diff --git a/data/jigcell_run_manager/jigcell_run_managerbioschemas.jsonld b/data/jigcell_run_manager/jigcell_run_managerbioschemas.jsonld index 1145ce540c78e..0c4738e2ba8b1 100644 --- a/data/jigcell_run_manager/jigcell_run_managerbioschemas.jsonld +++ b/data/jigcell_run_manager/jigcell_run_managerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "JigCell Run Manager", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://copasi.org/Projects/JigCell_Run_Manager_2_0//" } \ No newline at end of file diff --git a/data/jmrui/jmruibioschemas.jsonld b/data/jmrui/jmruibioschemas.jsonld index d6580516c9db4..310713d0e5909 100644 --- a/data/jmrui/jmruibioschemas.jsonld +++ b/data/jmrui/jmruibioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Michał Jabłoński", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5260066", { "@id": "https://doi.org/10.1186/s12859-017-1459-5" }, + "pmcid:PMC5260066", "pubmed:28114896" ], "sc:description": "Software package for advanced time-domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data. Through a user-friendly graphical interface biomedical researchers and clinical radiologists can use state-of-the-art signal processing algorithms to analyse and quantify spectroscopic data: from a single spectrum to a full multidimensional MRSI dataset.", diff --git a/data/jmztab-m/jmztab-mbioschemas.jsonld b/data/jmztab-m/jmztab-mbioschemas.jsonld index 4f85d271feec0..96ab879fa64f5 100644 --- a/data/jmztab-m/jmztab-mbioschemas.jsonld +++ b/data/jmztab-m/jmztab-mbioschemas.jsonld @@ -23,15 +23,15 @@ "sc:license": "Apache-2.0", "sc:name": "jmztab-m", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/lifs-tools/jmzTab-m", "sc:version": [ - "0.9.6", "1.0.4", "1.0.1", + "0.9.6", "1.0.2" ] }, diff --git a/data/jmztab/jmztabbioschemas.jsonld b/data/jmztab/jmztabbioschemas.jsonld index b1621fa361be2..1a02c81d863e2 100644 --- a/data/jmztab/jmztabbioschemas.jsonld +++ b/data/jmztab/jmztabbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Provides reading and writing capabilities, as well as supporting the validation of mzTab and the conversion of PRIDE XML and mzIdentML files to mzTab.", "sc:name": "jmzTab", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://code.google.com/p/mztab/" diff --git a/data/jnmf/jnmfbioschemas.jsonld b/data/jnmf/jnmfbioschemas.jsonld index 04be4326527d8..9b511dfa4c66b 100644 --- a/data/jnmf/jnmfbioschemas.jsonld +++ b/data/jnmf/jnmfbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Package which implemented the joint matrix factorization technique to integrating multi-dimensional genomics data for the discovery of combinatorial patterns.", "sc:name": "jNMF", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://page.amss.ac.cn/shihua.zhang/software.html" } \ No newline at end of file diff --git a/data/joa/joabioschemas.jsonld b/data/joa/joabioschemas.jsonld index 01f513aadd38f..b5d5791cd9055 100644 --- a/data/joa/joabioschemas.jsonld +++ b/data/joa/joabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2698-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/JOA", "@type": "sc:SoftwareApplication", @@ -20,18 +16,18 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC6408804", - "pubmed:30849961", { "@id": "https://doi.org/10.1186/s12859-019-2698-4" - } + }, + "pubmed:30849961" ], "sc:description": "Joint Overlap Analysis (JOA) of multiple genomic interval sets. Takes n interval sets and finds overlapping intervals with no constraints on the given intervals.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_3798" }, { - "@id": "edam:operation_3798" + "@id": "edam:operation_3501" } ], "sc:name": "JOA", @@ -40,6 +36,10 @@ "Mac" ], "sc:url": "https://joa.readthedocs.org" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2698-4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/joda/jodabioschemas.jsonld b/data/joda/jodabioschemas.jsonld index d754e2b5cb238..4b64f352a7563 100644 --- a/data/joda/jodabioschemas.jsonld +++ b/data/joda/jodabioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-12-249", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-1320-6695", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/joda", "@type": "sc:SoftwareApplication", @@ -33,20 +41,12 @@ "sc:license": "GPL-2.0", "sc:name": "joda", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/joda.html", "sc:version": "1.22.0" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-12-249", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-1320-6695", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/joinerml/joinermlbioschemas.jsonld b/data/joinerml/joinermlbioschemas.jsonld index fba217915b289..3d6869b1a8aed 100644 --- a/data/joinerml/joinermlbioschemas.jsonld +++ b/data/joinerml/joinermlbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12874-018-0502-1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/joinerml", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Pete Philipson", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:9879902", { "@id": "https://doi.org/10.1186/s12874-018-0502-1" }, - "pmcid:PMC6047371", - "pubmed:9879902" + "pmcid:PMC6047371" ], "sc:description": "Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes.", "sc:featureList": { @@ -33,10 +29,14 @@ "sc:name": "joineRML", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/joineRML/" + }, + { + "@id": "https://doi.org/10.1186/s12874-018-0502-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/jointslm/jointslmbioschemas.jsonld b/data/jointslm/jointslmbioschemas.jsonld index 880901df0f202..129df0f7058c0 100644 --- a/data/jointslm/jointslmbioschemas.jsonld +++ b/data/jointslm/jointslmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Copy number estimation from read depth information.", "sc:name": "JointSLM", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/inutano/docker-ngs-tools/tree/master/JointSLM" } \ No newline at end of file diff --git a/data/joy/joybioschemas.jsonld b/data/joy/joybioschemas.jsonld index 39f9b80ceefef..49c941e0f64c5 100644 --- a/data/joy/joybioschemas.jsonld +++ b/data/joy/joybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "JOY is a program for displaying 3D structural information in a multiple sequence alignment.", "sc:name": "JOY", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mizuguchilab.org/joy/" } \ No newline at end of file diff --git a/data/jpcr/jpcrbioschemas.jsonld b/data/jpcr/jpcrbioschemas.jsonld index 90529f3dfdab9..295d309179ecd 100644 --- a/data/jpcr/jpcrbioschemas.jsonld +++ b/data/jpcr/jpcrbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A java application based on FastPCR software and provides comprehensive and professional facilities for designing primers for most PCR applications and their combinations: standard, multiplex, long distance, inverse, real-time, unique, group-specific, bisulphite modification assays, polymerase extension PCR multi-fragments assembly cloning (OE-PCR); and microarray design;", "sc:name": "jPCR", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://primerdigital.com/tools/pcr.html", diff --git a/data/jphmm/jphmmbioschemas.jsonld b/data/jphmm/jphmmbioschemas.jsonld index 7fb579d417fd0..d1f76a5520e1e 100644 --- a/data/jphmm/jphmmbioschemas.jsonld +++ b/data/jphmm/jphmmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 or HBV genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 or HBV subtypes to predict the phylogenetic breakpoints and HIV/HBV subtype of the submitted sequence.", "sc:name": "jpHMM", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://jphmm.gobics.de/" diff --git a/data/jphyloio/jphyloiobioschemas.jsonld b/data/jphyloio/jphyloiobioschemas.jsonld index d821a79893647..e4a2791b8f5f9 100644 --- a/data/jphyloio/jphyloiobioschemas.jsonld +++ b/data/jphyloio/jphyloiobioschemas.jsonld @@ -21,9 +21,9 @@ "sc:license": "LGPL-3.0", "sc:name": "JPhyloIO", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfweb.info/JPhyloIO/", "sc:version": "0.5.4" diff --git a/data/jpop/jpopbioschemas.jsonld b/data/jpop/jpopbioschemas.jsonld index 14f5382ef2864..f83e5a1458da0 100644 --- a/data/jpop/jpopbioschemas.jsonld +++ b/data/jpop/jpopbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Aset java programs and Mathlab scripts to aid in the prediction of operon structures. JPOP integrates three sources of genomic information to predict operon structures in a sequenced genome:\n1) COG (cluster of orthologs) assignments;\n2) Phylogenetic profiles of genes;\n3) Intergenic distances between gene pairs.", "sc:name": "JPOP", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://csbl.bmb.uga.edu/downloads/indexa.php#jpop", diff --git a/data/jpred_3/jpred_3bioschemas.jsonld b/data/jpred_3/jpred_3bioschemas.jsonld index b7e1365b657a8..9811f5fc363b8 100644 --- a/data/jpred_3/jpred_3bioschemas.jsonld +++ b/data/jpred_3/jpred_3bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Improved web server for predicting protein secondary structure in three states (alpha helix, beta strand and coil). Improvements include better usability, batch submission of sequences and updates to the search databases.", "sc:name": "Jpred 3", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.compbio.dundee.ac.uk/jpred" } \ No newline at end of file diff --git a/data/jpred_ws_jabaws/jpred_ws_jabawsbioschemas.jsonld b/data/jpred_ws_jabaws/jpred_ws_jabawsbioschemas.jsonld index 05a61bbfe7193..634073a72812f 100644 --- a/data/jpred_ws_jabaws/jpred_ws_jabawsbioschemas.jsonld +++ b/data/jpred_ws_jabaws/jpred_ws_jabawsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Jpred WS (jabaws)", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.compbio.dundee.ac.uk/jabaws/", "sc:version": "1" diff --git a/data/jprofilegrid/jprofilegridbioschemas.jsonld b/data/jprofilegrid/jprofilegridbioschemas.jsonld index 2c6559078e9ff..2c596d96f50dc 100644 --- a/data/jprofilegrid/jprofilegridbioschemas.jsonld +++ b/data/jprofilegrid/jprofilegridbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Java-based multiple sequence alignment tool that generates ProfileGrids for analysis and export. ProfileGrids are a new paradigm for visualizing and analyzing MSAs in a concise representation. For a protein sequence, a ProfileGrid matrix contains positional amino acid counts highlighted according to the frequency of the characters in the alignment.", "sc:name": "JProfileGrid", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.profilegrid.org/" } \ No newline at end of file diff --git a/data/jronn_ws_jabaws/jronn_ws_jabawsbioschemas.jsonld b/data/jronn_ws_jabaws/jronn_ws_jabawsbioschemas.jsonld index c3a13fb459e8c..62589a85006e6 100644 --- a/data/jronn_ws_jabaws/jronn_ws_jabawsbioschemas.jsonld +++ b/data/jronn_ws_jabaws/jronn_ws_jabawsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Jronn WS (jabaws)", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.compbio.dundee.ac.uk/jabaws/", "sc:version": "1" diff --git a/data/jsbml/jsbmlbioschemas.jsonld b/data/jsbml/jsbmlbioschemas.jsonld index 48983dc0dae13..08fd2474ea7f4 100644 --- a/data/jsbml/jsbmlbioschemas.jsonld +++ b/data/jsbml/jsbmlbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Free, open-source, pure-Java library for working with SBML. It emulates libSBML’s API, with more Java idioms and without native object code.", "sc:name": "JSBML 1.1", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://sbml.org/Software/JSBML" } \ No newline at end of file diff --git a/data/jsparklines/jsparklinesbioschemas.jsonld b/data/jsparklines/jsparklinesbioschemas.jsonld index 7247e297273ee..8af3fb4b82170 100644 --- a/data/jsparklines/jsparklinesbioschemas.jsonld +++ b/data/jsparklines/jsparklinesbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Makes it straightforward to visualize numbers in Java tables by the use of sparklines.", "sc:name": "JSparklines", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://compomics.github.io/projects/jsparklines.html", diff --git a/data/jsphylosvg/jsphylosvgbioschemas.jsonld b/data/jsphylosvg/jsphylosvgbioschemas.jsonld index 20a2189396f76..4d197a4c7d8de 100644 --- a/data/jsphylosvg/jsphylosvgbioschemas.jsonld +++ b/data/jsphylosvg/jsphylosvgbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Open-source javascript library specifically built for rendering highly-extensible, customizable phylogenetic trees. It can render complex trees, yet offers a simple method to do so. It leverages the recent XML schema definition specified for phylogenetic trees, phyloXML.", "sc:name": "jsPhyloSVG", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/guyleonard/jsPhyloSVG", "sc:version": "1.55" diff --git a/data/jsquid/jsquidbioschemas.jsonld b/data/jsquid/jsquidbioschemas.jsonld index 74ea6b88b435b..15c3925e8d799 100644 --- a/data/jsquid/jsquidbioschemas.jsonld +++ b/data/jsquid/jsquidbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A java tool to visualize networks and edge scores.", "sc:name": "jSquid", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "bils.se", "sc:url": "http://jsquid.sbc.su.se/", diff --git a/data/jtraml/jtramlbioschemas.jsonld b/data/jtraml/jtramlbioschemas.jsonld index 970a493ae8b8e..6e47c04935fb5 100644 --- a/data/jtraml/jtramlbioschemas.jsonld +++ b/data/jtraml/jtramlbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/jtraml", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Java implementation of the PSI-MS Transitions Markup Language (TraML) specification.", "sc:name": "Jtraml", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/compomics/jtraml", diff --git a/data/jump3/jump3bioschemas.jsonld b/data/jump3/jump3bioschemas.jsonld index ab14c0e4e2704..0f304dc449476 100644 --- a/data/jump3/jump3bioschemas.jsonld +++ b/data/jump3/jump3bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Based on a formal on/off model of gene expression, but uses a non-parametric procedure based on decision trees (called “jump trees”) to reconstruct the GRN topology, allowing the inference of networks of hundreds of genes.", "sc:name": "jump3", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://homepages.inf.ed.ac.uk/vhuynht/software.html" } \ No newline at end of file diff --git a/data/junctionseq/junctionseqbioschemas.jsonld b/data/junctionseq/junctionseqbioschemas.jsonld index 7fb574e07730e..8d045062ccfc7 100644 --- a/data/junctionseq/junctionseqbioschemas.jsonld +++ b/data/junctionseq/junctionseqbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkw501", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/junctionseq", "@type": "sc:SoftwareApplication", @@ -22,10 +18,10 @@ "Library" ], "sc:citation": [ - "pmcid:PMC5009739", { "@id": "https://doi.org/10.1093/nar/gkw501" }, + "pmcid:PMC5009739", "pubmed:27257077" ], "sc:description": "A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data.", @@ -34,12 +30,16 @@ }, "sc:name": "JunctionSeq", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/JunctionSeq.html", "sc:version": "1.4.0" + }, + { + "@id": "https://doi.org/10.1093/nar/gkw501", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/jvarkit/jvarkitbioschemas.jsonld b/data/jvarkit/jvarkitbioschemas.jsonld index 46383fc2f6da0..a4327cf436933 100644 --- a/data/jvarkit/jvarkitbioschemas.jsonld +++ b/data/jvarkit/jvarkitbioschemas.jsonld @@ -21,8 +21,8 @@ "Linux" ], "sc:provider": [ - "Institut du Thorax, Nantes, France", - "univ-nantes.fr" + "univ-nantes.fr", + "Institut du Thorax, Nantes, France" ], "sc:url": "https://github.com/lindenb/jvarkit/wiki/Biostar178713", "sc:version": "1.0" diff --git a/data/jvenn/jvennbioschemas.jsonld b/data/jvenn/jvennbioschemas.jsonld index ac9a6e4df4959..d5380ddfc1e3a 100644 --- a/data/jvenn/jvennbioschemas.jsonld +++ b/data/jvenn/jvennbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "jvenn", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinfo.genotoul.fr/jvenn/" } \ No newline at end of file diff --git a/data/jvirgel/jvirgelbioschemas.jsonld b/data/jvirgel/jvirgelbioschemas.jsonld index a72da9fb16de0..59e2e3ba002e7 100644 --- a/data/jvirgel/jvirgelbioschemas.jsonld +++ b/data/jvirgel/jvirgelbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.", "sc:name": "JVirGel", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.jvirgel.de/" diff --git a/data/k-branches/k-branchesbioschemas.jsonld b/data/k-branches/k-branchesbioschemas.jsonld index 22ce39e0cd0c0..c565a80a9d621 100644 --- a/data/k-branches/k-branchesbioschemas.jsonld +++ b/data/k-branches/k-branchesbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Model-based branching point detection in single-cell data by K-branches clustering.", "sc:name": "K-Branches", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/theislab/kbranches" } \ No newline at end of file diff --git a/data/k-link/k-linkbioschemas.jsonld b/data/k-link/k-linkbioschemas.jsonld index e48aaa076816c..c92813a8298bd 100644 --- a/data/k-link/k-linkbioschemas.jsonld +++ b/data/k-link/k-linkbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "k-link", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.bioinformatics.csiro.au/k-link/" } \ No newline at end of file diff --git a/data/k-map/k-mapbioschemas.jsonld b/data/k-map/k-mapbioschemas.jsonld index 436f08aa9d5d6..85b32c3dc0bce 100644 --- a/data/k-map/k-mapbioschemas.jsonld +++ b/data/k-map/k-mapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Novel and user-friendly web-based program that systematically connects a set of query kinases to kinase inhibitors based on quantitative profiles of the kinase inhibitor activities. Users can find kinase inhibitors for a set of query kinases (obtained from high-throughput “omics” experiments) or to reveal new interactions between kinases and kinase inhibitors for rational drug combination studies.", "sc:name": "K-Map", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://tanlab.ucdenver.edu/kMap/" } \ No newline at end of file diff --git a/data/k-tope/k-topebioschemas.jsonld b/data/k-tope/k-topebioschemas.jsonld index 4c0dd1a313414..b6ce74688cf03 100644 --- a/data/k-tope/k-topebioschemas.jsonld +++ b/data/k-tope/k-topebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "MIT", "sc:name": "K-TOPE", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/mlpaull/KTOPE" } \ No newline at end of file diff --git a/data/k2n/k2nbioschemas.jsonld b/data/k2n/k2nbioschemas.jsonld index bd88a485e7ce7..489f7ad688838 100644 --- a/data/k2n/k2nbioschemas.jsonld +++ b/data/k2n/k2nbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web service to get from knotted to nested RNA structures. This site provides access to a variety of methods for pseudoknot removal.", "sc:name": "K2N", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.ibi.vu.nl/programs/k2nwww/" } \ No newline at end of file diff --git a/data/kaas/kaasbioschemas.jsonld b/data/kaas/kaasbioschemas.jsonld index 6c52a43e4f641..4d16de2362f56 100644 --- a/data/kaas/kaasbioschemas.jsonld +++ b/data/kaas/kaasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for ortholog assignment and pathway mapping. It provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.", "sc:name": "KAAS", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.genome.jp/kegg/kaas/" } \ No newline at end of file diff --git a/data/kaiju/kaijubioschemas.jsonld b/data/kaiju/kaijubioschemas.jsonld index 0672fddfb59fc..70e1decc3397b 100644 --- a/data/kaiju/kaijubioschemas.jsonld +++ b/data/kaiju/kaijubioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/kaiju", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": [ "Anders Krogh", @@ -23,8 +23,8 @@ "sc:license": "GPL-3.0", "sc:name": "Kaiju", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Section for Bioinformatics, Department of Biology, University of Copenhagen", "sc:url": "http://kaiju.binf.ku.dk", diff --git a/data/kalign/kalignbioschemas.jsonld b/data/kalign/kalignbioschemas.jsonld index 772e0719b47a4..ef834af023ecd 100644 --- a/data/kalign/kalignbioschemas.jsonld +++ b/data/kalign/kalignbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Fast and accurate multiple sequence alignment which handles large sequences.", "sc:name": "Kalign", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "EMBL-EBI", diff --git a/data/kanalyze/kanalyzebioschemas.jsonld b/data/kanalyze/kanalyzebioschemas.jsonld index da7e3b385c6c2..b8f57fcf12a7e 100644 --- a/data/kanalyze/kanalyzebioschemas.jsonld +++ b/data/kanalyze/kanalyzebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Java toolkit designed to convert DNA and RNA sequences into k-mers.", "sc:name": "KAnalyze", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://vannberg.biology.gatech.edu:8080/VannbergLab/kanalyze.html" diff --git a/data/kappa-view4/kappa-view4bioschemas.jsonld b/data/kappa-view4/kappa-view4bioschemas.jsonld index ebd276ae6587c..da7189705befa 100644 --- a/data/kappa-view4/kappa-view4bioschemas.jsonld +++ b/data/kappa-view4/kappa-view4bioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "It is a metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG version.", "sc:name": "KaPPA-View4", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://kpv.kazusa.or.jp/kpv4/" } \ No newline at end of file diff --git a/data/karyoploter/karyoploterbioschemas.jsonld b/data/karyoploter/karyoploterbioschemas.jsonld index d61b42a636c3e..2561c158b43a4 100644 --- a/data/karyoploter/karyoploterbioschemas.jsonld +++ b/data/karyoploter/karyoploterbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btx346", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/karyoploter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bernat Gel", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5870550", + "pubmed:28575171", { "@id": "https://doi.org/10.1093/bioinformatics/btx346" - }, - "pubmed:28575171", - "pmcid:PMC5870550" + } ], "sc:description": "Plot customizable linear genomes displaying arbitrary data.", "sc:featureList": { @@ -33,11 +29,15 @@ "sc:name": "karyoploteR", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/karyoploteR.html", "sc:version": "1.6.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btx346", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kaspspoon/kaspspoonbioschemas.jsonld b/data/kaspspoon/kaspspoonbioschemas.jsonld index c18a05708a8a8..9277f176bf30a 100644 --- a/data/kaspspoon/kaspspoonbioschemas.jsonld +++ b/data/kaspspoon/kaspspoonbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "KASPspoon", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon" } \ No newline at end of file diff --git a/data/kassiopeia/kassiopeiabioschemas.jsonld b/data/kassiopeia/kassiopeiabioschemas.jsonld index 76e517e27ee4a..e05871a3f0e08 100644 --- a/data/kassiopeia/kassiopeiabioschemas.jsonld +++ b/data/kassiopeia/kassiopeiabioschemas.jsonld @@ -21,8 +21,8 @@ { "@id": "https://doi.org/10.1186/1471-2164-15-115" }, - "pubmed:24507667", - "pmcid:PMC3923563" + "pmcid:PMC3923563", + "pubmed:24507667" ], "sc:description": "A web application for the generation, storage, and presentation of genome-wide analyses of mutually exclusive exonomes.", "sc:featureList": { @@ -30,8 +30,8 @@ }, "sc:name": "Kassiopeia", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://kassiopeia.motorprotein.de/kassiopeia" diff --git a/data/kat/katbioschemas.jsonld b/data/kat/katbioschemas.jsonld index dac23faa8cee8..a1a78d48aaaa6 100644 --- a/data/kat/katbioschemas.jsonld +++ b/data/kat/katbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btw663", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/kat", "@type": "sc:SoftwareApplication", @@ -21,26 +17,30 @@ { "@id": "https://doi.org/10.1093/bioinformatics/btw663" }, - "pmcid:PMC5408915", - "pubmed:27797770" + "pubmed:27797770", + "pmcid:PMC5408915" ], "sc:description": "Suite of tools that generate, analyse and compare k-mer spectra produced from sequence files", "sc:featureList": [ { - "@id": "edam:operation_0236" + "@id": "edam:operation_0253" }, { - "@id": "edam:operation_0253" + "@id": "edam:operation_0236" } ], "sc:license": "GPL-3.0", "sc:name": "KAT", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.earlham.ac.uk/kat-tools" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btw663", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kaustnmf/kaustnmfbioschemas.jsonld b/data/kaustnmf/kaustnmfbioschemas.jsonld index a1cc6444b93b4..cb3fef5531358 100644 --- a/data/kaustnmf/kaustnmfbioschemas.jsonld +++ b/data/kaustnmf/kaustnmfbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "KAUSTNMF", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://sfb.kaust.edu.sa/Pages/Software.aspx" } \ No newline at end of file diff --git a/data/kaviar/kaviarbioschemas.jsonld b/data/kaviar/kaviarbioschemas.jsonld index 65b0f05f517b6..4094119eec8f8 100644 --- a/data/kaviar/kaviarbioschemas.jsonld +++ b/data/kaviar/kaviarbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Compilation of human SNVs collected from many and diverse sources, stressing accessibility and ease of use. Kaviar (~Known VARiants) is a very simple tool for answering a very specific question: What variants have been reported already for a given specific genomic location?", "sc:name": "Kaviar", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://db.systemsbiology.net/kaviar/cgi-pub/Kaviar.pl" diff --git a/data/kb-rank/kb-rankbioschemas.jsonld b/data/kb-rank/kb-rankbioschemas.jsonld index 747c9ec01f81c..9c874cbb662cf 100644 --- a/data/kb-rank/kb-rankbioschemas.jsonld +++ b/data/kb-rank/kb-rankbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1007/s10969-012-9125-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/kb-rank", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC3375009", + "pubmed:22270457", { "@id": "https://doi.org/10.1007/s10969-012-9125-7" - }, - "pmcid:PMC3375009", - "pubmed:22270457" + } ], "sc:contributor": "5U01 GM093324-02", "sc:description": "Search tool takes a text input and retrieves relevant proteins structures. Example searches include diseases, drug names, and protein functions.", @@ -38,10 +42,6 @@ ], "sc:provider": "The Commonwealth Medical College", "sc:url": "http://protein.tcmc.edu/kb-rank" - }, - { - "@id": "https://doi.org/10.1007/s10969-012-9125-7", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kbase/kbasebioschemas.jsonld b/data/kbase/kbasebioschemas.jsonld index 4f2101198bbe3..5fbd2de2d4144 100644 --- a/data/kbase/kbasebioschemas.jsonld +++ b/data/kbase/kbasebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.", "sc:name": "KBASE", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://kbase.us/" } \ No newline at end of file diff --git a/data/kbat/kbatbioschemas.jsonld b/data/kbat/kbatbioschemas.jsonld index b56fca352a576..48149f2462cd5 100644 --- a/data/kbat/kbatbioschemas.jsonld +++ b/data/kbat/kbatbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Convenient analysis tool for genome-wide and candiate-region association mapping.", "sc:name": "KBAT", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.stat.sinica.edu.tw/hsinchou/genetics/association/KBAT.htm", "sc:version": "1.2" diff --git a/data/kcam/kcambioschemas.jsonld b/data/kcam/kcambioschemas.jsonld index 969fc92087cd4..045a2b07e7e0a 100644 --- a/data/kcam/kcambioschemas.jsonld +++ b/data/kcam/kcambioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Takes glycan structures as input and returns a list of similar glycan structures using a tree-structure alignment algorithm.", "sc:name": "KCaM", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.genome.jp/tools/kcam/" } \ No newline at end of file diff --git a/data/kcsmart/kcsmartbioschemas.jsonld b/data/kcsmart/kcsmartbioschemas.jsonld index 823209f17560a..e1336e9b7e176 100644 --- a/data/kcsmart/kcsmartbioschemas.jsonld +++ b/data/kcsmart/kcsmartbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jorma de Ronde", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Multi sample aCGH analysis package using kernel convolution.", "sc:license": "GPL-3.0", diff --git a/data/kd4v/kd4vbioschemas.jsonld b/data/kd4v/kd4vbioschemas.jsonld index b67e434be5f3e..d44177a081f07 100644 --- a/data/kd4v/kd4vbioschemas.jsonld +++ b/data/kd4v/kd4vbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Comprehensive Knowledge Discovery System for Missense Variant (KD4v) webserver allows users to characterize and predict the phenotypic effects of missense variants.", "sc:name": "KD4v", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://decrypthon.igbmc.fr/kd4v" } \ No newline at end of file diff --git a/data/kddn/kddnbioschemas.jsonld b/data/kddn/kddnbioschemas.jsonld index da47e89fe5645..c89c4d7364a6e 100644 --- a/data/kddn/kddnbioschemas.jsonld +++ b/data/kddn/kddnbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Cytoscape app to learn biological network topology and its changes using profiling data and domain knowledge. It takes input data and runs KDDN algorithm to construct the dependency network.", "sc:name": "KDDN", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://apps.cytoscape.org/apps/kddn" diff --git a/data/kdetrees/kdetreesbioschemas.jsonld b/data/kdetrees/kdetreesbioschemas.jsonld index 006defa1ec6f2..0cbb99bc4e4f6 100644 --- a/data/kdetrees/kdetreesbioschemas.jsonld +++ b/data/kdetrees/kdetreesbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "kdetrees", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/grady/kdetrees" } \ No newline at end of file diff --git a/data/kea/keabioschemas.jsonld b/data/kea/keabioschemas.jsonld index bccba32503a1e..02e6291722780 100644 --- a/data/kea/keabioschemas.jsonld +++ b/data/kea/keabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "KEA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://amp.pharm.mssm.edu/lib/kea.jsp" } \ No newline at end of file diff --git a/data/kebabs/kebabsbioschemas.jsonld b/data/kebabs/kebabsbioschemas.jsonld index 006cb696faade..bd51ca72e9692 100644 --- a/data/kebabs/kebabsbioschemas.jsonld +++ b/data/kebabs/kebabsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-6859-8828", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/kebabs", "@type": "sc:SoftwareApplication", @@ -28,12 +24,16 @@ "sc:license": "GPL-2.0", "sc:name": "KeBABS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.bioinf.jku.at/software/kebabs/", "sc:version": "1.8.0" + }, + { + "@id": "http://orcid.org/0000-0001-6859-8828", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/kegarray/kegarraybioschemas.jsonld b/data/kegarray/kegarraybioschemas.jsonld index 4abcbf5bde1a7..35ecb06258348 100644 --- a/data/kegarray/kegarraybioschemas.jsonld +++ b/data/kegarray/kegarraybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Java application that provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). Tightly integrated with the KEGG database, KegArray enables you to easily map those data to KEGG resources including PATHWAY, BRITE and genome maps.", "sc:name": "KegArray", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.genome.jp/kegg/expression/" } \ No newline at end of file diff --git a/data/kegdraw/kegdrawbioschemas.jsonld b/data/kegdraw/kegdrawbioschemas.jsonld index 68207b5be948d..d9b6586690072 100644 --- a/data/kegdraw/kegdrawbioschemas.jsonld +++ b/data/kegdraw/kegdrawbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "KegDraw is a java application for drawing compound and glycan structures with capabilities to search against the KEGG databases.", "sc:name": "KegDraw 0.1.14 beta", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.kegg.jp/kegg/download/kegtools.html" } \ No newline at end of file diff --git a/data/kegg/keggbioschemas.jsonld b/data/kegg/keggbioschemas.jsonld index 2880d57db3cb7..bf2e36b2de985 100644 --- a/data/kegg/keggbioschemas.jsonld +++ b/data/kegg/keggbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. This tool comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). Its Atlas is a new tool for the global analysis of metabolic pathways.", "sc:name": "Kyoto encyclopedia of genes and genomes (KEGG)", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.genome.ad.jp/kegg/" } \ No newline at end of file diff --git a/data/kegganim/kegganimbioschemas.jsonld b/data/kegganim/kegganimbioschemas.jsonld index a09f5267cb796..1134659c99b8c 100644 --- a/data/kegganim/kegganimbioschemas.jsonld +++ b/data/kegganim/kegganimbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "KEGGanim", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://biit.cs.ut.ee/kegganim", diff --git a/data/kegggraph/kegggraphbioschemas.jsonld b/data/kegggraph/kegggraphbioschemas.jsonld index 2429b72ecc9cc..37c793370009c 100644 --- a/data/kegggraph/kegggraphbioschemas.jsonld +++ b/data/kegggraph/kegggraphbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btp167", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/kegggraph", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Command-line tool" ], "sc:citation": [ - "pubmed:19307239", { "@id": "https://doi.org/10.1093/bioinformatics/btp167" }, - "pmcid:PMC2682514" + "pmcid:PMC2682514", + "pubmed:19307239" ], "sc:description": "Interface between a KEGG pathway and a graph object, as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers other functionalities including parsing, graph operation, visualization, etc.", "sc:featureList": [ @@ -40,12 +36,16 @@ "sc:license": "GPL-2.0", "sc:name": "KEGGgraph", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/KEGGgraph.html", "sc:version": "1.32.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btp167", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kegglincs/kegglincsbioschemas.jsonld b/data/kegglincs/kegglincsbioschemas.jsonld index 5f3e32fd6489b..4c21e8a16d5ce 100644 --- a/data/kegglincs/kegglincsbioschemas.jsonld +++ b/data/kegglincs/kegglincsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Shana White", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.", "sc:license": "GPL-3.0", "sc:name": "KEGGlincs", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/KEGGlincs.html", "sc:version": "1.0.0" diff --git a/data/keggorthology/bioconda_keggorthology.yaml b/data/keggorthology/bioconda_keggorthology.yaml index 7d5b1319689b2..9ee4c621bff00 100644 --- a/data/keggorthology/bioconda_keggorthology.yaml +++ b/data/keggorthology/bioconda_keggorthology.yaml @@ -4,7 +4,6 @@ description: graphical representation of the Feb 2010 KEGG Orthology. The KEGG o home: https://bioconductor.org/packages/3.10/bioc/html/keggorthology.html identifiers: - biotools:keggorthology -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-keggorthology summary: graph support for KO, KEGG Orthology diff --git a/data/keggorthology/keggorthologybioschemas.jsonld b/data/keggorthology/keggorthologybioschemas.jsonld index dcde4ed759d42..ff8c601e918e6 100644 --- a/data/keggorthology/keggorthologybioschemas.jsonld +++ b/data/keggorthology/keggorthologybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "VJ Carey", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.", "sc:license": "Artistic-2.0", "sc:name": "keggorthology", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/keggorthology.html", "sc:version": "2.26.0" diff --git a/data/keggparser/keggparserbioschemas.jsonld b/data/keggparser/keggparserbioschemas.jsonld index 9257ff27a9adc..b1613029fb0a1 100644 --- a/data/keggparser/keggparserbioschemas.jsonld +++ b/data/keggparser/keggparserbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment.", "sc:name": "KEGGParser", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.mathworks.com/matlabcentral/fileexchange/37561" } \ No newline at end of file diff --git a/data/keggprofile/keggprofilebioschemas.jsonld b/data/keggprofile/keggprofilebioschemas.jsonld index 9b73ec4adc7da..45890cc100f42 100644 --- a/data/keggprofile/keggprofilebioschemas.jsonld +++ b/data/keggprofile/keggprofilebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Shilin Zhao", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Annotation and visualization tool which integrated the expression profiles and the function annotation in KEGG pathway maps. The multi-types and multi-groups expression data can be visualized in one pathway map. It facilitated more detailed analysis about the specific function changes inner pathway or temporal correlations in different genes and samples.", "sc:license": "GPL-2.0", "sc:name": "KEGGprofile", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/KEGGprofile.html", "sc:version": "1.16.0" diff --git a/data/keggrest/keggrestbioschemas.jsonld b/data/keggrest/keggrestbioschemas.jsonld index 96223dcaba8f8..97955683c0b13 100644 --- a/data/keggrest/keggrestbioschemas.jsonld +++ b/data/keggrest/keggrestbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A package that provides a client interface to the KEGG REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.", "sc:license": "Artistic-2.0", "sc:name": "KEGGREST", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/KEGGREST.html", "sc:version": "1.14.0" diff --git a/data/keller/kellerbioschemas.jsonld b/data/keller/kellerbioschemas.jsonld index 2baf5e186682c..442c579fde9a9 100644 --- a/data/keller/kellerbioschemas.jsonld +++ b/data/keller/kellerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "KELLER", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.sailing.cs.cmu.edu/main/?page_id=430" } \ No newline at end of file diff --git a/data/ketcher-rails/ketcher-railsbioschemas.jsonld b/data/ketcher-rails/ketcher-railsbioschemas.jsonld index 96ebadcf2252f..4f03a89f08121 100644 --- a/data/ketcher-rails/ketcher-railsbioschemas.jsonld +++ b/data/ketcher-rails/ketcher-railsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "ketcher-rails", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/ComPlat/ketcher-rails" } \ No newline at end of file diff --git a/data/key_pathway_miner/key_pathway_minerbioschemas.jsonld b/data/key_pathway_miner/key_pathway_minerbioschemas.jsonld index 639e317c3ee71..43fa7733c7560 100644 --- a/data/key_pathway_miner/key_pathway_minerbioschemas.jsonld +++ b/data/key_pathway_miner/key_pathway_minerbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jan Baumbach", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "Extracts all maximal connected sub-networks that contain the genes that are differentially expressed. The exact quantities are modeled with two easy-to-interpret parameters (K, L) that allows the user to control the number of outliers (not dysregulated genes/cases) in the solutions. We developed two slightly varying models (INES and GLONE) that fall into the class of NP-Hard optimization problems.", "sc:name": "Key Pathway Miner", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "bmb.sdu.dk", "sc:url": "http://keypathwayminer.compbio.sdu.dk/", diff --git a/data/kfc/kfcbioschemas.jsonld b/data/kfc/kfcbioschemas.jsonld index 96287a449a29b..4cd7a04f4b2c5 100644 --- a/data/kfc/kfcbioschemas.jsonld +++ b/data/kfc/kfcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "KFC Server", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://mitchell-lab.biochem.wisc.edu/KFC_Server/index.php" diff --git a/data/kfits/kfitsbioschemas.jsonld b/data/kfits/kfitsbioschemas.jsonld index 30c02f10287d9..030402c55494b 100644 --- a/data/kfits/kfitsbioschemas.jsonld +++ b/data/kfits/kfitsbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dana Reichmann", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Framework for fitting and cleaning outliers in kinetic measurements.", "sc:name": "Kfits", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://kfits.reichmannlab.com/fitter/" } \ No newline at end of file diff --git a/data/kgem/kgembioschemas.jsonld b/data/kgem/kgembioschemas.jsonld index 18962d6246ea9..b82c39755e345 100644 --- a/data/kgem/kgembioschemas.jsonld +++ b/data/kgem/kgembioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "kGEM (k-Genotype Expectation Maximization algorithm) tool finds haplotypes for Single-amplicon sequencing data. This tool requires aligned reads in special internal format and auxiliary program ERIF could help to convert reads in this format either from fasta (unaligned) format or from SAM (pairwise alignment) format.", "sc:name": "kGEM", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://alan.cs.gsu.edu/NGS/?q=content/kgem", "sc:version": "0.3.1" diff --git a/data/kggseq/kggseqbioschemas.jsonld b/data/kggseq/kggseqbioschemas.jsonld index 29d9a8347a699..07c460f9ecdd4 100644 --- a/data/kggseq/kggseqbioschemas.jsonld +++ b/data/kggseq/kggseqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software platform constituted of Bioinformatics and statistical genetics functions making use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants/genes responsible for human diseases/traits.", "sc:name": "KGGSeq", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://statgenpro.psychiatry.hku.hk/limx/kggseq/" } \ No newline at end of file diff --git a/data/khmer/khmerbioschemas.jsonld b/data/khmer/khmerbioschemas.jsonld index a2b8b983a3c08..4352c0b09c61d 100644 --- a/data/khmer/khmerbioschemas.jsonld +++ b/data/khmer/khmerbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/khmer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Getting help guide", "khmer-project@idyll.org", - "Gitter Chat" + "Gitter Chat", + "Getting help guide" ], "sc:additionalType": "Command-line tool", "sc:description": "khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.", @@ -24,8 +24,8 @@ "Mac" ], "sc:provider": [ - "Michigan State University", "University of California, Davis", + "Michigan State University", "ucdavis.edu" ], "sc:url": "http://khmer.readthedocs.org/en/v2.0/", diff --git a/data/kic/kicbioschemas.jsonld b/data/kic/kicbioschemas.jsonld index cc3951a79d2c2..67642232c4373 100644 --- a/data/kic/kicbioschemas.jsonld +++ b/data/kic/kicbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "FASTQ compressor based on a new integer-mapped k-mer indexing method.", "sc:name": "KIC", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ysunlab.org/kic.jsp" diff --git a/data/kimod/bioconda_kimod.yaml b/data/kimod/bioconda_kimod.yaml index 449e1e1006dc0..7f8840611e365 100644 --- a/data/kimod/bioconda_kimod.yaml +++ b/data/kimod/bioconda_kimod.yaml @@ -16,7 +16,6 @@ description: 'This package allows to work with mixed omics data (transcriptomics home: https://bioconductor.org/packages/3.10/bioc/html/kimod.html identifiers: - biotools:kimod -- doi:10.1038/nmeth.3252 license: GPL (>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-kimod diff --git a/data/kimosys/kimosysbioschemas.jsonld b/data/kimosys/kimosysbioschemas.jsonld index 6bc1abfd6e175..30c57c5ea658b 100644 --- a/data/kimosys/kimosysbioschemas.jsonld +++ b/data/kimosys/kimosysbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12918-014-0085-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/kimosys", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact form", "sc:additionalType": "Database portal", "sc:citation": [ + "pmcid:PMC4236735", { "@id": "https://doi.org/10.1186/S12918-014-0085-3" }, - "pubmed:25115331", - "pmcid:PMC4236735" + "pubmed:25115331" ], "sc:description": "Web-based repository of experimental data for KInetic MOdels of biological SYStems.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "GPL-2.0", "sc:name": "KiMoSys", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://kimosys.org/" + }, + { + "@id": "https://doi.org/10.1186/S12918-014-0085-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kinact/kinactbioschemas.jsonld b/data/kinact/kinactbioschemas.jsonld index f7bfa62dcbe1b..1fb71ea264f46 100644 --- a/data/kinact/kinactbioschemas.jsonld +++ b/data/kinact/kinactbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/kinact", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Douglas E. V. Pires", "Dr. David B. Ascher", - "Carlos H. M. Rodrigues" + "Carlos H. M. Rodrigues", + "Dr. Douglas E. V. Pires" ], "sc:additionalType": "Web application", "sc:description": "Novel computational method for predicting activating mutations in kinases. It is a machine learning approach that relies on structural and sequence data of proteins, such as environment residue, stability changes predictions, atomic interactions, graph-based signatures and residue conservation.", diff --git a/data/kinari-web/kinari-webbioschemas.jsonld b/data/kinari-web/kinari-webbioschemas.jsonld index 007eda2da4442..b6aa20b37e414 100644 --- a/data/kinari-web/kinari-webbioschemas.jsonld +++ b/data/kinari-web/kinari-webbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "KINARI-Web is a web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions.", "sc:name": "KINARI-Web", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://kinari.cs.umass.edu/" } \ No newline at end of file diff --git a/data/kinase_sarfari_blast_search/kinase_sarfari_blast_searchbioschemas.jsonld b/data/kinase_sarfari_blast_search/kinase_sarfari_blast_searchbioschemas.jsonld index 17f043ecf7c01..26a345935cac6 100644 --- a/data/kinase_sarfari_blast_search/kinase_sarfari_blast_searchbioschemas.jsonld +++ b/data/kinase_sarfari_blast_search/kinase_sarfari_blast_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "BLAST search against Kinase domains stored in Kinase SARfari.", "sc:name": "Kinase SARfari BLAST Search", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "https://www.ebi.ac.uk/chembl/sarfari/kinasesarfari/protein", diff --git a/data/kinase_sarfari_small_molecule_search/kinase_sarfari_small_molecule_searchbioschemas.jsonld b/data/kinase_sarfari_small_molecule_search/kinase_sarfari_small_molecule_searchbioschemas.jsonld index ef9bbff6e5d58..a17c973114829 100644 --- a/data/kinase_sarfari_small_molecule_search/kinase_sarfari_small_molecule_searchbioschemas.jsonld +++ b/data/kinase_sarfari_small_molecule_search/kinase_sarfari_small_molecule_searchbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Kinase SARfari Small Molecule Search", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "https://www.ebi.ac.uk/chembl/sarfari/kinasesarfari/compound", diff --git a/data/kinasephos/kinasephosbioschemas.jsonld b/data/kinasephos/kinasephosbioschemas.jsonld index 10f4673c1e549..982178bc91ab6 100644 --- a/data/kinasephos/kinasephosbioschemas.jsonld +++ b/data/kinasephos/kinasephosbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Identify kinase-specific phosphorylation sites in protein sequences.", "sc:name": "KinasePhos", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://kinasephos.mbc.nctu.edu.tw/" } \ No newline at end of file diff --git a/data/kinefold/kinefoldbioschemas.jsonld b/data/kinefold/kinefoldbioschemas.jsonld index 87eae9a4e9ba9..20d72e8e200ad 100644 --- a/data/kinefold/kinefoldbioschemas.jsonld +++ b/data/kinefold/kinefoldbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots.", "sc:name": "Kinefold", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://kinefold.curie.fr/" } \ No newline at end of file diff --git a/data/kinfer/kinferbioschemas.jsonld b/data/kinfer/kinferbioschemas.jsonld index b7949f97ac2fa..17651279a852c 100644 --- a/data/kinfer/kinferbioschemas.jsonld +++ b/data/kinfer/kinferbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Generates a generalized mass action model from the chemical equations of reactions and an estimation of the structural parameters of these reactions", "sc:name": "KInfer", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cosbi.eu/research/prototypes/kinfer" } \ No newline at end of file diff --git a/data/kinmap/kinmapbioschemas.jsonld b/data/kinmap/kinmapbioschemas.jsonld index e2fb628cb8515..8613a4c835324 100644 --- a/data/kinmap/kinmapbioschemas.jsonld +++ b/data/kinmap/kinmapbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5217312", { "@id": "https://doi.org/10.1186/S12859-016-1433-7" }, - "pubmed:28056780" + "pubmed:28056780", + "pmcid:PMC5217312" ], "sc:description": "Web-based tool for interactive navigation through human kinome data.", "sc:featureList": { @@ -27,8 +27,8 @@ }, "sc:name": "KinMap", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.kinhub.org/kinmap/" diff --git a/data/kinvis/kinvisbioschemas.jsonld b/data/kinvis/kinvisbioschemas.jsonld index 05cb6977474db..ae5fbaca9c6c3 100644 --- a/data/kinvis/kinvisbioschemas.jsonld +++ b/data/kinvis/kinvisbioschemas.jsonld @@ -11,21 +11,21 @@ "@id": "https://bio.tools/KinVis", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Ehsan Ullah", - "Dr. Halima Bensmail" + "Dr. Halima Bensmail", + "Dr. Ehsan Ullah" ], "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:author": "Dr. Ehsan Ullah", "sc:description": "Visualization tool to detect cryptic relatedness in genetic datasets.", "sc:license": "Unlicense", "sc:name": "KinVis", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://shiny-vis.qcri.org/public/kinvis/" } \ No newline at end of file diff --git a/data/kipar/kiparbioschemas.jsonld b/data/kipar/kiparbioschemas.jsonld index 4fb428b212135..103dff0b92408 100644 --- a/data/kipar/kiparbioschemas.jsonld +++ b/data/kipar/kiparbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "KiPar", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.mcisb.org/resources/kipar/index.html" } \ No newline at end of file diff --git a/data/kipper/kipperbioschemas.jsonld b/data/kipper/kipperbioschemas.jsonld index af9da0c6f2fd7..e7ce29992a3b2 100644 --- a/data/kipper/kipperbioschemas.jsonld +++ b/data/kipper/kipperbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The basic command-line file versioning solution is a key-value data store that keeps track of when particular items are inserted or deleted (updates are deletes followed by inserts).It can recall versions by date or version id. It can keep versions in one or more volume files.", "sc:name": "Kipper", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/Public-Health-Bioinformatics/kipper" } \ No newline at end of file diff --git a/data/kismeth/kismethbioschemas.jsonld b/data/kismeth/kismethbioschemas.jsonld index 67bd946d88277..5bcc62112e137 100644 --- a/data/kismeth/kismethbioschemas.jsonld +++ b/data/kismeth/kismethbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Kismeth", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://katahdin.mssm.edu/kismeth" } \ No newline at end of file diff --git a/data/kissde/kissdebioschemas.jsonld b/data/kissde/kissdebioschemas.jsonld index eac2376eebd2f..5bf037bab30a6 100644 --- a/data/kissde/kissdebioschemas.jsonld +++ b/data/kissde/kissdebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "kissDE", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/kissDE.html", "sc:version": "1.0.0" diff --git a/data/kit/kitbioschemas.jsonld b/data/kit/kitbioschemas.jsonld index 6bcdceb28e52d..f3392629bceca 100644 --- a/data/kit/kitbioschemas.jsonld +++ b/data/kit/kitbioschemas.jsonld @@ -25,11 +25,11 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:27153705", { "@id": "https://doi.org/10.1093/bioinformatics/btw087" }, - "pmcid:PMC4908324", - "pubmed:27153705" + "pmcid:PMC4908324" ], "sc:description": "Kinetochore Tracking (KiT) is an open-source software package for tracking kinetochores from live-cell fluorescent movies.", "sc:featureList": { @@ -38,8 +38,8 @@ "sc:license": "GPL-3.0", "sc:name": "KiT", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://bitbucket.org/jarmond/kit/overview" diff --git a/data/kiwi/kiwibioschemas.jsonld b/data/kiwi/kiwibioschemas.jsonld index 4f4e5a89dd23c..e2e17c339e925 100644 --- a/data/kiwi/kiwibioschemas.jsonld +++ b/data/kiwi/kiwibioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-014-0408-9", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/kiwi", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC4269931", "pubmed:25496126", + "pmcid:PMC4269931", { "@id": "https://doi.org/10.1186/S12859-014-0408-9" } @@ -41,6 +37,10 @@ "Linux" ], "sc:url": "https://pythonhosted.org/KiwiDist/index.html" + }, + { + "@id": "https://doi.org/10.1186/S12859-014-0408-9", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/klifs/klifsbioschemas.jsonld b/data/klifs/klifsbioschemas.jsonld index c3b2357b2045c..36c40403109fb 100644 --- a/data/klifs/klifsbioschemas.jsonld +++ b/data/klifs/klifsbioschemas.jsonld @@ -11,42 +11,42 @@ "@id": "https://bio.tools/klifs", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Chris de Graaf", - "Dr. Albert J. Kooistra" + "Dr. Albert J. Kooistra", + "Dr. Chris de Graaf" ], "sc:additionalType": [ - "Web application", "Command-line tool", - "Web API", - "Database portal" + "Database portal", + "Web application", + "Web API" ], "sc:author": [ + "Oscar P.J. van Linden", "Georgi K. Kanev", - "Albert J. Kooistra", "Chris de Graaf", - "Division of Medicinal Chemistry (Vrije Universiteit Amsterdam)", - "Oscar P.J. van Linden" + "Albert J. Kooistra", + "Division of Medicinal Chemistry (Vrije Universiteit Amsterdam)" ], "sc:contributor": [ "Amsterdam Academic Alliance", - "Iwan J.P. de Esch", "Netherlands eScience Center (NLeSC)", - "Rob Leurs" + "Rob Leurs", + "Iwan J.P. de Esch" ], "sc:description": "Revolves around the structure of kinases in PDB and the way kinase inhibitors can interact with them. It also features automated annotation methods for (i) the assessment of ligand-targeted subpockets; the analysis of (ii) DFG and (iii) α-helix conformations; improved and automated protocols for (iv) the generation of sequence/structure alignments; (v) the curation of ligand atom and bond typing for accurate IFP analysis and (vi) weekly database updates.", "sc:funder": [ - "Netherlands eScience Center (NLeSC)", - "Amsterdam Academic Alliance" + "Amsterdam Academic Alliance", + "Netherlands eScience Center (NLeSC)" ], "sc:name": "KLIFS", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ - "Vrije Universiteit Amsterdam", - "vu.nl" + "vu.nl", + "Vrije Universiteit Amsterdam" ], "sc:url": "http://klifs.vu-compmedchem.nl" } \ No newline at end of file diff --git a/data/km2gcn/km2gcnbioschemas.jsonld b/data/km2gcn/km2gcnbioschemas.jsonld index a2893e69b1932..34559a3da282e 100644 --- a/data/km2gcn/km2gcnbioschemas.jsonld +++ b/data/km2gcn/km2gcnbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Juan A. Botía", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:28403906", "pmcid:PMC5389000", { "@id": "https://doi.org/10.1186/s12918-017-0420-6" - } + }, + "pubmed:28403906" ], "sc:description": "Optimization process of WGCNA hierarchical clustering with k-means.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "km2gcn", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/juanbot/km2gcn" } diff --git a/data/kmasker/kmaskerbioschemas.jsonld b/data/kmasker/kmaskerbioschemas.jsonld index b4548398ef2ea..593c7de442bf5 100644 --- a/data/kmasker/kmaskerbioschemas.jsonld +++ b/data/kmasker/kmaskerbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-5444-9282", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0003-1073-6719", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/Kmasker", "@type": "sc:SoftwareApplication", @@ -29,29 +21,37 @@ } ], "sc:additionalType": [ - "Command-line tool", - "Web service" + "Web service", + "Command-line tool" ], "sc:author": [ { - "@id": "https://orcid.org/0000-0001-5444-9282" + "@id": "https://orcid.org/0000-0003-1073-6719" }, { - "@id": "https://orcid.org/0000-0003-1073-6719" + "@id": "https://orcid.org/0000-0001-5444-9282" } ], "sc:description": "Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity.", "sc:license": "GPL-3.0", "sc:name": "Kmasker", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://kmasker.ipk-gatersleben.de/", "sc:version": [ - "1.1.0", - "1.1.1" + "1.1.1", + "1.1.0" ] + }, + { + "@id": "https://orcid.org/0000-0003-1073-6719", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0001-5444-9282", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/kmc/kmcbioschemas.jsonld b/data/kmc/kmcbioschemas.jsonld index 64f47d57b89ae..cf181761dbeaa 100644 --- a/data/kmc/kmcbioschemas.jsonld +++ b/data/kmc/kmcbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.", "sc:name": "KMC", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about" } \ No newline at end of file diff --git a/data/kmcex/kmcexbioschemas.jsonld b/data/kmcex/kmcexbioschemas.jsonld index 572904826caf8..079e982bea616 100644 --- a/data/kmcex/kmcexbioschemas.jsonld +++ b/data/kmcex/kmcexbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/kmcEx", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Limsoon Wong", - "Liang Zhao" + "Liang Zhao", + "Limsoon Wong" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:31038666", @@ -20,8 +20,8 @@ "sc:license": "Unlicense", "sc:name": "kmcEx", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://github.com/lzhLab/kmcEx" diff --git a/data/kmech/kmechbioschemas.jsonld b/data/kmech/kmechbioschemas.jsonld index 44374dccca866..292d4e5cba915 100644 --- a/data/kmech/kmechbioschemas.jsonld +++ b/data/kmech/kmechbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "kMech", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.igb.uci.edu/tools/sb/metabolic-modeling/35-kmech.html" } \ No newline at end of file diff --git a/data/kmerfinder/kmerfinderbioschemas.jsonld b/data/kmerfinder/kmerfinderbioschemas.jsonld index 65415ff9e8e3e..71df25a4e6ba7 100644 --- a/data/kmerfinder/kmerfinderbioschemas.jsonld +++ b/data/kmerfinder/kmerfinderbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1128/JCM.02452-13", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0001-6314-2709", + "@type": "schema:Person" }, { "@id": "https://bio.tools/kmerfinder", @@ -19,9 +19,9 @@ "biotools:primaryContact": "Ole Lund", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:24574292", - "pmcid:PMC3911411", "pubmed:24172157", + "pmcid:PMC3911411", + "pubmed:24574292", { "@id": "https://doi.org/10.1128/JCM.02452-13" } @@ -38,8 +38,8 @@ "sc:version": "1.2" }, { - "@id": "http://orcid.org/0000-0001-6314-2709", - "@type": "schema:Person" + "@id": "https://doi.org/10.1128/JCM.02452-13", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kmerpyramid/kmerpyramidbioschemas.jsonld b/data/kmerpyramid/kmerpyramidbioschemas.jsonld index e3f40670d6a69..2834f23cc04fe 100644 --- a/data/kmerpyramid/kmerpyramidbioschemas.jsonld +++ b/data/kmerpyramid/kmerpyramidbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "kmerPyramid", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/jkruppa/kmerPyramid" } \ No newline at end of file diff --git a/data/kmerstream/kmerstreambioschemas.jsonld b/data/kmerstream/kmerstreambioschemas.jsonld index 926bb7d73dd9f..c1d733a0dcaee 100644 --- a/data/kmerstream/kmerstreambioschemas.jsonld +++ b/data/kmerstream/kmerstreambioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Streaming algorithm for estimating the number of distinct k-mers present in high throughput sequencing data.", "sc:name": "KmerStream", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/pmelsted/KmerStream" } \ No newline at end of file diff --git a/data/knet/knetbioschemas.jsonld b/data/knet/knetbioschemas.jsonld index d5042179bd8ca..227a2166fd26b 100644 --- a/data/knet/knetbioschemas.jsonld +++ b/data/knet/knetbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Finds pairs of genes with similar behavior across a gene expression dataset. It is intended to be used as a comparative tool to compare the network size (number of output rows) between N datasets with the same numbers of biological samples (input columns) and measured genes (input rows).", "sc:name": "Knet", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://compbio.med.wayne.edu/software/KNet/index.htm" } \ No newline at end of file diff --git a/data/knime/knimebioschemas.jsonld b/data/knime/knimebioschemas.jsonld index 68201dce3668f..a0e11794eb019 100644 --- a/data/knime/knimebioschemas.jsonld +++ b/data/knime/knimebioschemas.jsonld @@ -16,14 +16,14 @@ "sc:license": "GPL-3.0", "sc:name": "Konstanz Information Miner (KNIME)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.knime.org", "sc:version": [ - "3.5", + "3.7", "3.6", - "3.7" + "3.5" ] } \ No newline at end of file diff --git a/data/knime4bio/knime4biobioschemas.jsonld b/data/knime4bio/knime4biobioschemas.jsonld index deb3f05791786..444604656a67c 100644 --- a/data/knime4bio/knime4biobioschemas.jsonld +++ b/data/knime4bio/knime4biobioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "Knime4Bio", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://code.google.com/p/knime4bio/" } \ No newline at end of file diff --git a/data/knoto-id/knoto-idbioschemas.jsonld b/data/knoto-id/knoto-idbioschemas.jsonld index b3c589b6e1761..70c88900c9987 100644 --- a/data/knoto-id/knoto-idbioschemas.jsonld +++ b/data/knoto-id/knoto-idbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Knoto-ID", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.vital-it.ch/software/Knoto-ID" } \ No newline at end of file diff --git a/data/kobamin/kobaminbioschemas.jsonld b/data/kobamin/kobaminbioschemas.jsonld index 2238a2c2513b7..95b593e0806f6 100644 --- a/data/kobamin/kobaminbioschemas.jsonld +++ b/data/kobamin/kobaminbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "KoBaMIN", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://chopra-modules.science.purdue.edu/modules/kobamin/html/" } \ No newline at end of file diff --git a/data/kobas/kobasbioschemas.jsonld b/data/kobas/kobasbioschemas.jsonld index 7669a89ad92fa..2dbf641f3c661 100644 --- a/data/kobas/kobasbioschemas.jsonld +++ b/data/kobas/kobasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).", "sc:name": "KOBAS", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://kobas.cbi.pku.edu.cn" } \ No newline at end of file diff --git a/data/kobra/kobrabioschemas.jsonld b/data/kobra/kobrabioschemas.jsonld index 3ce42fa2b7b7e..dbdbd1de0ae9b 100644 --- a/data/kobra/kobrabioschemas.jsonld +++ b/data/kobra/kobrabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "KoBra", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://sourceforge.net/projects/kobra/" } \ No newline at end of file diff --git a/data/kodama/kodamabioschemas.jsonld b/data/kodama/kodamabioschemas.jsonld index 07b1186f8a13e..5058c9b832694 100644 --- a/data/kodama/kodamabioschemas.jsonld +++ b/data/kodama/kodamabioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Stefano Cacciatore", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27993774", { "@id": "https://doi.org/10.1093/bioinformatics/btw705" }, - "pubmed:27993774", "pmcid:PMC5408808" ], "sc:description": "KODAMA is an R package of the novel learning algorithm for unsupervised feature extraction. It is specifically designed for analysing noisy and high-dimensional datasets. It has additional functions that allow improved interpretation of high-dimensional data.", diff --git a/data/kolmogorov/kolmogorovbioschemas.jsonld b/data/kolmogorov/kolmogorovbioschemas.jsonld index bc9e001eea6c7..a07c581a38df9 100644 --- a/data/kolmogorov/kolmogorovbioschemas.jsonld +++ b/data/kolmogorov/kolmogorovbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Kolmogorov", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.math.unipa.it/~raffaele/kolmogorov/" } \ No newline at end of file diff --git a/data/komodo/komodobioschemas.jsonld b/data/komodo/komodobioschemas.jsonld index 665f03b6c7937..23b0ea6a91840 100644 --- a/data/komodo/komodobioschemas.jsonld +++ b/data/komodo/komodobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software to detect significantly under- or over-represented groups of homologous genes (KO groups) in one taxon (named test taxon) when compared with another (named background taxon) in a given biochemical pathway.", "sc:name": "KOMODO", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://www.komodo.cnptia.embrapa.br/" } \ No newline at end of file diff --git a/data/kosmos/kosmosbioschemas.jsonld b/data/kosmos/kosmosbioschemas.jsonld index 6b8775cfa30f3..1bf45fd06f79f 100644 --- a/data/kosmos/kosmosbioschemas.jsonld +++ b/data/kosmos/kosmosbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "KOSMOS is a web server for analysis of harmonic and anharmonic macromolecular structures for DNA, RNA, and proteins. Users can request thermal fluctuation study or transient pathway generation by submitting PDB ID or uploading personal data files. All the simulation outputs have been deposited into NMA and ENI database where most of data are disclosed to the public unless users requested.", "sc:name": "KOSMOS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioengineering.skku.ac.kr/kosmos" } \ No newline at end of file diff --git a/data/kpath/kpathbioschemas.jsonld b/data/kpath/kpathbioschemas.jsonld index 471c7edca5dff..60ca54c19ddc2 100644 --- a/data/kpath/kpathbioschemas.jsonld +++ b/data/kpath/kpathbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Reference-based compression software of short read data sets.", "sc:name": "Kpath", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.cs.cmu.edu/~ckingsf/software/pathenc/" } \ No newline at end of file diff --git a/data/kpdgui/kpdguibioschemas.jsonld b/data/kpdgui/kpdguibioschemas.jsonld index 407f19d979330..de33a3ec88dee 100644 --- a/data/kpdgui/kpdguibioschemas.jsonld +++ b/data/kpdgui/kpdguibioschemas.jsonld @@ -15,8 +15,8 @@ "biotools:primaryContact": "Mathieu Bray", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:31054501", "pmcid:PMC6538268", + "pubmed:31054501", { "@id": "https://doi.org/10.1016/J.COMPBIOMED.2019.03.013" } @@ -26,8 +26,8 @@ "sc:name": "KPDGUI", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/mathieubray/KPDGUI" }, diff --git a/data/kplogo/kplogobioschemas.jsonld b/data/kplogo/kplogobioschemas.jsonld index 22d4c8cadb6c9..5b403d5d24da4 100644 --- a/data/kplogo/kplogobioschemas.jsonld +++ b/data/kplogo/kplogobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkx323", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/kplogo", "@type": "sc:SoftwareApplication", @@ -24,8 +20,8 @@ "Command-line tool" ], "sc:citation": [ - "pubmed:28460012", "pmcid:PMC5570168", + "pubmed:28460012", { "@id": "https://doi.org/10.1093/nar/gkx323" } @@ -37,15 +33,19 @@ "sc:license": "MIT", "sc:name": "kpLogo", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://kplogo.wi.mit.edu/" }, { "@id": "http://orcid.org/0000-0003-0369-5269", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gkx323", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/krait/kraitbioschemas.jsonld b/data/krait/kraitbioschemas.jsonld index c3fbe325a0ace..3e51b9bad479c 100644 --- a/data/krait/kraitbioschemas.jsonld +++ b/data/krait/kraitbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "Krait", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/lmdu/krait" } \ No newline at end of file diff --git a/data/krds/krdsbioschemas.jsonld b/data/krds/krdsbioschemas.jsonld index 6ea81480e8272..183a5c8966a3b 100644 --- a/data/krds/krdsbioschemas.jsonld +++ b/data/krds/krdsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Evaluating drug resistance mutations in kinases by molecular docking.", "sc:name": "KRDS", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bcbl.kaist.ac.kr/KRDS/" } \ No newline at end of file diff --git a/data/krisp/krispbioschemas.jsonld b/data/krisp/krispbioschemas.jsonld index fee0abb915633..a8a5a13dd5720 100644 --- a/data/krisp/krispbioschemas.jsonld +++ b/data/krisp/krispbioschemas.jsonld @@ -9,16 +9,12 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PNTD.0007231", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/krisp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Luiz C. J. Alcantara", - "Tulio de Oliveira" + "Tulio de Oliveira", + "Luiz C. J. Alcantara" ], "sc:additionalType": "Web application", "sc:citation": [ @@ -34,10 +30,10 @@ "@id": "edam:operation_0552" }, { - "@id": "edam:operation_3478" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3478" } ], "sc:license": "Other", @@ -48,6 +44,10 @@ "Linux" ], "sc:url": "http://www.krisp.org.za/tools.php" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PNTD.0007231", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/krona/kronabioschemas.jsonld b/data/krona/kronabioschemas.jsonld index 7ece72fece48c..50f2c2b86fa1d 100644 --- a/data/krona/kronabioschemas.jsonld +++ b/data/krona/kronabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Proprietary", "sc:name": "Krona", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/marbl/Krona/wiki" } \ No newline at end of file diff --git a/data/kronaextract/kronaextractbioschemas.jsonld b/data/kronaextract/kronaextractbioschemas.jsonld index d73068052bc9d..da01cb52c7a31 100644 --- a/data/kronaextract/kronaextractbioschemas.jsonld +++ b/data/kronaextract/kronaextractbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Extract from krona xml file (obtained by rankoptimizer), list of reads and blast offset for a given taxonomic name.", "sc:name": "kronaextract", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/taxonomy_analysis/kronaExtract/0.0.2", "sc:version": "0.0.2" diff --git a/data/kronos/kronosbioschemas.jsonld b/data/kronos/kronosbioschemas.jsonld index afb6491b9d68d..236d43bd7a2a6 100644 --- a/data/kronos/kronosbioschemas.jsonld +++ b/data/kronos/kronosbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "Kronos", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/jtaghiyar/kronos" diff --git a/data/kronrls-mkl/kronrls-mklbioschemas.jsonld b/data/kronrls-mkl/kronrls-mklbioschemas.jsonld index 262260f42962b..e813a91a45dfc 100644 --- a/data/kronrls-mkl/kronrls-mklbioschemas.jsonld +++ b/data/kronrls-mkl/kronrls-mklbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-016-0890-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/KronRLS-MKL", "@type": "sc:SoftwareApplication", @@ -20,18 +16,18 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:26801218", - "pmcid:PMC4722636", { "@id": "https://doi.org/10.1186/s12859-016-0890-3" - } + }, + "pmcid:PMC4722636" ], "sc:description": "Matlab implementation of the Kronecker Regularized Least Squares with multiple kernels algorithm.", "sc:featureList": [ { - "@id": "edam:operation_2949" + "@id": "edam:operation_0272" }, { - "@id": "edam:operation_0272" + "@id": "edam:operation_2949" }, { "@id": "edam:operation_0303" @@ -43,6 +39,10 @@ "Mac" ], "sc:url": "https://github.com/andrecamara/kronrlsmkl" + }, + { + "@id": "https://doi.org/10.1186/s12859-016-0890-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ksea_app/ksea_appbioschemas.jsonld b/data/ksea_app/ksea_appbioschemas.jsonld index 23cfbb9175fc2..0d9d850735913 100644 --- a/data/ksea_app/ksea_appbioschemas.jsonld +++ b/data/ksea_app/ksea_appbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/KSEA_App", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mark R. Chance", - "Danica D. Wiredja" + "Danica D. Wiredja", + "Mark R. Chance" ], "sc:additionalType": [ - "Web application", - "Library" + "Library", + "Web application" ], "sc:description": "Kinase-Substrate Enrichment Analysis (KSEA) App - web-based tool for kinase activity inference from quantitative phosphoproteomics.", "sc:license": "MIT", "sc:name": "KSEA App", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://casecpb.shinyapps.io/ksea/" } \ No newline at end of file diff --git a/data/ksp-puel/ksp-puelbioschemas.jsonld b/data/ksp-puel/ksp-puelbioschemas.jsonld index 8a1403e5cc140..a6f53e2a92e70 100644 --- a/data/ksp-puel/ksp-puelbioschemas.jsonld +++ b/data/ksp-puel/ksp-puelbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Application developed for predicting novel substrates of kinases of interest.", "sc:name": "KSP-PUEL", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/PengyiYang/KSP-PUEL" } \ No newline at end of file diff --git a/data/ksrepo/ksrepobioschemas.jsonld b/data/ksrepo/ksrepobioschemas.jsonld index bec99b987ec2e..602a71527a227 100644 --- a/data/ksrepo/ksrepobioschemas.jsonld +++ b/data/ksrepo/ksrepobioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-016-0931-Y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ksrepo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Adam Brown", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:26860211", "pmcid:PMC4746802", { "@id": "https://doi.org/10.1186/S12859-016-0931-Y" - } + }, + "pubmed:26860211" ], "sc:description": "Generalized platform for computational drug repositioning.", "sc:featureList": { @@ -37,6 +33,10 @@ "Windows" ], "sc:url": "https://github.com/adam-sam-brown/ksRepo" + }, + { + "@id": "https://doi.org/10.1186/S12859-016-0931-Y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kth-package/kth-packagebioschemas.jsonld b/data/kth-package/kth-packagebioschemas.jsonld index 142af371e51c3..7968f7402909a 100644 --- a/data/kth-package/kth-packagebioschemas.jsonld +++ b/data/kth-package/kth-packagebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "KTH-package provides a collection of tools designed to make the microarray data analysis easier.", "sc:name": "KTH-package", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.biotech.kth.se/molbio/microarray/dataanalysis/index.html", "sc:version": "1.2.1" diff --git a/data/ktreedist/ktreedistbioschemas.jsonld b/data/ktreedist/ktreedistbioschemas.jsonld index 787cc24c122f9..c67652f1671a3 100644 --- a/data/ktreedist/ktreedistbioschemas.jsonld +++ b/data/ktreedist/ktreedistbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Computer program written in Perl that calculates the minimum branch length distance from one phylogenetic tree to another, providing a measure of the difference in topology and relative branch lengths (shape) between two trees.", "sc:name": "Ktreedist", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://molevol.cmima.csic.es/castresana/Ktreedist.html" } \ No newline at end of file diff --git a/data/kuenm/kuenmbioschemas.jsonld b/data/kuenm/kuenmbioschemas.jsonld index 3f888ca5e3d5e..41cf15195d332 100644 --- a/data/kuenm/kuenmbioschemas.jsonld +++ b/data/kuenm/kuenmbioschemas.jsonld @@ -9,30 +9,30 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.7717/peerj.6281", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/kuenm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Marlon E. Cobos", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6368831", { "@id": "https://doi.org/10.7717/peerj.6281" }, + "pmcid:PMC6368831", "pubmed:30755826" ], "sc:description": "R package for detailed development of Maxent Ecological Niche Models.", "sc:name": "kuenm", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/marlonecobos/kuenm" - }, - { - "@id": "https://doi.org/10.7717/peerj.6281", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kups/kupsbioschemas.jsonld b/data/kups/kupsbioschemas.jsonld index af62e38a610bd..df1de5a009462 100644 --- a/data/kups/kupsbioschemas.jsonld +++ b/data/kups/kupsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Provides protein-protein interaction (PPI) data. It allows users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs) and associated features. Multiple filters and options allow the user to control the make-up of the IPPs and NIPs as well as the quality of the resultant data sets. Each data set is built from the overall database, from five primary databases.", "sc:name": "KUPS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.ittc.ku.edu/chenlab" } \ No newline at end of file diff --git a/data/kvarq/kvarqbioschemas.jsonld b/data/kvarq/kvarqbioschemas.jsonld index c85846ad7ae0b..350a85b12f677 100644 --- a/data/kvarq/kvarqbioschemas.jsonld +++ b/data/kvarq/kvarqbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2164-15-881", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/kvarq", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:25297886", { "@id": "https://doi.org/10.1186/1471-2164-15-881" }, - "pmcid:PMC4197298" + "pmcid:PMC4197298", + "pubmed:25297886" ], "sc:description": "This program performs rapid in silico genotyping for selected loci (e.g. phylogenetic SNPs, drug resistance mutations) in bacterial genome sequences in FastQ format. Mapping to a whole-genome reference sequence or de novo assembly or the short reads is not necessary.", "sc:featureList": { @@ -30,12 +26,16 @@ }, "sc:name": "KvarQ", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://www.swisstph.ch/en/about/mpi/tuberculosis-research/kvarq-targeted-and-direct-variant-calling-in-fastq-reads-of-bacterial-genomes/", "sc:version": "0.12.2" + }, + { + "@id": "https://doi.org/10.1186/1471-2164-15-881", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kvik/kvikbioschemas.jsonld b/data/kvik/kvikbioschemas.jsonld index 6c1e8847c86dc..91c52c5f69f1f 100644 --- a/data/kvik/kvikbioschemas.jsonld +++ b/data/kvik/kvikbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.6238.2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/kvik", "@type": "sc:SoftwareApplication", @@ -21,16 +17,16 @@ { "@id": "https://doi.org/10.12688/F1000RESEARCH.6238.2" }, - "pmcid:PMC4574765", - "pubmed:26425340" + "pubmed:26425340", + "pmcid:PMC4574765" ], "sc:description": "Develope interactive data exploration applications in genomics and systems biology. Collection of packages in the Go programming language that help application developers i) interface with the R statistical programming language; ii) specify and run statistical analysis pipelines; and iii) interface with online databases such as MsigDB and KEGG.", "sc:featureList": [ { - "@id": "edam:operation_0533" + "@id": "edam:operation_2403" }, { - "@id": "edam:operation_2403" + "@id": "edam:operation_0533" } ], "sc:license": "MIT", @@ -41,6 +37,10 @@ "Linux" ], "sc:url": "https://github.com/fjukstad/kvik" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.6238.2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kwip/kwipbioschemas.jsonld b/data/kwip/kwipbioschemas.jsonld index 4f906d9104163..93c257056c153 100644 --- a/data/kwip/kwipbioschemas.jsonld +++ b/data/kwip/kwipbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1005727", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/kwip", "@type": "sc:SoftwareApplication", @@ -25,26 +29,26 @@ "@id": "edam:topic_0622" }, { - "@id": "edam:topic_0797" + "@id": "edam:topic_0080" }, { - "@id": "edam:topic_0080" + "@id": "edam:topic_0797" } ], "sc:citation": [ - "pmcid:PMC5600398", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1005727" }, - "pubmed:28873405" + "pubmed:28873405", + "pmcid:PMC5600398" ], "sc:description": "The k-mer weighted inner product (kWIP) is a method for a de novo estimator of genetic similarity without the need of reference genome.", "sc:featureList": [ { - "@id": "edam:operation_3731" + "@id": "edam:operation_0289" }, { - "@id": "edam:operation_0289" + "@id": "edam:operation_3731" }, { "@id": "edam:operation_0346" @@ -57,10 +61,6 @@ "@id": "https://kwip.readthedocs.io/en/latest/" }, "sc:url": "https://github.com/kdmurray91/kwip" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1005727", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/kymoanalyzer/kymoanalyzerbioschemas.jsonld b/data/kymoanalyzer/kymoanalyzerbioschemas.jsonld index 35c872a40d338..7281cb600916c 100644 --- a/data/kymoanalyzer/kymoanalyzerbioschemas.jsonld +++ b/data/kymoanalyzer/kymoanalyzerbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Plug-in", "sc:citation": [ - "pmcid:PMC5473519", - "pubmed:27770501", { "@id": "https://doi.org/10.1111/tra.12456" - } + }, + "pubmed:27770501", + "pmcid:PMC5473519" ], "sc:description": "KymoAnalyzer is an open-source software that automatically classifies particle trajectories and systematically calculates velocities, run lengths, pauses, and a wealth of other parameters that are characteristic of motor-based transport.", "sc:featureList": { @@ -31,9 +31,9 @@ "sc:license": "Other", "sc:name": "KymoAnalyzer", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://www.encalada.scripps.edu/kymoanalyzer", "sc:version": "1.01" diff --git a/data/kymorod/kymorodbioschemas.jsonld b/data/kymorod/kymorodbioschemas.jsonld index 30de6caf619e0..fd16eb0dcc7f6 100644 --- a/data/kymorod/kymorodbioschemas.jsonld +++ b/data/kymorod/kymorodbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Method for automated kinematic analysis of rod-shaped plant organs.", "sc:name": "KymoRod", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/ijpb/KymoRod" } \ No newline at end of file diff --git a/data/l-measure/l-measurebioschemas.jsonld b/data/l-measure/l-measurebioschemas.jsonld index 1b8734d9b9be8..fd7123eacfb63 100644 --- a/data/l-measure/l-measurebioschemas.jsonld +++ b/data/l-measure/l-measurebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "L-Measure", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cng.gmu.edu:8080/Lm/" } \ No newline at end of file diff --git a/data/l1kdeconv/l1kdeconvbioschemas.jsonld b/data/l1kdeconv/l1kdeconvbioschemas.jsonld index 8d2cfb705e6e4..615767983278a 100644 --- a/data/l1kdeconv/l1kdeconvbioschemas.jsonld +++ b/data/l1kdeconv/l1kdeconvbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "l1kdeconv", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/l1kdeconv/index.html" } \ No newline at end of file diff --git a/data/l2l/l2lbioschemas.jsonld b/data/l2l/l2lbioschemas.jsonld index 3351031349ece..5c240e7d7bbcb 100644 --- a/data/l2l/l2lbioschemas.jsonld +++ b/data/l2l/l2lbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "L2L is a simple but powerful tool for discovering the hidden biological significance in microarray data. Through an easy-to-use web interface, L2L will mine a list of up- or down-regulated genes for Gene Ontology terms that are significantly enriched. L2L can also compare the list of genes to a database of hundreds of published microarray experiments, in order to identify common patterns of gene regulation. A downloadable command-line version can run customized and batch analyses.", "sc:name": "L2L", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://depts.washington.edu/l2l/", "sc:version": "1.2" diff --git a/data/la-images/la-imagesbioschemas.jsonld b/data/la-images/la-imagesbioschemas.jsonld index a11ccaee8a3cd..a5e6eb1827790 100644 --- a/data/la-images/la-imagesbioschemas.jsonld +++ b/data/la-images/la-imagesbioschemas.jsonld @@ -16,14 +16,14 @@ "sc:license": "GPL-3.0", "sc:name": "LA-iMageS", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "Bioscope Group, University Nova of Lisbon", "SING Group, University of Vigo", - "GEPAM Group, University of Campinas" + "GEPAM Group, University of Campinas", + "Bioscope Group, University Nova of Lisbon" ], "sc:url": "http://www.la-images.net", "sc:version": "1.1.3" diff --git a/data/lab7/lab7bioschemas.jsonld b/data/lab7/lab7bioschemas.jsonld index 36daf4099c889..65d1dbf982145 100644 --- a/data/lab7/lab7bioschemas.jsonld +++ b/data/lab7/lab7bioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Data workflow management platform to streamline NGS analyses.", "sc:name": "Lab7", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.lab7.io" } \ No newline at end of file diff --git a/data/ladderfinder/ladderfinderbioschemas.jsonld b/data/ladderfinder/ladderfinderbioschemas.jsonld index 2ed8122641b92..54068710f3f7d 100644 --- a/data/ladderfinder/ladderfinderbioschemas.jsonld +++ b/data/ladderfinder/ladderfinderbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Designed to solve a problem in DNA genotyping. It helps in the construction of allelic ladders that drive the sizing and binning of SSR fragments produced by PCR. The algorithm scans a spreadsheet containing a database of individual profiles and finds a minimum set of individuals, that covers the maximum number of alleles represented in the database, with all alleles represented only once.", "sc:name": "LadderFinder", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://services.appliedgenomics.org/software/ladderfinder/", diff --git a/data/lahedes/lahedesbioschemas.jsonld b/data/lahedes/lahedesbioschemas.jsonld index e07a6d5b4fea3..00e94ac69babc 100644 --- a/data/lahedes/lahedesbioschemas.jsonld +++ b/data/lahedes/lahedesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The LAGLIDADG Homing Endonuclease Database and Engineering Server (LAHEDES) is a database listing basic properties of LAGLIDADG homing endonucleases (LHEs) with validated biochemical activity and known target site specificity. It also supports web-based searches of DNA sequences (ranging from single or multiple genes to entire genomic reads) for potential target sites that might be recognized either by wild-type or by engineered variants of those endonucleases.", "sc:name": "LAHEDES", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://homingendonuclease.net" } \ No newline at end of file diff --git a/data/lailaps-qsm/lailaps-qsmbioschemas.jsonld b/data/lailaps-qsm/lailaps-qsmbioschemas.jsonld index f18bcb666a594..df548e8eb6cd3 100644 --- a/data/lailaps-qsm/lailaps-qsmbioschemas.jsonld +++ b/data/lailaps-qsm/lailaps-qsmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "LAILAPS-QSM", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://bitbucket.org/ipk_bit_team/bioescorte-suggestion" } \ No newline at end of file diff --git a/data/lailaps/lailapsbioschemas.jsonld b/data/lailaps/lailapsbioschemas.jsonld index cfa308a02c6e4..31356b5e9f7cc 100644 --- a/data/lailaps/lailapsbioschemas.jsonld +++ b/data/lailaps/lailapsbioschemas.jsonld @@ -19,13 +19,13 @@ "sc:description": "A search engine which provides an exploration of plant genomic data for forward genetic research and comprises millions of quarterly updated and indexed information from major life science databases as well as millions of evidence ranked gene annotations to associate these facts to plant genome loci.", "sc:name": "LAILAPS Search Engine (transPLANT instance)", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ - "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben", - "ipk" + "ipk", + "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben" ], "sc:url": "http://webapps.ipk-gatersleben.de/lailaps/app", "sc:version": "1" diff --git a/data/lailapsipk/lailapsipkbioschemas.jsonld b/data/lailapsipk/lailapsipkbioschemas.jsonld index 6a3e4b1f749b4..1fc6704ddd928 100644 --- a/data/lailapsipk/lailapsipkbioschemas.jsonld +++ b/data/lailapsipk/lailapsipkbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/lailapsipk", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Matthias Lange", - "Jinbo Chen" + "Jinbo Chen", + "Dr. Matthias Lange" ], "sc:additionalType": "Web application", "sc:author": "Jinbo Chen", "sc:description": "Search engine which provides an exploration of plant genomic data for forward genetic research and comprises millions of quarterly updated and indexed information from major life science databases as well as millions of evidence ranked gene annotations to associate these facts to plant genome loci. This instance serve for index of IPK hosted databases. It comprise search indexes for IPK plant genome databases, molecular databases and germplasm collections.", "sc:name": "LAILAPS Search Engine (IPK instance)", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "ipk", diff --git a/data/laj/lajbioschemas.jsonld b/data/laj/lajbioschemas.jsonld index 80fcb0e4b77bf..f425e5015d723 100644 --- a/data/laj/lajbioschemas.jsonld +++ b/data/laj/lajbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.", "sc:name": "Laj", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://globin.cse.psu.edu/dist/laj/" } \ No newline at end of file diff --git a/data/laj_1/laj_1bioschemas.jsonld b/data/laj_1/laj_1bioschemas.jsonld index a0469866af256..586e09275130c 100644 --- a/data/laj_1/laj_1bioschemas.jsonld +++ b/data/laj_1/laj_1bioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "laj_1", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", "sc:version": "1.3.1" diff --git a/data/lakemorpho/lakemorphobioschemas.jsonld b/data/lakemorpho/lakemorphobioschemas.jsonld index 6bc21ac3f0f7d..974b766454ecd 100644 --- a/data/lakemorpho/lakemorphobioschemas.jsonld +++ b/data/lakemorpho/lakemorphobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/f1000research.12512.1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/lakemorpho", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:29188019", + "pmcid:PMC5698920", { "@id": "https://doi.org/10.12688/f1000research.12512.1" - }, - "pmcid:PMC5698920" + } ], "sc:description": "Calculating lake morphometry metrics.", "sc:featureList": { @@ -32,10 +36,6 @@ "Windows" ], "sc:url": "https://github.com/usepa/lakemorpho" - }, - { - "@id": "https://doi.org/10.12688/f1000research.12512.1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/lalign/lalignbioschemas.jsonld b/data/lalign/lalignbioschemas.jsonld index 2ba24105f31b2..6243b023a3767 100644 --- a/data/lalign/lalignbioschemas.jsonld +++ b/data/lalign/lalignbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Find internal duplications by calculating non-intersecting local sequence alignments.", "sc:name": "LALIGN", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "EMBL-EBI", diff --git a/data/lalign_sib/lalign_sibbioschemas.jsonld b/data/lalign_sib/lalign_sibbioschemas.jsonld index 2197c7c5e84bd..54cb9a5cbea8e 100644 --- a/data/lalign_sib/lalign_sibbioschemas.jsonld +++ b/data/lalign_sib/lalign_sibbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally.", "sc:name": "LALIGN (SIB)", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://embnet.vital-it.ch/software/LALIGN_form.html" } \ No newline at end of file diff --git a/data/lambda/lambdabioschemas.jsonld b/data/lambda/lambdabioschemas.jsonld index 459e198b2116f..70cae87bed237 100644 --- a/data/lambda/lambdabioschemas.jsonld +++ b/data/lambda/lambdabioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "Unlicense", "sc:name": "LAmbDA", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://github.com/tsteelejohnson91/LAmbDA" } \ No newline at end of file diff --git a/data/lamp/lampbioschemas.jsonld b/data/lamp/lampbioschemas.jsonld index 84a584a2d2ee1..7ba04cc76c681 100644 --- a/data/lamp/lampbioschemas.jsonld +++ b/data/lamp/lampbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0066557", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/lamp", "@type": "sc:SoftwareApplication", @@ -31,11 +27,15 @@ }, "sc:name": "LAMP", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://biotechlab.fudan.edu.cn/database/lamp/" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0066557", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/lanceletdb/lanceletdbbioschemas.jsonld b/data/lanceletdb/lanceletdbbioschemas.jsonld index d9be0831c4e45..159576c973a51 100644 --- a/data/lanceletdb/lanceletdbbioschemas.jsonld +++ b/data/lanceletdb/lanceletdbbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Anlong Xu", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species.", "sc:license": "Unlicense", "sc:name": "LanceletDB", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://genome.bucm.edu.cn/lancelet/" } \ No newline at end of file diff --git a/data/lara/larabioschemas.jsonld b/data/lara/larabioschemas.jsonld index 16bb85f6061a0..b5a0bf4e45055 100644 --- a/data/lara/larabioschemas.jsonld +++ b/data/lara/larabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-8-271", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/lara", "@type": "sc:SoftwareApplication", @@ -22,8 +18,8 @@ { "@id": "https://doi.org/10.1186/1471-2105-8-271" }, - "pmcid:PMC1955456", - "pubmed:17662141" + "pubmed:17662141", + "pmcid:PMC1955456" ], "sc:description": "“lagrangian relaxed structural alignment” is a tool for the sequence-structure alignment of RNA sequences.", "sc:featureList": { @@ -33,6 +29,10 @@ "sc:operatingSystem": "Linux", "sc:url": "http://www.mi.fu-berlin.de/w/LiSA/Lara", "sc:version": "1.3.2a" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-8-271", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/larva/larvabioschemas.jsonld b/data/larva/larvabioschemas.jsonld index 27aea6f58ea0f..d1489fa8f42e0 100644 --- a/data/larva/larvabioschemas.jsonld +++ b/data/larva/larvabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKV803", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/larva", "@type": "sc:SoftwareApplication", @@ -28,10 +32,6 @@ "sc:name": "LARVA", "sc:operatingSystem": "Linux", "sc:url": "http://larva.gersteinlab.org/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKV803", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/larvalign/larvalignbioschemas.jsonld b/data/larvalign/larvalignbioschemas.jsonld index 0dbfde4a69957..a53815b6cce88 100644 --- a/data/larvalign/larvalignbioschemas.jsonld +++ b/data/larvalign/larvalignbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Dorit Merhof", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:29127664", - "pmcid:PMC5797188", { "@id": "https://doi.org/10.1007/s12021-017-9349-6" - } + }, + "pubmed:29127664", + "pmcid:PMC5797188" ], "sc:description": "Aligning Gene Expression Patterns from the Larval Brain of Drosophila melanogaster.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "larvalign", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/larvalign/larvalign/releases/tag/v1.0", "sc:version": "1.0" diff --git a/data/laser/laserbioschemas.jsonld b/data/laser/laserbioschemas.jsonld index c4ec4172019db..6f91d18841226 100644 --- a/data/laser/laserbioschemas.jsonld +++ b/data/laser/laserbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "C++ software package that can estimate individual ancestry directly from genome-wide shortgun sequencing reads without calling genotypes.", "sc:name": "LASER", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://genome.sph.umich.edu/wiki/LASER" } \ No newline at end of file diff --git a/data/lassim/lassimbioschemas.jsonld b/data/lassim/lassimbioschemas.jsonld index 9cc9c6ec46ad9..e61ea44a83e91 100644 --- a/data/lassim/lassimbioschemas.jsonld +++ b/data/lassim/lassimbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Mika Gustafsson", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:28640810", + "pmcid:PMC5501685", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1005608" - }, - "pubmed:28640810", - "pmcid:PMC5501685" + } ], "sc:description": "A network inference toolbox for genome-wide mechanistic modeling.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "LASSIM", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://gitlab.com/Gustafsson-lab/lassim" } diff --git a/data/lastz/lastzbioschemas.jsonld b/data/lastz/lastzbioschemas.jsonld index e507c84f4bf05..47f302523f2ce 100644 --- a/data/lastz/lastzbioschemas.jsonld +++ b/data/lastz/lastzbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.", "sc:name": "LASTZ", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bx.psu.edu/~rsharris/lastz/" } \ No newline at end of file diff --git a/data/layers/layersbioschemas.jsonld b/data/layers/layersbioschemas.jsonld index 7925ef4b9be8d..b62d717da11e1 100644 --- a/data/layers/layersbioschemas.jsonld +++ b/data/layers/layersbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Molecular surface peeling algorithm and its applications to analyze protein structures.", "sc:name": "Layers", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.csb.iitkgp.ernet.in/applications/mol_layers/main" } \ No newline at end of file diff --git a/data/lbe/lbebioschemas.jsonld b/data/lbe/lbebioschemas.jsonld index 39f2affb8e0cd..af67a1cd04edf 100644 --- a/data/lbe/lbebioschemas.jsonld +++ b/data/lbe/lbebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Cyril Dalmasso", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.", "sc:license": "GPL-2.0", "sc:name": "LBE", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LBE.html", diff --git a/data/lca/lcabioschemas.jsonld b/data/lca/lcabioschemas.jsonld index 077b07dd749b5..0746bed885c84 100644 --- a/data/lca/lcabioschemas.jsonld +++ b/data/lca/lcabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Find the lowest common ancestor from a BLAST tabular file.", "sc:name": "lca", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/LCA/0.1%20beta", "sc:version": "0.1 beta" diff --git a/data/lcmix/lcmixbioschemas.jsonld b/data/lcmix/lcmixbioschemas.jsonld index ab7d04fc848f2..d11e7f989a5d0 100644 --- a/data/lcmix/lcmixbioschemas.jsonld +++ b/data/lcmix/lcmixbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "R package using hierarchical mixture models for genomic data integration.", "sc:name": "lcmix", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://lcmix.r-forge.r-project.org/" } \ No newline at end of file diff --git a/data/ld_select/ld_selectbioschemas.jsonld b/data/ld_select/ld_selectbioschemas.jsonld index 766622f69b30c..10cad1f7ba852 100644 --- a/data/ld_select/ld_selectbioschemas.jsonld +++ b/data/ld_select/ld_selectbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Analysis the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2.", "sc:name": "LD Select", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://droog.gs.washington.edu/ldSelect.html" } \ No newline at end of file diff --git a/data/lda/ldabioschemas.jsonld b/data/lda/ldabioschemas.jsonld index f1c93c3eb7fac..f92e2ae01ff9d 100644 --- a/data/lda/ldabioschemas.jsonld +++ b/data/lda/ldabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Lipid Data Analyzer (LDA)", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://genome.tugraz.at/lda2" } \ No newline at end of file diff --git a/data/ldblock/ldblockbioschemas.jsonld b/data/ldblock/ldblockbioschemas.jsonld index 5959698d01aa4..95daf2e0b3d4d 100644 --- a/data/ldblock/ldblockbioschemas.jsonld +++ b/data/ldblock/ldblockbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "ldblock", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ldblock.html", "sc:version": "1.10.0" diff --git a/data/ldlink/ldlinkbioschemas.jsonld b/data/ldlink/ldlinkbioschemas.jsonld index dd6e752450009..e23465b05f59b 100644 --- a/data/ldlink/ldlinkbioschemas.jsonld +++ b/data/ldlink/ldlinkbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "LDlink", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://analysistools.nci.nih.gov/LDlink/" } \ No newline at end of file diff --git a/data/ldpac/ldpacbioschemas.jsonld b/data/ldpac/ldpacbioschemas.jsonld index 5e432bb07bc17..0cb4d86852370 100644 --- a/data/ldpac/ldpacbioschemas.jsonld +++ b/data/ldpac/ldpacbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Buhm Han", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:21181893", "sc:description": "Method for detecting spurious associations using p-values. The strength of the method is its simplicity; it requires no other information but p-values.", "sc:name": "LDPAC", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://ldpac.cs.ucla.edu/" } \ No newline at end of file diff --git a/data/ldso/ldsobioschemas.jsonld b/data/ldso/ldsobioschemas.jsonld index 7526d990c8c5a..5e231f35488da 100644 --- a/data/ldso/ldsobioschemas.jsonld +++ b/data/ldso/ldsobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Completely self-contained program written in Fortran90. It is a complete computer program for simulations of whole diploid population histories under various historical scenarios based on the gene-dropping method (MacCluer et al. 1986).", "sc:name": "LDSO", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://qgsp.jouy.inra.fr/index.php?option=com_content&view=article&id=51&Itemid=56" } \ No newline at end of file diff --git a/data/lea/leabioschemas.jsonld b/data/lea/leabioschemas.jsonld index 5320f81cb8281..6448c46a14692 100644 --- a/data/lea/leabioschemas.jsonld +++ b/data/lea/leabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Eric Frichot", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "R package for landscape genomics and ecological association tests. It can run analyses of population structure and genome scans for local adaptation. It includes statistical methods for estimating ancestry coefficients from large genotypic matrices and evaluating the number of ancestral populations; identifying genetic polymorphisms that exhibit high correlation with an environmental gradient or with variables used as proxies for ecological pressures, and controlling the false discovery rate.", "sc:license": "GPL-3.0", "sc:name": "LEA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LEA.html", "sc:version": "1.6.0" diff --git a/data/leafoptimizer/leafoptimizerbioschemas.jsonld b/data/leafoptimizer/leafoptimizerbioschemas.jsonld index dd57c1b889c72..f4f009829408b 100644 --- a/data/leafoptimizer/leafoptimizerbioschemas.jsonld +++ b/data/leafoptimizer/leafoptimizerbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "leafoptimizer", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/cdmuir/leafoptimizer" } \ No newline at end of file diff --git a/data/learncoil/learncoilbioschemas.jsonld b/data/learncoil/learncoilbioschemas.jsonld index dc02240f7f006..9843537ffc317 100644 --- a/data/learncoil/learncoilbioschemas.jsonld +++ b/data/learncoil/learncoilbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The LearnCoil Histidase Kinase program uses an iterative learning algorithm to detect possible coiled-coil domains in histidase kinase receptors.", "sc:name": "LearnCoil", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://groups.csail.mit.edu/cb/learncoil/webcoil.html" } \ No newline at end of file diff --git a/data/learnpopgen/learnpopgenbioschemas.jsonld b/data/learnpopgen/learnpopgenbioschemas.jsonld index bdb6b2fb5db66..797d2d7134c04 100644 --- a/data/learnpopgen/learnpopgenbioschemas.jsonld +++ b/data/learnpopgen/learnpopgenbioschemas.jsonld @@ -19,26 +19,26 @@ "biotools:primaryContact": "Liam J. Revell", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:31380058", - "pmcid:PMC6662327", { "@id": "https://doi.org/10.1002/ece3.5412" - } + }, + "pmcid:PMC6662327", + "pubmed:31380058" ], "sc:description": "R package for population genetic simulation and numerical analysis.", "sc:featureList": [ { - "@id": "edam:operation_3799" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3799" } ], "sc:license": "GPL-3.0", "sc:name": "learnPopGen", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/learnPopGen/index.html" diff --git a/data/lebibipqp/lebibipqpbioschemas.jsonld b/data/lebibipqp/lebibipqpbioschemas.jsonld index 62b542fb7ba5e..bb6a232e76f85 100644 --- a/data/lebibipqp/lebibipqpbioschemas.jsonld +++ b/data/lebibipqp/lebibipqpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The BioInformatics Prokaryotes Quick Phylogeny is designed to reconstruct the phylogeny of an Archaea or a Bacteria from its nucleic acid sequence. It is also giving the useful informations if species identification is needed.", "sc:name": "leBIBIpqp", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "IFB ELIXIR-FR", "sc:url": "https://umr5558-bibiserv.univ-lyon1.fr/lebibi/lebibi.cgi", diff --git a/data/ledpred/ledpredbioschemas.jsonld b/data/ledpred/ledpredbioschemas.jsonld index 25b6d2d0dccfd..e87fc4a87ded3 100644 --- a/data/ledpred/ledpredbioschemas.jsonld +++ b/data/ledpred/ledpredbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Aitor Gonzalez", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package creates a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, NGS peaks and signals and other numerical scores of the sequences using supervised classification. It contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences.", "sc:license": "MIT", "sc:name": "LedPred", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LedPred.html", "sc:version": "1.8.0" diff --git a/data/legiolist/legiolistbioschemas.jsonld b/data/legiolist/legiolistbioschemas.jsonld index 119bc1e3254e4..d2c24474d975d 100644 --- a/data/legiolist/legiolistbioschemas.jsonld +++ b/data/legiolist/legiolistbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6350-5001", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/legiolist", "@type": "sc:SoftwareApplication", @@ -24,15 +28,11 @@ "sc:name": "Legionella pneumophila genome database", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "Institut Pasteur", "sc:url": "http://genolist.pasteur.fr/LegioList/" - }, - { - "@id": "http://orcid.org/0000-0002-6350-5001", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/legumeip/legumeipbioschemas.jsonld b/data/legumeip/legumeipbioschemas.jsonld index 34006bcbbd69e..e84adc64ea3c2 100644 --- a/data/legumeip/legumeipbioschemas.jsonld +++ b/data/legumeip/legumeipbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes.", "sc:name": "LegumeIP", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://plantgrn.noble.org/LegumeIP/" diff --git a/data/leishindb/leishindbbioschemas.jsonld b/data/leishindb/leishindbbioschemas.jsonld index 0055426950f45..8cdcafdee2977 100644 --- a/data/leishindb/leishindbbioschemas.jsonld +++ b/data/leishindb/leishindbbioschemas.jsonld @@ -25,8 +25,8 @@ "sc:license": "Other", "sc:name": "LeishInDB", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://leishindb.biomedinformri.com/" diff --git a/data/lemon-tree/lemon-treebioschemas.jsonld b/data/lemon-tree/lemon-treebioschemas.jsonld index 8e71141a6d887..1503b6c60cdd3 100644 --- a/data/lemon-tree/lemon-treebioschemas.jsonld +++ b/data/lemon-tree/lemon-treebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Algorithm to infer a module network from biological data. It can integrate heterogeneous data types such as expression data, copy number, microRNA, epigenetic profiles.", "sc:name": "lemon-tree", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/eb00/lemon-tree" } \ No newline at end of file diff --git a/data/leon/leonbioschemas.jsonld b/data/leon/leonbioschemas.jsonld index d192a0b7fda22..2c3fd00a5eb60 100644 --- a/data/leon/leonbioschemas.jsonld +++ b/data/leon/leonbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A software to compress Next Generation Sequencing data.", "sc:name": "Leon", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "GenOuest", diff --git a/data/leproma/lepromabioschemas.jsonld b/data/leproma/lepromabioschemas.jsonld index 30e0297ec1df6..e951556865dfd 100644 --- a/data/leproma/lepromabioschemas.jsonld +++ b/data/leproma/lepromabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Mycobacterium leprae genome database.", "sc:name": "Mycobacterium leprae genome database", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://genolist.pasteur.fr/Leproma/" } \ No newline at end of file diff --git a/data/lfa/lfabioschemas.jsonld b/data/lfa/lfabioschemas.jsonld index a434f287f4c8a..c5cf4fb9bbea5 100644 --- a/data/lfa/lfabioschemas.jsonld +++ b/data/lfa/lfabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btv641", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/lfa", "@type": "sc:SoftwareApplication", @@ -25,11 +21,11 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:26545820", "pmcid:PMC4795615", { "@id": "https://doi.org/10.1093/bioinformatics/btv641" - }, - "pubmed:26545820" + } ], "sc:description": "LFA is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.", "sc:featureList": { @@ -38,12 +34,16 @@ "sc:license": "GPL-3.0", "sc:name": "lfa", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/lfa.html", "sc:version": "1.4.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv641", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/lfmm/lfmmbioschemas.jsonld b/data/lfmm/lfmmbioschemas.jsonld index dcb5cae11e911..e21b7a2fa9739 100644 --- a/data/lfmm/lfmmbioschemas.jsonld +++ b/data/lfmm/lfmmbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Unified framework for inferring population genetic structure and gene-environment associations.", "sc:name": "LFMM", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://membres-timc.imag.fr/Eric.Frichot/lfmm/index.htm" } \ No newline at end of file diff --git a/data/lfpy/lfpybioschemas.jsonld b/data/lfpy/lfpybioschemas.jsonld index c867701d2fe93..a73145120f2dc 100644 --- a/data/lfpy/lfpybioschemas.jsonld +++ b/data/lfpy/lfpybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "LFPy", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://lfpy.github.io/", "sc:version": "1.1.3" diff --git a/data/lfqc/lfqcbioschemas.jsonld b/data/lfqc/lfqcbioschemas.jsonld index 1002eab20942b..b1373aca59225 100644 --- a/data/lfqc/lfqcbioschemas.jsonld +++ b/data/lfqc/lfqcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "New lossless non-reference based fastq compression algorithm.", "sc:name": "LFQC", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://engr.uconn.edu/~rajasek/" } \ No newline at end of file diff --git a/data/lga/lgabioschemas.jsonld b/data/lga/lgabioschemas.jsonld index 64ab5b6e7b076..7bfbcb9c2a897 100644 --- a/data/lga/lgabioschemas.jsonld +++ b/data/lga/lgabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Local-Global Alignment (LGA) performs structural alignments for two proteins structures or fragments of 3D protein structures.", "sc:name": "LGA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://proteinmodel.org/AS2TS/LGA/lga.html" } \ No newline at end of file diff --git a/data/lgicdb/lgicdbbioschemas.jsonld b/data/lgicdb/lgicdbbioschemas.jsonld index 9d80d918117c9..ac162ea804933 100644 --- a/data/lgicdb/lgicdbbioschemas.jsonld +++ b/data/lgicdb/lgicdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available.", "sc:name": "Ligand-gated ion channel database (LGICdb)", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php" } \ No newline at end of file diff --git a/data/lgsfaligner/lgsfalignerbioschemas.jsonld b/data/lgsfaligner/lgsfalignerbioschemas.jsonld index cd73b361354e2..8003d84648111 100644 --- a/data/lgsfaligner/lgsfalignerbioschemas.jsonld +++ b/data/lgsfaligner/lgsfalignerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool to Align two RNA Secondary Structures Locally.", "sc:name": "LGSFAligner", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.comp.nus.edu.sg/~bioinfo/LGSFAligner/index.htm" } \ No newline at end of file diff --git a/data/libfid/libfidbioschemas.jsonld b/data/libfid/libfidbioschemas.jsonld index 1491a8a78f95e..ce621db6c4deb 100644 --- a/data/libfid/libfidbioschemas.jsonld +++ b/data/libfid/libfidbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "libfid", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "CeBiTec", diff --git a/data/libipaca/libipacabioschemas.jsonld b/data/libipaca/libipacabioschemas.jsonld index bec6d633cd10c..63ceedfebc7c4 100644 --- a/data/libipaca/libipacabioschemas.jsonld +++ b/data/libipaca/libipacabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Other", "sc:name": "libipaca", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/kirchnerlab/libipaca" diff --git a/data/libmaus/libmausbioschemas.jsonld b/data/libmaus/libmausbioschemas.jsonld index a5067b3da894c..03d9ec3fff092 100644 --- a/data/libmaus/libmausbioschemas.jsonld +++ b/data/libmaus/libmausbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-2.0", "sc:name": "libmaus", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/gt1/libmaus" } \ No newline at end of file diff --git a/data/libmgf/libmgfbioschemas.jsonld b/data/libmgf/libmgfbioschemas.jsonld index d686a98adadde..cc22ea9cf5ee0 100644 --- a/data/libmgf/libmgfbioschemas.jsonld +++ b/data/libmgf/libmgfbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "libmgf", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://kirchnerlab.github.io/libmgf/" } \ No newline at end of file diff --git a/data/libmsym/libmsymbioschemas.jsonld b/data/libmsym/libmsymbioschemas.jsonld index 680c5854985d0..59bbbe515e2fb 100644 --- a/data/libmsym/libmsymbioschemas.jsonld +++ b/data/libmsym/libmsymbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "libmsym", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/mcodev31/libmsym" } \ No newline at end of file diff --git a/data/libra/librabioschemas.jsonld b/data/libra/librabioschemas.jsonld index 18829564d0aec..3e0f435d7d043 100644 --- a/data/libra/librabioschemas.jsonld +++ b/data/libra/librabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/libra", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:citation": "pubmed:20101611", "sc:description": "Analyzes 4- and 8-channel iTRAQ data.", diff --git a/data/libra_k-mer/libra_k-merbioschemas.jsonld b/data/libra_k-mer/libra_k-merbioschemas.jsonld index 4c6d6df33ed7b..63f23f71f567f 100644 --- a/data/libra_k-mer/libra_k-merbioschemas.jsonld +++ b/data/libra_k-mer/libra_k-merbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/gigascience/giy165", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Libra_k-mer", "@type": "sc:SoftwareApplication", @@ -22,19 +18,19 @@ { "@id": "https://doi.org/10.1093/gigascience/giy165" }, - "pmcid:PMC6354030", - "pubmed:30597002" + "pubmed:30597002", + "pmcid:PMC6354030" ], "sc:description": "Scalable k-mer-based tool for massive all-vs-all metagenome comparisons.", "sc:featureList": [ { - "@id": "edam:operation_0310" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_3472" + "@id": "edam:operation_0310" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3472" } ], "sc:license": "Apache-2.0", @@ -44,6 +40,10 @@ "Linux" ], "sc:url": "https://github.com/iychoi/libra" + }, + { + "@id": "https://doi.org/10.1093/gigascience/giy165", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/libralign/libralignbioschemas.jsonld b/data/libralign/libralignbioschemas.jsonld index b08f99b89b217..49c4a19239f68 100644 --- a/data/libralign/libralignbioschemas.jsonld +++ b/data/libralign/libralignbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "LibrAlign", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfweb.info/LibrAlign/", "sc:version": "0.8.0" diff --git a/data/libroadrunner/libroadrunnerbioschemas.jsonld b/data/libroadrunner/libroadrunnerbioschemas.jsonld index 3acc21331acf7..b8187dddf798b 100644 --- a/data/libroadrunner/libroadrunnerbioschemas.jsonld +++ b/data/libroadrunner/libroadrunnerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML).", "sc:name": "libRoadRunner", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.libroadrunner.org" } \ No newline at end of file diff --git a/data/libsbml/libsbmlbioschemas.jsonld b/data/libsbml/libsbmlbioschemas.jsonld index 13853fbd4ab89..ef9c1254088a1 100644 --- a/data/libsbml/libsbmlbioschemas.jsonld +++ b/data/libsbml/libsbmlbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications.", "sc:name": "LibSBML", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sbml.org/Software/libSBML" } \ No newline at end of file diff --git a/data/licebase/licebasebioschemas.jsonld b/data/licebase/licebasebioschemas.jsonld index 1d9743cc37b65..8346c4b4cf0fd 100644 --- a/data/licebase/licebasebioschemas.jsonld +++ b/data/licebase/licebasebioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/LiceBase", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:description": "Database for Sea lice (Lepeophtheirus salmonis and Caligus spp.), which are the major pathogens affecting the global salmon farming industry and have a significant impact in many areas", "sc:license": "Other", "sc:name": "LiceBase", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://licebase.org/" diff --git a/data/lichee/licheebioschemas.jsonld b/data/lichee/licheebioschemas.jsonld index 4ed3a07f6ba54..68e4604df2cde 100644 --- a/data/lichee/licheebioschemas.jsonld +++ b/data/lichee/licheebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution) is a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples.", "sc:name": "LICHeE", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://viq854.github.io/lichee/" diff --git a/data/lichem/lichembioschemas.jsonld b/data/lichem/lichembioschemas.jsonld index 577cabcce5568..22eb3cdf96501 100644 --- a/data/lichem/lichembioschemas.jsonld +++ b/data/lichem/lichembioschemas.jsonld @@ -9,14 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1002/jcc.24295", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/lichem", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "G. Andrés Cisneros", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4808410", "pubmed:26781073", + "pmcid:PMC4808410", { "@id": "https://doi.org/10.1002/jcc.24295" } @@ -28,14 +32,10 @@ "sc:license": "GPL-3.0", "sc:name": "LICHEM", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/kratman/LICHEM_QMMM" - }, - { - "@id": "https://doi.org/10.1002/jcc.24295", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/lifeexplorer/lifeexplorerbioschemas.jsonld b/data/lifeexplorer/lifeexplorerbioschemas.jsonld index efa06a0098376..80c3f10fc5429 100644 --- a/data/lifeexplorer/lifeexplorerbioschemas.jsonld +++ b/data/lifeexplorer/lifeexplorerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "3D navigation tool for cells. Molecular Biology is a booming science with enormous scope and potential. In many ways its current status can be compared with the early days of the computer industry: it has the capacity to change the way we approach certain key technologies, such as medicine and manufacturing.", "sc:name": "LifeExplorer", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.lifeexplorer.info/" } \ No newline at end of file diff --git a/data/lifemap/lifemapbioschemas.jsonld b/data/lifemap/lifemapbioschemas.jsonld index 0c2efa33f5b65..53a0d8e7a990c 100644 --- a/data/lifemap/lifemapbioschemas.jsonld +++ b/data/lifemap/lifemapbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:license": "CC-BY-NC-4.0", "sc:name": "Lifemap", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://lifemap.univ-lyon1.fr", diff --git a/data/lifewatchgreece/lifewatchgreecebioschemas.jsonld b/data/lifewatchgreece/lifewatchgreecebioschemas.jsonld index f19b2d983f408..15a2969036e92 100644 --- a/data/lifewatchgreece/lifewatchgreecebioschemas.jsonld +++ b/data/lifewatchgreece/lifewatchgreecebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "LifeWatchGreece MicroCT vLab", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://microct.portal.lifewatchgreece.eu/", "sc:version": "1" diff --git a/data/ligalign/ligalignbioschemas.jsonld b/data/ligalign/ligalignbioschemas.jsonld index 0132652c4858d..20221a2276924 100644 --- a/data/ligalign/ligalignbioschemas.jsonld +++ b/data/ligalign/ligalignbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "LigAlign: an automated system and structure visualization tool for flexible ligand alignment and analysis. When performing rigid alignments, LigAlign produces results consistent with manually annotated structural motifs. In performing flexible alignments, LigAlign automatically produces biochemically reasonable ligand fragmentations and subsequently identifies conserved structural motifs that are not detected by rigid alignment.", "sc:name": "LigAlign", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://compbio.cs.toronto.edu/ligalign/" } \ No newline at end of file diff --git a/data/ligandrna/ligandrnabioschemas.jsonld b/data/ligandrna/ligandrnabioschemas.jsonld index d1a019b98d9e2..20c5936274aa1 100644 --- a/data/ligandrna/ligandrnabioschemas.jsonld +++ b/data/ligandrna/ligandrnabioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/ligandrna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Janusz Bujnicki - Project coordinator", + "Anna Philips - Program developer", "Kaja Milanowska - Server developer", - "Anna Philips - Program developer" + "Janusz Bujnicki - Project coordinator" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:25726469", "sc:description": "A novel computational tool for scoring and ranking three-dimensional poses of small molecule ligands bound to RNA 3D structures.", "sc:name": "LigandRNA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://ligandrna.genesilico.pl/" } \ No newline at end of file diff --git a/data/ligap/ligapbioschemas.jsonld b/data/ligap/ligapbioschemas.jsonld index d82b6978cd580..061ad69aa5a3d 100644 --- a/data/ligap/ligapbioschemas.jsonld +++ b/data/ligap/ligapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Allows integrative analysis and visualization of multiple lineages over whole time-course profiles.", "sc:name": "LIGAP", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://research.ics.aalto.fi/csb/software/ligap/" } \ No newline at end of file diff --git a/data/lightcpg/lightcpgbioschemas.jsonld b/data/lightcpg/lightcpgbioschemas.jsonld index fa21d7edc2a8b..0e2b9b8bf4873 100644 --- a/data/lightcpg/lightcpgbioschemas.jsonld +++ b/data/lightcpg/lightcpgbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-8346-0798", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/S12864-019-5742-X", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/LightCpG", "@type": "sc:SoftwareApplication", @@ -20,26 +28,18 @@ { "@id": "https://doi.org/10.1186/S12864-019-5742-X" }, - "pmcid:PMC6513517", - "pubmed:31084602" + "pubmed:31084602", + "pmcid:PMC6513517" ], "sc:description": "Multi-view CpG sites detection on single-cell whole genome sequence data.", "sc:license": "Unlicense", "sc:name": "LightCpG", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/guofei-tju/LightCpG" - }, - { - "@id": "https://orcid.org/0000-0001-8346-0798", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/S12864-019-5742-X", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/lightdock/lightdockbioschemas.jsonld b/data/lightdock/lightdockbioschemas.jsonld index 82571594ade48..30bb2905d5616 100644 --- a/data/lightdock/lightdockbioschemas.jsonld +++ b/data/lightdock/lightdockbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Other", "sc:name": "LightDock", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://life.bsc.es/pid/lightdock/", "sc:version": "0.4.0" diff --git a/data/lighter/lighterbioschemas.jsonld b/data/lighter/lighterbioschemas.jsonld index 57fdcb3fd56c2..d06409fb8f217 100644 --- a/data/lighter/lighterbioschemas.jsonld +++ b/data/lighter/lighterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.", "sc:name": "Lighter", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/mourisl/Lighter" } \ No newline at end of file diff --git a/data/ligmerge/ligmergebioschemas.jsonld b/data/ligmerge/ligmergebioschemas.jsonld index 076f6d87e8cdc..6646851ff5554 100644 --- a/data/ligmerge/ligmergebioschemas.jsonld +++ b/data/ligmerge/ligmergebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Novel drug-design algorithm which combines structures of known binders to generate similar but structurally distinct compounds that can be tested for binding.", "sc:name": "LigMerge", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://nbcr.ucsd.edu/data/sw/hosted/ligmerge/" } \ No newline at end of file diff --git a/data/ligplot/ligplotbioschemas.jsonld b/data/ligplot/ligplotbioschemas.jsonld index 488d4072ed662..b2a0689666cf7 100644 --- a/data/ligplot/ligplotbioschemas.jsonld +++ b/data/ligplot/ligplotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Program which plots schematic diagrams of protein-ligand interactions.", "sc:name": "LIGPLOT", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/" } \ No newline at end of file diff --git a/data/ligsearch/ligsearchbioschemas.jsonld b/data/ligsearch/ligsearchbioschemas.jsonld index ef979bf96d38d..299df7684e11d 100644 --- a/data/ligsearch/ligsearchbioschemas.jsonld +++ b/data/ligsearch/ligsearchbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "LigSearch", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/thornton-srv/databases/LigSearch", diff --git a/data/likeltd/likeltdbioschemas.jsonld b/data/likeltd/likeltdbioschemas.jsonld index 66c4e2c18c6e0..85b73c091ebd5 100644 --- a/data/likeltd/likeltdbioschemas.jsonld +++ b/data/likeltd/likeltdbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "LikeLTD", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://sites.google.com/site/baldingstatisticalgenetics/", diff --git a/data/lilikoi/lilikoibioschemas.jsonld b/data/lilikoi/lilikoibioschemas.jsonld index 9744ad376d568..8897a08ed522a 100644 --- a/data/lilikoi/lilikoibioschemas.jsonld +++ b/data/lilikoi/lilikoibioschemas.jsonld @@ -18,27 +18,27 @@ { "@id": "https://doi.org/10.1093/gigascience/giy136" }, - "pmcid:PMC6290884", - "pubmed:30535020" + "pubmed:30535020", + "pmcid:PMC6290884" ], "sc:description": "R package for personalized pathway-based classification modeling using metabolomics data.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_0533" }, { - "@id": "edam:operation_3659" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_0533" + "@id": "edam:operation_3659" } ], "sc:license": "GPL-2.0", "sc:name": "Lilikoi", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/lilikoi/index.html" }, diff --git a/data/limani/limanibioschemas.jsonld b/data/limani/limanibioschemas.jsonld index accefaa09b2d1..645803054dd31 100644 --- a/data/limani/limanibioschemas.jsonld +++ b/data/limani/limanibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Online framework for the analysis of vascular networks in leaves.", "sc:name": "LIMANI", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "PSB", "sc:url": "http://limani.psb.ugent.be", diff --git a/data/limix/limixbioschemas.jsonld b/data/limix/limixbioschemas.jsonld index 246ed1565f430..547b3d8e7edf5 100644 --- a/data/limix/limixbioschemas.jsonld +++ b/data/limix/limixbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:description": "Flexible and efficient linear mixed model library with interfaces to Python.", "sc:name": "Limix", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/PMBio/limix" } \ No newline at end of file diff --git a/data/limma/limmabioschemas.jsonld b/data/limma/limmabioschemas.jsonld index e097f0fc288ea..53cca091a313c 100644 --- a/data/limma/limmabioschemas.jsonld +++ b/data/limma/limmabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-9221-2892", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/limma", "@type": "sc:SoftwareApplication", @@ -26,22 +22,22 @@ "@id": "edam:data_2884" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3053" + "@id": "edam:topic_3047" }, { - "@id": "edam:topic_3047" + "@id": "edam:topic_3053" } ], "sc:citation": [ + "pmcid:PMC4402510", { "@id": "https://doi.org/10.1093/nar/gkv007" }, - "pmcid:PMC4402510", "pubmed:25605792" ], "sc:description": "Data analysis, linear models and differential expression for microarray data.", @@ -51,13 +47,17 @@ "sc:license": "GPL-2.0", "sc:name": "limma", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/limma.html", "sc:version": "3.30.7" }, + { + "@id": "http://orcid.org/0000-0001-9221-2892", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/nar/gkv007", "@type": "sc:CreativeWork" diff --git a/data/limmagui/limmaguibioschemas.jsonld b/data/limmagui/limmaguibioschemas.jsonld index 186371fb055a6..14b3dfd7cd323 100644 --- a/data/limmagui/limmaguibioschemas.jsonld +++ b/data/limmagui/limmaguibioschemas.jsonld @@ -9,35 +9,35 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-9221-2892", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/limmagui", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Yifang Hu", + "Keith Satterley", { "@id": "http://orcid.org/0000-0001-9221-2892" - }, - "Keith Satterley", - "Yifang Hu" + } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:15297296", "sc:description": "A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package.", "sc:license": "GPL-2.0", "sc:name": "limmaGUI", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/limmaGUI.html", "sc:version": "1.50.0" + }, + { + "@id": "http://orcid.org/0000-0001-9221-2892", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/limmarp/limmarpbioschemas.jsonld b/data/limmarp/limmarpbioschemas.jsonld index 7bd8738852e66..5e54963e7b513 100644 --- a/data/limmarp/limmarpbioschemas.jsonld +++ b/data/limmarp/limmarpbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:description": "Shiny app to determine differentially regulated features in data with few replicates and presence of missing values.", "sc:name": "LimmaRP", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "bmb.sdu.dk", diff --git a/data/limtox/limtoxbioschemas.jsonld b/data/limtox/limtoxbioschemas.jsonld index a1cd4a8d0455c..1b10996e926c7 100644 --- a/data/limtox/limtoxbioschemas.jsonld +++ b/data/limtox/limtoxbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Text mining for toxicology.", "sc:name": "LimTox", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "cnio.es", "sc:url": "http://limtox.bioinfo.cnio.es/", diff --git a/data/linc/bioconda_linc.yaml b/data/linc/bioconda_linc.yaml index 0becd678c150e..0d4950249f2f6 100644 --- a/data/linc/bioconda_linc.yaml +++ b/data/linc/bioconda_linc.yaml @@ -6,7 +6,6 @@ description: This package provides methods to compute co-expression networks of home: https://bioconductor.org/packages/3.10/bioc/html/LINC.html identifiers: - biotools:linc -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-linc summary: co-expression of lincRNAs and protein-coding genes diff --git a/data/linclust/linclustbioschemas.jsonld b/data/linclust/linclustbioschemas.jsonld index 97807e25c7467..6ff10d62d9f8f 100644 --- a/data/linclust/linclustbioschemas.jsonld +++ b/data/linclust/linclustbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Linclust", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://mmseqs.com" diff --git a/data/lincrna_predict/lincrna_predictbioschemas.jsonld b/data/lincrna_predict/lincrna_predictbioschemas.jsonld index 1b269332bd9d9..8e83648c12516 100644 --- a/data/lincrna_predict/lincrna_predictbioschemas.jsonld +++ b/data/lincrna_predict/lincrna_predictbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Deep learning method for lincRNA detection using auto-encoder algorithm.", "sc:name": "lincRNA predict", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/ningyu12/lincRNA_predict/" } \ No newline at end of file diff --git a/data/lincs_canvas_browser/lincs_canvas_browserbioschemas.jsonld b/data/lincs_canvas_browser/lincs_canvas_browserbioschemas.jsonld index b450bcac00052..aaf38916cb783 100644 --- a/data/lincs_canvas_browser/lincs_canvas_browserbioschemas.jsonld +++ b/data/lincs_canvas_browser/lincs_canvas_browserbioschemas.jsonld @@ -20,34 +20,34 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:24906883", - "pmcid:PMC4086130", { "@id": "https://doi.org/10.1093/nar/gku476" - } + }, + "pmcid:PMC4086130" ], "sc:description": "Interactive web server to query, browse and interrogate LINCS L1000 gene expression signatures.", "sc:featureList": [ { - "@id": "edam:operation_3223" + "@id": "edam:operation_0314" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_2436" + "@id": "edam:operation_3223" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_0314" + "@id": "edam:operation_2436" } ], "sc:name": "LINCS Canvas Browser (LCB)", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.maayanlab.net/LINCS/LCB" } diff --git a/data/lincsnp/lincsnpbioschemas.jsonld b/data/lincsnp/lincsnpbioschemas.jsonld index 61ddad3f9edad..3859260c74e49 100644 --- a/data/lincsnp/lincsnpbioschemas.jsonld +++ b/data/lincsnp/lincsnpbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-15-152", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/lincsnp", "@type": "sc:SoftwareApplication", @@ -27,15 +31,11 @@ }, "sc:name": "LincSNP", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://210.46.80.146/lincsnp/" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-15-152", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/lindna/lindnabioschemas.jsonld b/data/lindna/lindnabioschemas.jsonld index 79f669f2fce3f..927b7c390c8aa 100644 --- a/data/lindna/lindnabioschemas.jsonld +++ b/data/lindna/lindnabioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", - "UK BBSRC", "Wellcome Trust", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:description": "Draw linear maps of DNA constructs.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", + "UK BBSRC", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "lindna", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/lindna.html", "sc:version": "r6" diff --git a/data/lineagepulse/lineagepulsebioschemas.jsonld b/data/lineagepulse/lineagepulsebioschemas.jsonld index 93f186257f2a1..cafa67932d227 100644 --- a/data/lineagepulse/lineagepulsebioschemas.jsonld +++ b/data/lineagepulse/lineagepulsebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "LineagePulse", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LineagePulse.html", "sc:version": "1.0.0" diff --git a/data/linkage/linkagebioschemas.jsonld b/data/linkage/linkagebioschemas.jsonld index e201528546169..9a419baffe618 100644 --- a/data/linkage/linkagebioschemas.jsonld +++ b/data/linkage/linkagebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:6587361", - "pmcid:PMC345524" + "pmcid:PMC345524", + "pubmed:6587361" ], "sc:description": "The core of this package is a series of programs for maximum likelihood estimation of recombination rates, calculation of lod score tables, and analysis of genetic risks. The analysis programs are divided into two groups. The first group can be used for general pedigrees with marker and disease loci. Programs in the second group are for three- generation families and codominant marker loci, and are primarily intended for the construction of genetic maps from data on reference families.", "sc:license": "Not licensed", "sc:name": "LINKAGE", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.jurgott.org/linkage/LinkagePC.html" } \ No newline at end of file diff --git a/data/linkcomm/linkcommbioschemas.jsonld b/data/linkcomm/linkcommbioschemas.jsonld index d6b23cfb5f9c8..b6357f6b4f0fc 100644 --- a/data/linkcomm/linkcommbioschemas.jsonld +++ b/data/linkcomm/linkcommbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "linkcomm", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/linkcomm/index.html" } \ No newline at end of file diff --git a/data/linked_registries/linked_registriesbioschemas.jsonld b/data/linked_registries/linked_registriesbioschemas.jsonld index abe4aacc9905d..2432acb452e25 100644 --- a/data/linked_registries/linked_registriesbioschemas.jsonld +++ b/data/linked_registries/linked_registriesbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1155/2017/8327980", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Linked_Registries", "@type": "sc:SoftwareApplication", @@ -17,16 +21,16 @@ { "@id": "https://doi.org/10.1155/2017/8327980" }, - "pubmed:29214177", - "pmcid:PMC5682045" + "pmcid:PMC5682045", + "pubmed:29214177" ], "sc:description": "Connects rare diseases patient registries through a Semantic Web Layer.", "sc:featureList": [ { - "@id": "edam:operation_2422" + "@id": "edam:operation_3283" }, { - "@id": "edam:operation_3283" + "@id": "edam:operation_2422" } ], "sc:name": "Linked Registries", @@ -36,10 +40,6 @@ "Mac" ], "sc:url": "http://bioinformatics.ua.pt/linked-registries-app/#" - }, - { - "@id": "https://doi.org/10.1155/2017/8327980", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/linkedomics/linkedomicsbioschemas.jsonld b/data/linkedomics/linkedomicsbioschemas.jsonld index 927f340f496e6..6b77c15664bdf 100644 --- a/data/linkedomics/linkedomicsbioschemas.jsonld +++ b/data/linkedomics/linkedomicsbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Xiaohua Chen", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31124967", { "@id": "https://doi.org/10.1097/MD.0000000000015774" }, - "pmcid:PMC6571408", - "pubmed:31124967" + "pmcid:PMC6571408" ], "sc:description": "Publicly available portal that includes multi-omics data from all 32 TCGA Cancer types. It also includes mass spectrometry-based proteomics data generated by the Clinical Proteomics Tumor Analysis Consortium (CPTAC) for TCGA breast, colorectal and ovarian tumors.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "Unlicense", "sc:name": "LinkeDomics", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.linkedomics.org" }, diff --git a/data/linnorm/linnormbioschemas.jsonld b/data/linnorm/linnormbioschemas.jsonld index c6a13f349a2e0..b9ebfe417c468 100644 --- a/data/linnorm/linnormbioschemas.jsonld +++ b/data/linnorm/linnormbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ken Shun Hang Yip", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large-scale count data. It transforms such datasets for parametric tests. Also the following pipelines are implemented: 1. Cell subpopluation analysis and visualization using PCA clustering, 2. Differential expression analysis or differential peak detection using limma, 3. Highly variable gene discovery and visualization, 4. Gene correlation network analysis and visualization. 5. Hierarchical clustering and plotting.", "sc:license": "MIT", "sc:name": "Linnorm", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Linnorm.html", "sc:version": "1.2.0" diff --git a/data/lion-web/lion-webbioschemas.jsonld b/data/lion-web/lion-webbioschemas.jsonld index d005693333820..72f62e817e7f4 100644 --- a/data/lion-web/lion-webbioschemas.jsonld +++ b/data/lion-web/lion-webbioschemas.jsonld @@ -21,11 +21,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31141612", { "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ061" }, - "pmcid:PMC6541037", - "pubmed:31141612" + "pmcid:PMC6541037" ], "sc:description": "Web-based ontology enrichment tool for lipidomic data analysis.", "sc:featureList": [ @@ -42,9 +42,9 @@ "sc:license": "GPL-3.0", "sc:name": "LION-web", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.lipidontology.com/" }, diff --git a/data/lipid_maps/lipid_mapsbioschemas.jsonld b/data/lipid_maps/lipid_mapsbioschemas.jsonld index 0a955d9ada6bb..c72762a74f506 100644 --- a/data/lipid_maps/lipid_mapsbioschemas.jsonld +++ b/data/lipid_maps/lipid_mapsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.", "sc:name": "LIPID MAPS", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.lipidmaps.org/tools/index.html" } \ No newline at end of file diff --git a/data/lipid_mini-on/lipid_mini-onbioschemas.jsonld b/data/lipid_mini-on/lipid_mini-onbioschemas.jsonld index 0b84684ab7401..af817da86adf7 100644 --- a/data/lipid_mini-on/lipid_mini-onbioschemas.jsonld +++ b/data/lipid_mini-on/lipid_mini-onbioschemas.jsonld @@ -15,15 +15,15 @@ "Geremy Clair" ], "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:description": "Lipid Mining and Ontology (Lipid Mini-On) - mining and ontology tool for enrichment analysis of lipidomic data.", "sc:license": "BSD-2-Clause", "sc:name": "Lipid Mini-On", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://omicstools.pnnl.gov/shiny/lipid-mini-on/" diff --git a/data/lipidex/lipidexbioschemas.jsonld b/data/lipidex/lipidexbioschemas.jsonld index 2684178173399..a0565871d3bd0 100644 --- a/data/lipidex/lipidexbioschemas.jsonld +++ b/data/lipidex/lipidexbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/lipidex", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Workbench", - "Desktop application" + "Desktop application", + "Workbench" ], "sc:description": "A tool for high-confidence LC-MS/MS (Liquid Chromatography-Mass Spectrometry) lipid identification.", "sc:license": "MIT", "sc:name": "LipiDex", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/coongroup/LipiDex" } \ No newline at end of file diff --git a/data/lipidmatch_normalizer/lipidmatch_normalizerbioschemas.jsonld b/data/lipidmatch_normalizer/lipidmatch_normalizerbioschemas.jsonld index 25958d49635d0..4a40d72aab972 100644 --- a/data/lipidmatch_normalizer/lipidmatch_normalizerbioschemas.jsonld +++ b/data/lipidmatch_normalizer/lipidmatch_normalizerbioschemas.jsonld @@ -13,16 +13,16 @@ "@id": "https://bio.tools/LipidMatch_Normalizer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jeremy Koelmel", - "Jason Cochran" + "Jason Cochran", + "Jeremy Koelmel" ], "sc:additionalType": "Script", "sc:citation": [ - "pubmed:31035918", - "pmcid:PMC6489209", { "@id": "https://doi.org/10.1186/s12859-019-2803-8" - } + }, + "pubmed:31035918", + "pmcid:PMC6489209" ], "sc:description": "Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values.", "sc:featureList": [ @@ -39,9 +39,9 @@ "sc:license": "GPL-3.0", "sc:name": "LipidMatch Normalizer", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://secim.ufl.edu/secim-tools/lipidmatch-normalizer/", "sc:version": "1.0.2" diff --git a/data/lipidwrapper/lipidwrapperbioschemas.jsonld b/data/lipidwrapper/lipidwrapperbioschemas.jsonld index 4b5451a6f2544..0531b2e82c805 100644 --- a/data/lipidwrapper/lipidwrapperbioschemas.jsonld +++ b/data/lipidwrapper/lipidwrapperbioschemas.jsonld @@ -22,19 +22,19 @@ "Library" ], "sc:citation": [ + "pubmed:25032790", + "pmcid:PMC4102414", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1003720" - }, - "pmcid:PMC4102414", - "pubmed:25032790" + } ], "sc:description": "An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry.", "sc:featureList": [ { - "@id": "edam:operation_0477" + "@id": "edam:operation_0270" }, { - "@id": "edam:operation_0270" + "@id": "edam:operation_0477" } ], "sc:name": "LipidWrapper", diff --git a/data/lipidxplorer/lipidxplorerbioschemas.jsonld b/data/lipidxplorer/lipidxplorerbioschemas.jsonld index bc44795319767..11f49a4309a65 100644 --- a/data/lipidxplorer/lipidxplorerbioschemas.jsonld +++ b/data/lipidxplorer/lipidxplorerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "LipidXplorer is a software that supports the quantitative characterization of complex lipidomes by interpreting large datasets of shotgun mass spectra.", "sc:name": "LipidXplorer", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "BioInfra.Prot", diff --git a/data/liplike/liplikebioschemas.jsonld b/data/liplike/liplikebioschemas.jsonld index eae8df1d93d89..f65b609f765b1 100644 --- a/data/liplike/liplikebioschemas.jsonld +++ b/data/liplike/liplikebioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/LiPLike", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rasmus Magnusson", - "Mika Gustafsson" + "Mika Gustafsson", + "Rasmus Magnusson" ], "sc:additionalType": "Library", "sc:description": "Towards gene regulatory network predictions of high-certainty | Abstract Motivation Reverse engineering of gene regulatory networks has for years struggled with high correlation in expression between regulatory elements. If two regulators have matching expression patterns it is impossible to differentiate between the two, and thus false positive identifications are abundant. Results To allow for gene regulation predictions of high confidence, we propose a novel method, LiPLike, that assumes a regression model and iteratively searches for interactions that cannot be replaced by a linear combination of other predictors. To compare the performance of LiPLike with other available inference methods, we benchmarked LiPLike using three independent datasets from the previous DREAM5 challenge", "sc:license": "AGPL-3.0", "sc:name": "LiPLike", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://gitlab.com/Gustafsson-lab/liplike" } \ No newline at end of file diff --git a/data/lipo/lipobioschemas.jsonld b/data/lipo/lipobioschemas.jsonld index 046ed64785cdc..cb9c8456887c0 100644 --- a/data/lipo/lipobioschemas.jsonld +++ b/data/lipo/lipobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool can analyse polypeptide sequences encoded within the genome of Gram-negative bacteria and report the sequences with a possible lipo-box. The lipo-box is recognised on the basis of given the critera.", "sc:name": "LIPO", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://services.cbu.uib.no/tools/lipo" } \ No newline at end of file diff --git a/data/liquid/liquidbioschemas.jsonld b/data/liquid/liquidbioschemas.jsonld index c941b8900706a..6ab97bf498a52 100644 --- a/data/liquid/liquidbioschemas.jsonld +++ b/data/liquid/liquidbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Pymol Plugin for Fuzzy Pharmacophore Models", "sc:name": "LIQUID", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://gecco.org.chemie.uni-frankfurt.de/liquid/index.html" diff --git a/data/liquidassociation/bioconda_liquidassociation.yaml b/data/liquidassociation/bioconda_liquidassociation.yaml index 280a5f664bdf6..9e480a9a72694 100644 --- a/data/liquidassociation/bioconda_liquidassociation.yaml +++ b/data/liquidassociation/bioconda_liquidassociation.yaml @@ -5,7 +5,6 @@ description: The package contains functions for calculate direct and model-based home: https://bioconductor.org/packages/3.10/bioc/html/LiquidAssociation.html identifiers: - biotools:liquidassociation -- doi:10.1038/nmeth.3252 license: GPL (>=3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-liquidassociation diff --git a/data/liquidassociation/liquidassociationbioschemas.jsonld b/data/liquidassociation/liquidassociationbioschemas.jsonld index 7ab3337ec37fb..219454a57d002 100644 --- a/data/liquidassociation/liquidassociationbioschemas.jsonld +++ b/data/liquidassociation/liquidassociationbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "LiquidAssociation", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LiquidAssociation.html", diff --git a/data/lise/lisebioschemas.jsonld b/data/lise/lisebioschemas.jsonld index a207658f0f129..2a166ced5c7a5 100644 --- a/data/lise/lisebioschemas.jsonld +++ b/data/lise/lisebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "LISE is a web server for a novel method of predicting small molecule binding sites on proteins.", "sc:name": "LISE", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://lise.ibms.sinica.edu.tw" diff --git a/data/listannotation/listannotationbioschemas.jsonld b/data/listannotation/listannotationbioschemas.jsonld index d0f8e27bc129f..bdaae304274f9 100644 --- a/data/listannotation/listannotationbioschemas.jsonld +++ b/data/listannotation/listannotationbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "listannotation", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/listor/listorbioschemas.jsonld b/data/listor/listorbioschemas.jsonld index 0cbfcf4b96164..8d9099be8658f 100644 --- a/data/listor/listorbioschemas.jsonld +++ b/data/listor/listorbioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", + "UK MRC", "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK BBSRC" ], "sc:description": "Write a list file of the logical OR of two sets of sequences.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "listor", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/listor.html", "sc:version": "r6" diff --git a/data/litinspector/litinspectorbioschemas.jsonld b/data/litinspector/litinspectorbioschemas.jsonld index 7ebefcdbe7652..64dfc11e6e792 100644 --- a/data/litinspector/litinspectorbioschemas.jsonld +++ b/data/litinspector/litinspectorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "LitInspector", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.litinspector.org/" } \ No newline at end of file diff --git a/data/litpathexplorer/litpathexplorerbioschemas.jsonld b/data/litpathexplorer/litpathexplorerbioschemas.jsonld index c7c0f09bffcbd..2a13ccdbbda75 100644 --- a/data/litpathexplorer/litpathexplorerbioschemas.jsonld +++ b/data/litpathexplorer/litpathexplorerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Confidence-based visual text analytics tool for exploring literature-enriched pathway models.", "sc:name": "LitPathExplorer", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://nactem.ac.uk/LitPathExplorer_BI/" diff --git a/data/livebench/livebenchbioschemas.jsonld b/data/livebench/livebenchbioschemas.jsonld index 851bc470033e9..083706fbd0afc 100644 --- a/data/livebench/livebenchbioschemas.jsonld +++ b/data/livebench/livebenchbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "LiveBench", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://meta.bioinfo.pl/livebench.pl" } \ No newline at end of file diff --git a/data/lmap/lmapbioschemas.jsonld b/data/lmap/lmapbioschemas.jsonld index cf17ddad61cf8..4e232dc71d99c 100644 --- a/data/lmap/lmapbioschemas.jsonld +++ b/data/lmap/lmapbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:27597435", + "pmcid:PMC5011788", { "@id": "https://doi.org/10.1186/S12859-016-1204-5" - }, - "pmcid:PMC5011788" + } ], "sc:description": "Lightweight Multigene Analyses in PAML.", "sc:featureList": { diff --git a/data/lmdme/lmdmebioschemas.jsonld b/data/lmdme/lmdmebioschemas.jsonld index fc2d106218f1f..e1a762ef906f6 100644 --- a/data/lmdme/lmdmebioschemas.jsonld +++ b/data/lmdme/lmdmebioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6537-3575", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/lmdme", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Cristobal Fresno", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:20800686", "sc:contributor": { @@ -25,16 +29,12 @@ "sc:license": "GPL-2.0", "sc:name": "lmdme", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/lmdme.html", "sc:version": "1.16.0" - }, - { - "@id": "http://orcid.org/0000-0002-6537-3575", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/lme4/lme4bioschemas.jsonld b/data/lme4/lme4bioschemas.jsonld index eb52fb90e2957..1a4f93aa3e444 100644 --- a/data/lme4/lme4bioschemas.jsonld +++ b/data/lme4/lme4bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "lme4", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/lme4/index.html" } \ No newline at end of file diff --git a/data/lme4qtl/lme4qtlbioschemas.jsonld b/data/lme4qtl/lme4qtlbioschemas.jsonld index ab87e04dc3c1c..a07d4aaedd644 100644 --- a/data/lme4qtl/lme4qtlbioschemas.jsonld +++ b/data/lme4qtl/lme4qtlbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-018-2057-x", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/lme4qtl", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:29486711", { "@id": "https://doi.org/10.1186/s12859-018-2057-x" }, + "pubmed:29486711", "pmcid:PMC5830078" ], "sc:description": "Linear mixed models with flexible covariance structure for genetic studies of related individuals.", @@ -33,10 +37,6 @@ "Windows" ], "sc:url": "https://github.com/variani/lme4qtl" - }, - { - "@id": "https://doi.org/10.1186/s12859-018-2057-x", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/lmgene/bioconda_lmgene.yaml b/data/lmgene/bioconda_lmgene.yaml index d2abbca742baa..576dd416af95e 100644 --- a/data/lmgene/bioconda_lmgene.yaml +++ b/data/lmgene/bioconda_lmgene.yaml @@ -4,7 +4,6 @@ description: LMGene package for analysis of microarray data using a linear model home: https://bioconductor.org/packages/3.10/bioc/html/LMGene.html identifiers: - biotools:lmgene -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-lmgene diff --git a/data/lmgene/lmgenebioschemas.jsonld b/data/lmgene/lmgenebioschemas.jsonld index 8a2e4cd40b0d3..09979f72b4f9b 100644 --- a/data/lmgene/lmgenebioschemas.jsonld +++ b/data/lmgene/lmgenebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Blythe Durbin-Johnson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A package for analysis of microarray data using a linear model and glog data transformation.", "sc:license": "GPL-3.0", "sc:name": "LMGene", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LMGene.html", "sc:version": "2.30.0" diff --git a/data/lmm-lasso/lmm-lassobioschemas.jsonld b/data/lmm-lasso/lmm-lassobioschemas.jsonld index e3428955a71f2..bd0d2a63dfd85 100644 --- a/data/lmm-lasso/lmm-lassobioschemas.jsonld +++ b/data/lmm-lasso/lmm-lassobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "LMM-Lasso is a linear mixed models that allows for both multi-locus mapping and correction for confounding effects.", "sc:name": "LMM-Lasso", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bsse.ethz.ch/mlcb/research/bioinformatics-and-computational-biology/lmm-lasso.html" } \ No newline at end of file diff --git a/data/lmm2met/lmm2metbioschemas.jsonld b/data/lmm2met/lmm2metbioschemas.jsonld index d38f05cb6354e..c692266de7d3a 100644 --- a/data/lmm2met/lmm2metbioschemas.jsonld +++ b/data/lmm2met/lmm2metbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1016/J.CSBJ.2019.04.009", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/lmm2met", "@type": "sc:SoftwareApplication", @@ -24,24 +28,20 @@ "sc:description": "Linear mixed-effects modeling to improve clinical metabolomics information.", "sc:featureList": [ { - "@id": "edam:operation_3803" + "@id": "edam:operation_3891" }, { - "@id": "edam:operation_3891" + "@id": "edam:operation_3803" } ], "sc:license": "MIT", "sc:name": "lmm2met", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/kwanjeeraw/lmm2met" - }, - { - "@id": "https://doi.org/10.1016/J.CSBJ.2019.04.009", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/lnatools/lnatoolsbioschemas.jsonld b/data/lnatools/lnatoolsbioschemas.jsonld index 39ea55c5a7541..a72d86073c58c 100644 --- a/data/lnatools/lnatoolsbioschemas.jsonld +++ b/data/lnatools/lnatoolsbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/lnatools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Support in other countries", - "Support in the US" + "Support in the US", + "Support in other countries" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:12824412", "sc:description": "Collection of tools for the design of LNA (locked nucleic acid) substituted oligonucleotides including: melting temperature (Tm) analysis, secondary structure prediction, and probe design for expression arrays, real time PCR, and SNP genotyping.", "sc:name": "LNAtools", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.exiqon.com/oligo-tools" } \ No newline at end of file diff --git a/data/lncident/lncidentbioschemas.jsonld b/data/lncident/lncidentbioschemas.jsonld index ce0b19a269c52..cf883d6448ff6 100644 --- a/data/lncident/lncidentbioschemas.jsonld +++ b/data/lncident/lncidentbioschemas.jsonld @@ -32,8 +32,8 @@ "sc:license": "GPL-3.0", "sc:name": "Lncident", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://csbl.bmb.uga.edu/mirrors/JLU/Lncident/index.php" diff --git a/data/lncipedia/lncipediabioschemas.jsonld b/data/lncipedia/lncipediabioschemas.jsonld index 38494d7feb4da..ea5a12b4cfcd1 100644 --- a/data/lncipedia/lncipediabioschemas.jsonld +++ b/data/lncipedia/lncipediabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "LNCipedia", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://www.lncipedia.org/" diff --git a/data/lncrnadb/lncrnadbbioschemas.jsonld b/data/lncrnadb/lncrnadbbioschemas.jsonld index be4a1cf06987e..0995adbfd24a4 100644 --- a/data/lncrnadb/lncrnadbbioschemas.jsonld +++ b/data/lncrnadb/lncrnadbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database containing a comprehensive list of long noncoding RNAs (lncRNAs) that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information.", "sc:name": "lncRNAdb", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.lncrnadb.org/" } \ No newline at end of file diff --git a/data/lncrnator/lncrnatorbioschemas.jsonld b/data/lncrnator/lncrnatorbioschemas.jsonld index b85a80c1d1796..3fa15dfc75d79 100644 --- a/data/lncrnator/lncrnatorbioschemas.jsonld +++ b/data/lncrnator/lncrnatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool aims to be the lncRNA (long non-coding RNA) portal encompassing expression profile, interacting (binding) protein, integrated sequence curation, evolutionary scores, and coding potential. Data sets were collected from TCGA, GEO, ENCODE, and modENCODE (Organism: Human, Mouse, Fly, Worm, and Yeast).", "sc:name": "lncRNAtor", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://lncrnator.ewha.ac.kr/" } \ No newline at end of file diff --git a/data/lnctar/lnctarbioschemas.jsonld b/data/lnctar/lnctarbioschemas.jsonld index d55f13f48d35c..54d49b1a23fc7 100644 --- a/data/lnctar/lnctarbioschemas.jsonld +++ b/data/lnctar/lnctarbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr. Qinghua Cui", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:25524864", "sc:description": "Efficient tool for predicting RNA targets of lncRNAs (Long noncoding RNAs)", diff --git a/data/lncvar/lncvarbioschemas.jsonld b/data/lncvar/lncvarbioschemas.jsonld index 36d6da02643fe..b3b9b04d31985 100644 --- a/data/lncvar/lncvarbioschemas.jsonld +++ b/data/lncvar/lncvarbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Database of genetic variations associated with long noncoding genes.", "sc:name": "LncVar", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioinfo.ibp.ac.cn/LncVar" diff --git a/data/lnetwork/lnetworkbioschemas.jsonld b/data/lnetwork/lnetworkbioschemas.jsonld index 5f442cca43417..6b4c4822781c7 100644 --- a/data/lnetwork/lnetworkbioschemas.jsonld +++ b/data/lnetwork/lnetworkbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Efficient and effective method for constructing phylogenetic networks. It takes as input a set of rooted phylogenetic trees given in Newick format (inputfile shows an example of input data).", "sc:name": "LNETWORK", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://nclab.hit.edu.cn/~wangjuan/LNETWORK/" } \ No newline at end of file diff --git a/data/lnsignal/lnsignalbioschemas.jsonld b/data/lnsignal/lnsignalbioschemas.jsonld index 7d27ea6c2e0b9..120b2def7a07e 100644 --- a/data/lnsignal/lnsignalbioschemas.jsonld +++ b/data/lnsignal/lnsignalbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "The web server LnSignal (Labelling N-terminal Signal petide cleavage site) was developed by integrating position-specific amino acid propensities based on the highest average positions and conditional random fields.", "sc:name": "LnSignal", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/LnSignal/" diff --git a/data/load_multifastq/load_multifastqbioschemas.jsonld b/data/load_multifastq/load_multifastqbioschemas.jsonld index a48105185bef4..a5481197249e5 100644 --- a/data/load_multifastq/load_multifastqbioschemas.jsonld +++ b/data/load_multifastq/load_multifastqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "load_multifastq", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/lobo/lobobioschemas.jsonld b/data/lobo/lobobioschemas.jsonld index 9797cf2e7a9a3..997fe480b5c9b 100644 --- a/data/lobo/lobobioschemas.jsonld +++ b/data/lobo/lobobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Loop modelling server for protein structures.", "sc:name": "LOBO", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/lobo/", diff --git a/data/lobstahs/lobstahsbioschemas.jsonld b/data/lobstahs/lobstahsbioschemas.jsonld index 4275627af8053..0e5b45dfe3724 100644 --- a/data/lobstahs/lobstahsbioschemas.jsonld +++ b/data/lobstahs/lobstahsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-5705-9682", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/lobstahs", "@type": "sc:SoftwareApplication", @@ -24,16 +28,12 @@ "sc:license": "GPL-3.0", "sc:name": "LOBSTAHS", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LOBSTAHS.html", "sc:version": "1.0.0" - }, - { - "@id": "http://orcid.org/0000-0002-5705-9682", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/lobstr/lobstrbioschemas.jsonld b/data/lobstr/lobstrbioschemas.jsonld index 7e5f1178743f6..3f5fa76013229 100644 --- a/data/lobstr/lobstrbioschemas.jsonld +++ b/data/lobstr/lobstrbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/lobstr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Melissa Gymrek", - "lobSTR user group mailing list" + "lobSTR user group mailing list", + "Melissa Gymrek" ], "sc:additionalType": "Workflow", "sc:citation": "pubmed:22522390", diff --git a/data/localcider/localciderbioschemas.jsonld b/data/localcider/localciderbioschemas.jsonld index 509f6ca0763f5..057078dc0608c 100644 --- a/data/localcider/localciderbioschemas.jsonld +++ b/data/localcider/localciderbioschemas.jsonld @@ -10,22 +10,22 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1016/j.bpj.2016.11.3200", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0002-4155-5729", + "@type": "schema:Person" }, { "@id": "https://bio.tools/localcider", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Rohit V. Pappu", { "@id": "http://orcid.org/0000-0002-4155-5729" - }, - "Rohit V. Pappu" + } ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5232785", "pubmed:28076807", + "pmcid:PMC5232785", { "@id": "https://doi.org/10.1016/j.bpj.2016.11.3200" } @@ -37,15 +37,15 @@ "sc:license": "GPL-2.0", "sc:name": "localCIDER", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/Pappulab/localCIDER" }, { - "@id": "http://orcid.org/0000-0002-4155-5729", - "@type": "schema:Person" + "@id": "https://doi.org/10.1016/j.bpj.2016.11.3200", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/localizome/localizomebioschemas.jsonld b/data/localizome/localizomebioschemas.jsonld index 0731e5d1e3e52..34eedee032cb3 100644 --- a/data/localizome/localizomebioschemas.jsonld +++ b/data/localizome/localizomebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.", "sc:name": "Localizome", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/katur/localizome" diff --git a/data/localmove/localmovebioschemas.jsonld b/data/localmove/localmovebioschemas.jsonld index be3ce0a2ba01c..4b8be23abf0bc 100644 --- a/data/localmove/localmovebioschemas.jsonld +++ b/data/localmove/localmovebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "LocalMove", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinformatics.bc.edu/clotelab/localmove/" } \ No newline at end of file diff --git a/data/locarna-p/locarna-pbioschemas.jsonld b/data/locarna-p/locarna-pbioschemas.jsonld index 342017e6a4415..8d6fe0e200fb6 100644 --- a/data/locarna-p/locarna-pbioschemas.jsonld +++ b/data/locarna-p/locarna-pbioschemas.jsonld @@ -9,36 +9,44 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-8231-3323", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1261/rna.029041.111", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/locarna-p", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Sebastian Will", { "@id": "http://orcid.org/0000-0001-8231-3323" - }, - "Sebastian Will" + } ], "edam:has_input": { "@id": "edam:data_3495" }, "edam:has_output": [ { - "@id": "edam:data_1465" + "@id": "edam:data_1916" }, { - "@id": "edam:data_0872" + "@id": "edam:data_1465" }, { - "@id": "edam:data_1916" + "@id": "edam:data_0872" } ], "sc:additionalType": "Command-line tool", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0080" + "@id": "edam:topic_0097" }, { - "@id": "edam:topic_0097" + "@id": "edam:topic_0080" } ], "sc:author": [ @@ -48,11 +56,11 @@ } ], "sc:citation": [ - "pubmed:22450757", { "@id": "https://doi.org/10.1261/rna.029041.111" }, - "pmcid:PMC3334699" + "pmcid:PMC3334699", + "pubmed:22450757" ], "sc:description": "Probabilistic structure-based multiple alignment of RNAs.", "sc:featureList": { @@ -65,22 +73,14 @@ "Linux" ], "sc:provider": [ - "rnateam", - "University Freiburg" + "University Freiburg", + "rnateam" ], "sc:softwareHelp": { "@id": "http://www.bioinf.uni-freiburg.de/Software/LocARNA/" }, "sc:url": "http://www.bioinf.uni-freiburg.de/Software/LocARNA/", "sc:version": "1.8.9" - }, - { - "@id": "https://doi.org/10.1261/rna.029041.111", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-8231-3323", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/locarna/locarnabioschemas.jsonld b/data/locarna/locarnabioschemas.jsonld index 678897dcceec4..388932d73c4f2 100644 --- a/data/locarna/locarnabioschemas.jsonld +++ b/data/locarna/locarnabioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pcbi.0030065", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/locarna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sebastian Will", { "@id": "http://orcid.org/0000-0001-8231-3323" - } + }, + "Sebastian Will" ], "edam:has_input": { "@id": "edam:data_3495" @@ -47,11 +43,11 @@ } ], "sc:citation": [ + "pmcid:PMC1851984", + "pubmed:17432929", { "@id": "https://doi.org/10.1371/journal.pcbi.0030065" - }, - "pmcid:PMC1851984", - "pubmed:17432929" + } ], "sc:description": "Structure-based multiple alignment of RNAs.", "sc:featureList": { @@ -74,6 +70,10 @@ { "@id": "http://orcid.org/0000-0001-8231-3323", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1371/journal.pcbi.0030065", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/locate/locatebioschemas.jsonld b/data/locate/locatebioschemas.jsonld index 7c89df6225add..c3fd9a43b9723 100644 --- a/data/locate/locatebioschemas.jsonld +++ b/data/locate/locatebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of mouse proteins.", "sc:name": "LOCATE", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://locate.imb.uq.edu.au/" } \ No newline at end of file diff --git a/data/locdb/locdbbioschemas.jsonld b/data/locdb/locdbbioschemas.jsonld index abe324c6e9d72..9743671c5931b 100644 --- a/data/locdb/locdbbioschemas.jsonld +++ b/data/locdb/locdbbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/locdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Burkhard Rost", - "Shruti Rastogi" + "Shruti Rastogi", + "Burkhard Rost" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:21071420", diff --git a/data/lochap/lochapbioschemas.jsonld b/data/lochap/lochapbioschemas.jsonld index b8a2ee4bcfe60..f0c87aee1ced0 100644 --- a/data/lochap/lochapbioschemas.jsonld +++ b/data/lochap/lochapbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "LocHap is an ultra-fast computational pipeline for calling local haplotype variant using deep DNA-sequencing data to reveal cellular heterogeneity and somatic mosaicism.", "sc:name": "LocHap", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://compgenome.org/lochap/", "sc:version": "1.0" diff --git a/data/loci2path/loci2pathbioschemas.jsonld b/data/loci2path/loci2pathbioschemas.jsonld index e971927f4bb7e..c5b600332972d 100644 --- a/data/loci2path/loci2pathbioschemas.jsonld +++ b/data/loci2path/loci2pathbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "loci2path", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/loci2path.html", "sc:version": "1.0.0" diff --git a/data/locnes/locnesbioschemas.jsonld b/data/locnes/locnesbioschemas.jsonld index 266a319e54370..698def441bb23 100644 --- a/data/locnes/locnesbioschemas.jsonld +++ b/data/locnes/locnesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Support Vector Machine (SVM) predictor that locates classical nuclear export signals (NESs) in CRM1 cargoes. Export-Karyopherinβ CRM1 recognizes hundreds of broadly functioning proteins. Most CRM1 cargoes contain the classical NES (also known as leucine-rich NESs), a peptide with 8-15 amino acids, regularly spaced with conserved hydrophobic residues.", "sc:name": "LocNES", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://prodata.swmed.edu/LocNES/LocNES.php" } \ No newline at end of file diff --git a/data/locp/locpbioschemas.jsonld b/data/locp/locpbioschemas.jsonld index 8e1509044c350..1f23e25391309 100644 --- a/data/locp/locpbioschemas.jsonld +++ b/data/locp/locpbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-4714-9481", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/locp", "@type": "sc:SoftwareApplication", @@ -21,10 +25,6 @@ "sc:name": "LOCP", "sc:operatingSystem": "Linux", "sc:url": "http://ekhidna.biocenter.helsinki.fi/locp/" - }, - { - "@id": "http://orcid.org/0000-0002-4714-9481", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/loctree3/loctree3bioschemas.jsonld b/data/loctree3/loctree3bioschemas.jsonld index df81f60324529..7acc04acd8ff8 100644 --- a/data/loctree3/loctree3bioschemas.jsonld +++ b/data/loctree3/loctree3bioschemas.jsonld @@ -15,15 +15,15 @@ "Web application" ], "sc:author": [ - "Tatyana Goldberg", + "Guy Yachdav", "Maximilian Hecht", - "Timothy Karl", "Tobias Hamp", - "Guy Yachdav" + "Tatyana Goldberg", + "Timothy Karl" ], "sc:contributor": [ - "Henrik Nielsen", "Burkhard Rost", + "Henrik Nielsen", "Alexander von Humboldt Foundation through German Federal Ministry for Education and Research", "Ernst Ludwig Ehrlich Studienwerk" ], @@ -36,8 +36,8 @@ "sc:name": "LocTree3", "sc:operatingSystem": "Linux", "sc:provider": [ - "Technische Universität München", - "RostLab" + "RostLab", + "Technische Universität München" ], "sc:url": "https://rostlab.org/services/loctree3/", "sc:version": "1.0.8" diff --git a/data/locus/locusbioschemas.jsonld b/data/locus/locusbioschemas.jsonld index 036dfb5283f00..129ca788e09ea 100644 --- a/data/locus/locusbioschemas.jsonld +++ b/data/locus/locusbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "LOCUS (Length Optimized Characterization of Unknown Spliceforms) is a dynamic-programming algorithm for finding the optimal set of splice sites in a genomic region of interest with estimated prior length information.", "sc:name": "LOCUS", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://stormo.wustl.edu/resources.html" } \ No newline at end of file diff --git a/data/locusexplorer/locusexplorerbioschemas.jsonld b/data/locusexplorer/locusexplorerbioschemas.jsonld index 46d741b4ddbb8..e65340929632d 100644 --- a/data/locusexplorer/locusexplorerbioschemas.jsonld +++ b/data/locusexplorer/locusexplorerbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "LocusExplorer", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/oncogenetics/LocusExplorer" } \ No newline at end of file diff --git a/data/locusmap/locusmapbioschemas.jsonld b/data/locusmap/locusmapbioschemas.jsonld index a5855ba1caa9d..3353f38aa7346 100644 --- a/data/locusmap/locusmapbioschemas.jsonld +++ b/data/locusmap/locusmapbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Computer package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. The current version offers linkage analysis between codominant loci, between dominant loci, between codominant loci and dominant loci, and between codominant and sex-influenced, sex-linked, and imprinted loci.", "sc:name": "LOCUSMAP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://animalgene.umn.edu/locusmap/index.html", "sc:version": "2.1" diff --git a/data/lodgwas/lodgwasbioschemas.jsonld b/data/lodgwas/lodgwasbioschemas.jsonld index a1c4f79936605..1d8943cc111b6 100644 --- a/data/lodgwas/lodgwasbioschemas.jsonld +++ b/data/lodgwas/lodgwasbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "lodGWAS", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/lodGWAS/" } \ No newline at end of file diff --git a/data/logicfs/logicfsbioschemas.jsonld b/data/logicfs/logicfsbioschemas.jsonld index be08d4482924c..ca14241e12804 100644 --- a/data/logicfs/logicfsbioschemas.jsonld +++ b/data/logicfs/logicfsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "logicFS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/logicFS.html", diff --git a/data/logiqa/logiqabioschemas.jsonld b/data/logiqa/logiqabioschemas.jsonld index 6c34ffd1be157..cf48726c3913a 100644 --- a/data/logiqa/logiqabioschemas.jsonld +++ b/data/logiqa/logiqabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12864-016-2642-1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/logiqa", "@type": "sc:SoftwareApplication", @@ -22,8 +18,8 @@ { "@id": "https://doi.org/10.1186/S12864-016-2642-1" }, - "pubmed:27185059", - "pmcid:PMC4868109" + "pmcid:PMC4868109", + "pubmed:27185059" ], "sc:description": "A database dedicated to long-range genome interactions quality assessment.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "LOGIQA", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.ngs-qc.org/logiqa/" + }, + { + "@id": "https://doi.org/10.1186/S12864-016-2642-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/logitt/bioconda_logitt.yaml b/data/logitt/bioconda_logitt.yaml index bdfcfaeb02bf8..16cabda9961a4 100644 --- a/data/logitt/bioconda_logitt.yaml +++ b/data/logitt/bioconda_logitt.yaml @@ -6,7 +6,6 @@ description: The logitT library implements the Logit-t algorithm introduced in - home: https://bioconductor.org/packages/3.10/bioc/html/logitT.html identifiers: - biotools:logitt -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-logitt diff --git a/data/logitt/logittbioschemas.jsonld b/data/logitt/logittbioschemas.jsonld index 0c17e84b0902b..fecae4d8e377b 100644 --- a/data/logitt/logittbioschemas.jsonld +++ b/data/logitt/logittbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "logitT", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/logitT.html", diff --git a/data/logminer/logminerbioschemas.jsonld b/data/logminer/logminerbioschemas.jsonld index 17fd3f25d1ad8..c00d5dd076e16 100644 --- a/data/logminer/logminerbioschemas.jsonld +++ b/data/logminer/logminerbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "LogMiNeR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://bitbucket.org/kleinstein/logminer" } \ No newline at end of file diff --git a/data/logobar/logobarbioschemas.jsonld b/data/logobar/logobarbioschemas.jsonld index d044254331b94..5b65226dc237c 100644 --- a/data/logobar/logobarbioschemas.jsonld +++ b/data/logobar/logobarbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "LogoBar is a Java application to display protein sequence logos. With this application you can generate protein sequence logos from multiple sequence alignments that show the amino acid incidence at every position.", "sc:name": "LogoBar", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.biosci.ki.se/groups/tbu/logobar/" diff --git a/data/logoddslogo/logoddslogobioschemas.jsonld b/data/logoddslogo/logoddslogobioschemas.jsonld index 34ec70d624525..1a7be6da05ab2 100644 --- a/data/logoddslogo/logoddslogobioschemas.jsonld +++ b/data/logoddslogo/logoddslogobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web based application designed to make the generation of sequence logos from biological sequence alignments simple.", "sc:name": "LogOddsLogo", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html" diff --git a/data/logol/logolbioschemas.jsonld b/data/logol/logolbioschemas.jsonld index ac27221128df9..90e8324c1a2f2 100644 --- a/data/logol/logolbioschemas.jsonld +++ b/data/logol/logolbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "CECILL-2.0", "sc:name": "Logol", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "GenOuest", diff --git a/data/logolas/logolasbioschemas.jsonld b/data/logolas/logolasbioschemas.jsonld index e498db28064d9..d52ee9b81f7ea 100644 --- a/data/logolas/logolasbioschemas.jsonld +++ b/data/logolas/logolasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "Logolas", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Logolas.html", "sc:version": "1.4.0" diff --git a/data/logomaker/logomakerbioschemas.jsonld b/data/logomaker/logomakerbioschemas.jsonld index 2d0448e1f1349..77e609e4dbb35 100644 --- a/data/logomaker/logomakerbioschemas.jsonld +++ b/data/logomaker/logomakerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/Logomaker", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ammar Tareen", - "Justin Kinney" + "Justin Kinney", + "Ammar Tareen" ], "sc:additionalType": "Library", "sc:description": "Beautiful sequence logos in python | Software for the visualization of sequence-function relationships | beautiful sequence logos in Python — logomaker 0.8 documentation | Logomaker can be installed from PyPI by executing | Software for creating highly customized sequence logos | Free document hosting provided by Read the Docs", diff --git a/data/loinc2hpo/loinc2hpobioschemas.jsonld b/data/loinc2hpo/loinc2hpobioschemas.jsonld index 4dce5c3e31b57..d583213061fc9 100644 --- a/data/loinc2hpo/loinc2hpobioschemas.jsonld +++ b/data/loinc2hpo/loinc2hpobioschemas.jsonld @@ -25,19 +25,19 @@ }, "sc:additionalType": "Library", "sc:citation": [ + "pubmed:31119199", "pmcid:PMC6527418", { "@id": "https://doi.org/10.1038/S41746-019-0110-4" - }, - "pubmed:31119199" + } ], "sc:description": "Annotation tool that recommends candidate Human Phenotype Ontology (HPO) terms to a LOINC (Laboratory Observation Identifier Names and Codes) test based on lexical matching between HPO term definitions and the name of a laboratory test.", "sc:license": "BSD-3-Clause", "sc:name": "LOINC2HPO", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/monarch-initiative/loinc2hpo" } diff --git a/data/lol/bioconda_lol.yaml b/data/lol/bioconda_lol.yaml index db4e27c1dd833..76b67fa341239 100644 --- a/data/lol/bioconda_lol.yaml +++ b/data/lol/bioconda_lol.yaml @@ -3,7 +3,6 @@ description: Various optimization methods for Lasso inference with matrix warppe home: https://bioconductor.org/packages/3.10/bioc/html/lol.html identifiers: - biotools:lol -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-lol diff --git a/data/lol/lolbioschemas.jsonld b/data/lol/lolbioschemas.jsonld index 54cae7ce0013d..c6393fe3eb2a5 100644 --- a/data/lol/lolbioschemas.jsonld +++ b/data/lol/lolbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yinyin Yuan", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Various optimization methods for Lasso inference with matrix warpper.", "sc:license": "GPL-2.0", diff --git a/data/lola/lolabioschemas.jsonld b/data/lola/lolabioschemas.jsonld index 35845130663c2..3ab476229b3cb 100644 --- a/data/lola/lolabioschemas.jsonld +++ b/data/lola/lolabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nathan Sheffield", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This make is possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.", "sc:license": "GPL-3.0", "sc:name": "LOLA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LOLA.html", "sc:version": "1.4.0" diff --git a/data/lolaweb/lolawebbioschemas.jsonld b/data/lolaweb/lolawebbioschemas.jsonld index 626d19dd005a6..09ace7e911f79 100644 --- a/data/lolaweb/lolawebbioschemas.jsonld +++ b/data/lolaweb/lolawebbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Interactive genomic locus overlap enrichment analysis.", "sc:name": "LOLAweb", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://lolaweb.databio.org", "sc:version": "9a42c57c9" diff --git a/data/lomets2/lomets2bioschemas.jsonld b/data/lomets2/lomets2bioschemas.jsonld index 378952b47c3be..400124ce984ae 100644 --- a/data/lomets2/lomets2bioschemas.jsonld +++ b/data/lomets2/lomets2bioschemas.jsonld @@ -9,42 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKZ384", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/LOMETS2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yang Zhang", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31081035", - "pmcid:PMC6602514", { "@id": "https://doi.org/10.1093/NAR/GKZ384" - } + }, + "pmcid:PMC6602514", + "pubmed:31081035" ], "sc:description": "LOMETS (Local Meta-Threading Server) is meta-threading method for template-based protein structure prediction.", "sc:featureList": [ - { - "@id": "edam:operation_0267" - }, { "@id": "edam:operation_0474" }, { "@id": "edam:operation_0302" + }, + { + "@id": "edam:operation_0267" } ], "sc:license": "Unlicense", "sc:name": "LOMETS2", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://zhanglab.ccmb.med.umich.edu/LOMETS/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ384", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/long-bone-diaphyseal-csg-toolkit/long-bone-diaphyseal-csg-toolkitbioschemas.jsonld b/data/long-bone-diaphyseal-csg-toolkit/long-bone-diaphyseal-csg-toolkitbioschemas.jsonld index c68837cfa8de5..9d1aae77077d8 100644 --- a/data/long-bone-diaphyseal-csg-toolkit/long-bone-diaphyseal-csg-toolkitbioschemas.jsonld +++ b/data/long-bone-diaphyseal-csg-toolkit/long-bone-diaphyseal-csg-toolkitbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "long-bone-diaphyseal-CSG-Toolkit", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/pr0m1th3as/long-bone-diaphyseal-CSG-Toolkit" } \ No newline at end of file diff --git a/data/longgwas/longgwasbioschemas.jsonld b/data/longgwas/longgwasbioschemas.jsonld index a41fa4ab49b4e..3cac553284c91 100644 --- a/data/longgwas/longgwasbioschemas.jsonld +++ b/data/longgwas/longgwasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Mixed-model-based approach for performing association mapping which utilizes multiple phenotype measurements for each individual.", "sc:name": "longGWAS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://genetics.cs.ucla.edu/longGWAS/" diff --git a/data/longislnd/longislndbioschemas.jsonld b/data/longislnd/longislndbioschemas.jsonld index e37eb38b2f555..2ffee8438b99e 100644 --- a/data/longislnd/longislndbioschemas.jsonld +++ b/data/longislnd/longislndbioschemas.jsonld @@ -13,20 +13,16 @@ "@id": "https://doi.org/10.1093/bioinformatics/btw602", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0001-7243-9221", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/longislnd", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27667791", - "pmcid:PMC5167071", { "@id": "https://doi.org/10.1093/bioinformatics/btw602" - } + }, + "pmcid:PMC5167071", + "pubmed:27667791" ], "sc:contributor": { "@id": "http://orcid.org/0000-0001-7243-9221" @@ -39,6 +35,10 @@ "sc:name": "LongISLND", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/bioinform/longislnd" + }, + { + "@id": "http://orcid.org/0000-0001-7243-9221", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/longo/longobioschemas.jsonld b/data/longo/longobioschemas.jsonld index 07604ca68bd2c..679b0da7e50a1 100644 --- a/data/longo/longobioschemas.jsonld +++ b/data/longo/longobioschemas.jsonld @@ -31,9 +31,9 @@ }, "sc:name": "LONGO", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/biohpc/longo" } diff --git a/data/lookseq/lookseqbioschemas.jsonld b/data/lookseq/lookseqbioschemas.jsonld index 712a10f06518b..d645899595493 100644 --- a/data/lookseq/lookseqbioschemas.jsonld +++ b/data/lookseq/lookseqbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "LookSeq", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.sanger.ac.uk/science/tools/lookseq" } \ No newline at end of file diff --git a/data/looping/loopingbioschemas.jsonld b/data/looping/loopingbioschemas.jsonld index 426b8822ff68e..b6844ab91c790 100644 --- a/data/looping/loopingbioschemas.jsonld +++ b/data/looping/loopingbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Method based on the Random Forest automatic learning technique, designed to select structural templates for protein loops among a dataset of candidates.", "sc:name": "LoopIng", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://circe.med.uniroma1.it/looping/" } \ No newline at end of file diff --git a/data/loqum/loqumbioschemas.jsonld b/data/loqum/loqumbioschemas.jsonld index f90fb7c8d3ff5..e54af168f4017 100644 --- a/data/loqum/loqumbioschemas.jsonld +++ b/data/loqum/loqumbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Assigns reliable mapping quality scores to mappings of Illumina reads returned by an alignment tool.", "sc:name": "LoQuM", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://compbio.case.edu/loqum/" } \ No newline at end of file diff --git a/data/lord/lordbioschemas.jsonld b/data/lord/lordbioschemas.jsonld index fbae2662e9c06..df69aca6f8514 100644 --- a/data/lord/lordbioschemas.jsonld +++ b/data/lord/lordbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "LORD (linking opendata for rare diseases) - tool for browsing information about rare diseases. It aggregates the information from Orphanet, HPO and OMIM database.", "sc:name": "LORD", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://enlord.bndmr.fr/#homepage" diff --git a/data/lorean/loreanbioschemas.jsonld b/data/lorean/loreanbioschemas.jsonld index 7c6ad98062861..a41ad474daa96 100644 --- a/data/lorean/loreanbioschemas.jsonld +++ b/data/lorean/loreanbioschemas.jsonld @@ -15,19 +15,19 @@ "biotools:primaryContact": "Luigi Faino", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6324239", "pubmed:30401722", { "@id": "https://doi.org/10.1104/pp.18.00848" - }, - "pmcid:PMC6324239" + } ], "sc:description": "Automated eukaryotic genome annotation based on long-read cDNA sequencing.", "sc:featureList": [ { - "@id": "edam:operation_0362" + "@id": "edam:operation_0476" }, { - "@id": "edam:operation_0476" + "@id": "edam:operation_0362" }, { "@id": "edam:operation_0308" @@ -36,8 +36,8 @@ "sc:license": "MIT", "sc:name": "LoReAn", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/lfaino/LoReAn" }, diff --git a/data/lors/lorsbioschemas.jsonld b/data/lors/lorsbioschemas.jsonld index 7a93ea1247b73..a7b8ba44db902 100644 --- a/data/lors/lorsbioschemas.jsonld +++ b/data/lors/lorsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "LOw-Rank representation and Sparse regression for eQTL mapping. This algorithm accounts for confounding factors such as unobserved covariates, experimental artifacts, and unknown environmental perturbations.", "sc:name": "LORS", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://zhaocenter.org/software/#Genomic_Expression_Pathway_Analysis" } \ No newline at end of file diff --git a/data/lot/lotbioschemas.jsonld b/data/lot/lotbioschemas.jsonld index 444342d72456d..0865a74989603 100644 --- a/data/lot/lotbioschemas.jsonld +++ b/data/lot/lotbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "LOT (Linkage analysis of Ordinal Traits) is a software program that performs linkage analysis of ordinal traits for pedigree data. It implements a latent-variable proportional-odds logistic model that relates inheritance patterns to the distribution of the ordinal trait.", "sc:name": "LOT", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://c2s2.yale.edu/software/LOT/", diff --git a/data/lovd/lovdbioschemas.jsonld b/data/lovd/lovdbioschemas.jsonld index fa0ab11fbcc78..d68f9698a4c3b 100644 --- a/data/lovd/lovdbioschemas.jsonld +++ b/data/lovd/lovdbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/lovd", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data, even of variants outside of genes.", "sc:license": "GPL-3.0", "sc:name": "LOVD", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ELIXIR-NL", "sc:url": "http://www.lovd.nl/3.0/home", diff --git a/data/lowcomplexity/lowcomplexitybioschemas.jsonld b/data/lowcomplexity/lowcomplexitybioschemas.jsonld index 4c7bc4dacf410..b5ab0956ef612 100644 --- a/data/lowcomplexity/lowcomplexitybioschemas.jsonld +++ b/data/lowcomplexity/lowcomplexitybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool that searches for low complexity regions of DNA or protein sequences. Using it you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences.", "sc:name": "LowComplexity", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/" } \ No newline at end of file diff --git a/data/lowmaca/lowmacabioschemas.jsonld b/data/lowmaca/lowmacabioschemas.jsonld index a37d869f5b350..acbbf6ae3f9fa 100644 --- a/data/lowmaca/lowmacabioschemas.jsonld +++ b/data/lowmaca/lowmacabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-016-0935-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/lowmaca", "@type": "sc:SoftwareApplication", @@ -22,10 +26,10 @@ ], "edam:has_input": [ { - "@id": "edam:data_2295" + "@id": "edam:data_1138" }, { - "@id": "edam:data_1138" + "@id": "edam:data_2295" } ], "edam:has_output": [ @@ -36,10 +40,10 @@ "@id": "edam:data_2166" }, { - "@id": "edam:data_0867" + "@id": "edam:data_2884" }, { - "@id": "edam:data_2884" + "@id": "edam:data_0867" } ], "sc:additionalType": [ @@ -55,10 +59,10 @@ } ], "sc:citation": [ + "pubmed:26860319", { "@id": "https://doi.org/10.1186/s12859-016-0935-7" }, - "pubmed:26860319", "pmcid:PMC4748640" ], "sc:description": "This package is a simple suite of tools to investigate and analyze the mutation profile of several proteins or PFAM domains via consensus alignment. You can conduct an hypothesis driven exploratory analysis using our package simply providing a set of genes or PFAM domains of your interest.", @@ -67,32 +71,28 @@ "@id": "edam:operation_0296" }, { - "@id": "edam:operation_0492" + "@id": "edam:operation_2479" }, { - "@id": "edam:operation_2479" + "@id": "edam:operation_0492" } ], "sc:license": "GPL-3.0", "sc:name": "LowMACA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LowMACA.html", "sc:version": "1.6.0" }, { - "@id": "http://orcid.org/0000-0003-1103-7688", + "@id": "http://orcid.org/0000-0001-6371-1334", "@type": "schema:Person" }, { - "@id": "https://doi.org/10.1186/s12859-016-0935-7", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-6371-1334", + "@id": "http://orcid.org/0000-0003-1103-7688", "@type": "schema:Person" } ] diff --git a/data/lox/loxbioschemas.jsonld b/data/lox/loxbioschemas.jsonld index 0d956c1e12e66..1be5f4d5540b9 100644 --- a/data/lox/loxbioschemas.jsonld +++ b/data/lox/loxbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.", "sc:name": "LOX", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://medicine.yale.edu/lab/townsend/sand/index.aspx#page1" diff --git a/data/lpe/lpebioschemas.jsonld b/data/lpe/lpebioschemas.jsonld index bedbb5a9d8451..0c867d7cd09b2 100644 --- a/data/lpe/lpebioschemas.jsonld +++ b/data/lpe/lpebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "LPE", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LPE.html", "sc:version": "1.48.0" diff --git a/data/lpeadj/bioconda_lpeadj.yaml b/data/lpeadj/bioconda_lpeadj.yaml index 0bc576e6bfccc..17bdb90313876 100644 --- a/data/lpeadj/bioconda_lpeadj.yaml +++ b/data/lpeadj/bioconda_lpeadj.yaml @@ -7,7 +7,6 @@ description: Two options are added to the LPE algorithm. The original LPE method home: https://bioconductor.org/packages/3.10/bioc/html/LPEadj.html identifiers: - biotools:lpeadj -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-lpeadj diff --git a/data/lpeadj/lpeadjbioschemas.jsonld b/data/lpeadj/lpeadjbioschemas.jsonld index 300130f6dd284..e11b9a34d6985 100644 --- a/data/lpeadj/lpeadjbioschemas.jsonld +++ b/data/lpeadj/lpeadjbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Carl Murie", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Two options are added to the LPE algorithm, which original version sets all variances below the max variance in the ordered distribution of variances to the maximum variance. In the present version, this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default, the tool uses the sample size based variance adjustment.", "sc:license": "GPL-3.0", "sc:name": "LPEadj", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LPEadj.html", "sc:version": "1.34.0" diff --git a/data/lpicom/lpicombioschemas.jsonld b/data/lpicom/lpicombioschemas.jsonld index a373ce1b0d641..51903526d71c7 100644 --- a/data/lpicom/lpicombioschemas.jsonld +++ b/data/lpicom/lpicombioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web server developed for understanding protein-ligand interaction for almost all ligands available in Protein Data Bank.", "sc:name": "LPIcom", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://crdd.osdd.net/raghava/lpicom/" diff --git a/data/lpnet/lpnetbioschemas.jsonld b/data/lpnet/lpnetbioschemas.jsonld index c84978b6d3763..d64410e898b96 100644 --- a/data/lpnet/lpnetbioschemas.jsonld +++ b/data/lpnet/lpnetbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "lpNet", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/lpNet.html", "sc:version": "2.6.0" diff --git a/data/lpsymphony/lpsymphonybioschemas.jsonld b/data/lpsymphony/lpsymphonybioschemas.jsonld index 10afad6706a5e..6ec19983b745f 100644 --- a/data/lpsymphony/lpsymphonybioschemas.jsonld +++ b/data/lpsymphony/lpsymphonybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Vladislav Kim", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users' system. Thus, the intention is to provide an easy to install interface to SYMPHONY.", "sc:license": "EPL-1.0", "sc:name": "lpsymphony", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/lpsymphony.html", "sc:version": "1.2.0" diff --git a/data/lrc/lrcbioschemas.jsonld b/data/lrc/lrcbioschemas.jsonld index f9a02dfde90f8..dc2c638131789 100644 --- a/data/lrc/lrcbioschemas.jsonld +++ b/data/lrc/lrcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A computational method based on a combination of physicochemical and structural properties to predict the B-cell epitopes.", "sc:name": "LRC", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bs.ipm.ir/softwares/LRC/" } \ No newline at end of file diff --git a/data/lrcstats/lrcstatsbioschemas.jsonld b/data/lrcstats/lrcstatsbioschemas.jsonld index 0524904e359a6..e81a735d1b235 100644 --- a/data/lrcstats/lrcstatsbioschemas.jsonld +++ b/data/lrcstats/lrcstatsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/LRCstats", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Script", - "Command-line tool" + "Command-line tool", + "Script" ], "sc:description": "Tool for evaluating Long Reads Correction methods.", "sc:license": "GPL-3.0", diff --git a/data/lrensemble/lrensemblebioschemas.jsonld b/data/lrensemble/lrensemblebioschemas.jsonld index 35c9b37baf926..1c898d8808b22 100644 --- a/data/lrensemble/lrensemblebioschemas.jsonld +++ b/data/lrensemble/lrensemblebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "LRensemble (LR Ensemble Localization Predictor) predicts 4 major locations for Yeast Proteins: Cytosol, Mitochondrion, Nucleus, Secretory. The prediction method is to build an ensemble over different available localization predictors. In the current version, our predict collects prediction results from up to 6 predictors and Logistic Regression is used as the ensemble algorithm.", "sc:name": "LRensemble", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://mleg.cse.sc.edu/LRensemble/cgi-bin/index.html" } \ No newline at end of file diff --git a/data/lriscan/lriscanbioschemas.jsonld b/data/lriscan/lriscanbioschemas.jsonld index dc3f87fdc805e..98061e7282ed5 100644 --- a/data/lriscan/lriscanbioschemas.jsonld +++ b/data/lriscan/lriscanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for the LRI prediction in full viral genomes based on a multiple genome alignment.", "sc:name": "LRIscan", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.rna.uni-jena.de/en/software/" } \ No newline at end of file diff --git a/data/lrpath/lrpathbioschemas.jsonld b/data/lrpath/lrpathbioschemas.jsonld index 2bc19cc55fac0..41c7cf25d7954 100644 --- a/data/lrpath/lrpathbioschemas.jsonld +++ b/data/lrpath/lrpathbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "LRpath performs gene set enrichment testing using logistic regression, and allows the data to remain on a continuous scale.", "sc:name": "LRpath", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://lrpath.ncibi.org/" } \ No newline at end of file diff --git a/data/lrrr/lrrrbioschemas.jsonld b/data/lrrr/lrrrbioschemas.jsonld index 697f67813524e..cebec6dae39e6 100644 --- a/data/lrrr/lrrrbioschemas.jsonld +++ b/data/lrrr/lrrrbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Method that determines binding sites of small compounds (ligands) on the surface of proteinsExtraction of binding sites of ligands and search for unknown binding sites on apoproteins. Some call it docking. Some call it binding site detections. Some call it knowledge based.", "sc:name": "lrrr 1.4", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://sourceforge.net/projects/lrrr/", "sc:version": "beta1" diff --git a/data/lrrsearch/lrrsearchbioschemas.jsonld b/data/lrrsearch/lrrsearchbioschemas.jsonld index 754d0f558375e..a04c6dc839ed2 100644 --- a/data/lrrsearch/lrrsearchbioschemas.jsonld +++ b/data/lrrsearch/lrrsearchbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "LRRsearch", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.lrrsearch.com/" } \ No newline at end of file diff --git a/data/ls-snp/ls-snpbioschemas.jsonld b/data/ls-snp/ls-snpbioschemas.jsonld index fbc9293da2d2b..2b02be487420c 100644 --- a/data/ls-snp/ls-snpbioschemas.jsonld +++ b/data/ls-snp/ls-snpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web tool for genome-wide annotation of human SNPs. The current version provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological function. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features, inferred from three-dimensional experimental structures.", "sc:name": "LS-SNP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://ls-snp.icm.jhu.edu/ls-snp-pdb/" } \ No newline at end of file diff --git a/data/lsd/lsdbioschemas.jsonld b/data/lsd/lsdbioschemas.jsonld index 9f54ddac22398..17e75df6d0279 100644 --- a/data/lsd/lsdbioschemas.jsonld +++ b/data/lsd/lsdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This database contains senescence associated genes (SAGs) from 21 species retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and classified into different categories according to their functions in leaf senescence or morphological phenotypes. Users can browse or search the database to obtain information including literatures, mutants, phenotypes, expression profiles, miRNA interactions, orthologs in other plants and cross links to other databases.", "sc:name": "LSD", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://psd.cbi.pku.edu.cn/" } \ No newline at end of file diff --git a/data/lskb/lskbbioschemas.jsonld b/data/lskb/lskbbioschemas.jsonld index f0345d8487dcc..3049f6eec91d3 100644 --- a/data/lskb/lskbbioschemas.jsonld +++ b/data/lskb/lskbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Comprehensive drug discovery and genomic research workbench, knowledgebase and data management system.", "sc:name": "Life Science Knowledge Bank (LSKB)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.lskb.w-fusionus.com" } \ No newline at end of file diff --git a/data/lspr/lsprbioschemas.jsonld b/data/lspr/lsprbioschemas.jsonld index abaace305ebab..6c28b01c23bac 100644 --- a/data/lspr/lsprbioschemas.jsonld +++ b/data/lspr/lsprbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "LSPR is a Matlab package used to detect periodic expression profiles in DNA microarray time-series data.", "sc:name": "LSPR", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinformatics.cau.edu.cn/LSPR/" } \ No newline at end of file diff --git a/data/lst/lstbioschemas.jsonld b/data/lst/lstbioschemas.jsonld index 21fbfaccf034c..976882caeb7ad 100644 --- a/data/lst/lstbioschemas.jsonld +++ b/data/lst/lstbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "LST", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.statistical-modeling.de/lst.html" } \ No newline at end of file diff --git a/data/lter-marechiara/lter-marechiarabioschemas.jsonld b/data/lter-marechiara/lter-marechiarabioschemas.jsonld index 23e4d511e7f13..dfad0a8d72a23 100644 --- a/data/lter-marechiara/lter-marechiarabioschemas.jsonld +++ b/data/lter-marechiara/lter-marechiarabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "LTER-MARECHIARA", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://szn.macisteweb.com/" } \ No newline at end of file diff --git a/data/ltrtype/ltrtypebioschemas.jsonld b/data/ltrtype/ltrtypebioschemas.jsonld index abe55099d5ef4..3d5c487d401e8 100644 --- a/data/ltrtype/ltrtypebioschemas.jsonld +++ b/data/ltrtype/ltrtypebioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3389/fpls.2017.00402", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ltrtype", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Li-Zhi Gao", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:28421083", "pmcid:PMC5379124", { "@id": "https://doi.org/10.3389/fpls.2017.00402" - } + }, + "pubmed:28421083" ], "sc:description": "Efficient tool to characterize structurally complex LTR retrotransposons and nested insertions on genomes.", "sc:featureList": { @@ -31,10 +35,6 @@ "Mac" ], "sc:url": "http://www.plantkingdomgdb.com/LTRtype/index.html" - }, - { - "@id": "https://doi.org/10.3389/fpls.2017.00402", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/luca/lucabioschemas.jsonld b/data/luca/lucabioschemas.jsonld index a7ef5fab1f246..2f831949885fc 100644 --- a/data/luca/lucabioschemas.jsonld +++ b/data/luca/lucabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R package implementing the methods for case-control inference of statistical interaction between genetic and nongenetic risk factors under covariate assumptions.", "sc:name": "LUCA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://stat.sfu.ca/statgen/research/luca.html" } \ No newline at end of file diff --git a/data/lucegene/lucegenebioschemas.jsonld b/data/lucegene/lucegenebioschemas.jsonld index f8e36995b1900..0b4e1cd743994 100644 --- a/data/lucegene/lucegenebioschemas.jsonld +++ b/data/lucegene/lucegenebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "LuceGene", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.gmod.org/wiki/LuceGene", "sc:version": "1.4" diff --git a/data/luciphor2/luciphor2bioschemas.jsonld b/data/luciphor2/luciphor2bioschemas.jsonld index 76314b705671e..3468b5d860bbe 100644 --- a/data/luciphor2/luciphor2bioschemas.jsonld +++ b/data/luciphor2/luciphor2bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data.", "sc:name": "Luciphor2", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://luciphor2.sourceforge.net/" } \ No newline at end of file diff --git a/data/lucy/lucybioschemas.jsonld b/data/lucy/lucybioschemas.jsonld index 2ea5f90a1d5f0..765a2b3aae101 100644 --- a/data/lucy/lucybioschemas.jsonld +++ b/data/lucy/lucybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/lucy", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Michael Holmes", - "Hui-Hsien Chou" + "Hui-Hsien Chou", + "Michael Holmes" ], "sc:additionalType": "Command-line tool", "sc:description": "A program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly.", diff --git a/data/lumi/lumibioschemas.jsonld b/data/lumi/lumibioschemas.jsonld index 541a33267d18b..b47129c62c064 100644 --- a/data/lumi/lumibioschemas.jsonld +++ b/data/lumi/lumibioschemas.jsonld @@ -22,10 +22,10 @@ "Library" ], "sc:citation": [ - "pubmed:17540033", { "@id": "https://doi.org/10.1186/1745-6150-2-16" }, + "pubmed:17540033", "pmcid:PMC1891274" ], "sc:description": "This package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.", diff --git a/data/lunggens/lunggensbioschemas.jsonld b/data/lunggens/lunggensbioschemas.jsonld index 4788a1506eb1d..b5b7367af65f3 100644 --- a/data/lunggens/lunggensbioschemas.jsonld +++ b/data/lunggens/lunggensbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1136/thoraxjnl-2015-207035", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/lunggens", "@type": "sc:SoftwareApplication", @@ -25,21 +21,21 @@ }, "sc:additionalType": "Database portal", "sc:applicationSubCategory": [ - { - "@id": "edam:topic_0203" - }, { "@id": "edam:topic_3512" }, { "@id": "edam:topic_3170" + }, + { + "@id": "edam:topic_0203" } ], "sc:citation": [ - "pubmed:26130332", { "@id": "https://doi.org/10.1136/thoraxjnl-2015-207035" }, + "pubmed:26130332", "pmcid:PMC4641439" ], "sc:description": "Query single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query returns associated selective gene signatures and genes encoding cell surface markers and transcription factors in interactive heatmap and tables.", @@ -53,6 +49,10 @@ "Linux" ], "sc:url": "https://research.cchmc.org/pbge/lunggens/default.html" + }, + { + "@id": "https://doi.org/10.1136/thoraxjnl-2015-207035", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/lutefisk/lutefiskbioschemas.jsonld b/data/lutefisk/lutefiskbioschemas.jsonld index 9ae928ae1e0b6..2a7476906df89 100644 --- a/data/lutefisk/lutefiskbioschemas.jsonld +++ b/data/lutefisk/lutefiskbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "\"De novo\" peptide sequencing from MS/MS data.", "sc:name": "lutefisk", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.hairyfatguy.com/lutefisk" } \ No newline at end of file diff --git a/data/lux_score/lux_scorebioschemas.jsonld b/data/lux_score/lux_scorebioschemas.jsonld index ca7030a157f3b..0751454b6be0a 100644 --- a/data/lux_score/lux_scorebioschemas.jsonld +++ b/data/lux_score/lux_scorebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "LUX Score", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://lifs.isas.de/index.php/lux-score" } \ No newline at end of file diff --git a/data/lwgv/lwgvbioschemas.jsonld b/data/lwgv/lwgvbioschemas.jsonld index 05f3e981fdfa3..d467da61bfb45 100644 --- a/data/lwgv/lwgvbioschemas.jsonld +++ b/data/lwgv/lwgvbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Uses a simple language for describing features on a genome or biological sequence and provides a browsable image of these features.", "sc:name": "lwgv", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://lwgv.sourceforge.net/" } \ No newline at end of file diff --git a/data/lymphoseq/lymphoseqbioschemas.jsonld b/data/lymphoseq/lymphoseqbioschemas.jsonld index bf49a62b885e1..f40fbba40503b 100644 --- a/data/lymphoseq/lymphoseqbioschemas.jsonld +++ b/data/lymphoseq/lymphoseqbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David Coffey", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.", "sc:license": "Artistic-2.0", "sc:name": "LymphoSeq", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/LymphoSeq.html", "sc:version": "1.2.0" diff --git a/data/lynx_multi-gene_annotations/lynx_multi-gene_annotationsbioschemas.jsonld b/data/lynx_multi-gene_annotations/lynx_multi-gene_annotationsbioschemas.jsonld index 52f763b7bbe4f..39727f6bc5787 100644 --- a/data/lynx_multi-gene_annotations/lynx_multi-gene_annotationsbioschemas.jsonld +++ b/data/lynx_multi-gene_annotations/lynx_multi-gene_annotationsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Programmatic access to the analytical tools (Enrichment Analysis, and Network-based gene prioritization) and annotations on the genes (integrated from over 35 databases).", "sc:name": "Lynx Multi-Gene Annotations", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://lynx.ci.uchicago.edu/webservices.html", "sc:version": "1" diff --git a/data/m-bison/m-bisonbioschemas.jsonld b/data/m-bison/m-bisonbioschemas.jsonld index 6c967172fff24..53a0400149be7 100644 --- a/data/m-bison/m-bisonbioschemas.jsonld +++ b/data/m-bison/m-bisonbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "M-BISON", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://simtk.org/home/m-bison", "sc:version": "1.0" diff --git a/data/m-iolite/m-iolitebioschemas.jsonld b/data/m-iolite/m-iolitebioschemas.jsonld index 105dc92097c1d..f829dbb975ffd 100644 --- a/data/m-iolite/m-iolitebioschemas.jsonld +++ b/data/m-iolite/m-iolitebioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Maria I Klapa", "sc:additionalType": [ - "Database portal", - "Suite", "Workflow", - "Desktop application" + "Desktop application", + "Suite", + "Database portal" ], "sc:description": "MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems Laboratory, appropriately filtered GOLM database peak information and Human Metabolome database information.", "sc:license": "Other", diff --git a/data/m1cr0b1al1z3r/m1cr0b1al1z3rbioschemas.jsonld b/data/m1cr0b1al1z3r/m1cr0b1al1z3rbioschemas.jsonld index 70ad3d0bb0335..79da7e3b0b851 100644 --- a/data/m1cr0b1al1z3r/m1cr0b1al1z3rbioschemas.jsonld +++ b/data/m1cr0b1al1z3r/m1cr0b1al1z3rbioschemas.jsonld @@ -9,45 +9,45 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKZ423", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/M1CR0B1AL1Z3R", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Tal Pupko", "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:citation": [ "pubmed:31114912", + "pmcid:PMC6602433", { "@id": "https://doi.org/10.1093/NAR/GKZ423" - }, - "pmcid:PMC6602433" + } ], "sc:description": "Web server for the analysis of large-scale microbial genomics data.", "sc:featureList": [ { - "@id": "edam:operation_0306" + "@id": "edam:operation_3745" }, { - "@id": "edam:operation_3478" + "@id": "edam:operation_0306" }, { - "@id": "edam:operation_3745" + "@id": "edam:operation_3478" } ], "sc:license": "GPL-2.0", "sc:name": "M1CR0B1AL1Z3R", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://microbializer.tau.ac.il/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ423", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/m2lite/m2litebioschemas.jsonld b/data/m2lite/m2litebioschemas.jsonld index 41a0c1b4690ea..201b35b9bd70a 100644 --- a/data/m2lite/m2litebioschemas.jsonld +++ b/data/m2lite/m2litebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Lightweight, easily pluggable, and extremely fast conversion software tool. It converts msf files to the proteomics community standard mzIdentML file format.", "sc:name": "M2Lite", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://bitbucket.org/paiyetan/m2lite" } \ No newline at end of file diff --git a/data/m3/m3bioschemas.jsonld b/data/m3/m3bioschemas.jsonld index 52f1ec939e770..e3e38450741d2 100644 --- a/data/m3/m3bioschemas.jsonld +++ b/data/m3/m3bioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "An improved SNP calling algorithm for Illumina BeadArray Data.", "sc:name": "M3", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://zhaocenter.org/software/#Genomic_Expression_Pathway_Analysis", diff --git a/data/m3d/m3dbioschemas.jsonld b/data/m3d/m3dbioschemas.jsonld index 79e2b214eaafd..ee3f9c711af85 100644 --- a/data/m3d/m3dbioschemas.jsonld +++ b/data/m3d/m3dbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Tom Mayo", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.", "sc:license": "Artistic-2.0", "sc:name": "M3D", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/M3D.html", "sc:version": "1.8.0" diff --git a/data/m3drop/m3dropbioschemas.jsonld b/data/m3drop/m3dropbioschemas.jsonld index 5cdfb80ea9e71..65906badb4c0b 100644 --- a/data/m3drop/m3dropbioschemas.jsonld +++ b/data/m3drop/m3dropbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "M3Drop", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/M3Drop.html", diff --git a/data/m4t/m4tbioschemas.jsonld b/data/m4t/m4tbioschemas.jsonld index 187c4579daa8c..f91f73cbc4f9d 100644 --- a/data/m4t/m4tbioschemas.jsonld +++ b/data/m4t/m4tbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "M4T", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://manaslu.fiserlab.org/M4T/" } \ No newline at end of file diff --git a/data/m6acomet/m6acometbioschemas.jsonld b/data/m6acomet/m6acometbioschemas.jsonld index 7aaee1df371e3..acb942811dc71 100644 --- a/data/m6acomet/m6acometbioschemas.jsonld +++ b/data/m6acomet/m6acometbioschemas.jsonld @@ -18,33 +18,33 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jia Meng", "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:citation": [ + "pmcid:PMC6498663", + "pubmed:31046660", { "@id": "https://doi.org/10.1186/s12859-019-2840-3" - }, - "pubmed:31046660", - "pmcid:PMC6498663" + } ], "sc:description": "Large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network.", "sc:featureList": [ { - "@id": "edam:operation_3207" + "@id": "edam:operation_0417" }, { - "@id": "edam:operation_3766" + "@id": "edam:operation_3207" }, { - "@id": "edam:operation_0417" + "@id": "edam:operation_3766" } ], "sc:name": "m6Acomet", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://xjtlu.edu.cn/biologicalsciences/m6acomet" } diff --git a/data/m_ia/m_iabioschemas.jsonld b/data/m_ia/m_iabioschemas.jsonld index 78bbfa7408622..5eba0e3e15225 100644 --- a/data/m_ia/m_iabioschemas.jsonld +++ b/data/m_ia/m_iabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This environment offers an interactive multi-user interface which includes all steps of a microarray study: from MIAME-compliant storage of experiments and raw data processing to analysis of differentially regulated genes. In addition, it offers functional insight into gene expression data by using an original approach combining biological knowledge annotation with gene expression data through interactive graph.", "sc:name": "M IA", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://maia.genouest.org/" } \ No newline at end of file diff --git a/data/ma/mabioschemas.jsonld b/data/ma/mabioschemas.jsonld index 7946977085c5a..d09f1a219def2 100644 --- a/data/ma/mabioschemas.jsonld +++ b/data/ma/mabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ma", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.emouseatlas.org/emap/home.html", "sc:version": "1" diff --git a/data/ma2c/ma2cbioschemas.jsonld b/data/ma2c/ma2cbioschemas.jsonld index 2694fbc5fc695..79f5159294af4 100644 --- a/data/ma2c/ma2cbioschemas.jsonld +++ b/data/ma2c/ma2cbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Model-based Analysis of 2-Color Arrays is a model-based algorithm for analyzing 2-color microarrays.A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. A robust algorithm for detecting peak regions is also formulated and shown to perform well compared to other approaches.", "sc:name": "MA2C", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://liulab.dfci.harvard.edu/MA2C/MA2C.htm", "sc:version": "1.4.1" diff --git a/data/maanova/maanovabioschemas.jsonld b/data/maanova/maanovabioschemas.jsonld index 1fcd551248db8..b60df4e320464 100644 --- a/data/maanova/maanovabioschemas.jsonld +++ b/data/maanova/maanovabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "maanova", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/maanova.html", "sc:version": "1.44.0" diff --git a/data/macaron/macaronbioschemas.jsonld b/data/macaron/macaronbioschemas.jsonld index 5b2543449cec0..01e5129e8e6df 100644 --- a/data/macaron/macaronbioschemas.jsonld +++ b/data/macaron/macaronbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/bty382", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/macaron", "@type": "sc:SoftwareApplication", @@ -32,11 +36,11 @@ } ], "sc:citation": [ - "pubmed:29726922", - "pmcid:PMC29726922", { "@id": "https://doi.org/10.1093/bioinformatics/bty382" - } + }, + "pubmed:29726922", + "pmcid:PMC29726922" ], "sc:description": "MACARON (Multi-bAse Codon-Associated variant Re-annotatiON) is a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data. Starting from a standard VCF file, MACARON identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon.", "sc:featureList": { @@ -51,10 +55,6 @@ }, "sc:url": "http://www.genmed.fr/index.php/fr/recherche/publications", "sc:version": "0.6" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/bty382", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/macat/macatbioschemas.jsonld b/data/macat/macatbioschemas.jsonld index e2229c57b0365..0e9860102264d 100644 --- a/data/macat/macatbioschemas.jsonld +++ b/data/macat/macatbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-1471-1295", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/macat", "@type": "sc:SoftwareApplication", @@ -24,16 +28,12 @@ "sc:license": "Artistic-2.0", "sc:name": "macat", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/macat.html", "sc:version": "1.48.0" - }, - { - "@id": "http://orcid.org/0000-0003-1471-1295", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mach-admix/mach-admixbioschemas.jsonld b/data/mach-admix/mach-admixbioschemas.jsonld index 7eae75cb8a7e5..9fa0f1ef79f26 100644 --- a/data/mach-admix/mach-admixbioschemas.jsonld +++ b/data/mach-admix/mach-admixbioschemas.jsonld @@ -26,10 +26,10 @@ "@id": "edam:operation_3557" }, { - "@id": "edam:operation_0487" + "@id": "edam:operation_3703" }, { - "@id": "edam:operation_3703" + "@id": "edam:operation_0487" } ], "sc:license": "Not licensed", diff --git a/data/mach/machbioschemas.jsonld b/data/mach/machbioschemas.jsonld index 764b37e8eab16..41327af7ba8d4 100644 --- a/data/mach/machbioschemas.jsonld +++ b/data/mach/machbioschemas.jsonld @@ -18,27 +18,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC3175618", + "pubmed:21058334", { "@id": "https://doi.org/10.1002/gepi.20533" - }, - "pmcid:PMC3175618", - "pubmed:21058334" + } ], "sc:description": "Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.", "sc:featureList": [ { - "@id": "edam:operation_3557" + "@id": "edam:operation_0487" }, { - "@id": "edam:operation_0487" + "@id": "edam:operation_3557" } ], "sc:license": "Not licensed", "sc:name": "MACH", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://csg.sph.umich.edu/abecasis/mach/" } diff --git a/data/mach2dat/mach2datbioschemas.jsonld b/data/mach2dat/mach2datbioschemas.jsonld index 3ccbc4b5b76b4..43d1101c24ad8 100644 --- a/data/mach2dat/mach2datbioschemas.jsonld +++ b/data/mach2dat/mach2datbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Not licensed", "sc:name": "mach2dat", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.nitrc.org/projects/mach2dat/" } \ No newline at end of file diff --git a/data/mach2qtl/mach2qtlbioschemas.jsonld b/data/mach2qtl/mach2qtlbioschemas.jsonld index 8b986194fc741..b9cb27695d1b1 100644 --- a/data/mach2qtl/mach2qtlbioschemas.jsonld +++ b/data/mach2qtl/mach2qtlbioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC2925172", + "pubmed:19715440", { "@id": "https://doi.org/10.1146/annurev.genom.9.081307.164242" }, - "pubmed:19715440" + "pmcid:PMC2925172" ], "sc:description": "QTL analysis based on imputed dosages/posterior_probabilities", "sc:featureList": { diff --git a/data/macie/maciebioschemas.jsonld b/data/macie/maciebioschemas.jsonld index c25f7ac2328b9..5c78bbe6a77bf 100644 --- a/data/macie/maciebioschemas.jsonld +++ b/data/macie/maciebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Mechanism, Annotation, and Classification in Enzymes: database of enzyme reaction mechanisms.", "sc:name": "MACIE", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/thornton-srv/databases/MACiE/" } \ No newline at end of file diff --git a/data/macleaps/macleapsbioschemas.jsonld b/data/macleaps/macleapsbioschemas.jsonld index c100315fee9e0..885c52bfe68b5 100644 --- a/data/macleaps/macleapsbioschemas.jsonld +++ b/data/macleaps/macleapsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MACLEAPS", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ra.cs.uni-tuebingen.de/software/MACLEAPS/index.htm" } \ No newline at end of file diff --git a/data/macorrplot/bioconda_macorrplot.yaml b/data/macorrplot/bioconda_macorrplot.yaml index d116bcba3beae..306efa867df33 100644 --- a/data/macorrplot/bioconda_macorrplot.yaml +++ b/data/macorrplot/bioconda_macorrplot.yaml @@ -4,7 +4,6 @@ description: Graphically displays correlation in microarray data that is due to home: https://bioconductor.org/packages/3.10/bioc/html/maCorrPlot.html identifiers: - biotools:macorrplot -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-macorrplot diff --git a/data/macorrplot/macorrplotbioschemas.jsonld b/data/macorrplot/macorrplotbioschemas.jsonld index 47c8ad1ce7de1..34fa4f8370e55 100644 --- a/data/macorrplot/macorrplotbioschemas.jsonld +++ b/data/macorrplot/macorrplotbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "maCorrPlot", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/maCorrPlot.html", "sc:version": "1.44.0" diff --git a/data/macpet/macpetbioschemas.jsonld b/data/macpet/macpetbioschemas.jsonld index 0f4fc185820ac..6165dc649e526 100644 --- a/data/macpet/macpetbioschemas.jsonld +++ b/data/macpet/macpetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MACPET", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MACPET.html", "sc:version": "1.0.0" diff --git a/data/macsims/macsimsbioschemas.jsonld b/data/macsims/macsimsbioschemas.jsonld index 5ff561501b1ce..10886ee798fde 100644 --- a/data/macsims/macsimsbioschemas.jsonld +++ b/data/macsims/macsimsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Multiple alignment-based information management system that combines the advantages of both knowledge-based and ab initio sequence analysis methods.", "sc:name": "MACSIMS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "IFB ELIXIR-FR", diff --git a/data/macsyfinder/macsyfinderbioschemas.jsonld b/data/macsyfinder/macsyfinderbioschemas.jsonld index fa28ed60aa688..7162c495e07f1 100644 --- a/data/macsyfinder/macsyfinderbioschemas.jsonld +++ b/data/macsyfinder/macsyfinderbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/macsyfinder", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems to reflect these conserved features, and to allow their efficient detection.", "sc:license": "GPL-3.0", "sc:name": "MacSyFinder", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Institut Pasteur", "sc:url": "https://github.com/gem-pasteur/macsyfinder", diff --git a/data/madap/madapbioschemas.jsonld b/data/madap/madapbioschemas.jsonld index 59571a136c1e1..e5474d9a584a2 100644 --- a/data/madap/madapbioschemas.jsonld +++ b/data/madap/madapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MADAP", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ccg.vital-it.ch/madap/" } \ No newline at end of file diff --git a/data/madcat/madcatbioschemas.jsonld b/data/madcat/madcatbioschemas.jsonld index 67bc613449480..0d2bde98fd62b 100644 --- a/data/madcat/madcatbioschemas.jsonld +++ b/data/madcat/madcatbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Mapping of Distances for the Categorization of Topology is a protein structure search tool", "sc:name": "MaDCaT", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.grigoryanlab.org/madcat/" } \ No newline at end of file diff --git a/data/made4/made4bioschemas.jsonld b/data/made4/made4bioschemas.jsonld index b73dde7adb89c..084a78d6eadaa 100644 --- a/data/made4/made4bioschemas.jsonld +++ b/data/made4/made4bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-1395-9734", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/made4", "@type": "sc:SoftwareApplication", @@ -24,16 +28,12 @@ "sc:license": "Artistic-2.0", "sc:name": "made4", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/made4.html", "sc:version": "1.48.0" - }, - { - "@id": "http://orcid.org/0000-0002-1395-9734", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/madora/madorabioschemas.jsonld b/data/madora/madorabioschemas.jsonld index 9150a6930387e..245ef3d9a080d 100644 --- a/data/madora/madorabioschemas.jsonld +++ b/data/madora/madorabioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:author": [ - "Lucie Houdová", - "Daniel Georgiev" + "Daniel Georgiev", + "Lucie Houdová" ], "sc:description": "A web application for processing and visualization of statistics for bone marrow donors registry - especially statistics of donors, executed searches for suitable donor, the typing and harvests before transplantation.", "sc:name": "MADORA", diff --git a/data/madseq/madseqbioschemas.jsonld b/data/madseq/madseqbioschemas.jsonld index c225c3eb6b754..40b51b94e9348 100644 --- a/data/madseq/madseqbioschemas.jsonld +++ b/data/madseq/madseqbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yu Kong", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides a group of hierarchical Bayesian models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.", "sc:license": "GPL-2.0", "sc:name": "MADSEQ", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MADSEQ.html", "sc:version": "1.0.0" diff --git a/data/maf/mafbioschemas.jsonld b/data/maf/mafbioschemas.jsonld index 5fae32792b023..991bfae95f3e6 100644 --- a/data/maf/mafbioschemas.jsonld +++ b/data/maf/mafbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it supports the widely used glass microarrays and oligo-chips, it was designed with the specific idiosyncrasies of Nylon based microarrays in mind.", "sc:name": "MAF", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://tagc.univ-mrs.fr/bioinformatics/maf/" diff --git a/data/mafft-dash/mafft-dashbioschemas.jsonld b/data/mafft-dash/mafft-dashbioschemas.jsonld index 9dbe41afb345e..be97c6d665c64 100644 --- a/data/mafft-dash/mafft-dashbioschemas.jsonld +++ b/data/mafft-dash/mafft-dashbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1093/NAR/GKZ342", "@type": "sc:CreativeWork" }, + { + "@id": "https://orcid.org/0000-0003-4133-8393", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/MAFFT-DASH", "@type": "sc:SoftwareApplication", @@ -23,40 +27,36 @@ } ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": [ - "pmcid:PMC6602451", - "pubmed:31062021", { "@id": "https://doi.org/10.1093/NAR/GKZ342" - } + }, + "pmcid:PMC6602451", + "pubmed:31062021" ], "sc:description": "Multiple alignment program for amino acid or nucleotide sequences.", "sc:featureList": [ { - "@id": "edam:operation_0509" + "@id": "edam:operation_0504" }, { "@id": "edam:operation_0503" }, { - "@id": "edam:operation_0504" + "@id": "edam:operation_0509" } ], "sc:license": "GPL-1.0", "sc:name": "MAFFT-DASH", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://mafft.cbrc.jp/alignment/server/" - }, - { - "@id": "https://orcid.org/0000-0003-4133-8393", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mafft/mafftbioschemas.jsonld b/data/mafft/mafftbioschemas.jsonld index 2e5aba484c7d2..1fe5a0c62e471 100644 --- a/data/mafft/mafftbioschemas.jsonld +++ b/data/mafft/mafftbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "MAFFT", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mafft.cbrc.jp/alignment/server/index.html" } \ No newline at end of file diff --git a/data/mafft_ebi/mafft_ebibioschemas.jsonld b/data/mafft_ebi/mafft_ebibioschemas.jsonld index 982da31e35d97..c3b0cafda5d1d 100644 --- a/data/mafft_ebi/mafft_ebibioschemas.jsonld +++ b/data/mafft_ebi/mafft_ebibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MAFFT (EBI)", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.ebi.ac.uk/Tools/msa/mafft/", "sc:version": "1" diff --git a/data/mafsnp/mafsnpbioschemas.jsonld b/data/mafsnp/mafsnpbioschemas.jsonld index 84db10d62f9d2..5820621d8c170 100644 --- a/data/mafsnp/mafsnpbioschemas.jsonld +++ b/data/mafsnp/mafsnpbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MAFsnp", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://homepage.fudan.edu.cn/zhangh/softwares/mafsnp/" } \ No newline at end of file diff --git a/data/maftools/maftoolsbioschemas.jsonld b/data/maftools/maftoolsbioschemas.jsonld index 5958bb6e1910f..021c9f273246c 100644 --- a/data/maftools/maftoolsbioschemas.jsonld +++ b/data/maftools/maftoolsbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Anand Mayakonda", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.", "sc:license": "MIT", "sc:name": "maftools", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/maftools.html", "sc:version": "1.0.30" diff --git a/data/magallanes/magallanesbioschemas.jsonld b/data/magallanes/magallanesbioschemas.jsonld index 165c203bb08ed..40af494e92fc4 100644 --- a/data/magallanes/magallanesbioschemas.jsonld +++ b/data/magallanes/magallanesbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-1554-8987", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-10-334", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/magallanes", "@type": "sc:SoftwareApplication", @@ -30,16 +38,16 @@ "sc:description": "A Platform-independent Java library of algorithms to built-up search engines to help in the discovery of services and datatypes specially oriented to deal with repositories of web-services and associated datatypes.", "sc:featureList": [ { - "@id": "edam:operation_3763" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_3695" + "@id": "edam:operation_3761" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_3695" }, { - "@id": "edam:operation_3761" + "@id": "edam:operation_3763" } ], "sc:license": "GPL-3.0", @@ -52,14 +60,6 @@ "sc:provider": "uma.es", "sc:url": "http://bitlab-es.com/magallanes/", "sc:version": "1" - }, - { - "@id": "https://orcid.org/0000-0003-1554-8987", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-10-334", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mage-ml_visualize/mage-ml_visualizebioschemas.jsonld b/data/mage-ml_visualize/mage-ml_visualizebioschemas.jsonld index 7b8c29ccc2a3d..4a14412c870cf 100644 --- a/data/mage-ml_visualize/mage-ml_visualizebioschemas.jsonld +++ b/data/mage-ml_visualize/mage-ml_visualizebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MAGE-ML visualize script will read any MAGE-ML file and generate a graph showing the links between BioMaterials all the way through to BioAssays, and include information on sample characteristics and experimental factor values in the output.", "sc:name": "MAGE-ML Visualize", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://tab2mage.sourceforge.net/#other_packages", "sc:version": "1.0" diff --git a/data/mageckflute/mageckflutebioschemas.jsonld b/data/mageckflute/mageckflutebioschemas.jsonld index 386028fa5dda4..fa5d04342cdbc 100644 --- a/data/mageckflute/mageckflutebioschemas.jsonld +++ b/data/mageckflute/mageckflutebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "MAGeCKFlute", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MAGeCKFlute.html", diff --git a/data/magecomet/magecometbioschemas.jsonld b/data/magecomet/magecometbioschemas.jsonld index 8180c02b27439..adb0c4462003a 100644 --- a/data/magecomet/magecometbioschemas.jsonld +++ b/data/magecomet/magecometbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An online tool that facilitates curation of MAGE-TAB. It combines text-mining and the Experimental Factor Ontology (EFO) to create a semi-automatic environment for faster annotation, guided data-manipulation and content summary.", "sc:name": "MageComet", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "EMBL-EBI", diff --git a/data/magellan/magellanbioschemas.jsonld b/data/magellan/magellanbioschemas.jsonld index a5dcb5296d4fb..edc0792dff14d 100644 --- a/data/magellan/magellanbioschemas.jsonld +++ b/data/magellan/magellanbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1186/s12711-016-0242-9", "@type": "sc:CreativeWork" }, + { + "@id": "http://orcid.org/0000-0001-6039-0838", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/magellan", "@type": "sc:SoftwareApplication", @@ -21,11 +25,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27613390", - "pmcid:PMC5018160", { "@id": "https://doi.org/10.1186/s12711-016-0242-9" - } + }, + "pmcid:PMC5018160", + "pubmed:27613390" ], "sc:description": "MaGelLAn is a software that facilitates quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information", "sc:featureList": { @@ -34,16 +38,12 @@ "sc:license": "Other", "sc:name": "MaGelLAn", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://lissp.irb.hr/software/magellan-1-0/", "sc:version": "1.0" - }, - { - "@id": "http://orcid.org/0000-0001-6039-0838", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/maggottracker/maggottrackerbioschemas.jsonld b/data/maggottracker/maggottrackerbioschemas.jsonld index 707d7eebbe4eb..016376d7526dd 100644 --- a/data/maggottracker/maggottrackerbioschemas.jsonld +++ b/data/maggottracker/maggottrackerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Single-animal tracking system for Drosophila larval locomotion analysis.", "sc:name": "MaggotTracker", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://wormloco.org/mag/doc/" diff --git a/data/magi/magibioschemas.jsonld b/data/magi/magibioschemas.jsonld index 968bb9c226d6f..cbb0fb8c79892 100644 --- a/data/magi/magibioschemas.jsonld +++ b/data/magi/magibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Publicly available web application to explore and annotate cancer genomics data.", "sc:name": "MAGI", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://magi.brown.edu/" diff --git a/data/magia2/magia2bioschemas.jsonld b/data/magia2/magia2bioschemas.jsonld index 53735f59080b7..cff10476d39cf 100644 --- a/data/magia2/magia2bioschemas.jsonld +++ b/data/magia2/magia2bioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Web tool for the integrative analysis of in silico target prediction, and reconstruction of post-transcriptional regulatory and mixed regulatory networks from miRNA and gene expression data.", "sc:name": "MAGIA2", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://gencomp.bio.unipd.it/magia2/start/" } \ No newline at end of file diff --git a/data/magic/magicbioschemas.jsonld b/data/magic/magicbioschemas.jsonld index 97cfa2a031d82..116de67a25d22 100644 --- a/data/magic/magicbioschemas.jsonld +++ b/data/magic/magicbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Magic", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/magic/", diff --git a/data/magic_ms/magic_msbioschemas.jsonld b/data/magic_ms/magic_msbioschemas.jsonld index 8cfb0cbf17c91..f9348021f7faf 100644 --- a/data/magic_ms/magic_msbioschemas.jsonld +++ b/data/magic_ms/magic_msbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 Approach.", "sc:name": "MAGIC", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://ms.iis.sinica.edu.tw/COmics/Software_MAGIC.html" } \ No newline at end of file diff --git a/data/magic_tool/magic_toolbioschemas.jsonld b/data/magic_tool/magic_toolbioschemas.jsonld index e7392f785b1c0..8a68b60e2759d 100644 --- a/data/magic_tool/magic_toolbioschemas.jsonld +++ b/data/magic_tool/magic_toolbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "MAGIC Tool is an integrated microarray data analysis software.", "sc:name": "MAGIC Tool", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.bio.davidson.edu/projects/magic/magic.html", diff --git a/data/magicviewer/magicviewerbioschemas.jsonld b/data/magicviewer/magicviewerbioschemas.jsonld index 724993856e5ff..077e2cfc5abcd 100644 --- a/data/magicviewer/magicviewerbioschemas.jsonld +++ b/data/magicviewer/magicviewerbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/magicviewer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Linglin Zhou", "Erle Zhu", - "Jinyu Wu", "Huabin Hou", + "Linglin Zhou", + "Jinyu Wu", "Zhongsheng Sun" ], "sc:additionalType": "Desktop application", "sc:description": "Large-scale short reads and sequencing depth visualization.", "sc:name": "MagicViewer", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioinformatics.zj.cn/magicviewer/index.php" } \ No newline at end of file diff --git a/data/magna/magnabioschemas.jsonld b/data/magna/magnabioschemas.jsonld index 20c3977fb95fd..188b2b8b94186 100644 --- a/data/magna/magnabioschemas.jsonld +++ b/data/magna/magnabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software tool for pairwise global network alignment. It is an extension of MAGNA. An example of an application domain where this tool is useful is computational biology – It can be used for biological network alignment.", "sc:name": "MAGNA++", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www3.nd.edu/~cone/MAGNA++/" } \ No newline at end of file diff --git a/data/magnet/magnetbioschemas.jsonld b/data/magnet/magnetbioschemas.jsonld index 4cf1ef98933b4..6046c443004dc 100644 --- a/data/magnet/magnetbioschemas.jsonld +++ b/data/magnet/magnetbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Microarray Gene Expression and Network Evaluation Toolkit (MAGNET) is a web tool with three components: generation of coexpression networks, weighted protein-protein interaction networks and bimodality of coexpression.", "sc:name": "MAGNET", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://magnet.case.edu" diff --git a/data/maigespack/bioconda_maigespack.yaml b/data/maigespack/bioconda_maigespack.yaml index 96c32f0970a4e..b040c359e7da3 100644 --- a/data/maigespack/bioconda_maigespack.yaml +++ b/data/maigespack/bioconda_maigespack.yaml @@ -4,7 +4,6 @@ description: This package uses functions of various other packages together with home: https://bioconductor.org/packages/3.10/bioc/html/maigesPack.html identifiers: - biotools:maigespack -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-maigespack diff --git a/data/maigespack/maigespackbioschemas.jsonld b/data/maigespack/maigespackbioschemas.jsonld index 4192e0a2b5022..cded98614b567 100644 --- a/data/maigespack/maigespackbioschemas.jsonld +++ b/data/maigespack/maigespackbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "maigesPack", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/maigesPack.html", "sc:version": "1.38.0" diff --git a/data/maistas/maistasbioschemas.jsonld b/data/maistas/maistasbioschemas.jsonld index 816b0992e4228..696eea434315e 100644 --- a/data/maistas/maistasbioschemas.jsonld +++ b/data/maistas/maistasbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/maistas", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Matteo Floris", - "Domenico Raimondo" + "Domenico Raimondo", + "Matteo Floris" ], "sc:additionalType": "Web application", "sc:description": "Fully automatic pipeline aimed at building and assessing three-dimensional models for alternative splicing isoforms.", "sc:name": "Maistas", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "ELIXIR-ITA-SAPIENZA", "sc:url": "http://maistas.bioinformatica.crs4.it/", diff --git a/data/mait/maitbioschemas.jsonld b/data/mait/maitbioschemas.jsonld index bd21c461545fd..10211021e9fd7 100644 --- a/data/mait/maitbioschemas.jsonld +++ b/data/mait/maitbioschemas.jsonld @@ -18,13 +18,13 @@ }, "edam:has_output": [ { - "@id": "edam:data_1636" + "@id": "edam:data_2884" }, { - "@id": "edam:data_2048" + "@id": "edam:data_1636" }, { - "@id": "edam:data_2884" + "@id": "edam:data_2048" } ], "sc:additionalType": [ @@ -41,10 +41,10 @@ ], "sc:citation": [ "pubmed:24642061", - "pmcid:PMC4071204", { "@id": "https://doi.org/10.1093/bioinformatics/btu136" - } + }, + "pmcid:PMC4071204" ], "sc:description": "This package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.", "sc:featureList": [ diff --git a/data/majiq-spel/majiq-spelbioschemas.jsonld b/data/majiq-spel/majiq-spelbioschemas.jsonld index 818e54a9f12c8..8bdeb057aa27c 100644 --- a/data/majiq-spel/majiq-spelbioschemas.jsonld +++ b/data/majiq-spel/majiq-spelbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yoseph Barash", "sc:additionalType": [ - "Web API", + "Web service", "Command-line tool", - "Web service" + "Web API" ], "sc:description": "Web-tool to interrogate classical and complex splicing variations from RNA-Seq data.", "sc:license": "Unlicense", diff --git a/data/makecdfenv/makecdfenvbioschemas.jsonld b/data/makecdfenv/makecdfenvbioschemas.jsonld index ac21d318a36b9..81cb74134ed5a 100644 --- a/data/makecdfenv/makecdfenvbioschemas.jsonld +++ b/data/makecdfenv/makecdfenvbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "makecdfenv", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/makecdfenv.html", "sc:version": "1.50.0" diff --git a/data/makenucseq/makenucseqbioschemas.jsonld b/data/makenucseq/makenucseqbioschemas.jsonld index 2d22894ced0dd..284da7c623df4 100644 --- a/data/makenucseq/makenucseqbioschemas.jsonld +++ b/data/makenucseq/makenucseqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Create random nucleotide sequences.", "sc:funder": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "makenucseq", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/makenucseq.html", "sc:version": "r6" diff --git a/data/makeprotseq/makeprotseqbioschemas.jsonld b/data/makeprotseq/makeprotseqbioschemas.jsonld index 66881e8463e7c..426cd23a66c52 100644 --- a/data/makeprotseq/makeprotseqbioschemas.jsonld +++ b/data/makeprotseq/makeprotseqbioschemas.jsonld @@ -13,9 +13,9 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "UK BBSRC", "UK MRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Create random protein sequences.", "sc:funder": [ @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "makeprotseq", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/maker/makerbioschemas.jsonld b/data/maker/makerbioschemas.jsonld index 2bc9353d0dbb0..dd986998015cb 100644 --- a/data/maker/makerbioschemas.jsonld +++ b/data/maker/makerbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1101/gr.6743907", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/maker", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC2134774", { "@id": "https://doi.org/10.1101/gr.6743907" }, - "pubmed:18025269", - "pmcid:PMC2134774" + "pubmed:18025269" ], "sc:description": "Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.", "sc:featureList": { @@ -32,6 +28,10 @@ "sc:name": "MAKER", "sc:operatingSystem": "Linux", "sc:url": "http://www.yandell-lab.org/software/maker.html" + }, + { + "@id": "https://doi.org/10.1101/gr.6743907", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/maketssdist/maketssdistbioschemas.jsonld b/data/maketssdist/maketssdistbioschemas.jsonld index a992f4d36b7d1..6dd6d09ca68d2 100644 --- a/data/maketssdist/maketssdistbioschemas.jsonld +++ b/data/maketssdist/maketssdistbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Get peak distribution around TSS.", "sc:name": "maketssdist", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/maketssdist/makeTSSdist/1.0", "sc:version": "1.0" diff --git a/data/mala/malabioschemas.jsonld b/data/mala/malabioschemas.jsonld index 73d9ba9e77ef5..1444ee9c3a23b 100644 --- a/data/mala/malabioschemas.jsonld +++ b/data/mala/malabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Designed for the analysis of Microarray data. The rational data representing the gene expressions is discretized into a limited number of intervals for each cell of the array; the obtained discrete variables are then used to select a small subset of the genes that have strong discriminating power for the considered classes. The optimization algorithms for feature selection and logic formula extraction are then used to identify networks of genes that characterize the classes.", "sc:name": "MALA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://dmb.iasi.cnr.it/mala.php" } \ No newline at end of file diff --git a/data/malakite/malakitebioschemas.jsonld b/data/malakite/malakitebioschemas.jsonld index b11864352ea62..a514437913d18 100644 --- a/data/malakite/malakitebioschemas.jsonld +++ b/data/malakite/malakitebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A program for automatic detection of aligned blocks in multiple protein alignment.", "sc:name": "Malakite", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://mouse.belozersky.msu.ru/tools/malakite.html" } \ No newline at end of file diff --git a/data/malaria_data_small_molecule_search/malaria_data_small_molecule_searchbioschemas.jsonld b/data/malaria_data_small_molecule_search/malaria_data_small_molecule_searchbioschemas.jsonld index 8d1fdda54078b..f163ab1b04059 100644 --- a/data/malaria_data_small_molecule_search/malaria_data_small_molecule_searchbioschemas.jsonld +++ b/data/malaria_data_small_molecule_search/malaria_data_small_molecule_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Search against small molecules stored in Malaria Data database.", "sc:name": "Malaria Data Small Molecule Search", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "https://www.ebi.ac.uk/chembl/malaria/compound", diff --git a/data/malax/malaxbioschemas.jsonld b/data/malax/malaxbioschemas.jsonld index e27f7e7f0d890..7acb3350f1940 100644 --- a/data/malax/malaxbioschemas.jsonld +++ b/data/malax/malaxbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/malax", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Eran Halperin", - "Omer Weissbrod" + "Omer Weissbrod", + "Eran Halperin" ], "sc:additionalType": "Command-line tool", "sc:description": "Association testing of bisulfite sequencing methylation data via a Laplace approximation.", "sc:name": "MALAX", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/omerwe/MALAX" } \ No newline at end of file diff --git a/data/maldipepquant/maldipepquantbioschemas.jsonld b/data/maldipepquant/maldipepquantbioschemas.jsonld index ec4753046a5f0..5745eac0c9a26 100644 --- a/data/maldipepquant/maldipepquantbioschemas.jsonld +++ b/data/maldipepquant/maldipepquantbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool to quantify MALDI peptides (SILAC) from Phenyx output", "sc:name": "MALDIPepQuant", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://web.expasy.org/maldipepquant/" } \ No newline at end of file diff --git a/data/maldsoft/maldsoftbioschemas.jsonld b/data/maldsoft/maldsoftbioschemas.jsonld index 3f9f7e67440a7..b1d83cde5daae 100644 --- a/data/maldsoft/maldsoftbioschemas.jsonld +++ b/data/maldsoft/maldsoftbioschemas.jsonld @@ -15,10 +15,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC1182107", + "pubmed:15386213", { "@id": "https://doi.org/10.1086/425281" - }, - "pubmed:15386213" + } ], "sc:description": "Admixture mapping of complex trait loci, using case-control data.", "sc:featureList": { @@ -27,9 +27,9 @@ "sc:license": "Not licensed", "sc:name": "MALDsoft", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://web.stanford.edu/group/pritchardlab/software/maldsoft_download.html" }, diff --git a/data/maltcms/maltcmsbioschemas.jsonld b/data/maltcms/maltcmsbioschemas.jsonld index 099e517b8daef..ff190dea79334 100644 --- a/data/maltcms/maltcmsbioschemas.jsonld +++ b/data/maltcms/maltcmsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Maltcms", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://maltcms.sourceforge.net/", "sc:version": "1.3.0" diff --git a/data/mammalian_gene_collection/mammalian_gene_collectionbioschemas.jsonld b/data/mammalian_gene_collection/mammalian_gene_collectionbioschemas.jsonld index 4dbba2b200e4d..efaee1e875596 100644 --- a/data/mammalian_gene_collection/mammalian_gene_collectionbioschemas.jsonld +++ b/data/mammalian_gene_collection/mammalian_gene_collectionbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Mammalian Gene Collection", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://mgc.nci.nih.gov/" } \ No newline at end of file diff --git a/data/mamodel/mamodelbioschemas.jsonld b/data/mamodel/mamodelbioschemas.jsonld index cdb3885422394..56dee67a79c32 100644 --- a/data/mamodel/mamodelbioschemas.jsonld +++ b/data/mamodel/mamodelbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It is a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization.", "sc:name": "MAmodel", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.cs.tut.fi/sgn/csb/mamodel/", "sc:version": "20060511" diff --git a/data/mamphea/mampheabioschemas.jsonld b/data/mamphea/mampheabioschemas.jsonld index 64274b6d1c5ad..5354b89a7db83 100644 --- a/data/mamphea/mampheabioschemas.jsonld +++ b/data/mamphea/mampheabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MamPhEA is a web application dedicated to understanding functional properties of mammalian gene sets based on mouse-mutant phenotypes.", "sc:name": "MamPhEA", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://evol.nhri.org.tw/phenome/index.jsp?platform=mmus" } \ No newline at end of file diff --git a/data/manhattan_harvester/manhattan_harvesterbioschemas.jsonld b/data/manhattan_harvester/manhattan_harvesterbioschemas.jsonld index 7941f084f22ea..9dbd2635314a1 100644 --- a/data/manhattan_harvester/manhattan_harvesterbioschemas.jsonld +++ b/data/manhattan_harvester/manhattan_harvesterbioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2600-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Manhattan_Harvester", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "T. Haller", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6330393", "pubmed:30634901", + "pmcid:PMC6330393", { "@id": "https://doi.org/10.1186/s12859-019-2600-4" } @@ -28,10 +24,10 @@ "sc:description": "Tool for automatically detecting and characterizing peaks from GWAS output files (Manhattan Plots).", "sc:featureList": [ { - "@id": "edam:operation_3222" + "@id": "edam:operation_3215" }, { - "@id": "edam:operation_3215" + "@id": "edam:operation_3222" }, { "@id": "edam:operation_3557" @@ -41,10 +37,14 @@ "sc:name": "Manhattan Harvester", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.geenivaramu.ee/en/tools/manhattan-harvester" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2600-4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/manor/manorbioschemas.jsonld b/data/manor/manorbioschemas.jsonld index e6a0056cb801b..5148cb14d5158 100644 --- a/data/manor/manorbioschemas.jsonld +++ b/data/manor/manorbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "MANOR", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MANOR.html", diff --git a/data/manorm/manormbioschemas.jsonld b/data/manorm/manormbioschemas.jsonld index a7fac4f59d2be..fbcb133fb845e 100644 --- a/data/manorm/manormbioschemas.jsonld +++ b/data/manorm/manormbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Simple and effective method for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications.", "sc:name": "MAnorm", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm" } \ No newline at end of file diff --git a/data/manta/bioconda_manta.yaml b/data/manta/bioconda_manta.yaml index 2ac49b1740e9c..13b181599a46f 100644 --- a/data/manta/bioconda_manta.yaml +++ b/data/manta/bioconda_manta.yaml @@ -3,7 +3,6 @@ description: Tools for robust comparative metatranscriptomics. home: https://bioconductor.org/packages/3.10/bioc/html/manta.html identifiers: - biotools:manta -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-manta summary: Microbial Assemblage Normalized Transcript Analysis diff --git a/data/manta/mantabioschemas.jsonld b/data/manta/mantabioschemas.jsonld index e70d311f945c3..c9956d5537392 100644 --- a/data/manta/mantabioschemas.jsonld +++ b/data/manta/mantabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/manta", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Adrian Marchetti", - "Chris Berthiaume" + "Chris Berthiaume", + "Adrian Marchetti" ], "sc:additionalType": [ "Command-line tool", @@ -22,9 +22,9 @@ "sc:license": "Artistic-2.0", "sc:name": "manta", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/manta.html", "sc:version": "1.20.0" diff --git a/data/mantelcorr/bioconda_mantelcorr.yaml b/data/mantelcorr/bioconda_mantelcorr.yaml index a630a6c5c979c..b49b1f859340c 100644 --- a/data/mantelcorr/bioconda_mantelcorr.yaml +++ b/data/mantelcorr/bioconda_mantelcorr.yaml @@ -4,7 +4,6 @@ description: Computes Mantel cluster correlations from a (p x n) numeric data ma home: https://bioconductor.org/packages/3.10/bioc/html/MantelCorr.html identifiers: - biotools:mantelcorr -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-mantelcorr diff --git a/data/mantis/mantisbioschemas.jsonld b/data/mantis/mantisbioschemas.jsonld index c34730d915e24..599c4615c711a 100644 --- a/data/mantis/mantisbioschemas.jsonld +++ b/data/mantis/mantisbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:26017358", - "pmcid:PMC4445977", { "@id": "https://doi.org/10.1186/S12859-015-0598-9" - } + }, + "pmcid:PMC4445977" ], "sc:description": "An R package that simulates multilocus models of pathogen evolution.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "MANTIS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://www.eeid.ox.ac.uk/mantis" } diff --git a/data/mantra/mantrabioschemas.jsonld b/data/mantra/mantrabioschemas.jsonld index 2e8f60dc5c4f4..1afca269d8083 100644 --- a/data/mantra/mantrabioschemas.jsonld +++ b/data/mantra/mantrabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computational tool for the analysis of the Mode of Action (MoA) of novel drugs and the identification of known and approved candidates for “drug repositioning”. It is based on network theory and non-parametric statistics on gene expression data.", "sc:name": "MANTRA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mantra.tigem.it/" } \ No newline at end of file diff --git a/data/mapanalyzer/mapanalyzerbioschemas.jsonld b/data/mapanalyzer/mapanalyzerbioschemas.jsonld index 4d68c24dbfa44..ba953e1688d44 100644 --- a/data/mapanalyzer/mapanalyzerbioschemas.jsonld +++ b/data/mapanalyzer/mapanalyzerbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/mapanalyzer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Shiping Yang (for database-related issues)", - "Yuan Zhou (for prediction server-related issues)" + "Yuan Zhou (for prediction server-related issues)", + "Shiping Yang (for database-related issues)" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:26568329", "sc:description": "MAP (Microtubule-associated Proteins) analysis tool.", "sc:name": "MAPanalyzer", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://systbio.cau.edu.cn/mappred/" diff --git a/data/mapdamage/mapdamagebioschemas.jsonld b/data/mapdamage/mapdamagebioschemas.jsonld index ec132a63cac7b..663325d31e329 100644 --- a/data/mapdamage/mapdamagebioschemas.jsonld +++ b/data/mapdamage/mapdamagebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:description": "Identify and quantify DNA damage patterns in ancient DNA.", "sc:name": "MapDamage", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ginolhac.github.io/mapDamage/" } \ No newline at end of file diff --git a/data/mapdia/mapdiabioschemas.jsonld b/data/mapdia/mapdiabioschemas.jsonld index 36d3f67e1208c..a5ef185fb5d41 100644 --- a/data/mapdia/mapdiabioschemas.jsonld +++ b/data/mapdia/mapdiabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Performs essential data preprocessing, including novel retention time-based normalization method and a sequence of peptide/fragment selection steps, and more importantly, hierarchical model-based statistical significance analysis for multi-group comparisons under representative experimental designs.", "sc:name": "MAPDIA", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sourceforge.net/projects/mapdia/." } \ No newline at end of file diff --git a/data/mapdisto/mapdistobioschemas.jsonld b/data/mapdisto/mapdistobioschemas.jsonld index 7b566c6aff8e3..e97e5cb41a26d 100644 --- a/data/mapdisto/mapdistobioschemas.jsonld +++ b/data/mapdisto/mapdistobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MAPDISTO", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://mapdisto.free.fr/MapDisto/", "sc:version": "1.8.1" diff --git a/data/mapexr/mapexrbioschemas.jsonld b/data/mapexr/mapexrbioschemas.jsonld index 2b54c0b5cf899..1ab6f26a883ec 100644 --- a/data/mapexr/mapexrbioschemas.jsonld +++ b/data/mapexr/mapexrbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Brian K Mannakee", - "Erik S Knudsen", - "Ryan N Gutenkunst" + "Ryan N Gutenkunst", + "Erik S Knudsen" ], "sc:additionalType": "Library", "sc:description": "The algorithm is a post-variant-calling filter for variants that uses BLASTN to determine the fraction of reads supporting a variant call that align best to the site of the variant.", "sc:license": "MIT", "sc:name": "mapexr", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/bmannakee/mapexr" } \ No newline at end of file diff --git a/data/mapi/mapibioschemas.jsonld b/data/mapi/mapibioschemas.jsonld index d0e0443a62c4c..196415b208403 100644 --- a/data/mapi/mapibioschemas.jsonld +++ b/data/mapi/mapibioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bib/bbs017", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mapi", "@type": "sc:SoftwareApplication", @@ -20,21 +16,21 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC3558448", + "pubmed:22517427", { "@id": "https://doi.org/10.1093/bib/bbs017" - }, - "pubmed:22517427" + } ], "sc:description": "Framework for the development of desktop client applications. It is able to integrate meta-data of different Web-services catalogues. Its main characteristic is that it is modular and adaptable to different usage scenarios.", "sc:featureList": [ { - "@id": "edam:operation_3760" + "@id": "edam:operation_3436" }, { "@id": "edam:operation_3429" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_3760" } ], "sc:license": "GPL-3.0", @@ -43,6 +39,10 @@ "sc:provider": "uma.es", "sc:url": "http://bitlab-es.com/mapi/", "sc:version": "1" + }, + { + "@id": "https://doi.org/10.1093/bib/bbs017", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mapkl/mapklbioschemas.jsonld b/data/mapkl/mapklbioschemas.jsonld index 5bd4fb07c53d0..78b5ed758d5da 100644 --- a/data/mapkl/mapklbioschemas.jsonld +++ b/data/mapkl/mapklbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Argiris Sakellariou", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "We propose a hybrid FS method, which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes.", "sc:license": "GPL-2.0", diff --git a/data/mapman/mapmanbioschemas.jsonld b/data/mapman/mapmanbioschemas.jsonld index 998010359c03a..dc526d26a35cd 100644 --- a/data/mapman/mapmanbioschemas.jsonld +++ b/data/mapman/mapmanbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MapMan", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://mapman.gabipd.org/web/guest/home" } \ No newline at end of file diff --git a/data/mapmi/mapmibioschemas.jsonld b/data/mapmi/mapmibioschemas.jsonld index fe9ae30d123c2..b8a2b6eebc13a 100644 --- a/data/mapmi/mapmibioschemas.jsonld +++ b/data/mapmi/mapmibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MapMi", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/enright-srv/MapMi/", diff --git a/data/mapoptics/mapopticsbioschemas.jsonld b/data/mapoptics/mapopticsbioschemas.jsonld index 0e6b2879cbc06..47d7561841d38 100644 --- a/data/mapoptics/mapopticsbioschemas.jsonld +++ b/data/mapoptics/mapopticsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MapOptics", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/FadyMohareb/mapoptics" } \ No newline at end of file diff --git a/data/mapp/mappbioschemas.jsonld b/data/mapp/mappbioschemas.jsonld index 726536b04fe73..127876156bac1 100644 --- a/data/mapp/mappbioschemas.jsonld +++ b/data/mapp/mappbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Not licensed", "sc:name": "MAPP", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://mendel.stanford.edu/SidowLab/downloads/MAPP/index.html" } \ No newline at end of file diff --git a/data/mapping_tool/mapping_toolbioschemas.jsonld b/data/mapping_tool/mapping_toolbioschemas.jsonld index c7e1a00d5e2ee..6a71b46c2f12f 100644 --- a/data/mapping_tool/mapping_toolbioschemas.jsonld +++ b/data/mapping_tool/mapping_toolbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Mapping Tool", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.csb.ethz.ch/tools/mapping-tool", "sc:version": "1.3" diff --git a/data/mappinghsp4taxo/mappinghsp4taxobioschemas.jsonld b/data/mappinghsp4taxo/mappinghsp4taxobioschemas.jsonld index 04ed71f63087f..a696d50a919ee 100644 --- a/data/mappinghsp4taxo/mappinghsp4taxobioschemas.jsonld +++ b/data/mappinghsp4taxo/mappinghsp4taxobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Analyses taxoptimizer output file to find the most relevant database's sequence using taxonomics informations (kronaextract output) and draw picture(s) with the mapping of all hsp on it.", "sc:name": "mappinghsp4taxo", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/taxonomy_analysis/mappinghsp4taxo/0.0.2", diff --git a/data/mappis/mappisbioschemas.jsonld b/data/mappis/mappisbioschemas.jsonld index ed60c5a37dfb2..bf1755c1f5dde 100644 --- a/data/mappis/mappisbioschemas.jsonld +++ b/data/mappis/mappisbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Multiple Alignment of Protein-Protein Interfaces (MAPPIS) is a tool for the recognition of spatially conserved chemical interactions shared by a set of protein-protein interfaces or regions of protein interaction. Users input a set of protein-protein complexes and MAPPIS returns a list of shared interaction properties of the interfaces.", "sc:name": "MAPPIS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/MAPPIS" } \ No newline at end of file diff --git a/data/mappop/mappopbioschemas.jsonld b/data/mappop/mappopbioschemas.jsonld index ec7264de0f870..96bd272c27e50 100644 --- a/data/mappop/mappopbioschemas.jsonld +++ b/data/mappop/mappopbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:10790413", - "pmcid:PMC1461083" + "pmcid:PMC1461083", + "pubmed:10790413" ], "sc:description": "MapPop is a software for choosing good samples from mapping populations and for locating new markers on pre-existing maps.", "sc:name": "MapPop", diff --git a/data/mapredictdsc/mapredictdscbioschemas.jsonld b/data/mapredictdsc/mapredictdscbioschemas.jsonld index 2c55d571585c8..b76977a1ffbe5 100644 --- a/data/mapredictdsc/mapredictdscbioschemas.jsonld +++ b/data/mapredictdsc/mapredictdscbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Adi Laurentiu Tarca", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.", "sc:license": "GPL-2.0", diff --git a/data/maps/mapsbioschemas.jsonld b/data/maps/mapsbioschemas.jsonld index 1584dd6a57d8c..bf8758ee37186 100644 --- a/data/maps/mapsbioschemas.jsonld +++ b/data/maps/mapsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pcbi.1006982", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/MAPS", "@type": "sc:SoftwareApplication", @@ -18,8 +22,8 @@ ], "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC6483256", "pubmed:30986246", + "pmcid:PMC6483256", { "@id": "https://doi.org/10.1371/journal.pcbi.1006982" } @@ -27,13 +31,13 @@ "sc:description": "MAPS (Model-based Analysis of PLAC-Seq data) pipeline is a a set of multiple scripts used to analyze PLAC-Seq and HiChIP data.", "sc:featureList": [ { - "@id": "edam:operation_3798" + "@id": "edam:operation_3222" }, { "@id": "edam:operation_2429" }, { - "@id": "edam:operation_3222" + "@id": "edam:operation_3798" } ], "sc:name": "MAPS", @@ -42,10 +46,6 @@ "Mac" ], "sc:url": "https://github.com/ijuric/MAPS" - }, - { - "@id": "https://doi.org/10.1371/journal.pcbi.1006982", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mapscape/mapscapebioschemas.jsonld b/data/mapscape/mapscapebioschemas.jsonld index 14f77240e374e..c6f1c926c3f32 100644 --- a/data/mapscape/mapscapebioschemas.jsonld +++ b/data/mapscape/mapscapebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "MapScape", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bioconductor.org/packages/release/bioc/html/mapscape.html" } \ No newline at end of file diff --git a/data/mapview/mapviewbioschemas.jsonld b/data/mapview/mapviewbioschemas.jsonld index 9cac9ece0fc16..677c1ea110081 100644 --- a/data/mapview/mapviewbioschemas.jsonld +++ b/data/mapview/mapviewbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/mapview", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hua Bao", - "Suhua Shi" + "Suhua Shi", + "Hua Bao" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:19369497", "sc:description": "An information-rich short reads alignment viewer with genetic detection capability for next-generation sequencing technologies. It supports a compact alignment view for both single-end and pair-end short reads, multiple navigation and zoom modes, and multi-thread processing. It offers automated genetic variation detection.", "sc:name": "MapView", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://evolution.sysu.edu.cn/mapview/" } \ No newline at end of file diff --git a/data/maq/maqbioschemas.jsonld b/data/maq/maqbioschemas.jsonld index 3b220eedf3721..378ccd28fd649 100644 --- a/data/maq/maqbioschemas.jsonld +++ b/data/maq/maqbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-14-184", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/maq", "@type": "sc:SoftwareApplication", @@ -21,13 +17,13 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:23758764", "pmcid:PMC2577856", "pmcid:PMC3694458", + "pubmed:23758764", + "pubmed:18714091", { "@id": "https://doi.org/10.1101/gr.078212.108" }, - "pubmed:18714091", { "@id": "https://doi.org/10.1186/1471-2105-14-184" } @@ -44,6 +40,10 @@ ], "sc:url": "http://maq.sourceforge.net/" }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-184", + "@type": "sc:CreativeWork" + }, { "@id": "https://doi.org/10.1101/gr.078212.108", "@type": "sc:CreativeWork" diff --git a/data/marcat/marcatbioschemas.jsonld b/data/marcat/marcatbioschemas.jsonld index 99bc9ac0d80cf..dfda3d42fc550 100644 --- a/data/marcat/marcatbioschemas.jsonld +++ b/data/marcat/marcatbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "CC-BY-NC-ND-3.0", "sc:name": "MarCat", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://mmp.sfb.uit.no/databases/", diff --git a/data/marcoil/marcoilbioschemas.jsonld b/data/marcoil/marcoilbioschemas.jsonld index a5839b101261d..28425f5775bc2 100644 --- a/data/marcoil/marcoilbioschemas.jsonld +++ b/data/marcoil/marcoilbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "predicting coiled-coils in protein sequences", "sc:name": "MARCOIL", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bcf.isb-sib.ch/webmarcoil/webmarcoilINFOC1.html" } \ No newline at end of file diff --git a/data/mardb/mardbbioschemas.jsonld b/data/mardb/mardbbioschemas.jsonld index 9e67e3e887cb2..5e9ea228b6fe7 100644 --- a/data/mardb/mardbbioschemas.jsonld +++ b/data/mardb/mardbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-NC-ND-3.0", "sc:name": "MarDB", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://mmp.sfb.uit.no/databases/mardb/", "sc:version": "1.0" diff --git a/data/marea/mareabioschemas.jsonld b/data/marea/mareabioschemas.jsonld index 41f1ee060e482..45720c85d21d1 100644 --- a/data/marea/mareabioschemas.jsonld +++ b/data/marea/mareabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool to evaluate the effectiveness of no-take marine reserves.", "sc:name": "MAREA", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/turfeffect/MAREA" diff --git a/data/marginalcausality/marginalcausalitybioschemas.jsonld b/data/marginalcausality/marginalcausalitybioschemas.jsonld index dd297e85f057e..e486bf36cfa2e 100644 --- a/data/marginalcausality/marginalcausalitybioschemas.jsonld +++ b/data/marginalcausality/marginalcausalitybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MarginalCausality", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/Monneret/MarginalCausality" } \ No newline at end of file diff --git a/data/mariboes/mariboesbioschemas.jsonld b/data/mariboes/mariboesbioschemas.jsonld index 172c287ecc36f..93f2b6b59110e 100644 --- a/data/mariboes/mariboesbioschemas.jsonld +++ b/data/mariboes/mariboesbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MaRIboES", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://trac.nbic.nl/mariboes/" } \ No newline at end of file diff --git a/data/markduplicates_ip/markduplicates_ipbioschemas.jsonld b/data/markduplicates_ip/markduplicates_ipbioschemas.jsonld index f2389c45646ea..af373f4bbc4cb 100644 --- a/data/markduplicates_ip/markduplicates_ipbioschemas.jsonld +++ b/data/markduplicates_ip/markduplicates_ipbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Marks all duplicate reads in a provided SAM or BAM file and either removes them or flags them.", "sc:name": "MarkDuplicates (IP)", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/picard_pasteur_wrapper/rgPicardMarkDups/1.56.0", "sc:version": "1.56.0" diff --git a/data/markophylo/markophylobioschemas.jsonld b/data/markophylo/markophylobioschemas.jsonld index 4b944fa8c93a9..09f1235a11cdf 100644 --- a/data/markophylo/markophylobioschemas.jsonld +++ b/data/markophylo/markophylobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data.", "sc:name": "markophylo", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/markophylo/" } \ No newline at end of file diff --git a/data/markus/markusbioschemas.jsonld b/data/markus/markusbioschemas.jsonld index a723b7d789f57..e0a02db7a0d4e 100644 --- a/data/markus/markusbioschemas.jsonld +++ b/data/markus/markusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "MarkUs is a web server for analysis and comparison of the structural and functional properties of proteins.", "sc:name": "MarkUs", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-Us" } \ No newline at end of file diff --git a/data/marmoset/marmosetbioschemas.jsonld b/data/marmoset/marmosetbioschemas.jsonld index 3d64324d6fd29..b3ff85404fc05 100644 --- a/data/marmoset/marmosetbioschemas.jsonld +++ b/data/marmoset/marmosetbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/MARMoSET", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Johannes Graumann", - "Mario Looso" + "Mario Looso", + "Johannes Graumann" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:31097673", @@ -20,9 +20,9 @@ "sc:license": "MIT", "sc:name": "MARMoSET", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.molgen.mpg.de/loosolab/MARMoSET_C" } \ No newline at end of file diff --git a/data/marna/marnabioschemas.jsonld b/data/marna/marnabioschemas.jsonld index 62f6847cb509c..b71ace158ef76 100644 --- a/data/marna/marnabioschemas.jsonld +++ b/data/marna/marnabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-8231-3323", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/marna", "@type": "sc:SoftwareApplication", @@ -24,20 +28,16 @@ "sc:description": "Sequence-structure alignment of RNAs.", "sc:name": "MARNA web server", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ - "rnateam", - "University Freiburg" + "University Freiburg", + "rnateam" ], "sc:url": "http://rna.informatik.uni-freiburg.de/MARNA/", "sc:version": "1.0.0" - }, - { - "@id": "http://orcid.org/0000-0001-8231-3323", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/marray/marraybioschemas.jsonld b/data/marray/marraybioschemas.jsonld index 19e41431ce88a..2672c71a4504c 100644 --- a/data/marray/marraybioschemas.jsonld +++ b/data/marray/marraybioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yee Hwa (Jean) Yang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.", "sc:license": "GPL-3.0", diff --git a/data/marref/marrefbioschemas.jsonld b/data/marref/marrefbioschemas.jsonld index 9161f67d6b619..f54f5163bfa40 100644 --- a/data/marref/marrefbioschemas.jsonld +++ b/data/marref/marrefbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "CC-BY-NC-ND-3.0", "sc:name": "MarRef", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://mmp.sfb.uit.no/databases/", "sc:version": "1.0" diff --git a/data/marscan/marscanbioschemas.jsonld b/data/marscan/marscanbioschemas.jsonld index f83cbbacfc9d5..e42ec5b018242 100644 --- a/data/marscan/marscanbioschemas.jsonld +++ b/data/marscan/marscanbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK MRC", + "EMBOSS Contributors", "UK BBSRC", - "EMBOSS Contributors" + "Wellcome Trust", + "UK MRC" ], "sc:description": "Find matrix/scaffold recognition (MRS) signatures in DNA sequences.", "sc:funder": [ - "Wellcome Trust", "UK MRC", + "Wellcome Trust", "UK BBSRC" ], "sc:license": "GPL-3.0", @@ -31,8 +31,8 @@ "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/marscan.html", "sc:version": "r6" diff --git a/data/marspred/marspredbioschemas.jsonld b/data/marspred/marspredbioschemas.jsonld index 479d231bec011..226f958f30c70 100644 --- a/data/marspred/marspredbioschemas.jsonld +++ b/data/marspred/marspredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Prediction method  for discrimination between Mitochondrial-AARSs and Cytosolic-AARSs.", "sc:name": "MARSpred", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/marspred/" diff --git a/data/martini/martinibioschemas.jsonld b/data/martini/martinibioschemas.jsonld index 749699af94970..6af98396dfbb2 100644 --- a/data/martini/martinibioschemas.jsonld +++ b/data/martini/martinibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "martini", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/martini.html", "sc:version": "1.0.0" diff --git a/data/martview/martviewbioschemas.jsonld b/data/martview/martviewbioschemas.jsonld index 4a3434c9f22af..60d315df746f0 100644 --- a/data/martview/martviewbioschemas.jsonld +++ b/data/martview/martviewbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for data retrieval and data mining that integrates data from Ensembl. Through the web interface it allows you to apply a series of filters to create custom datasets which can be converted to several useful output formats.", "sc:name": "MartView", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.biomart.org/biomart/martview/" } \ No newline at end of file diff --git a/data/marv/marvbioschemas.jsonld b/data/marv/marvbioschemas.jsonld index 56a77cb042021..ed141ab52747f 100644 --- a/data/marv/marvbioschemas.jsonld +++ b/data/marv/marvbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1530-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/marv", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Marika Kaakinen", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5311849", "pubmed:28209135", { "@id": "https://doi.org/10.1186/s12859-017-1530-2" - }, - "pmcid:PMC5311849" + } ], "sc:description": "Multi-phenotype Analysis of Rare Variants.", "sc:featureList": { @@ -36,6 +32,10 @@ "Linux" ], "sc:url": "https://github.com/ImperialStatGen/MARV" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1530-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/masc/mascbioschemas.jsonld b/data/masc/mascbioschemas.jsonld index d0b73eed65f4e..85773a5e006bf 100644 --- a/data/masc/mascbioschemas.jsonld +++ b/data/masc/mascbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Perl implementation of our MaSC approach to estimating fragment length from short-read high-throughput sequencing data.", "sc:name": "MaSC", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.perkinslab.ca/Software.html" diff --git a/data/mascot/mascotbioschemas.jsonld b/data/mascot/mascotbioschemas.jsonld index 4a190d77c7e85..4966a74976b2a 100644 --- a/data/mascot/mascotbioschemas.jsonld +++ b/data/mascot/mascotbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Proprietary", "sc:name": "Mascot Server", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.matrixscience.com/server.html" } \ No newline at end of file diff --git a/data/mascot2xml/mascot2xmlbioschemas.jsonld b/data/mascot2xml/mascot2xmlbioschemas.jsonld index 2efa70067e22e..b67acc91c2d6d 100644 --- a/data/mascot2xml/mascot2xmlbioschemas.jsonld +++ b/data/mascot2xml/mascot2xmlbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mascot2xml", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "Converts Mascot search results in .dat files to pepXML (.xml) format.", "sc:name": "Mascot2XML", diff --git a/data/mascot_parser/mascot_parserbioschemas.jsonld b/data/mascot_parser/mascot_parserbioschemas.jsonld index 70bc98d2a813e..fb4f3baee0d06 100644 --- a/data/mascot_parser/mascot_parserbioschemas.jsonld +++ b/data/mascot_parser/mascot_parserbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Proprietary", "sc:name": "Mascot Parser", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.matrixscience.com/msparser.html" } \ No newline at end of file diff --git a/data/mascotdatfile/mascotdatfilebioschemas.jsonld b/data/mascotdatfile/mascotdatfilebioschemas.jsonld index f265e0c6bbe0a..702d51fb0f370 100644 --- a/data/mascotdatfile/mascotdatfilebioschemas.jsonld +++ b/data/mascotdatfile/mascotdatfilebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A library to fully parse and analyse MASCOT MS/MS search results.", "sc:name": "Mascotdatfile", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://compomics.github.io/projects/mascotdatfile.html", diff --git a/data/mascp_gator/mascp_gatorbioschemas.jsonld b/data/mascp_gator/mascp_gatorbioschemas.jsonld index ab4d314bd67a4..cd31410cd0ecc 100644 --- a/data/mascp_gator/mascp_gatorbioschemas.jsonld +++ b/data/mascp_gator/mascp_gatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Proteomics aggregation utility  that queries and aggregates information from a variety of online Arabidopsis proteomic resources.", "sc:name": "MASCP Gator", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://gator.masc-proteomics.org/" } \ No newline at end of file diff --git a/data/mase/masebioschemas.jsonld b/data/mase/masebioschemas.jsonld index 308794eeee3a6..7b16e5ae46a32 100644 --- a/data/mase/masebioschemas.jsonld +++ b/data/mase/masebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool designed to simplify the manipulation of aligned sequence sets. It contains functionality for many of the common tasks related to this goal. In addition, mase was designed with a very modular approach, making additions or modifications to the code straightforward.", "sc:name": "MASE", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.girinst.org/downloads/software/mase/" } \ No newline at end of file diff --git a/data/masigpro/masigprobioschemas.jsonld b/data/masigpro/masigprobioschemas.jsonld index b0b556a917aed..74d865775918e 100644 --- a/data/masigpro/masigprobioschemas.jsonld +++ b/data/masigpro/masigprobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Maria Jose Nueda", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.", "sc:license": "GPL-2.0", "sc:name": "maSigPro", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/maSigPro.html", "sc:version": "1.46.0" diff --git a/data/maskambignuc/maskambignucbioschemas.jsonld b/data/maskambignuc/maskambignucbioschemas.jsonld index caad66dd40ebf..c5a8ebb4f9330 100644 --- a/data/maskambignuc/maskambignucbioschemas.jsonld +++ b/data/maskambignuc/maskambignucbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "EMBOSS Contributors", "Wellcome Trust", - "UK BBSRC" + "EMBOSS Contributors", + "UK BBSRC", + "UK MRC" ], "sc:description": "Mask all ambiguity characters in nucleotide sequences with N.", "sc:funder": [ @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "maskambignuc", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/maskambignuc.html", "sc:version": "r6" diff --git a/data/maskambigprot/maskambigprotbioschemas.jsonld b/data/maskambigprot/maskambigprotbioschemas.jsonld index 369dd01f1e9e1..dd0ad08d4ec1a 100644 --- a/data/maskambigprot/maskambigprotbioschemas.jsonld +++ b/data/maskambigprot/maskambigprotbioschemas.jsonld @@ -13,8 +13,8 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "UK MRC", "UK BBSRC", + "UK MRC", "EMBOSS Contributors" ], "sc:description": "Mask all ambiguity characters in protein sequences with X.", @@ -27,12 +27,12 @@ "sc:name": "maskambigprot", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/maskambigprot.html", "sc:version": "r6" diff --git a/data/maskbad/maskbadbioschemas.jsonld b/data/maskbad/maskbadbioschemas.jsonld index 75c81364c28f0..f97aa30e64456 100644 --- a/data/maskbad/maskbadbioschemas.jsonld +++ b/data/maskbad/maskbadbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Dannemann", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Package includes functions to analyze and mask microarray expression data.", "sc:license": "GPL-2.0", diff --git a/data/maskfeat/maskfeatbioschemas.jsonld b/data/maskfeat/maskfeatbioschemas.jsonld index a1fad5a5666da..d5151c85b03d6 100644 --- a/data/maskfeat/maskfeatbioschemas.jsonld +++ b/data/maskfeat/maskfeatbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", + "UK BBSRC", "UK MRC", - "EMBOSS Contributors", - "UK BBSRC" + "Wellcome Trust", + "EMBOSS Contributors" ], "sc:description": "Write a sequence with masked features.", "sc:funder": [ - "UK BBSRC", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "maskfeat", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/maskfeat.html", "sc:version": "r6" diff --git a/data/maskseq/maskseqbioschemas.jsonld b/data/maskseq/maskseqbioschemas.jsonld index 14872eec38912..71311de9b7f95 100644 --- a/data/maskseq/maskseqbioschemas.jsonld +++ b/data/maskseq/maskseqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", + "EMBOSS Contributors", "UK MRC", "Wellcome Trust", - "EMBOSS Contributors" + "UK BBSRC" ], "sc:description": "Write a sequence with masked regions.", "sc:funder": [ "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "maskseq", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/maskseq.html", "sc:version": "r6" diff --git a/data/massarray/massarraybioschemas.jsonld b/data/massarray/massarraybioschemas.jsonld index 821f694359989..b3c842cfdec08 100644 --- a/data/massarray/massarraybioschemas.jsonld +++ b/data/massarray/massarraybioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Reid F. Thompson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package.", "sc:license": "GPL-2.0", "sc:name": "MassArray", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MassArray.html", diff --git a/data/masschroq/masschroqbioschemas.jsonld b/data/masschroq/masschroqbioschemas.jsonld index 641b287888c91..e0efb78fd7ec1 100644 --- a/data/masschroq/masschroqbioschemas.jsonld +++ b/data/masschroq/masschroqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "XIC extraction and quantitation from LC-MS data.", "sc:name": "MassChroQ", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://pappso.inra.fr/bioinfo/masschroq/" } \ No newline at end of file diff --git a/data/masshunter_file_reader/masshunter_file_readerbioschemas.jsonld b/data/masshunter_file_reader/masshunter_file_readerbioschemas.jsonld index 6341f24674cb9..832d5ea687c5e 100644 --- a/data/masshunter_file_reader/masshunter_file_readerbioschemas.jsonld +++ b/data/masshunter_file_reader/masshunter_file_readerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Access raw data from Agilent MassHunter GC/MS and GC/MS/MS, export to plain text.", "sc:name": "MassHunter File Reader", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.quadtechassociates.com/freeware.html" diff --git a/data/massifquant/massifquantbioschemas.jsonld b/data/massifquant/massifquantbioschemas.jsonld index 6d3b61738cd97..c5609edcc0ffd 100644 --- a/data/massifquant/massifquantbioschemas.jsonld +++ b/data/massifquant/massifquantbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Kalman filter based on binless peak picking and quantitation in XCMS.", "sc:name": "massifquant", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.bioconductor.org/packages/release/bioc/html/xcms.html" } \ No newline at end of file diff --git a/data/massir/massirbioschemas.jsonld b/data/massir/massirbioschemas.jsonld index 2a7385d961cc6..7d28d6b9b02d7 100644 --- a/data/massir/massirbioschemas.jsonld +++ b/data/massir/massirbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1093/bioinformatics/btu161", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0003-2388-6046", + "@type": "schema:Person" }, { "@id": "https://bio.tools/massir", @@ -27,15 +27,15 @@ "@id": "edam:data_2884" }, { - "@id": "edam:data_1772" + "@id": "edam:data_1636" }, { - "@id": "edam:data_1636" + "@id": "edam:data_1772" } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { @@ -46,11 +46,11 @@ } ], "sc:citation": [ - "pmcid:PMC4080740", - "pubmed:24659105", { "@id": "https://doi.org/10.1093/bioinformatics/btu161" - } + }, + "pmcid:PMC4080740", + "pubmed:24659105" ], "sc:description": "Predicts the sex of samples in gene expression microarray datasets.", "sc:featureList": { @@ -59,16 +59,16 @@ "sc:license": "GPL-3.0", "sc:name": "massiR", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/massiR.html", "sc:version": "1.10.0" }, { - "@id": "http://orcid.org/0000-0003-2388-6046", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/bioinformatics/btu161", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/massmap/massmapbioschemas.jsonld b/data/massmap/massmapbioschemas.jsonld index eedf0f9f183df..2ed3df82b0169 100644 --- a/data/massmap/massmapbioschemas.jsonld +++ b/data/massmap/massmapbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s40168-018-0517-1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/massmap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jiyuan Hu", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:30045760", "pmcid:PMC6060480", { "@id": "https://doi.org/10.1186/s40168-018-0517-1" - } + }, + "pubmed:30045760" ], "sc:description": "A two-stage microbial association mapping framework with advanced FDR control.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "GPL-2.0", "sc:name": "massMap", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/JiyuanHu/massMap" + }, + { + "@id": "https://doi.org/10.1186/s40168-018-0517-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/massmatrix/massmatrixbioschemas.jsonld b/data/massmatrix/massmatrixbioschemas.jsonld index 9069c03f23257..f5e70010e7f7e 100644 --- a/data/massmatrix/massmatrixbioschemas.jsonld +++ b/data/massmatrix/massmatrixbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/massmatrix", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:description": "Web based tools for peptide identification and quantitation.", "sc:name": "MassMatrix", diff --git a/data/masspix/masspixbioschemas.jsonld b/data/masspix/masspixbioschemas.jsonld index 5f2e084f9c658..f784985f219e3 100644 --- a/data/masspix/masspixbioschemas.jsonld +++ b/data/masspix/masspixbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1007/s11306-017-1252-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/masspix", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Julian L. Griffin", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5608769", { "@id": "https://doi.org/10.1007/s11306-017-1252-5" }, + "pmcid:PMC5608769", "pubmed:28989334" ], "sc:description": "Processes high resolution mass spectrometry imaging data, performs multivariate statistics (PCA, clustering) and lipid identification.", @@ -36,11 +32,15 @@ ], "sc:name": "massPix", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/hallz/massPix" + }, + { + "@id": "https://doi.org/10.1007/s11306-017-1252-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/massspecapi/massspecapibioschemas.jsonld b/data/massspecapi/massspecapibioschemas.jsonld index 09c358f37a704..ad3b18fcbe904 100644 --- a/data/massspecapi/massspecapibioschemas.jsonld +++ b/data/massspecapi/massspecapibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MassSpecAPI", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.chemspider.com/MassSpecAPI.asmx", "sc:version": "1" diff --git a/data/massspecwavelet/massspecwaveletbioschemas.jsonld b/data/massspecwavelet/massspecwaveletbioschemas.jsonld index 130585e1d6407..ec663991d8ccd 100644 --- a/data/massspecwavelet/massspecwaveletbioschemas.jsonld +++ b/data/massspecwavelet/massspecwaveletbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Pan Du", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:16820428", "sc:description": "Processing Mass Spectrometry spectrum by using wavelet based algorithm.", @@ -21,8 +21,8 @@ "sc:name": "MassSpecWavelet", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MassSpecWavelet.html", "sc:version": "1.40.0" diff --git a/data/masstrix/masstrixbioschemas.jsonld b/data/masstrix/masstrixbioschemas.jsonld index c0624001add51..672e3a4a3a930 100644 --- a/data/masstrix/masstrixbioschemas.jsonld +++ b/data/masstrix/masstrixbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "With applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.", "sc:name": "MassTRIX", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://masstrix.org" } \ No newline at end of file diff --git a/data/massytools/massytoolsbioschemas.jsonld b/data/massytools/massytoolsbioschemas.jsonld index c7e125a934e74..91c3044048cba 100644 --- a/data/massytools/massytoolsbioschemas.jsonld +++ b/data/massytools/massytoolsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Data processing tool for targeted high-throughput MALDI-MS data extraction.", "sc:name": "MassyTools", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/Tarskin/MassyTools" } \ No newline at end of file diff --git a/data/mast/mastbioschemas.jsonld b/data/mast/mastbioschemas.jsonld index 53e6160d13eb5..607f1cd6bfe58 100644 --- a/data/mast/mastbioschemas.jsonld +++ b/data/mast/mastbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Andrew McDavid", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Methods and models for handling zero-inflated single cell assay data.", "sc:license": "GPL-2.0", diff --git a/data/mastr/mastrbioschemas.jsonld b/data/mastr/mastrbioschemas.jsonld index 27ad9ea764083..963925e4ec086 100644 --- a/data/mastr/mastrbioschemas.jsonld +++ b/data/mastr/mastrbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Stinus Lindgreen", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Multiple alignment and secondary structure prediction on a set of structural RNA sequences.", "sc:name": "MASTR", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "binf.ku.dk", "sc:url": "http://servers.binf.ku.dk/mastr/", diff --git a/data/masttreedist/masttreedistbioschemas.jsonld b/data/masttreedist/masttreedistbioschemas.jsonld index 407715ed6c846..f1a893d236f96 100644 --- a/data/masttreedist/masttreedistbioschemas.jsonld +++ b/data/masttreedist/masttreedistbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Software for phylogenetic tree-to-tree distance comparison by calculating these trees’ “Maximum Agreemen SubTrees” in order to improve the visualization of tree “landscape”", "sc:name": "MASTtreedist", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.rc.usf.edu/MASTtree/" diff --git a/data/masurca/masurcabioschemas.jsonld b/data/masurca/masurcabioschemas.jsonld index c8af84eca23be..fdb935be3eaff 100644 --- a/data/masurca/masurcabioschemas.jsonld +++ b/data/masurca/masurcabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/masurca", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Aleksey Zimin", - "Guillaume Marçais" + "Guillaume Marçais", + "Aleksey Zimin" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:23990416", diff --git a/data/matapax/matapaxbioschemas.jsonld b/data/matapax/matapaxbioschemas.jsonld index 74576d1c9b120..4073b47b8753e 100644 --- a/data/matapax/matapaxbioschemas.jsonld +++ b/data/matapax/matapaxbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Platform for high throughput collaborative genome wide association studies (GWAS). Computational time is reduced by processing user-supplied trait data in parallel. Result analysis is facilitated by displaying annotated candidate markers in tabular format and in a genome browser.", "sc:name": "Matapax", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://matapax.mpimp-golm.mpg.de/" diff --git a/data/matataki/matatakibioschemas.jsonld b/data/matataki/matatakibioschemas.jsonld index 978a64bf0d086..a42b3b8c53f83 100644 --- a/data/matataki/matatakibioschemas.jsonld +++ b/data/matataki/matatakibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Matataki", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/informationsea/Matataki" } \ No newline at end of file diff --git a/data/matav3/matav3bioschemas.jsonld b/data/matav3/matav3bioschemas.jsonld index b19f196bdf7dc..bf7789171b942 100644 --- a/data/matav3/matav3bioschemas.jsonld +++ b/data/matav3/matav3bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool to compute history tree.", "sc:name": "matav3", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/matav3/matav3" } \ No newline at end of file diff --git a/data/match/matchbioschemas.jsonld b/data/match/matchbioschemas.jsonld index d2ec6be893fd3..f049c4166c41e 100644 --- a/data/match/matchbioschemas.jsonld +++ b/data/match/matchbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use it.", "sc:name": "Match", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.gene-regulation.com/pub/programs.html#match" } \ No newline at end of file diff --git a/data/match_box/match_boxbioschemas.jsonld b/data/match_box/match_boxbioschemas.jsonld index 46b7cde7726a9..f2246318c12b1 100644 --- a/data/match_box/match_boxbioschemas.jsonld +++ b/data/match_box/match_boxbioschemas.jsonld @@ -22,30 +22,30 @@ ], "sc:author": "MacArthur Lab", "sc:citation": [ + "pmcid:PMC6250066", + "pubmed:30240502", { "@id": "https://doi.org/10.1002/humu.23655" - }, - "pmcid:PMC6250066", - "pubmed:30240502" + } ], "sc:description": "Open source software matching patients across genomic centers and finding the individual patients with the same candidate gene and overlapping phenotypic feature. Search for novel genetic causes of rare disease is based on the algorithm that determines the similarity between two distinct patients.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_3431" }, { "@id": "edam:operation_2422" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_3196" } ], "sc:license": "BSD-3-Clause", "sc:name": "matchbox", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://seqr.broadinstitute.org/matchmaker/matchbox" } diff --git a/data/matchbox/matchboxbioschemas.jsonld b/data/matchbox/matchboxbioschemas.jsonld index 39ffc30484896..c1b0904ca425c 100644 --- a/data/matchbox/matchboxbioschemas.jsonld +++ b/data/matchbox/matchboxbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/matchbox", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Luigi Marchionni", - "Anuj Gupta" + "Anuj Gupta", + "Luigi Marchionni" ], "sc:additionalType": [ "Library", @@ -23,8 +23,8 @@ "sc:license": "Artistic-2.0", "sc:name": "matchBox", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/matchBox.html", diff --git a/data/matcher-api-ebi/matcher-api-ebibioschemas.jsonld b/data/matcher-api-ebi/matcher-api-ebibioschemas.jsonld index 1e2f506028ef6..931d7ef385a20 100644 --- a/data/matcher-api-ebi/matcher-api-ebibioschemas.jsonld +++ b/data/matcher-api-ebi/matcher-api-ebibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Pairwise sequence alignment of DNA or protein sequences using Waterman-Eggert local alignment.", "sc:name": "matcher-api (EBI)", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/psa/emboss_matcher_rest", diff --git a/data/matcher-ebi/matcher-ebibioschemas.jsonld b/data/matcher-ebi/matcher-ebibioschemas.jsonld index 9866e391e23ac..5056407af1161 100644 --- a/data/matcher-ebi/matcher-ebibioschemas.jsonld +++ b/data/matcher-ebi/matcher-ebibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Waterman-Eggert local alignment of two sequences.", "sc:name": "matcher (EBI)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/psa/emboss_matcher/", diff --git a/data/matcher/matcherbioschemas.jsonld b/data/matcher/matcherbioschemas.jsonld index 58f47ec5bb578..a2d34fe41040f 100644 --- a/data/matcher/matcherbioschemas.jsonld +++ b/data/matcher/matcherbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "EMBOSS Contributors", + "Wellcome Trust", "UK MRC", "UK BBSRC" ], @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "matcher", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/matcher.html", "sc:version": "r6" diff --git a/data/matchmaker_exchange/matchmaker_exchangebioschemas.jsonld b/data/matchmaker_exchange/matchmaker_exchangebioschemas.jsonld index 1daac6b56ee77..52a926cd8c846 100644 --- a/data/matchmaker_exchange/matchmaker_exchangebioschemas.jsonld +++ b/data/matchmaker_exchange/matchmaker_exchangebioschemas.jsonld @@ -17,15 +17,15 @@ "@id": "https://bio.tools/matchmaker_exchange", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web API", - "Web application" + "Web application", + "Web API" ], "sc:citation": [ - "pmcid:PMC4610002", - "pubmed:26295439", { "@id": "https://doi.org/10.1002/humu.22858" - } + }, + "pubmed:26295439", + "pmcid:PMC4610002" ], "sc:description": "A platform for rare disease gene discovery. It connects databases of genotypes and rare phenotypes via a common application programming interface (API).", "sc:featureList": [ @@ -36,18 +36,18 @@ "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3197" + "@id": "edam:operation_3760" }, { - "@id": "edam:operation_3760" + "@id": "edam:operation_3197" } ], "sc:license": "Other", "sc:name": "Matchmaker exchange", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.matchmakerexchange.org" } diff --git a/data/matchminer/matchminerbioschemas.jsonld b/data/matchminer/matchminerbioschemas.jsonld index 0f897619a4661..bdd64b202a1a1 100644 --- a/data/matchminer/matchminerbioschemas.jsonld +++ b/data/matchminer/matchminerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MatchMiner", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://discover.nci.nih.gov/matchminer/" } \ No newline at end of file diff --git a/data/matcol/matcolbioschemas.jsonld b/data/matcol/matcolbioschemas.jsonld index ea7beb5659296..9898395bf1e5b 100644 --- a/data/matcol/matcolbioschemas.jsonld +++ b/data/matcol/matcolbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Measure fluorescence signal colocalisation in biological systems.", "sc:name": "MatCol", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinformatics.cmri.org.au/bioinformatics.htm" } \ No newline at end of file diff --git a/data/mathdamp/mathdampbioschemas.jsonld b/data/mathdamp/mathdampbioschemas.jsonld index 27c0caaca0dd0..bb1f7d036cfdf 100644 --- a/data/mathdamp/mathdampbioschemas.jsonld +++ b/data/mathdamp/mathdampbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Facilitates the visualization of differences between metabolite profiles acquired by hyphenated mass spectrometry techniques. Differences are highlighted by applying arithmetic operations to all corresponding signal intensities from whole raw (automatically preprocessed and normalized) datasets on a datapoint-by-datapoint basis. The results are visualized using density plots", "sc:name": "MathDAMP", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://mathdamp.iab.keio.ac.jp/" } \ No newline at end of file diff --git a/data/matras/matrasbioschemas.jsonld b/data/matras/matrasbioschemas.jsonld index 6c00bf11e491f..a519edeb3dfa3 100644 --- a/data/matras/matrasbioschemas.jsonld +++ b/data/matras/matrasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.", "sc:name": "MATRAS", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://strcomp.protein.osaka-u.ac.jp/matras/" } \ No newline at end of file diff --git a/data/matrix-clustering/matrix-clusteringbioschemas.jsonld b/data/matrix-clustering/matrix-clusteringbioschemas.jsonld index 1889f6986551c..0a5e8f37e10c8 100644 --- a/data/matrix-clustering/matrix-clusteringbioschemas.jsonld +++ b/data/matrix-clustering/matrix-clusteringbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Morgane Thomas-Chollier", - "Jacques van Helden", - "Jaime Castro-Mondragon" + "Jaime Castro-Mondragon", + "Jacques van Helden" ], "sc:additionalType": [ "Web application", @@ -21,9 +21,9 @@ ], "sc:author": "Jaime Castro-Mondragon", "sc:contributor": [ - "Morgane Thomas-Chollier", + "Jacques van Helden", "Denis Thieffry", - "Jacques van Helden" + "Morgane Thomas-Chollier" ], "sc:description": "Taking as input one or several sets of position-specific scoring matrices, this program applies hierarchical clustering to identify clusters of similar motifs. It produces a set of trees (one per cluster) and builds branch motifs at each node of each tree by merging the matrices of all descendent nodes.", "sc:name": "matrix-clustering", diff --git a/data/matrix_eqtl/matrix_eqtlbioschemas.jsonld b/data/matrix_eqtl/matrix_eqtlbioschemas.jsonld index 8436dec02a6d5..e32d69982eff7 100644 --- a/data/matrix_eqtl/matrix_eqtlbioschemas.jsonld +++ b/data/matrix_eqtl/matrix_eqtlbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Model and test for association using both linear regression and ANOVA models. The models can include covariates to account for such factors as population structure, gender, and clinical variables. It also supports testing of heteroscedastic models and models with correlated errors.", "sc:name": "Matrix eQTL", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/" } \ No newline at end of file diff --git a/data/matrixcgh/matrixcghbioschemas.jsonld b/data/matrixcgh/matrixcghbioschemas.jsonld index 6d76aa29c862e..71f503c73ab98 100644 --- a/data/matrixcgh/matrixcghbioschemas.jsonld +++ b/data/matrixcgh/matrixcghbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MatrixCGH is an extensible software framework for array CGH processing", "sc:name": "MatrixCGH", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.informatik.uni-ulm.de/ni/staff/HKestler/mcgh2/doc.html", "sc:version": "0.52" diff --git a/data/matrixdb/matrixdbbioschemas.jsonld b/data/matrixdb/matrixdbbioschemas.jsonld index 153e75fcd6513..703b8682efb73 100644 --- a/data/matrixdb/matrixdbbioschemas.jsonld +++ b/data/matrixdb/matrixdbbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-9263-1851", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/matrixdb", "@type": "sc:SoftwareApplication", @@ -21,10 +25,6 @@ "sc:name": "MatrixDB", "sc:operatingSystem": "Linux", "sc:url": "http://matrixdb.univ-lyon1.fr/" - }, - { - "@id": "https://orcid.org/0000-0001-9263-1851", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/matrixepistasis/matrixepistasisbioschemas.jsonld b/data/matrixepistasis/matrixepistasisbioschemas.jsonld index 3302bb68f1c89..b1f028353df77 100644 --- a/data/matrixepistasis/matrixepistasisbioschemas.jsonld +++ b/data/matrixepistasis/matrixepistasisbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "LGPL-3.0", "sc:name": "MatrixEpistasis", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/fanglab/MatrixEpistasis" } \ No newline at end of file diff --git a/data/matt/mattbioschemas.jsonld b/data/matt/mattbioschemas.jsonld index 50a41815b0483..e26046984929a 100644 --- a/data/matt/mattbioschemas.jsonld +++ b/data/matt/mattbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Matt", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://matt.cs.tufts.edu/", "sc:version": "1.0" diff --git a/data/mattbench/mattbenchbioschemas.jsonld b/data/mattbench/mattbenchbioschemas.jsonld index 3d3acbc69754b..c7b82a5a84796 100644 --- a/data/mattbench/mattbenchbioschemas.jsonld +++ b/data/mattbench/mattbenchbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Mattbench", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bcb.cs.tufts.edu/mattbench/Mattbench.html" } \ No newline at end of file diff --git a/data/matter/bioconda_matter.yaml b/data/matter/bioconda_matter.yaml index 5b142efd5a2d1..da50c9e55c4d4 100644 --- a/data/matter/bioconda_matter.yaml +++ b/data/matter/bioconda_matter.yaml @@ -4,7 +4,6 @@ description: Memory-efficient reading, writing, and manipulation of structured b home: https://bioconductor.org/packages/3.10/bioc/html/matter.html identifiers: - biotools:matter -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-matter summary: A framework for rapid prototyping with file-based data structures diff --git a/data/matter/matterbioschemas.jsonld b/data/matter/matterbioschemas.jsonld index 8c86dad00ce1c..c3eab66ae0bdd 100644 --- a/data/matter/matterbioschemas.jsonld +++ b/data/matter/matterbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "matter", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/matter.html", "sc:version": "1.0.0" diff --git a/data/mattfa/mattfabioschemas.jsonld b/data/mattfa/mattfabioschemas.jsonld index 5bc0b1654cf66..778f61eb6941f 100644 --- a/data/mattfa/mattfabioschemas.jsonld +++ b/data/mattfa/mattfabioschemas.jsonld @@ -9,31 +9,31 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/bty499", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/matTFA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laboratory of Computational Systems Biotechnology", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6298055", + "pubmed:30561545", { "@id": "https://doi.org/10.1093/bioinformatics/bty499" - }, - "pubmed:30561545", - "pmcid:PMC6298055" + } ], "sc:description": "Matlab implementation of Thermodynamics-based Flux Analysis.", "sc:license": "GPL-3.0", "sc:name": "matTFA", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/EPFL-LCSB/matTFA" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/bty499", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/maturebayes/maturebayesbioschemas.jsonld b/data/maturebayes/maturebayesbioschemas.jsonld index 569ebef65b040..47fa8b6a8b6b1 100644 --- a/data/maturebayes/maturebayesbioschemas.jsonld +++ b/data/maturebayes/maturebayesbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MatureBayes", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mirna.imbb.forth.gr/MatureBayes.html" } \ No newline at end of file diff --git a/data/mauve/mauvebioschemas.jsonld b/data/mauve/mauvebioschemas.jsonld index 697c560b3b0d4..9c0f0cad674a3 100644 --- a/data/mauve/mauvebioschemas.jsonld +++ b/data/mauve/mauvebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Mauve", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://darlinglab.org/mauve" diff --git a/data/mavisto/mavistobioschemas.jsonld b/data/mavisto/mavistobioschemas.jsonld index e837508ec8257..f675009121f03 100644 --- a/data/mavisto/mavistobioschemas.jsonld +++ b/data/mavisto/mavistobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MAVisto (Motif Analysis and VISualisation TOolkit)is a tool for the exploration of motifs in network. It provides a flexible motif search algorithm and different views for the analysis and visualisation of network motifs.", "sc:name": "MAVisto", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://mavisto.ipk-gatersleben.de/", "sc:version": "2.7.0" diff --git a/data/maxalign/maxalignbioschemas.jsonld b/data/maxalign/maxalignbioschemas.jsonld index b60e696fd0897..44ff2065ff34a 100644 --- a/data/maxalign/maxalignbioschemas.jsonld +++ b/data/maxalign/maxalignbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Other", "sc:name": "MaxAlign", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.cbs.dtu.dk/services/MaxAlign/" diff --git a/data/maxcluster/maxclusterbioschemas.jsonld b/data/maxcluster/maxclusterbioschemas.jsonld index 70458a415a0f4..07b53da7a672e 100644 --- a/data/maxcluster/maxclusterbioschemas.jsonld +++ b/data/maxcluster/maxclusterbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1110/ps.0215902", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/maxcluster", "@type": "sc:SoftwareApplication", @@ -30,11 +26,15 @@ }, "sc:name": "MaxCluster", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.sbg.bio.ic.ac.uk/~maxcluster" + }, + { + "@id": "https://doi.org/10.1110/ps.0215902", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/maxcounts/maxcountsbioschemas.jsonld b/data/maxcounts/maxcountsbioschemas.jsonld index 67a647451c44d..e78f1e44f8e78 100644 --- a/data/maxcounts/maxcountsbioschemas.jsonld +++ b/data/maxcounts/maxcountsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "Maxcounts", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://sysbiobig.dei.unipd.it/?q=Software#MAXCOUNTS", diff --git a/data/maxflow/maxflowbioschemas.jsonld b/data/maxflow/maxflowbioschemas.jsonld index d5b9577648550..3d667920a20d4 100644 --- a/data/maxflow/maxflowbioschemas.jsonld +++ b/data/maxflow/maxflowbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A greedy algorithm, using a novel consistency score to estimate the relative likelihood of alternative paths of transitive alignment. In contrast to traditional profile models of amino acid preferences, MaxFlow models the probability that two positions are structurally equivalent and retains high information content across large distances in sequence space.", "sc:name": "Maxflow", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ekhidna.biocenter.helsinki.fi/gtg/start" } \ No newline at end of file diff --git a/data/maxic-q/maxic-qbioschemas.jsonld b/data/maxic-q/maxic-qbioschemas.jsonld index 50bad30d93cd1..27ab1c98e171e 100644 --- a/data/maxic-q/maxic-qbioschemas.jsonld +++ b/data/maxic-q/maxic-qbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.", "sc:name": "MaXIC-Q", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://ms.iis.sinica.edu.tw/MaXIC-Q" diff --git a/data/maxillary-sinus-quantification/maxillary-sinus-quantificationbioschemas.jsonld b/data/maxillary-sinus-quantification/maxillary-sinus-quantificationbioschemas.jsonld index 37d3c33889fa9..226e635068fcb 100644 --- a/data/maxillary-sinus-quantification/maxillary-sinus-quantificationbioschemas.jsonld +++ b/data/maxillary-sinus-quantification/maxillary-sinus-quantificationbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Automated tool for quantifying the total and air-free volume of the maxillary sinus based on computed tomography images. The quantification tool seeks to standardize maxillary sinus volume measurements, thus allowing better comparisons and determinations of factors that influence maxillary sinus size. The automated tool utilized image processing techniques (watershed, threshold, and morphological operators).", "sc:name": "Maxillary-Sinus-Quantification", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/dianapina/Maxillary-Sinus-Quantification" diff --git a/data/maxlink/maxlinkbioschemas.jsonld b/data/maxlink/maxlinkbioschemas.jsonld index c169c04364453..af54599f4e0cb 100644 --- a/data/maxlink/maxlinkbioschemas.jsonld +++ b/data/maxlink/maxlinkbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MaxLink", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://maxlink.sbc.su.se/" } \ No newline at end of file diff --git a/data/maxocc/maxoccbioschemas.jsonld b/data/maxocc/maxoccbioschemas.jsonld index 48683680cea5a..3b3737373d6de 100644 --- a/data/maxocc/maxoccbioschemas.jsonld +++ b/data/maxocc/maxoccbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MaxOcc", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://py-enmr.cerm.unifi.it/access/index/maxocc", diff --git a/data/maxreport/maxreportbioschemas.jsonld b/data/maxreport/maxreportbioschemas.jsonld index 44e3cd85c05f9..171b98dd3545b 100644 --- a/data/maxreport/maxreportbioschemas.jsonld +++ b/data/maxreport/maxreportbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Tao Zhou", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC4803341", + "pubmed:27003708", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0152067" - }, - "pmcid:PMC4803341", - "pubmed:27003708" + } ], "sc:description": "An Enhanced Proteomic Result Reporting Tool for MaxQuant.", "sc:featureList": { diff --git a/data/maxsnippetmodel/maxsnippetmodelbioschemas.jsonld b/data/maxsnippetmodel/maxsnippetmodelbioschemas.jsonld index 5b363e0a82e34..106d67c59444a 100644 --- a/data/maxsnippetmodel/maxsnippetmodelbioschemas.jsonld +++ b/data/maxsnippetmodel/maxsnippetmodelbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "MaxSnippetModel", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/jostmey/MaxSnippetModel" } \ No newline at end of file diff --git a/data/maxsprout/maxsproutbioschemas.jsonld b/data/maxsprout/maxsproutbioschemas.jsonld index f0ef19728ed13..9dc7c83a99c92 100644 --- a/data/maxsprout/maxsproutbioschemas.jsonld +++ b/data/maxsprout/maxsproutbioschemas.jsonld @@ -20,12 +20,12 @@ "sc:name": "MaxSprout", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBL-EBI", - "University of Helsinki" + "University of Helsinki", + "EMBL-EBI" ], "sc:url": "http://www.ebi.ac.uk/Tools/structure/maxsprout/", "sc:version": "1" diff --git a/data/mba/mbabioschemas.jsonld b/data/mba/mbabioschemas.jsonld index b7f820abd286f..a533022d56d8a 100644 --- a/data/mba/mbabioschemas.jsonld +++ b/data/mba/mbabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Java program for automated assignment and assessment of uncertainty of protein backbone NMR. It is based on a statistical model for NMR spectra, and employs a tree-based algorithm of stochastic optimization.", "sc:name": "MBA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.stat.purdue.edu/~ovitek/mba/mba.html" diff --git a/data/mbamethyl/mbamethylbioschemas.jsonld b/data/mbamethyl/mbamethylbioschemas.jsonld index 65fb7c964e79f..bfab560b9dce5 100644 --- a/data/mbamethyl/mbamethylbioschemas.jsonld +++ b/data/mbamethyl/mbamethylbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Tao Wang", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences.", "sc:license": "Artistic-2.0", "sc:name": "MBAmethyl", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MBAmethyl.html", "sc:version": "1.8.0" diff --git a/data/mbased/mbasedbioschemas.jsonld b/data/mbased/mbasedbioschemas.jsonld index 8f0d1b7a77758..90c7e9b116b4b 100644 --- a/data/mbased/mbasedbioschemas.jsonld +++ b/data/mbased/mbasedbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "MBASED", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MBASED.html", "sc:version": "1.8.0" diff --git a/data/mbbc/mbbcbioschemas.jsonld b/data/mbbc/mbbcbioschemas.jsonld index 3cb01627e3663..1c8cc1d0e674a 100644 --- a/data/mbbc/mbbcbioschemas.jsonld +++ b/data/mbbc/mbbcbioschemas.jsonld @@ -17,9 +17,9 @@ "@id": "https://bio.tools/mbbc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Haiyan Hu", "Xiaoman Li", - "Ying Wang", - "Haiyan Hu" + "Ying Wang" ], "sc:additionalType": "Desktop application", "sc:citation": [ diff --git a/data/mbcb/mbcbbioschemas.jsonld b/data/mbcb/mbcbbioschemas.jsonld index bc50871e80728..24cd4501e7c65 100644 --- a/data/mbcb/mbcbbioschemas.jsonld +++ b/data/mbcb/mbcbbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "MBCB", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MBCB.html", "sc:version": "1.28.0" diff --git a/data/mbgd/mbgdbioschemas.jsonld b/data/mbgd/mbgdbioschemas.jsonld index 35345f47be8f0..d699d25173ed7 100644 --- a/data/mbgd/mbgdbioschemas.jsonld +++ b/data/mbgd/mbgdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The microbial genome database for comparative analysis is a platform for microbial comparative genomics based on automated ortholog group identification. A prominent feature is that it allows users to create ortholog groups using a specified subgroup of organisms.", "sc:name": "Microbial Genome Database (MBGD)", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mbgd.genome.ad.jp/" } \ No newline at end of file diff --git a/data/mblastall/mblastallbioschemas.jsonld b/data/mblastall/mblastallbioschemas.jsonld index 2ac0fab86b4cc..84e490ad07726 100644 --- a/data/mblastall/mblastallbioschemas.jsonld +++ b/data/mblastall/mblastallbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Search nucleotide database with nucleotide query sequence(s).", "sc:name": "mblastall", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://bioweb.pasteur.fr/packages/pack@ptools@0.99d", diff --git a/data/mbpcr/mbpcrbioschemas.jsonld b/data/mbpcr/mbpcrbioschemas.jsonld index 0ddd8f0c9c5fd..27ef5d1d8d269 100644 --- a/data/mbpcr/mbpcrbioschemas.jsonld +++ b/data/mbpcr/mbpcrbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "P.M.V. Rancoita", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Estimates the DNA copy number profile by detecting regions with copy number changes.", "sc:license": "GPL-2.0", "sc:name": "mBPCR", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mBPCR.html", diff --git a/data/mbppred/mbppredbioschemas.jsonld b/data/mbppred/mbppredbioschemas.jsonld index 1177a282a2bb8..daa7da3854163 100644 --- a/data/mbppred/mbppredbioschemas.jsonld +++ b/data/mbppred/mbppredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Profile Hidden Markov Model based method capable of predicting membrane binding proteins (MBPs).", "sc:name": "MBPpred", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://aias.biol.uoa.gr/MBPpred/" } \ No newline at end of file diff --git a/data/mbr/mbrbioschemas.jsonld b/data/mbr/mbrbioschemas.jsonld index ef58e6f08bac2..893c1b739a546 100644 --- a/data/mbr/mbrbioschemas.jsonld +++ b/data/mbr/mbrbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Microarray Blob Remover is a microarray tool which allows rapid visualization, detection, and removalof blob-like defects as an initial quality control step. The software allows rapid visualization, detection, and removal of blob defects of a variety of sizes and shapes from different types of microarrays using their .CEL files. Removal of the affected probes in the blob-defects using MBR was shown to improve sensitivity and FDR compared to leaving the affected probes in the analysis.", "sc:name": "MBR", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://liulab.dfci.harvard.edu/Software/MBR/MBR.htm.html", "sc:version": "20070206" diff --git a/data/mbrole/mbrolebioschemas.jsonld b/data/mbrole/mbrolebioschemas.jsonld index e2561c4d37755..7bbfd3e32fe47 100644 --- a/data/mbrole/mbrolebioschemas.jsonld +++ b/data/mbrole/mbrolebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms.", "sc:name": "MBRole", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://csbg.cnb.csic.es/mbrole2/" diff --git a/data/mbstar/mbstarbioschemas.jsonld b/data/mbstar/mbstarbioschemas.jsonld index bc50d45b9502b..be98efada317f 100644 --- a/data/mbstar/mbstarbioschemas.jsonld +++ b/data/mbstar/mbstarbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web server for accurate prediction of true or functional miRNA binding sites.", "sc:name": "MBSTAR", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.isical.ac.in/~bioinfo_miu/MBStar30.htm" diff --git a/data/mbttest/mbttestbioschemas.jsonld b/data/mbttest/mbttestbioschemas.jsonld index 0c1e1d71a2203..ef6e904f41e11 100644 --- a/data/mbttest/mbttestbioschemas.jsonld +++ b/data/mbttest/mbttestbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "MBttest", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MBttest.html", "sc:version": "1.2.0" diff --git a/data/mbv/mbvbioschemas.jsonld b/data/mbv/mbvbioschemas.jsonld index b1acbda4dc20c..a5c4a95a8f496 100644 --- a/data/mbv/mbvbioschemas.jsonld +++ b/data/mbv/mbvbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets.", "sc:name": "MBV", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://qtltools.github.io/qtltools/" } \ No newline at end of file diff --git a/data/mbwa_wrapper/mbwa_wrapperbioschemas.jsonld b/data/mbwa_wrapper/mbwa_wrapperbioschemas.jsonld index 98eb1c456ee3f..cb36cc57fe186 100644 --- a/data/mbwa_wrapper/mbwa_wrapperbioschemas.jsonld +++ b/data/mbwa_wrapper/mbwa_wrapperbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome.", "sc:name": "mbwa_wrapper", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://bioweb.pasteur.fr/packages/pack@ptools@0.99d", "sc:version": "0.7.4" diff --git a/data/mcbiclust/mcbiclustbioschemas.jsonld b/data/mcbiclust/mcbiclustbioschemas.jsonld index 567ecb2c60a4c..1c8e6c43ef26c 100644 --- a/data/mcbiclust/mcbiclustbioschemas.jsonld +++ b/data/mcbiclust/mcbiclustbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Robert Bentham", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:28911113", { "@id": "https://doi.org/10.1093/nar/gkx590" }, + "pubmed:28911113", "pmcid:PMC5587796" ], "sc:description": "Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.", @@ -28,9 +28,9 @@ "sc:license": "GPL-2.0", "sc:name": "MCbiclust", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MCbiclust.html", "sc:version": "1.4.0" diff --git a/data/mccortex/mccortexbioschemas.jsonld b/data/mccortex/mccortexbioschemas.jsonld index b72e419627bd4..7fc3d9dae63ed 100644 --- a/data/mccortex/mccortexbioschemas.jsonld +++ b/data/mccortex/mccortexbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "MIT", "sc:name": "McCortex", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/mcveanlab/mccortex" } \ No newline at end of file diff --git a/data/mcdgpa/mcdgpabioschemas.jsonld b/data/mcdgpa/mcdgpabioschemas.jsonld index 3d099639cfa6f..8ceb6d62fc5be 100644 --- a/data/mcdgpa/mcdgpabioschemas.jsonld +++ b/data/mcdgpa/mcdgpabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This tool is proposed to identify disease-related genes. It is divided into three steps: module partition, genes prioritization in each disease-associated module, and rank fusion for the global ranking.", "sc:name": "MCDGPA", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://doc.aporc.org/wiki/MCDGPA" } \ No newline at end of file diff --git a/data/mcf/mcfbioschemas.jsonld b/data/mcf/mcfbioschemas.jsonld index 0c5517f1609d2..58fead815679b 100644 --- a/data/mcf/mcfbioschemas.jsonld +++ b/data/mcf/mcfbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Image segmentation algorithms and example code for automated single cell analysis.", "sc:name": "MCF", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.stat.duke.edu/research/software/west/MCF/index.html" diff --git a/data/mcgh/mcghbioschemas.jsonld b/data/mcgh/mcghbioschemas.jsonld index 334145d11d0b0..9be0c10a9644a 100644 --- a/data/mcgh/mcghbioschemas.jsonld +++ b/data/mcgh/mcghbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Matlab toolbox with graphical interface to analysis DNA microarray-based comparative genomic hybridization (CGH) experiments. CGH on DNA microarray enable us to measure the copy numbers of thousands of genes through the genome.", "sc:name": "MCGH", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://folk.uio.no/junbaiw/mcgh/" } \ No newline at end of file diff --git a/data/mcmc_ibdfinder/mcmc_ibdfinderbioschemas.jsonld b/data/mcmc_ibdfinder/mcmc_ibdfinderbioschemas.jsonld index 8dd4a7da7ad19..a18bfd96d1620 100644 --- a/data/mcmc_ibdfinder/mcmc_ibdfinderbioschemas.jsonld +++ b/data/mcmc_ibdfinder/mcmc_ibdfinderbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "C++ program that estimates posterior probabilities of identity by descent (IBD) sharing between multiple individuals using unphased single nucleotide polymorphism (SNP) data.", "sc:name": "MCMC_IBDfinder", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://people.binf.ku.dk/ida/Software/MCMC_IBDfinder/" } \ No newline at end of file diff --git a/data/mcmccodonsite/mcmccodonsitebioschemas.jsonld b/data/mcmccodonsite/mcmccodonsitebioschemas.jsonld index 1cd253684ad16..c45e1ba2b5d1e 100644 --- a/data/mcmccodonsite/mcmccodonsitebioschemas.jsonld +++ b/data/mcmccodonsite/mcmccodonsitebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Program implementing some codon models allowing \\omega = d_N/d_S to vary among sites (M0, M2a, M3, M7, M8) in a Bayesian framework.", "sc:name": "MCMCcodonsite", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bioinformatics.uottawa.ca/stephane/downloads.html" } \ No newline at end of file diff --git a/data/mcode/mcodebioschemas.jsonld b/data/mcode/mcodebioschemas.jsonld index b74ade1fd035b..97a38cefb6ce3 100644 --- a/data/mcode/mcodebioschemas.jsonld +++ b/data/mcode/mcodebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A Cytoscape plugin that finds clusters in different types of networks. An automated method for finding molecular complexes in large protein interaction networks.", "sc:name": "MCODE", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://baderlab.org/Software/MCODE" } \ No newline at end of file diff --git a/data/mcpath/mcpathbioschemas.jsonld b/data/mcpath/mcpathbioschemas.jsonld index 55b896739817f..c0c7c3c7fcf9c 100644 --- a/data/mcpath/mcpathbioschemas.jsonld +++ b/data/mcpath/mcpathbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "MCPath is a Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.", "sc:name": "MCPath", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://safir.prc.boun.edu.tr/clbet_server" diff --git a/data/mcpd/mcpdbioschemas.jsonld b/data/mcpd/mcpdbioschemas.jsonld index 37ba09c8d7f61..b9a37b39d7112 100644 --- a/data/mcpd/mcpdbioschemas.jsonld +++ b/data/mcpd/mcpdbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Used in the analysis of pooling experiments for library screening. Pools are collections of clones, and screening a pool with a probe is a group test, determining whether any of these clones are positive for the probe. The results of the pool screenings are interpreted, or decoded, to infer which clones are candidates to be positive using a Markov chain Monte Carlo approach.", "sc:name": "MCPD", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioinformatics.rutgers.edu/Software/MCPD/" diff --git a/data/mcpep/mcpepbioschemas.jsonld b/data/mcpep/mcpepbioschemas.jsonld index c4800cbea65d7..ee941e1c428f0 100644 --- a/data/mcpep/mcpepbioschemas.jsonld +++ b/data/mcpep/mcpepbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MCPep", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "Instruct", "sc:url": "http://bental.tau.ac.il/MCPep/", diff --git a/data/mcqfold/mcqfoldbioschemas.jsonld b/data/mcqfold/mcqfoldbioschemas.jsonld index f29bdb92a071d..f4c249f539192 100644 --- a/data/mcqfold/mcqfoldbioschemas.jsonld +++ b/data/mcqfold/mcqfoldbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "McQFold", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www-stud.informatik.uni-frankfurt.de/~metzler/McQFold/" } \ No newline at end of file diff --git a/data/mcrestimate/bioconda_mcrestimate.yaml b/data/mcrestimate/bioconda_mcrestimate.yaml index f1101c62cb090..b4d298b1cb494 100644 --- a/data/mcrestimate/bioconda_mcrestimate.yaml +++ b/data/mcrestimate/bioconda_mcrestimate.yaml @@ -4,7 +4,6 @@ description: This package includes a function for combining preprocessing and cl home: https://bioconductor.org/packages/3.10/bioc/html/MCRestimate.html identifiers: - biotools:mcrestimate -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-mcrestimate diff --git a/data/mcrestimate/mcrestimatebioschemas.jsonld b/data/mcrestimate/mcrestimatebioschemas.jsonld index af712378411fc..ff31d9802c4d7 100644 --- a/data/mcrestimate/mcrestimatebioschemas.jsonld +++ b/data/mcrestimate/mcrestimatebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "MCRestimate", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MCRestimate.html", "sc:version": "2.30.0" diff --git a/data/mcsea/mcseabioschemas.jsonld b/data/mcsea/mcseabioschemas.jsonld index 83f2e45299637..646e145a55fac 100644 --- a/data/mcsea/mcseabioschemas.jsonld +++ b/data/mcsea/mcseabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "mCSEA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mCSEA.html", "sc:version": "1.0.1" diff --git a/data/mcsm-ab/mcsm-abbioschemas.jsonld b/data/mcsm-ab/mcsm-abbioschemas.jsonld index 0a0b67fc43edf..a7e71323406df 100644 --- a/data/mcsm-ab/mcsm-abbioschemas.jsonld +++ b/data/mcsm-ab/mcsm-abbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mcsm-ab", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Douglas E. V. Pires", - "Dr. David B. Ascher" + "Dr. David B. Ascher", + "Dr. Douglas E. V. Pires" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:27216816", @@ -20,8 +20,8 @@ "sc:name": "mCSM-AB", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bleoberis.bioc.cam.ac.uk/mcsm_ab/" } \ No newline at end of file diff --git a/data/mcsm-ppi2/mcsm-ppi2bioschemas.jsonld b/data/mcsm-ppi2/mcsm-ppi2bioschemas.jsonld index 2aaad51a86032..fdb429f202705 100644 --- a/data/mcsm-ppi2/mcsm-ppi2bioschemas.jsonld +++ b/data/mcsm-ppi2/mcsm-ppi2bioschemas.jsonld @@ -9,28 +9,36 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-3004-2119", + "@type": "schema:Person" + }, { "@id": "https://orcid.org/0000-0003-2948-2413", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ383", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mCSM-PPI2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "https://orcid.org/0000-0002-3004-2119" + "@id": "https://orcid.org/0000-0003-2948-2413" }, { - "@id": "https://orcid.org/0000-0003-2948-2413" + "@id": "https://orcid.org/0000-0002-3004-2119" } ], "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6602427", + "pubmed:31114883", { "@id": "https://doi.org/10.1093/NAR/GKZ383" }, - "pubmed:31114883" + "pmcid:PMC6602427" ], "sc:description": "Machine learning computational tool designed to more accurately predict the effects of missense mutations on protein–protein interaction binding affinity.", "sc:featureList": [ @@ -38,28 +46,20 @@ "@id": "edam:operation_0331" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_2492" }, { - "@id": "edam:operation_2492" + "@id": "edam:operation_3501" } ], "sc:license": "Unlicense", "sc:name": "mCSM-PPI2", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://biosig.unimelb.edu.au/mcsm_ppi2/" - }, - { - "@id": "https://orcid.org/0000-0002-3004-2119", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ383", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mcsm_na/mcsm_nabioschemas.jsonld b/data/mcsm_na/mcsm_nabioschemas.jsonld index efe220af18dff..1a3dd0e7ea5b9 100644 --- a/data/mcsm_na/mcsm_nabioschemas.jsonld +++ b/data/mcsm_na/mcsm_nabioschemas.jsonld @@ -9,28 +9,32 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKX236", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mcsm_na", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. David B. Ascher", - "Dr. Douglas E. V. Pires" + "Dr. Douglas E. V. Pires", + "Dr. David B. Ascher" ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28383703", + "pmcid:PMC5570212", { "@id": "https://doi.org/10.1093/NAR/GKX236" }, - "pmcid:PMC5570212" + "pubmed:28383703" ], "sc:description": "Quantitatively predict the effects of mutations in protein coding regions on nucleic acid binding affinities.", "sc:featureList": [ { - "@id": "edam:operation_0279" + "@id": "edam:operation_0331" }, { - "@id": "edam:operation_0331" + "@id": "edam:operation_0279" }, { "@id": "edam:operation_0420" @@ -38,10 +42,6 @@ ], "sc:name": "mCSM_NA", "sc:url": "http://structure.bioc.cam.ac.uk/mcsm_na" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKX236", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mcsnp/mcsnpbioschemas.jsonld b/data/mcsnp/mcsnpbioschemas.jsonld index 31ac5fd536243..0baed5a617124 100644 --- a/data/mcsnp/mcsnpbioschemas.jsonld +++ b/data/mcsnp/mcsnpbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "McSNP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.bioinformatics.org/mcsnp/wiki/", "sc:version": "1.0" diff --git a/data/mctbi/mctbibioschemas.jsonld b/data/mctbi/mctbibioschemas.jsonld index 4e5575b45e8aa..14bb2a272fd96 100644 --- a/data/mctbi/mctbibioschemas.jsonld +++ b/data/mctbi/mctbibioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1261/RNA.060947.117", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mctbi", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28450533", "pmcid:PMC5513060", { "@id": "https://doi.org/10.1261/RNA.060947.117" - } + }, + "pubmed:28450533" ], "sc:description": "A web server for predicting metal ion effects in RNA structures.", "sc:featureList": { @@ -27,10 +31,6 @@ }, "sc:name": "MCTBI", "sc:url": "http://rna.physics.missouri.edu/MCTBI/" - }, - { - "@id": "https://doi.org/10.1261/RNA.060947.117", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mdcs/mdcsbioschemas.jsonld b/data/mdcs/mdcsbioschemas.jsonld index 52cb5693f81ee..b8b1e125b6872 100644 --- a/data/mdcs/mdcsbioschemas.jsonld +++ b/data/mdcs/mdcsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MDCS", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mips.helmholtz-muenchen.de/proj/mdcs/" } \ No newline at end of file diff --git a/data/mdd-carb/mdd-carbbioschemas.jsonld b/data/mdd-carb/mdd-carbbioschemas.jsonld index d5642f45d5695..8cedc123a25f2 100644 --- a/data/mdd-carb/mdd-carbbioschemas.jsonld +++ b/data/mdd-carb/mdd-carbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server for identifying carbonylation sites. Protein carbonylation, is an irreversible non-enzymatic post-translational modification (PTM) which is often used as a marker of oxidative stress. Despite the used of Protein Carbonylation as a biomarker of oxidative stress, the substrate motif of carbonylation remains unknown.", "sc:name": "MDD-carb", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://140.138.150.145/~mddcarb/mddcarb/index.php" } \ No newline at end of file diff --git a/data/mddglutar/mddglutarbioschemas.jsonld b/data/mddglutar/mddglutarbioschemas.jsonld index a5842528782c5..b0a562dbd2d2f 100644 --- a/data/mddglutar/mddglutarbioschemas.jsonld +++ b/data/mddglutar/mddglutarbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/MDDGlutar", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": "pubmed:30717647", "sc:description": "Web server for identifying glutarylation sites.", "sc:name": "MDDGlutar", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://csb.cse.yzu.edu.tw/MDDGlutar/" diff --git a/data/mddmd/mddmdbioschemas.jsonld b/data/mddmd/mddmdbioschemas.jsonld index aada9b68ff561..27cd796f7ae31 100644 --- a/data/mddmd/mddmdbioschemas.jsonld +++ b/data/mddmd/mddmdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "MDdMD", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://mmb.irbbarcelona.org/MDdMD" } \ No newline at end of file diff --git a/data/mdgsa/mdgsabioschemas.jsonld b/data/mdgsa/mdgsabioschemas.jsonld index a51427d93bf88..5672c52bda561 100644 --- a/data/mdgsa/mdgsabioschemas.jsonld +++ b/data/mdgsa/mdgsabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-016-0989-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mdgsa", "@type": "sc:SoftwareApplication", @@ -21,40 +17,40 @@ "@id": "edam:data_3111" }, "edam:has_output": [ - { - "@id": "edam:data_1772" - }, { "@id": "edam:data_2884" }, { "@id": "edam:data_1669" + }, + { + "@id": "edam:data_1772" } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3518" + "@id": "edam:topic_0622" }, { - "@id": "edam:topic_2640" + "@id": "edam:topic_0203" }, { - "@id": "edam:topic_0622" + "@id": "edam:topic_2640" }, { - "@id": "edam:topic_0203" + "@id": "edam:topic_0659" }, { - "@id": "edam:topic_0659" + "@id": "edam:topic_3518" } ], "sc:citation": [ - "pmcid:PMC4804509", "pubmed:27005934", + "pmcid:PMC4804509", { "@id": "https://doi.org/10.1186/s12859-016-0989-6" } @@ -71,12 +67,16 @@ "sc:license": "GPL-3.0", "sc:name": "mdgsa", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mdgsa.html", "sc:version": "1.6.0" + }, + { + "@id": "https://doi.org/10.1186/s12859-016-0989-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mdi-gpu/mdi-gpubioschemas.jsonld b/data/mdi-gpu/mdi-gpubioschemas.jsonld index 33c94ae6974a7..7039d75c3e93d 100644 --- a/data/mdi-gpu/mdi-gpubioschemas.jsonld +++ b/data/mdi-gpu/mdi-gpubioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Improved implementation of a Bayesian correlated clustering algorithm, that permits integrated clustering to be routinely performed across multiple datasets, each with tens of thousands of items.", "sc:name": "MDI-GPU", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/" } \ No newline at end of file diff --git a/data/mdmoby/mdmobybioschemas.jsonld b/data/mdmoby/mdmobybioschemas.jsonld index cc792c07e0e0b..b254a8237d6ab 100644 --- a/data/mdmoby/mdmobybioschemas.jsonld +++ b/data/mdmoby/mdmobybioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Set of semantic Web-Services to help access to molecular dynamics (MD) simulations. Semantic information is added using the BioMoby library and a MD Ontology.", "sc:name": "MDMoby", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://mmb.irbbarcelona.org/MDWeb" } \ No newline at end of file diff --git a/data/mdp/mdpbioschemas.jsonld b/data/mdp/mdpbioschemas.jsonld index 88631e498815d..c85911a4c0d37 100644 --- a/data/mdp/mdpbioschemas.jsonld +++ b/data/mdp/mdpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "mdp", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mdp.html", "sc:version": "1.0.0" diff --git a/data/mdpbiome/mdpbiomebioschemas.jsonld b/data/mdpbiome/mdpbiomebioschemas.jsonld index b855140106683..0de6192903051 100644 --- a/data/mdpbiome/mdpbiomebioschemas.jsonld +++ b/data/mdpbiome/mdpbiomebioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-6960-357X", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0002-1977-9777", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/MDPBiome", "@type": "sc:SoftwareApplication", @@ -32,14 +40,6 @@ ], "sc:url": "https://github.com/beatrizgj/MDPbiome" }, - { - "@id": "https://orcid.org/0000-0001-6960-357X", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0002-1977-9777", - "@type": "schema:Person" - }, { "@id": "https://orcid.org/0000-0002-8129-6506", "@type": "schema:Person" diff --git a/data/mdpfinder/mdpfinderbioschemas.jsonld b/data/mdpfinder/mdpfinderbioschemas.jsonld index 0aab6d7482b9f..a579a7ea93744 100644 --- a/data/mdpfinder/mdpfinderbioschemas.jsonld +++ b/data/mdpfinder/mdpfinderbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Package for identifying driver pathways promoting cancer proliferation and filtering out the unfunctional and passenger ones.", "sc:name": "MDPFinder", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://page.amss.ac.cn/shihua.zhang/software.html" } \ No newline at end of file diff --git a/data/mdqc/mdqcbioschemas.jsonld b/data/mdqc/mdqcbioschemas.jsonld index 13ee0473806c9..b0769d53a2b95 100644 --- a/data/mdqc/mdqcbioschemas.jsonld +++ b/data/mdqc/mdqcbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "mdqc", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mdqc.html", "sc:version": "1.36.0" diff --git a/data/mdscan/mdscanbioschemas.jsonld b/data/mdscan/mdscanbioschemas.jsonld index 710b425b27d5d..a06e9b7992da8 100644 --- a/data/mdscan/mdscanbioschemas.jsonld +++ b/data/mdscan/mdscanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.", "sc:name": "MDscan", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://robotics.stanford.edu/~xsliu/MDscan/" } \ No newline at end of file diff --git a/data/mdsine/mdsinebioschemas.jsonld b/data/mdsine/mdsinebioschemas.jsonld index e15998153f7fb..6a5e716015eb5 100644 --- a/data/mdsine/mdsinebioschemas.jsonld +++ b/data/mdsine/mdsinebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "MDSINE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://bitbucket.org/MDSINE/mdsine/" } \ No newline at end of file diff --git a/data/mdts/mdtsbioschemas.jsonld b/data/mdts/mdtsbioschemas.jsonld index b76b7437bc313..97ddcdb293577 100644 --- a/data/mdts/mdtsbioschemas.jsonld +++ b/data/mdts/mdtsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "MDTS", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MDTS.html", "sc:version": "1.0.2" diff --git a/data/meadmix/meadmixbioschemas.jsonld b/data/meadmix/meadmixbioschemas.jsonld index 231cb850a4ff1..63cf2803889d5 100644 --- a/data/meadmix/meadmixbioschemas.jsonld +++ b/data/meadmix/meadmixbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Fortran program to estimate the admixture proportions and genetic drift using DNA sequence data, based on a coalescent estimator.", "sc:name": "MEAdmix", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.zsl.org/science/software/meadmix" } \ No newline at end of file diff --git a/data/meaga/meagabioschemas.jsonld b/data/meaga/meagabioschemas.jsonld index aab09e21fa83f..4e5ca094ec837 100644 --- a/data/meaga/meagabioschemas.jsonld +++ b/data/meaga/meagabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MEAGA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genome.sph.umich.edu/wiki/MEAGA" } \ No newline at end of file diff --git a/data/meal/mealbioschemas.jsonld b/data/meal/mealbioschemas.jsonld index 815bb244fb184..7bcfc7cf42c75 100644 --- a/data/meal/mealbioschemas.jsonld +++ b/data/meal/mealbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "MEAL", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MEAL.html", "sc:version": "1.4.2" diff --git a/data/means/meansbioschemas.jsonld b/data/means/meansbioschemas.jsonld index d33bd975d49b6..f976e6f8f00c8 100644 --- a/data/means/meansbioschemas.jsonld +++ b/data/means/meansbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btw229", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/means", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael P. H. Stumpf", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5018365", { "@id": "https://doi.org/10.1093/bioinformatics/btw229" }, + "pmcid:PMC5018365", "pubmed:27153663" ], "sc:description": "Moment Expansion Approximation, iNference and Simulation (MEANS) is a tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment", @@ -29,10 +33,6 @@ "sc:name": "MEANS", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/theosysbio/means" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btw229", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/measurementerror.cor/bioconda_measurementerror.cor.yaml b/data/measurementerror.cor/bioconda_measurementerror.cor.yaml index 4c3ed6b14efa1..1f5945806570f 100644 --- a/data/measurementerror.cor/bioconda_measurementerror.cor.yaml +++ b/data/measurementerror.cor/bioconda_measurementerror.cor.yaml @@ -4,7 +4,6 @@ description: Two-stage measurement error model for correlation estimation with s home: https://bioconductor.org/packages/3.10/bioc/html/MeasurementError.cor.html identifiers: - biotools:measurementerror.cor -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-measurementerror.cor diff --git a/data/mebs/mebsbioschemas.jsonld b/data/mebs/mebsbioschemas.jsonld index 4ca070e940469..550c09faeb22c 100644 --- a/data/mebs/mebsbioschemas.jsonld +++ b/data/mebs/mebsbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/mebs", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Augusto Cesar Poot-Hernandez", "Bruno Contreras Moreira", - "Valerie De Anda Torres" + "Valerie De Anda Torres", + "Augusto Cesar Poot-Hernandez" ], "sc:additionalType": "Command-line tool", "sc:description": "Software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle.", diff --git a/data/mecat/mecatbioschemas.jsonld b/data/mecat/mecatbioschemas.jsonld index b6b3afbc0386a..08e89f23acf2c 100644 --- a/data/mecat/mecatbioschemas.jsonld +++ b/data/mecat/mecatbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/mecat", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Chuan-Le Xiao", "Ying Chen", - "Feng Luo" + "Feng Luo", + "Chuan-Le Xiao" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:28945707", @@ -21,8 +21,8 @@ "sc:license": "GPL-3.0", "sc:name": "MECAT", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/xiaochuanle/MECAT" } \ No newline at end of file diff --git a/data/mechrna/mechrnabioschemas.jsonld b/data/mechrna/mechrnabioschemas.jsonld index 716263c788ca3..00b107a7053d0 100644 --- a/data/mechrna/mechrnabioschemas.jsonld +++ b/data/mechrna/mechrnabioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/mechrna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alexander R Gawronski", "Rolf Backofen", - "Support" + "Support", + "Alexander R Gawronski" ], "sc:additionalType": "Command-line tool", "sc:description": "Prediction of lncRNA mechanisms from RNA–RNA and RNA–protein interactions.", diff --git a/data/medecom/medecombioschemas.jsonld b/data/medecom/medecombioschemas.jsonld index e77a9bd243d54..cfe96fa5d1dfe 100644 --- a/data/medecom/medecombioschemas.jsonld +++ b/data/medecom/medecombioschemas.jsonld @@ -22,25 +22,25 @@ }, "edam:has_output": [ { - "@id": "edam:data_2048" + "@id": "edam:data_2884" }, { - "@id": "edam:data_2884" + "@id": "edam:data_2048" } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3518" + "@id": "edam:topic_0080" }, { - "@id": "edam:topic_3295" + "@id": "edam:topic_3518" }, { - "@id": "edam:topic_0080" + "@id": "edam:topic_3295" } ], "sc:author": [ @@ -48,11 +48,11 @@ "Pavlo Lutsik" ], "sc:citation": [ + "pubmed:28340624", + "pmcid:PMC5366155", { "@id": "https://doi.org/10.1186/s13059-017-1182-6" - }, - "pubmed:28340624", - "pmcid:PMC5366155" + } ], "sc:description": "Computational method for decomposition of heterogeneous DNA methylomes. It applies matrix factorization with biologically motivated constratints and regularization to discover and quantify latent components in methylomes of multi-cellual samples.", "sc:featureList": { @@ -65,8 +65,8 @@ "Linux" ], "sc:provider": [ - "Walter lab", "Hein Lab", + "Walter lab", "hdhub" ], "sc:softwareHelp": { diff --git a/data/medeller/medellerbioschemas.jsonld b/data/medeller/medellerbioschemas.jsonld index 6eda30c53a1b9..372ebfd3454e2 100644 --- a/data/medeller/medellerbioschemas.jsonld +++ b/data/medeller/medellerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MEDELLER", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://opig.stats.ox.ac.uk/webapps/medeller/home.pl?app=MEDELLER" } \ No newline at end of file diff --git a/data/medips/medipsbioschemas.jsonld b/data/medips/medipsbioschemas.jsonld index 9e624d0f4b483..782b6fd093f20 100644 --- a/data/medips/medipsbioschemas.jsonld +++ b/data/medips/medipsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btt650", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-8718-8848", "@type": "schema:Person" @@ -28,8 +24,8 @@ "Library" ], "sc:citation": [ - "pubmed:24227674", "pmcid:PMC3892689", + "pubmed:24227674", { "@id": "https://doi.org/10.1093/bioinformatics/btt650" } @@ -41,12 +37,16 @@ "sc:license": "GPL-2.0", "sc:name": "MEDIPS", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MEDIPS.html", "sc:version": "1.24.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btt650", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/medline_ranker/medline_rankerbioschemas.jsonld b/data/medline_ranker/medline_rankerbioschemas.jsonld index d60696f5aa3b3..afb72f328000d 100644 --- a/data/medline_ranker/medline_rankerbioschemas.jsonld +++ b/data/medline_ranker/medline_rankerbioschemas.jsonld @@ -32,26 +32,26 @@ "@id": "edam:topic_0218" }, "sc:citation": [ + "pubmed:19429696", "pmcid:PMC2703945", { "@id": "https://doi.org/10.1093/nar/gkp353" - }, - "pubmed:19429696" + } ], "sc:description": "This web server offers a flexible and fast statistical ranking of PubMed abstracts for topics of interest without expert knowledge.", "sc:featureList": [ { - "@id": "edam:operation_0306" + "@id": "edam:operation_0305" }, { - "@id": "edam:operation_0305" + "@id": "edam:operation_0306" } ], "sc:name": "Medline Ranker", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://cbdm.uni-mainz.de/medlineranker" }, diff --git a/data/medlineranker/medlinerankerbioschemas.jsonld b/data/medlineranker/medlinerankerbioschemas.jsonld index d5e44535dae5f..45c803386f5ba 100644 --- a/data/medlineranker/medlinerankerbioschemas.jsonld +++ b/data/medlineranker/medlinerankerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The MedlineRanker web server allows a flexible and fast ranking of Medline abstracts for a topic of interest without expert knowledge.", "sc:name": "MedlineRanker", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://cbdm-01.zdv.uni-mainz.de/~jfontain/cms/?page_id=4" } \ No newline at end of file diff --git a/data/medme/medmebioschemas.jsonld b/data/medme/medmebioschemas.jsonld index d3998bb86b0f6..0d45aab330e9f 100644 --- a/data/medme/medmebioschemas.jsonld +++ b/data/medme/medmebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "MEDME", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MEDME.html", "sc:version": "1.34.0" diff --git a/data/medock/medockbioschemas.jsonld b/data/medock/medockbioschemas.jsonld index 4b8f17f961a04..de74e04f938eb 100644 --- a/data/medock/medockbioschemas.jsonld +++ b/data/medock/medockbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "MEDock", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://medock.ee.ncku.edu.tw/" } \ No newline at end of file diff --git a/data/medsavant/medsavantbioschemas.jsonld b/data/medsavant/medsavantbioschemas.jsonld index 9fe2be3a0a205..b52438ef8b983 100644 --- a/data/medsavant/medsavantbioschemas.jsonld +++ b/data/medsavant/medsavantbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "MedSavant is a tool that helps find the genetic causes of disease.", "sc:name": "MedSavant", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.genomesavant.com/p/medsavant/index", diff --git a/data/medusa/medusabioschemas.jsonld b/data/medusa/medusabioschemas.jsonld index a8179d5e81d16..fc25d2f150e0d 100644 --- a/data/medusa/medusabioschemas.jsonld +++ b/data/medusa/medusabioschemas.jsonld @@ -11,13 +11,13 @@ "@id": "https://bio.tools/medusa", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Emanuele Bosi", "Marco Galardini", - "Marco Fondi", - "Emanuele Bosi" + "Marco Fondi" ], "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:author": "Emanuele Bosi", "sc:description": "Algorithm for genome scaffoldin which exploits information obtained from a set of genomes from related organisms to determine the correct order and orientation of the contigs. It formalizes the scaffolding problem by means of a combinatorial optimization formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. It does not require either prior knowledge on the microrganisms dataset under analysis or the availability of paired end read libraries.", diff --git a/data/medusa_motif/medusa_motifbioschemas.jsonld b/data/medusa_motif/medusa_motifbioschemas.jsonld index 4885ed6aeaa6b..314775eeb0c3e 100644 --- a/data/medusa_motif/medusa_motifbioschemas.jsonld +++ b/data/medusa_motif/medusa_motifbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MEDUSA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://cbio.mskcc.org/leslielab/software/medusa" } \ No newline at end of file diff --git a/data/medusa_pcr/medusa_pcrbioschemas.jsonld b/data/medusa_pcr/medusa_pcrbioschemas.jsonld index e2b2c47cff692..c136cc290d0f4 100644 --- a/data/medusa_pcr/medusa_pcrbioschemas.jsonld +++ b/data/medusa_pcr/medusa_pcrbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "medusa", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sonnhammer.sbc.su.se/download/software/medusa/" } \ No newline at end of file diff --git a/data/medyan/medyanbioschemas.jsonld b/data/medyan/medyanbioschemas.jsonld index d9a357640c5c3..f14503f87b621 100644 --- a/data/medyan/medyanbioschemas.jsonld +++ b/data/medyan/medyanbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "James Komianos", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27120189", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1004877" }, - "pubmed:27120189", "pmcid:PMC4847874" ], "sc:description": "Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks.", @@ -27,8 +27,8 @@ }, "sc:name": "MEDYAN", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.medyan.org/" }, diff --git a/data/meffil/meffilbioschemas.jsonld b/data/meffil/meffilbioschemas.jsonld index 470fdc7ef3354..48ab7eeca9233 100644 --- a/data/meffil/meffilbioschemas.jsonld +++ b/data/meffil/meffilbioschemas.jsonld @@ -13,8 +13,8 @@ "biotools:primaryContact": "Matthew Suderman", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:29931280", - "pmcid:PMC6247925" + "pmcid:PMC6247925", + "pubmed:29931280" ], "sc:description": "algorithms for analyzing DNA methylation data generated using Infinium HumanMethylation450 or MethylationEPIC BeadChips\nEpigenome-Wide Association Studies (EWAS)", "sc:license": "Artistic-2.0", diff --git a/data/mefit/mefitbioschemas.jsonld b/data/mefit/mefitbioschemas.jsonld index 9c575b966d7cb..a1ab8f23ff19c 100644 --- a/data/mefit/mefitbioschemas.jsonld +++ b/data/mefit/mefitbioschemas.jsonld @@ -9,25 +9,29 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-016-1358-1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mefit", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hardik I. Parikh", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27905885", + "pmcid:PMC5134250", { "@id": "https://doi.org/10.1186/S12859-016-1358-1" - }, - "pmcid:PMC5134250", - "pubmed:27905885" + } ], "sc:description": "This pipeline will merge overlapping paired-end reads, calculate merge statistics, and filter reads for quality.", "sc:featureList": [ { - "@id": "edam:operation_0232" + "@id": "edam:operation_3695" }, { - "@id": "edam:operation_3695" + "@id": "edam:operation_0232" } ], "sc:license": "Apache-1.0", @@ -37,10 +41,6 @@ "Mac" ], "sc:url": "https://github.com/nisheth/MeFiT" - }, - { - "@id": "https://doi.org/10.1186/S12859-016-1358-1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mega/megabioschemas.jsonld b/data/mega/megabioschemas.jsonld index b41d91e76d7ef..cd6b772363275 100644 --- a/data/mega/megabioschemas.jsonld +++ b/data/mega/megabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Proprietary", "sc:name": "MEGA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.megasoftware.net/" diff --git a/data/megadock-web/megadock-webbioschemas.jsonld b/data/megadock-web/megadock-webbioschemas.jsonld index 56bb983064758..4d24c156104dc 100644 --- a/data/megadock-web/megadock-webbioschemas.jsonld +++ b/data/megadock-web/megadock-webbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/megadock-web", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yutaka Akiyama", - "Masahito Ohue" + "Masahito Ohue", + "Yutaka Akiyama" ], "sc:additionalType": "Database portal", "sc:description": "It is an integrated database of high-throughput structure-based PPI predictions.", "sc:name": "MEGADOCK-Web", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.bi.cs.titech.ac.jp/megadock-web/" } \ No newline at end of file diff --git a/data/megamapper/megamapperbioschemas.jsonld b/data/megamapper/megamapperbioschemas.jsonld index db1e9aa044fa0..fd9c9e601f3ce 100644 --- a/data/megamapper/megamapperbioschemas.jsonld +++ b/data/megamapper/megamapperbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computational pipeline for positional cloning of mutations by whole genome sequencing.", "sc:name": "MegaMapper", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://wiki.med.harvard.edu/SysBio/Megason/MegaMapper" } \ No newline at end of file diff --git a/data/megamerger/megamergerbioschemas.jsonld b/data/megamerger/megamergerbioschemas.jsonld index 730b576577fc1..1c7bc0ba63e5d 100644 --- a/data/megamerger/megamergerbioschemas.jsonld +++ b/data/megamerger/megamergerbioschemas.jsonld @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "megamerger", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/megamerger_ws_husar/megamerger_ws_husarbioschemas.jsonld b/data/megamerger_ws_husar/megamerger_ws_husarbioschemas.jsonld index 367b6b069deb6..536c5db42c9e5 100644 --- a/data/megamerger_ws_husar/megamerger_ws_husarbioschemas.jsonld +++ b/data/megamerger_ws_husar/megamerger_ws_husarbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "megamerger WS (husar)", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/megamerger.html", "sc:version": "1" diff --git a/data/megan/meganbioschemas.jsonld b/data/megan/meganbioschemas.jsonld index e7edf3d0a7165..a9531f6c3c3c7 100644 --- a/data/megan/meganbioschemas.jsonld +++ b/data/megan/meganbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MEGAN", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ab.inf.uni-tuebingen.de/software/megan6/" } \ No newline at end of file diff --git a/data/megan6/megan6bioschemas.jsonld b/data/megan6/megan6bioschemas.jsonld index 99104773430b1..4af97004f91c2 100644 --- a/data/megan6/megan6bioschemas.jsonld +++ b/data/megan6/megan6bioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MEGAN6", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ab.inf.uni-tuebingen.de/software/megan6/" } \ No newline at end of file diff --git a/data/megante/megantebioschemas.jsonld b/data/megante/megantebioschemas.jsonld index 3b61e4b72e5d0..f707b1c97d054 100644 --- a/data/megante/megantebioschemas.jsonld +++ b/data/megante/megantebioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/pcp/pct157", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/megante", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web service", "sc:citation": [ - "pubmed:24253915", { "@id": "https://doi.org/10.1093/pcp/pct157" }, - "pmcid:PMC3894707" + "pmcid:PMC3894707", + "pubmed:24253915" ], "sc:description": "Perform genomic sequence annotations by uploading a sequence and selecting the species to query. Automatically runs several analysis and integrates the results to select the appropriate consensus exon-intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with GBrowse and the results can be downloaded in Microsoft Excel format.", "sc:featureList": { @@ -31,10 +35,6 @@ "Windows" ], "sc:url": "https://megante.dna.affrc.go.jp" - }, - { - "@id": "https://doi.org/10.1093/pcp/pct157", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/megraft/megraftbioschemas.jsonld b/data/megraft/megraftbioschemas.jsonld index 37ebbb3b46340..28e072fa74542 100644 --- a/data/megraft/megraftbioschemas.jsonld +++ b/data/megraft/megraftbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Megraft", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://microbiology.se/software/megraft" } \ No newline at end of file diff --git a/data/megu/megubioschemas.jsonld b/data/megu/megubioschemas.jsonld index 8980610638563..89ef0e60753ba 100644 --- a/data/megu/megubioschemas.jsonld +++ b/data/megu/megubioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "MEGU is a web application that visualizes complex omics data of multiple layers simultaneously, including transcriptome, pro-teome, and metabolome, onto an integrated pathway diagram de-rived by connecting the individual KEGG pathway maps; the mapped images are generated in Scalable Vector Graphics for easy editing by hand or with computer programs or drawing software.", "sc:name": "MEGU", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://megu.iab.keio.ac.jp/" } \ No newline at end of file diff --git a/data/meigo/meigobioschemas.jsonld b/data/meigo/meigobioschemas.jsonld index 05ec40541a490..7f907715c4b58 100644 --- a/data/meigo/meigobioschemas.jsonld +++ b/data/meigo/meigobioschemas.jsonld @@ -13,8 +13,8 @@ "@id": "https://bio.tools/meigo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Julio R. Banga", - "Julio Saez-Rodríguez" + "Julio Saez-Rodríguez", + "Julio R. Banga" ], "sc:additionalType": "Library", "sc:citation": [ @@ -30,9 +30,9 @@ }, "sc:name": "MEIGO", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://nautilus.iim.csic.es/~gingproc/meigo.html" }, diff --git a/data/meigor/meigorbioschemas.jsonld b/data/meigor/meigorbioschemas.jsonld index 9f7fc18508ebe..8a4d87b1e61ee 100644 --- a/data/meigor/meigorbioschemas.jsonld +++ b/data/meigor/meigorbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jose Egea", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A software suite based on metaheuristics for global optimization in systems biology and bioinformatics.", "sc:license": "GPL-3.0", "sc:name": "MEIGOR", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MEIGOR.html", "sc:version": "1.8.0" diff --git a/data/melanie/melaniebioschemas.jsonld b/data/melanie/melaniebioschemas.jsonld index e9405de65c995..dee6afe905c26 100644 --- a/data/melanie/melaniebioschemas.jsonld +++ b/data/melanie/melaniebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Offers a unique and flexible interface for the comprehensive visualization, exploration and analysis of 2D gel data. It provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE (Fluorescence Difference Gel Electrophoresis) gels.", "sc:name": "Melanie", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://world-2dpage.expasy.org/melanie/", diff --git a/data/melanomamine/melanomaminebioschemas.jsonld b/data/melanomamine/melanomaminebioschemas.jsonld index ce8e8be2f7932..d02f3adf63826 100644 --- a/data/melanomamine/melanomaminebioschemas.jsonld +++ b/data/melanomamine/melanomaminebioschemas.jsonld @@ -16,20 +16,20 @@ ], "sc:additionalType": "Web application", "sc:author": [ - "Andrés Cañada", - "Martin Krallinger" + "Martin Krallinger", + "Andrés Cañada" ], "sc:description": "Text mining for melanoma.", "sc:name": "MelanomaMine", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ + "Spanish Cancer Research Center", "Spanish National Bioinformatics Institute", - "cnio.es", - "Spanish Cancer Research Center" + "cnio.es" ], "sc:url": "http://melanomamine.bioinfo.cnio.es/", "sc:version": "0.1" diff --git a/data/meltdb/meltdbbioschemas.jsonld b/data/meltdb/meltdbbioschemas.jsonld index 3001536cd3a82..609e60ecd6442 100644 --- a/data/meltdb/meltdbbioschemas.jsonld +++ b/data/meltdb/meltdbbioschemas.jsonld @@ -15,13 +15,13 @@ "sc:license": "GPL-2.0", "sc:name": "MeltDB", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ - "bigi", "CeBiTec", + "bigi", "Bielefeld University" ], "sc:url": "http://meltdb.cebitec.uni-bielefeld.de", diff --git a/data/melting/meltingbioschemas.jsonld b/data/melting/meltingbioschemas.jsonld index 137d2a528de65..903d9cf32e173 100644 --- a/data/melting/meltingbioschemas.jsonld +++ b/data/melting/meltingbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA.", "sc:name": "Melting", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.ebi.ac.uk/compneur-srv/melting/" } \ No newline at end of file diff --git a/data/mem-adsvm/mem-adsvmbioschemas.jsonld b/data/mem-adsvm/mem-adsvmbioschemas.jsonld index dd687fc991324..d4394dc65b6b6 100644 --- a/data/mem-adsvm/mem-adsvmbioschemas.jsonld +++ b/data/mem-adsvm/mem-adsvmbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/mem-adsvm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Shibiao Wan", - "Man-Wai Mak" + "Man-Wai Mak", + "Shibiao Wan" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:27000774", "sc:description": "A two-layer multi-label predictor for identifying multi-functional types of membrane proteins.", "sc:name": "Mem-ADSVM", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioinfo.eie.polyu.edu.hk/MemADSVMServer/" } \ No newline at end of file diff --git a/data/mem/membioschemas.jsonld b/data/mem/membioschemas.jsonld index c3860e8dae844..13a8f97ec3002 100644 --- a/data/mem/membioschemas.jsonld +++ b/data/mem/membioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mem", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jaak Vilo", "Raivo Kolde", + "Jaak Vilo", "Priit Adler" ], "sc:additionalType": "Database portal", @@ -21,9 +21,9 @@ "sc:license": "Freeware", "sc:name": "Multi Experiment Matrix (MEM)", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://biit.cs.ut.ee/mem/" } \ No newline at end of file diff --git a/data/membplugin/membpluginbioschemas.jsonld b/data/membplugin/membpluginbioschemas.jsonld index 1b7ee66c7c308..6e210968cc4b2 100644 --- a/data/membplugin/membpluginbioschemas.jsonld +++ b/data/membplugin/membpluginbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/membplugin", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers.", "sc:license": "GPL-3.0", diff --git a/data/membrain/membrainbioschemas.jsonld b/data/membrain/membrainbioschemas.jsonld index be8a6953e0428..bb58cbadca83f 100644 --- a/data/membrain/membrainbioschemas.jsonld +++ b/data/membrain/membrainbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server developed for transmembrane protein structure prediction. It contains two main prediction functions, i.e., transmembrane helix (TMH) prediction and TMH-TMH residue contact prediction.", "sc:name": "MemBrain", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/MemBrain/" } \ No newline at end of file diff --git a/data/meme/memebioschemas.jsonld b/data/meme/memebioschemas.jsonld index 1a3be57be64fc..55dd16ac4a59a 100644 --- a/data/meme/memebioschemas.jsonld +++ b/data/meme/memebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for discovering motifs in a group of related DNA or protein sequences. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. This tool represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern.", "sc:name": "MEME", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://meme-suite.org/tools/meme" diff --git a/data/meme_meme/meme_memebioschemas.jsonld b/data/meme_meme/meme_memebioschemas.jsonld index dc99d8421abd4..3fee6ee455de1 100644 --- a/data/meme_meme/meme_memebioschemas.jsonld +++ b/data/meme_meme/meme_memebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.", "sc:name": "meme_meme", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://meme-suite.org/tools/meme", diff --git a/data/meme_suite/meme_suitebioschemas.jsonld b/data/meme_suite/meme_suitebioschemas.jsonld index 0ff584f2c8918..3d88467a98f28 100644 --- a/data/meme_suite/meme_suitebioschemas.jsonld +++ b/data/meme_suite/meme_suitebioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "MEME Suite Support", "sc:additionalType": [ - "Suite", + "Command-line tool", "Web application", - "Command-line tool" + "Suite" ], "sc:citation": "pubmed:7584402", "sc:description": "Unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.", diff --git a/data/memgen/memgenbioschemas.jsonld b/data/memgen/memgenbioschemas.jsonld index 82652c2752b6c..a12cb2d34a78a 100644 --- a/data/memgen/memgenbioschemas.jsonld +++ b/data/memgen/memgenbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Creates multi-component lipid bilayer membranes for molecular dynamics simulations.", "sc:name": "MemGen", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://memgen.uni-goettingen.de/" } \ No newline at end of file diff --git a/data/memhdx/memhdxbioschemas.jsonld b/data/memhdx/memhdxbioschemas.jsonld index e6a973b1d6493..ab7b2b9b46489 100644 --- a/data/memhdx/memhdxbioschemas.jsonld +++ b/data/memhdx/memhdxbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This tool allows users to perform an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure.", "sc:name": "MEMHDX", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Institut Pasteur", "sc:url": "http://memhdx.c3bi.pasteur.fr/", diff --git a/data/memloci/memlocibioschemas.jsonld b/data/memloci/memlocibioschemas.jsonld index 917e9ea0448c7..9d6c9e9ae2548 100644 --- a/data/memloci/memlocibioschemas.jsonld +++ b/data/memloci/memlocibioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/memloci", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Pier Luigi Martelli", - "Andrea Pierleoni" + "Andrea Pierleoni", + "Pier Luigi Martelli" ], "sc:additionalType": "Web application", "sc:description": "Predictor for the subcellular localization of proteins associated or inserted in eukaryotes membranes.", "sc:name": "MemLoci", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", diff --git a/data/memo/memobioschemas.jsonld b/data/memo/memobioschemas.jsonld index 148c2c6cab776..3bf6ef7580e3e 100644 --- a/data/memo/memobioschemas.jsonld +++ b/data/memo/memobioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM).", "sc:name": "MEMO", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/MEMO-toolbox/MEMO" diff --git a/data/memo_cancer/memo_cancerbioschemas.jsonld b/data/memo_cancer/memo_cancerbioschemas.jsonld index f47a3661e88a0..769255b67d990 100644 --- a/data/memo_cancer/memo_cancerbioschemas.jsonld +++ b/data/memo_cancer/memo_cancerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Method for identifying mutually exclusive driver networks in cancer. The method identifies networks defined by three properties: first, member genes are recurrently altered via somatic mutation or copy number changes; second, member genes are likely to participate in the same biological pathway or process, as determined from prior pathway and network knowledge; and third, genomic events within the network exhibit a statistically significant level of mutual exclusivity.", "sc:name": "MEMo", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://cbio.mskcc.org/tools/memo/" } \ No newline at end of file diff --git a/data/memoir/memoirbioschemas.jsonld b/data/memoir/memoirbioschemas.jsonld index 0e63233095cef..8038464f606a4 100644 --- a/data/memoir/memoirbioschemas.jsonld +++ b/data/memoir/memoirbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Memoir", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://opig.stats.ox.ac.uk/webapps/memoir" } \ No newline at end of file diff --git a/data/memosys/memosysbioschemas.jsonld b/data/memosys/memosysbioschemas.jsonld index ca4332a7ed4f2..b76de4804e8a1 100644 --- a/data/memosys/memosysbioschemas.jsonld +++ b/data/memosys/memosysbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web based bioinformatics platform for the management, storage, and development of metabolic models. It supports the development of new models by providing a built in version control system which offers access to the complete reconstruction history.", "sc:name": "MEMOSys", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://icbi.at/software/memosys/memosys.shtml" } \ No newline at end of file diff --git a/data/memotif/memotifbioschemas.jsonld b/data/memotif/memotifbioschemas.jsonld index 6545d59f0748d..77d0215d1a70d 100644 --- a/data/memotif/memotifbioschemas.jsonld +++ b/data/memotif/memotifbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MeMotif", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://projects.biotec.tu-dresden.de/memotif" } \ No newline at end of file diff --git a/data/mempype/mempypebioschemas.jsonld b/data/mempype/mempypebioschemas.jsonld index ed600ba8b0e6b..57038375d4f05 100644 --- a/data/mempype/mempypebioschemas.jsonld +++ b/data/mempype/mempypebioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Prediction of topology and subcellular localization of Eukaryotic membrane proteins.", "sc:name": "MemPype", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "https://mu2py.biocomp.unibo.it/mempype", diff --git a/data/memtype-2l/memtype-2lbioschemas.jsonld b/data/memtype-2l/memtype-2lbioschemas.jsonld index 8fe2289a01c4e..6094c6cc07777 100644 --- a/data/memtype-2l/memtype-2lbioschemas.jsonld +++ b/data/memtype-2l/memtype-2lbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "2-layer predictor for predicting membrane protein types, the first layer will predict whether the query sequence belongs to membrane proteins or not; and the second layer aims to predict exactly the membrane protein types when the output of the first layer is “membrane proteins”.", "sc:name": "MemType-2L", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/MemType/" diff --git a/data/mendel/mendelbioschemas.jsonld b/data/mendel/mendelbioschemas.jsonld index 6f22a34b1a991..0ff69cdc01f2c 100644 --- a/data/mendel/mendelbioschemas.jsonld +++ b/data/mendel/mendelbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "Other", "sc:name": "Mendel", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://software.genetics.ucla.edu/mendel" } \ No newline at end of file diff --git a/data/mendelian/mendelianbioschemas.jsonld b/data/mendelian/mendelianbioschemas.jsonld index d697190aeffb6..4919bc193b588 100644 --- a/data/mendelian/mendelianbioschemas.jsonld +++ b/data/mendelian/mendelianbioschemas.jsonld @@ -9,30 +9,30 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-6742-3911", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/mendelian", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Filip Van Nieuwerburgh", { "@id": "http://orcid.org/0000-0001-6742-3911" - } + }, + "Filip Van Nieuwerburgh" ], "sc:additionalType": "Command-line tool", "sc:description": "R-package for heuristic variant filtering.", "sc:license": "GPL-2.0", "sc:name": "Mendelian", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/BartBroeckx/Mendelian" + }, + { + "@id": "http://orcid.org/0000-0001-6742-3911", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mendelianrandomization/mendelianrandomizationbioschemas.jsonld b/data/mendelianrandomization/mendelianrandomizationbioschemas.jsonld index a45d79d37beb0..c582c0def97b7 100644 --- a/data/mendelianrandomization/mendelianrandomizationbioschemas.jsonld +++ b/data/mendelianrandomization/mendelianrandomizationbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Stephen Burgess", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5510723", { "@id": "https://doi.org/10.1093/ije/dyx034" }, - "pubmed:28398548", - "pmcid:PMC5510723" + "pubmed:28398548" ], "sc:description": "Encodes several methods for performing Mendelian randomization analyses with summarized data. Summarized data on genetic associations with the exposure and with the outcome can be obtained from large consortia. These data can be used for obtaining causal estimates using instrumental variable methods.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "MendelianRandomization", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/MendelianRandomization/" }, diff --git a/data/mendelmd/mendelmdbioschemas.jsonld b/data/mendelmd/mendelmdbioschemas.jsonld index 600d9a56f5a38..c4b698198d630 100644 --- a/data/mendelmd/mendelmdbioschemas.jsonld +++ b/data/mendelmd/mendelmdbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Mendel,MD", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://mendelmd.org/" } \ No newline at end of file diff --git a/data/meneco/menecobioschemas.jsonld b/data/meneco/menecobioschemas.jsonld index 8766eda465265..3b8fd1052fde9 100644 --- a/data/meneco/menecobioschemas.jsonld +++ b/data/meneco/menecobioschemas.jsonld @@ -25,29 +25,29 @@ "Script" ], "sc:citation": [ - "pmcid:PMC5302834", - "pubmed:28129330", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1005276" - } + }, + "pmcid:PMC5302834", + "pubmed:28129330" ], "sc:description": "Topological gap-filling of genome-scale draft metabolic networks.", "sc:featureList": [ { - "@id": "edam:operation_3715" + "@id": "edam:operation_3803" }, { - "@id": "edam:operation_3660" + "@id": "edam:operation_3715" }, { - "@id": "edam:operation_3803" + "@id": "edam:operation_3660" } ], "sc:license": "GPL-3.0", "sc:name": "meneco", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://bioasp.github.io/meneco/", "sc:version": "1.5" diff --git a/data/mentha/menthabioschemas.jsonld b/data/mentha/menthabioschemas.jsonld index fed196cc7c7da..da77a5e16cdd6 100644 --- a/data/mentha/menthabioschemas.jsonld +++ b/data/mentha/menthabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mentha", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Luana Licata", - "Alberto Calderone" + "Alberto Calderone", + "Luana Licata" ], "sc:additionalType": "Web application", "sc:author": "Alberto Calderone", @@ -21,9 +21,9 @@ "sc:description": "Resource for protein-protein interactions (PPI). It integrates data curated by experts in compliance with IMEx curation policies, using the PSICQUIC protocol to implement an automatic procedure that automatically aligns the integrated database with data regularly annotated by the primary databases", "sc:name": "mentha", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy", diff --git a/data/menu-builder/menu-builderbioschemas.jsonld b/data/menu-builder/menu-builderbioschemas.jsonld index 97e27bc225873..f0bb2b4437750 100644 --- a/data/menu-builder/menu-builderbioschemas.jsonld +++ b/data/menu-builder/menu-builderbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A simple menu builder.", "sc:name": "menu-builder", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "BioJS", "sc:url": "https://github.com/greenify/menu-builder", diff --git a/data/mepsa/mepsabioschemas.jsonld b/data/mepsa/mepsabioschemas.jsonld index 40a39495bad97..eaa0a14636c56 100644 --- a/data/mepsa/mepsabioschemas.jsonld +++ b/data/mepsa/mepsabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective.", "sc:name": "MEPSA", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioweb.cbm.uam.es/software/MEPSA/" diff --git a/data/merav/meravbioschemas.jsonld b/data/merav/meravbioschemas.jsonld index e62d28cc3e4ff..4475b1a14340f 100644 --- a/data/merav/meravbioschemas.jsonld +++ b/data/merav/meravbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web-based tool that can query a database comprising ～4300 microarrays, representing human gene expression in normal tissues, cancer cell lines and primary tumors.", "sc:name": "MERAV", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://merav.wi.mit.edu/" diff --git a/data/mercator_plant/mercator_plantbioschemas.jsonld b/data/mercator_plant/mercator_plantbioschemas.jsonld index 6cfa1d816ee08..277b8d50cc2f0 100644 --- a/data/mercator_plant/mercator_plantbioschemas.jsonld +++ b/data/mercator_plant/mercator_plantbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for genome scale functional annotation of plant sequence data.", "sc:name": "Mercator", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mapman.gabipd.org/web/guest/app/Mercator" } \ No newline at end of file diff --git a/data/mergemaid/mergemaidbioschemas.jsonld b/data/mergemaid/mergemaidbioschemas.jsonld index a963dc3c5de4e..9db9a9806eae8 100644 --- a/data/mergemaid/mergemaidbioschemas.jsonld +++ b/data/mergemaid/mergemaidbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xiaogang Zhong", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This R extension studies gene expression array data. Its main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculates the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival.", "sc:license": "GPL-2.0", "sc:name": "MergeMaid", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MergeMaid.html", "sc:version": "2.46.0" diff --git a/data/mergeomics/mergeomicsbioschemas.jsonld b/data/mergeomics/mergeomicsbioschemas.jsonld index c0822d1ce560b..1a7f21b16fb77 100644 --- a/data/mergeomics/mergeomicsbioschemas.jsonld +++ b/data/mergeomics/mergeomicsbioschemas.jsonld @@ -18,17 +18,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Douglas Arneson", "sc:additionalType": [ + "Web application", "Workflow", "Suite", - "Web application", "Library" ], "sc:citation": [ + "pubmed:27612452", "pmcid:PMC5016927", { "@id": "https://doi.org/10.1186/s12864-016-3057-8" - }, - "pubmed:27612452" + } ], "sc:description": "Multidimensional Data Integration. This web aplication serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts: a Marker Set Enrichment Analysis (MSEA) and a weighted Key Driver Analysis (wKDA).", "sc:featureList": { @@ -37,9 +37,9 @@ "sc:license": "GPL-2.0", "sc:name": "Mergeomics", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://mergeomics.research.idre.ucla.edu/home.php" } diff --git a/data/mergeomics_pipeline/mergeomics_pipelinebioschemas.jsonld b/data/mergeomics_pipeline/mergeomics_pipelinebioschemas.jsonld index e0151a8d5b90f..73228b72a1371 100644 --- a/data/mergeomics_pipeline/mergeomics_pipelinebioschemas.jsonld +++ b/data/mergeomics_pipeline/mergeomics_pipelinebioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5097440", + "pubmed:27814671", { "@id": "https://doi.org/10.1186/s12864-016-3198-9" - }, - "pubmed:27814671" + } ], "sc:description": "Mergeomics is a computational pipeline consisting of independent modules that 1) leverage multi-omics association data to identify biological processes that are perturbed in disease, and 2) overlay the disease-associated processes onto molecular interaction networks to pinpoint hubs as potential key regulators.", "sc:featureList": { diff --git a/data/merger/mergerbioschemas.jsonld b/data/merger/mergerbioschemas.jsonld index 24750677ddb60..00170dc16729d 100644 --- a/data/merger/mergerbioschemas.jsonld +++ b/data/merger/mergerbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "Wellcome Trust", "EMBOSS Contributors", + "UK BBSRC", "UK MRC" ], "sc:description": "Merge two overlapping sequences.", "sc:funder": [ "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "merger", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/mergeslidingwindowsclusters/mergeslidingwindowsclustersbioschemas.jsonld b/data/mergeslidingwindowsclusters/mergeslidingwindowsclustersbioschemas.jsonld index f50a45c3a50f7..1cdafe77757d5 100644 --- a/data/mergeslidingwindowsclusters/mergeslidingwindowsclustersbioschemas.jsonld +++ b/data/mergeslidingwindowsclusters/mergeslidingwindowsclustersbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Merges two files containing the results of a sliding windows clustering.", "sc:name": "mergeslidingwindowsclusters", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/mergetranscriptlists/mergetranscriptlistsbioschemas.jsonld b/data/mergetranscriptlists/mergetranscriptlistsbioschemas.jsonld index 41a06d0a7b41f..98bcc1ff4da0d 100644 --- a/data/mergetranscriptlists/mergetranscriptlistsbioschemas.jsonld +++ b/data/mergetranscriptlists/mergetranscriptlistsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "mergetranscriptlists", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/merip-pf/merip-pfbioschemas.jsonld b/data/merip-pf/merip-pfbioschemas.jsonld index 2290102c6a3e5..c469c1755b296 100644 --- a/data/merip-pf/merip-pfbioschemas.jsonld +++ b/data/merip-pf/merip-pfbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/J.GPB.2013.01.002", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/merip-pf", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "YU Jun", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4357668", "pubmed:23434047", { "@id": "https://doi.org/10.1016/J.GPB.2013.01.002" - }, - "pmcid:PMC4357668" + } ], "sc:description": "An easy-to-use pipeline for high-resolution peak-finding in MeRIP-Seq data.", "sc:featureList": { @@ -35,6 +31,10 @@ "Mac" ], "sc:url": "http://software.big.ac.cn/MeRIP-PF.html" + }, + { + "@id": "https://doi.org/10.1016/J.GPB.2013.01.002", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/merit/meritbioschemas.jsonld b/data/merit/meritbioschemas.jsonld index 162a5d32a8a49..b2599bef0a221 100644 --- a/data/merit/meritbioschemas.jsonld +++ b/data/merit/meritbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hossein Khiabanian", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Mutation Error Rare Identification Toolkit is a comprehensive pipeline designed for in-depth quantification of erroneous substitutions and small indels in high-throughput sequencing data, specifically, for ultra-deep applications.\nIt considers the genomic context of the errors, including the nucleotides immediately at their 5’ and 3’, and establishes error rates at 96 possible substitutions as well as four single-base and 16 double-base indels.", "sc:name": "MERIT", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.khiabanian-lab.org/pages/software.html" } \ No newline at end of file diff --git a/data/merlin/merlinbioschemas.jsonld b/data/merlin/merlinbioschemas.jsonld index e4187ad7e075a..8188943c85b12 100644 --- a/data/merlin/merlinbioschemas.jsonld +++ b/data/merlin/merlinbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "Merlin", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://csg.sph.umich.edu/abecasis/Merlin/" } \ No newline at end of file diff --git a/data/mermaid/mermaidbioschemas.jsonld b/data/mermaid/mermaidbioschemas.jsonld index 9d76aa554abf2..1ed9dd6161f9c 100644 --- a/data/mermaid/mermaidbioschemas.jsonld +++ b/data/mermaid/mermaidbioschemas.jsonld @@ -19,8 +19,8 @@ "biotools:primaryContact": "Alejandro Giorgetti", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31106328", "pmcid:PMC6602572", + "pubmed:31106328", { "@id": "https://doi.org/10.1093/NAR/GKZ416" } @@ -28,21 +28,21 @@ "sc:description": "Web server to prepare and run coarse-grained membrane protein dynamics.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_2476" }, { "@id": "edam:operation_0244" }, { - "@id": "edam:operation_2476" + "@id": "edam:operation_3431" } ], "sc:license": "CC-BY-4.0", "sc:name": "MERMAID", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://molsim.sci.univr.it/mermaid/" } diff --git a/data/merops/meropsbioschemas.jsonld b/data/merops/meropsbioschemas.jsonld index 069c43e1361e0..3df504f2ec6e5 100644 --- a/data/merops/meropsbioschemas.jsonld +++ b/data/merops/meropsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Collection of peptidases. The database has a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. The database can distinguish one peptidase from another through identifying the specificity of the peptidase in terms of where it will cleave substrates and with which inhibitors it will interact.", "sc:name": "MEROPS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://merops.sanger.ac.uk/" } \ No newline at end of file diff --git a/data/merops_blast/merops_blastbioschemas.jsonld b/data/merops_blast/merops_blastbioschemas.jsonld index a5f4df169814b..c826f793a3e2d 100644 --- a/data/merops_blast/merops_blastbioschemas.jsonld +++ b/data/merops_blast/merops_blastbioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "MEROPS group", "sc:additionalType": "Web application", "sc:author": [ - "Neil Rawlings", - "MEROPS group" + "MEROPS group", + "Neil Rawlings" ], "sc:contributor": "NCBI", "sc:description": "Search MEROPS sequences with BLAST.", "sc:name": "MEROPS Blast", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ diff --git a/data/merrill/merrillbioschemas.jsonld b/data/merrill/merrillbioschemas.jsonld index 7ee267e570ec3..952f794d93f46 100644 --- a/data/merrill/merrillbioschemas.jsonld +++ b/data/merrill/merrillbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Micromagnetic Earth Related Robust Interpretated Language Laboratory.", "sc:name": "MERRILL", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.geos.ed.ac.uk/geosciences/research/projects/rockmag" } \ No newline at end of file diff --git a/data/mesadb/mesadbbioschemas.jsonld b/data/mesadb/mesadbbioschemas.jsonld index b7639af23d990..8f414f466f51d 100644 --- a/data/mesadb/mesadbbioschemas.jsonld +++ b/data/mesadb/mesadbbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/mesadb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Koray D. Kaya", "Aybar C. Acar", - "Cengiz Yakicier", + "Koray D. Kaya", "Özlen Konu", - "Gökhan Karakülah" + "Gökhan Karakülah", + "Cengiz Yakicier" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:21177657", "sc:description": "microRNA expression and sequence analysis database is a database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets.", "sc:name": "mESAdb", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://konulab.fen.bilkent.edu.tr/mirna/" } \ No newline at end of file diff --git a/data/meshdbi/meshdbibioschemas.jsonld b/data/meshdbi/meshdbibioschemas.jsonld index c36e1e5c5c981..15f4c13008b8c 100644 --- a/data/meshdbi/meshdbibioschemas.jsonld +++ b/data/meshdbi/meshdbibioschemas.jsonld @@ -39,11 +39,11 @@ } ], "sc:citation": [ - "pmcid:PMC4343279", + "pubmed:25887539", { "@id": "https://doi.org/10.1186/s12859-015-0453-z" }, - "pubmed:25887539" + "pmcid:PMC4343279" ], "sc:description": "The package is a unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interfaced to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db.", "sc:featureList": { @@ -52,8 +52,8 @@ "sc:license": "Artistic-2.0", "sc:name": "MeSHDbi", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MeSHDbi.html", diff --git a/data/meshes/bioconda_meshes.yaml b/data/meshes/bioconda_meshes.yaml index 87e03c5d0cd1a..699615c081555 100644 --- a/data/meshes/bioconda_meshes.yaml +++ b/data/meshes/bioconda_meshes.yaml @@ -10,7 +10,6 @@ description: MeSH (Medical Subject Headings) is the NLM controlled vocabulary us home: https://bioconductor.org/packages/3.10/bioc/html/meshes.html identifiers: - biotools:meshes -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-meshes summary: MeSH Enrichment and Semantic analyses diff --git a/data/meshes/meshesbioschemas.jsonld b/data/meshes/meshesbioschemas.jsonld index abab721e2f0d2..071f6f48bdb25 100644 --- a/data/meshes/meshesbioschemas.jsonld +++ b/data/meshes/meshesbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Guangchuang Yu", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. This tool supports enrichment analysis of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups.", "sc:license": "Artistic-2.0", "sc:name": "meshes", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/meshes.html", diff --git a/data/meshr/meshrbioschemas.jsonld b/data/meshr/meshrbioschemas.jsonld index fa0b9924b9383..b2a51ed6c5a16 100644 --- a/data/meshr/meshrbioschemas.jsonld +++ b/data/meshr/meshrbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "http://orcid.org/0000-0003-3797-2148", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1111/age.12307", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/meshr", "@type": "sc:SoftwareApplication", @@ -25,18 +21,18 @@ }, "edam:has_input": [ { - "@id": "edam:data_0582" + "@id": "edam:data_2295" }, { - "@id": "edam:data_2295" + "@id": "edam:data_0582" } ], "edam:has_output": [ { - "@id": "edam:data_2048" + "@id": "edam:data_3509" }, { - "@id": "edam:data_3509" + "@id": "edam:data_2048" } ], "sc:additionalType": [ @@ -45,18 +41,18 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3063" + "@id": "edam:topic_3572" }, { - "@id": "edam:topic_3572" + "@id": "edam:topic_3063" } ], "sc:citation": [ + "pmcid:PMC5032990", { "@id": "https://doi.org/10.1111/age.12307" }, - "pubmed:26036323", - "pmcid:PMC5032990" + "pubmed:26036323" ], "sc:description": "A set of annotation maps describing the entire MeSH assembled using data from MeSH.", "sc:featureList": { @@ -65,12 +61,16 @@ "sc:license": "Artistic-2.0", "sc:name": "meshr", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/meshr.html", "sc:version": "1.10.0" + }, + { + "@id": "https://doi.org/10.1111/age.12307", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/meshsim/meshsimbioschemas.jsonld b/data/meshsim/meshsimbioschemas.jsonld index 5d802c20bfeec..5efbcfec217b5 100644 --- a/data/meshsim/meshsimbioschemas.jsonld +++ b/data/meshsim/meshsimbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jing ZHou", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Provide for measuring semantic similarity over MeSH headings and MEDLINE documents.", "sc:license": "GPL-2.0", "sc:name": "MeSHSim", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MeSHSim.html", "sc:version": "1.6.0" diff --git a/data/mesmer/mesmerbioschemas.jsonld b/data/mesmer/mesmerbioschemas.jsonld index e402a722c9afa..bb1cade8b70b6 100644 --- a/data/mesmer/mesmerbioschemas.jsonld +++ b/data/mesmer/mesmerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Scientific tool designed to identify characteristic structures or components in heterogenous solutions from bulk-average data. It does this by evolving a population of ensembles containing candidate components, selecting only ensembles that fit the available experimental data better than their peers.", "sc:name": "MESMER", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://code.google.com/p/mesmer/" } \ No newline at end of file diff --git a/data/messina/messinabioschemas.jsonld b/data/messina/messinabioschemas.jsonld index 4ca208f2de81b..f7ab9b928779b 100644 --- a/data/messina/messinabioschemas.jsonld +++ b/data/messina/messinabioschemas.jsonld @@ -30,21 +30,21 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0203" + "@id": "edam:topic_3344" }, { - "@id": "edam:topic_3360" + "@id": "edam:topic_0203" }, { - "@id": "edam:topic_3344" + "@id": "edam:topic_3360" } ], "sc:citation": [ - "pmcid:PMC2671167", + "pubmed:19399185", { "@id": "https://doi.org/10.1371/journal.pone.0005337" }, - "pubmed:19399185" + "pmcid:PMC2671167" ], "sc:description": "Collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.", "sc:featureList": [ @@ -61,9 +61,9 @@ "sc:license": "EPL-1.0", "sc:name": "messina", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/messina.html", "sc:version": "1.10.0" diff --git a/data/met/metbioschemas.jsonld b/data/met/metbioschemas.jsonld index d5fedc4094b13..2b97842693dbe 100644 --- a/data/met/metbioschemas.jsonld +++ b/data/met/metbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The Motif Enrichment Tool (MET) takes user-defined gene sets and identifies significantly associated sets of genes that share a regulatory motif. The tool is available for a number of model organisms (human, mouse, zebrafinch, stickleback, fruitfly, etc). It incorporates transcription factor DNA-specificity motifs taken from literature curation, bacterial one-hybrid assays, high-throughput SELEX experiments, and protein binding microarrays.", "sc:name": "MET", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://veda.cs.uiuc.edu/MET/" diff --git a/data/meta-4mcpred/meta-4mcpredbioschemas.jsonld b/data/meta-4mcpred/meta-4mcpredbioschemas.jsonld index f3514fa2d89ee..f93a990920977 100644 --- a/data/meta-4mcpred/meta-4mcpredbioschemas.jsonld +++ b/data/meta-4mcpred/meta-4mcpredbioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/J.OMTN.2019.04.019", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Meta-4mCpred", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Leyi Wei", "Balachandran Manavalan", - "Gwang Lee", - "Leyi Wei" + "Gwang Lee" ], "sc:additionalType": "Web application", "sc:citation": [ @@ -33,11 +29,15 @@ "sc:license": "Unlicense", "sc:name": "Meta-4mCpred", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://thegleelab.org/Meta-4mCpred" + }, + { + "@id": "https://doi.org/10.1016/J.OMTN.2019.04.019", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/meta-basic/meta-basicbioschemas.jsonld b/data/meta-basic/meta-basicbioschemas.jsonld index db2bb255ca018..9dd2fb4ea4baa 100644 --- a/data/meta-basic/meta-basicbioschemas.jsonld +++ b/data/meta-basic/meta-basicbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "A tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure.", "sc:name": "Meta-BASIC", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://basic.bioinfo.pl/" } \ No newline at end of file diff --git a/data/meta-gecko/meta-geckobioschemas.jsonld b/data/meta-gecko/meta-geckobioschemas.jsonld index aa57dc69ff747..ed7bbe63ff94b 100644 --- a/data/meta-gecko/meta-geckobioschemas.jsonld +++ b/data/meta-gecko/meta-geckobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Esteban Pérez-Wohlfeil", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Set of post-processing tools aimed at improving the taxonomical classification and at providing additional information to enhance metagenomics analyses. The developed tools provide additional proofs in the presence of low-abundant species, information of the mapping quality in coding and noncoding regions, etc.", "sc:license": "GPL-3.0", "sc:name": "META-GECKO", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "uma.es", "sc:url": "http://bitlab-es.com/gecko/template.php#META-GECKO", diff --git a/data/meta-meme/meta-memebioschemas.jsonld b/data/meta-meme/meta-memebioschemas.jsonld index 615c0ac72580e..f6828cde88cb3 100644 --- a/data/meta-meme/meta-memebioschemas.jsonld +++ b/data/meta-meme/meta-memebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif.", "sc:name": "Meta-MEME", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://metameme.sdsc.edu/" } \ No newline at end of file diff --git a/data/meta-pipe/meta-pipebioschemas.jsonld b/data/meta-pipe/meta-pipebioschemas.jsonld index ded4d19d6e565..dc3c5b2755f11 100644 --- a/data/meta-pipe/meta-pipebioschemas.jsonld +++ b/data/meta-pipe/meta-pipebioschemas.jsonld @@ -12,11 +12,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:author": [ + "Edvard Pedersen", "Erik Hjerde", "Inge Alexander Raknes", - "Espen Robert Mikalsen", - "Edvard Pedersen", - "Tim Kahlke" + "Tim Kahlke", + "Espen Robert Mikalsen" ], "sc:description": "Metagenome and genome annotation tool. Used for prokaryota analysis on assembled contigs. It include gene prediction and domain annotation using MGA, Glimmer, BLAST and UniProt. Output formats supported are EMBL and TSV.", "sc:name": "Meta-pipe", diff --git a/data/meta-snp/meta-snpbioschemas.jsonld b/data/meta-snp/meta-snpbioschemas.jsonld index 56dd8a1e09fe4..ae9ec428cdc0f 100644 --- a/data/meta-snp/meta-snpbioschemas.jsonld +++ b/data/meta-snp/meta-snpbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-2323-0963", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/1471-2164-14-S3-S2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/meta-snp", "@type": "sc:SoftwareApplication", @@ -37,21 +29,21 @@ "sc:additionalType": "Web service", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0634" + "@id": "edam:topic_0123" }, { - "@id": "edam:topic_0123" + "@id": "edam:topic_0634" } ], "sc:author": { "@id": "http://orcid.org/0000-0002-2323-0963" }, "sc:citation": [ + "pmcid:PMC3839641", { "@id": "https://doi.org/10.1186/1471-2164-14-S3-S2" }, - "pubmed:23819846", - "pmcid:PMC3839641" + "pubmed:23819846" ], "sc:description": "Meta-predictor of disease causing variants.", "sc:featureList": { @@ -68,6 +60,14 @@ "@id": "http://snps.biofold.org/meta-snp/pages/help.html" }, "sc:url": "http://snps.biofold.org/meta-snp" + }, + { + "@id": "https://doi.org/10.1186/1471-2164-14-S3-S2", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-2323-0963", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/meta/metabioschemas.jsonld b/data/meta/metabioschemas.jsonld index 5475e25bf1aa3..4d6bee05230bc 100644 --- a/data/meta/metabioschemas.jsonld +++ b/data/meta/metabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pcbi.0020049", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/meta", "@type": "sc:SoftwareApplication", @@ -32,20 +36,16 @@ "sc:license": "GPL-3.0", "sc:name": "meta", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "Lab Roderic Guigo Group", - "crg.eu" + "crg.eu", + "Lab Roderic Guigo Group" ], "sc:url": "http://big.crg.cat/services/meta", "sc:version": "1" - }, - { - "@id": "https://doi.org/10.1371/journal.pcbi.0020049", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metaarray/metaarraybioschemas.jsonld b/data/metaarray/metaarraybioschemas.jsonld index 13e475902d352..194356112db9c 100644 --- a/data/metaarray/metaarraybioschemas.jsonld +++ b/data/metaarray/metaarraybioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "metaArray", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/metaArray.html", diff --git a/data/metab/metabbioschemas.jsonld b/data/metab/metabbioschemas.jsonld index fe8fa395d08bb..e23cf91796288 100644 --- a/data/metab/metabbioschemas.jsonld +++ b/data/metab/metabbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "GPL-2.0", "sc:name": "Metab", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Metab.html", diff --git a/data/metabin/metabinbioschemas.jsonld b/data/metabin/metabinbioschemas.jsonld index 0c66bfae9a15d..8444815546ed4 100644 --- a/data/metabin/metabinbioschemas.jsonld +++ b/data/metabin/metabinbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Program for accurate, fast and highly sensitive taxonomic assignments of metagenomic sequences", "sc:name": "MetaBin", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://metabin.riken.jp/application" } \ No newline at end of file diff --git a/data/metabiome/metabiomebioschemas.jsonld b/data/metabiome/metabiomebioschemas.jsonld index f16c21836290f..a5b30789b50fc 100644 --- a/data/metabiome/metabiomebioschemas.jsonld +++ b/data/metabiome/metabiomebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "MetaBioiME is a web resource to find novel homologs for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and completed bacterial genomes.", "sc:name": "MetaBioME", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://metasystems.riken.jp/metabiome/" } \ No newline at end of file diff --git a/data/metabnorm/metabnormbioschemas.jsonld b/data/metabnorm/metabnormbioschemas.jsonld index b11d8813aac84..9d819b7118a79 100644 --- a/data/metabnorm/metabnormbioschemas.jsonld +++ b/data/metabnorm/metabnormbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "metabnorm", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sourceforge.net/projects/metabnorm/" } \ No newline at end of file diff --git a/data/metabocraft/metabocraftbioschemas.jsonld b/data/metabocraft/metabocraftbioschemas.jsonld index 52274416d76fa..64c601646748b 100644 --- a/data/metabocraft/metabocraftbioschemas.jsonld +++ b/data/metabocraft/metabocraftbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome.", "sc:name": "MetaboCraft", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/argymeg/MetaboCraft/" } \ No newline at end of file diff --git a/data/metabodiff/metabodiffbioschemas.jsonld b/data/metabodiff/metabodiffbioschemas.jsonld index 9b1cb15d2672a..a6ad05189dc2d 100644 --- a/data/metabodiff/metabodiffbioschemas.jsonld +++ b/data/metabodiff/metabodiffbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "MetaboDiff", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/andreasmock/MetaboDiff/" diff --git a/data/metabolic_network_sgl/metabolic_network_sglbioschemas.jsonld b/data/metabolic_network_sgl/metabolic_network_sglbioschemas.jsonld index d19c1e65bbf44..8052fddee2e9a 100644 --- a/data/metabolic_network_sgl/metabolic_network_sglbioschemas.jsonld +++ b/data/metabolic_network_sgl/metabolic_network_sglbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Linking metabolic network features to phenotypes using sparse group lasso.", "sc:name": "Metabolic Network SGL", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://sourceforge.net/p/metabolic-network-sgl/git/ci/master/tree/" } \ No newline at end of file diff --git a/data/metabolitedetector/metabolitedetectorbioschemas.jsonld b/data/metabolitedetector/metabolitedetectorbioschemas.jsonld index 4c50c079b8a6f..5c312de6f67ff 100644 --- a/data/metabolitedetector/metabolitedetectorbioschemas.jsonld +++ b/data/metabolitedetector/metabolitedetectorbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/metabolitedetector", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "K. Hiller - Software Developer", - "Nils koschnitzki - Administrator" + "Nils koschnitzki - Administrator", + "K. Hiller - Software Developer" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:19358599", "sc:description": "QT4 based software package for the analysis of GC-MS based metabolomics data. The software is especially intended for the analysis of high resoluted GC-MS chromatograms which accumulate during high throughput based metabolmics experiments.", "sc:name": "MetaboliteDetector", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://metabolitedetector.tu-bs.de/" } \ No newline at end of file diff --git a/data/metabolomexchange/metabolomexchangebioschemas.jsonld b/data/metabolomexchange/metabolomexchangebioschemas.jsonld index a25fa21d015ff..47e3332bb405d 100644 --- a/data/metabolomexchange/metabolomexchangebioschemas.jsonld +++ b/data/metabolomexchange/metabolomexchangebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MetabolomeXchange", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ELIXIR-NL", "sc:url": "http://metabolomexchange.org" diff --git a/data/metabolomicstools/metabolomicstoolsbioschemas.jsonld b/data/metabolomicstools/metabolomicstoolsbioschemas.jsonld index 48336ba140551..664666c608caf 100644 --- a/data/metabolomicstools/metabolomicstoolsbioschemas.jsonld +++ b/data/metabolomicstools/metabolomicstoolsbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1007/s11306-017-1242-7", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/metabolomicstools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christoph Steinbeck", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC5550549", - "pubmed:28890673", { "@id": "https://doi.org/10.1007/s11306-017-1242-7" - } + }, + "pubmed:28890673", + "pmcid:PMC5550549" ], "sc:description": "Freely-available software tools for metabolomics analysis.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "MetabolomicsTools", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/RASpicer/MetabolomicsTools" + }, + { + "@id": "https://doi.org/10.1007/s11306-017-1242-7", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metabomxtr/metabomxtrbioschemas.jsonld b/data/metabomxtr/metabomxtrbioschemas.jsonld index d8ab5ace9c02f..5f1fa06810083 100644 --- a/data/metabomxtr/metabomxtrbioschemas.jsonld +++ b/data/metabomxtr/metabomxtrbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Nodzenski", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.", "sc:license": "GPL-2.0", "sc:name": "metabomxtr", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/metabomxtr.html", "sc:version": "1.8.0" diff --git a/data/metabosearch/metabosearchbioschemas.jsonld b/data/metabosearch/metabosearchbioschemas.jsonld index 8b8c7e83fbf2c..80bb734ccb0c1 100644 --- a/data/metabosearch/metabosearchbioschemas.jsonld +++ b/data/metabosearch/metabosearchbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Performs mass-based metabolite search simultaneously against the four major metabolite databases: Human Metabolome DataBase (HMDB), Madison Metabolomics Consortium Database (MMCD), Metlin, and LipidMaps.", "sc:name": "metabosearch", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://omics.georgetown.edu/metabosearch.html" } \ No newline at end of file diff --git a/data/metabosignal/metabosignalbioschemas.jsonld b/data/metabosignal/metabosignalbioschemas.jsonld index 670e2856df819..059849763c7be 100644 --- a/data/metabosignal/metabosignalbioschemas.jsonld +++ b/data/metabosignal/metabosignalbioschemas.jsonld @@ -9,16 +9,12 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btw697", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/metabosignal", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rafael Ayala", - "Andrea Rodriguez-Martinez" + "Andrea Rodriguez-Martinez", + "Rafael Ayala" ], "sc:additionalType": [ "Library", @@ -38,12 +34,16 @@ "sc:license": "GPL-3.0", "sc:name": "MetaboSignal", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MetaboSignal.html", "sc:version": "1.4.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btw697", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metabridge/metabridgebioschemas.jsonld b/data/metabridge/metabridgebioschemas.jsonld index 995990083cd8e..2132622ffbe40 100644 --- a/data/metabridge/metabridgebioschemas.jsonld +++ b/data/metabridge/metabridgebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MetaBridge", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.metabridge.org/" } \ No newline at end of file diff --git a/data/metacca/metaccabioschemas.jsonld b/data/metacca/metaccabioschemas.jsonld index 00b9e4403a5ca..2649c95ad4179 100644 --- a/data/metacca/metaccabioschemas.jsonld +++ b/data/metacca/metaccabioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btw052", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-1072-8858", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/metacca", "@type": "sc:SoftwareApplication", @@ -16,15 +24,15 @@ "@id": "http://orcid.org/0000-0003-1072-8858" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4920109", - "pubmed:27153689", { "@id": "https://doi.org/10.1093/bioinformatics/btw052" - } + }, + "pubmed:27153689", + "pmcid:PMC4920109" ], "sc:description": "Performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. It extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.", "sc:featureList": { @@ -33,20 +41,12 @@ "sc:license": "MIT", "sc:name": "metaCCA", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/metaCCA.html", "sc:version": "1.2.0" - }, - { - "@id": "http://orcid.org/0000-0003-1072-8858", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btw052", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metacoder/metacoderbioschemas.jsonld b/data/metacoder/metacoderbioschemas.jsonld index e8902f8e30edd..9eedeafb8fcc7 100644 --- a/data/metacoder/metacoderbioschemas.jsonld +++ b/data/metacoder/metacoderbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/metacoder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Niklaus J. Grünwald", - "GitHub Issues" + "GitHub Issues", + "Niklaus J. Grünwald" ], "sc:additionalType": "Library", "sc:description": "Package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data.", "sc:license": "MIT", "sc:name": "Metacoder", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/grunwaldlab/metacoder" } \ No newline at end of file diff --git a/data/metacomp/metacompbioschemas.jsonld b/data/metacomp/metacompbioschemas.jsonld index e55af26929239..95083a50e68e9 100644 --- a/data/metacomp/metacompbioschemas.jsonld +++ b/data/metacomp/metacompbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Tool for meta-omics comparative analysis.", "sc:name": "MetaComp", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cqb.pku.edu.cn/ZhuLab/MetaComp/" } \ No newline at end of file diff --git a/data/metacram/metacrambioschemas.jsonld b/data/metacram/metacrambioschemas.jsonld index 7b66dbcc897f6..72e4deb640dce 100644 --- a/data/metacram/metacrambioschemas.jsonld +++ b/data/metacram/metacrambioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "MetaCRAM", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://web.engr.illinois.edu/~mkim158/metacram.html" } \ No newline at end of file diff --git a/data/metacrop/metacropbioschemas.jsonld b/data/metacrop/metacropbioschemas.jsonld index ea92aec5b949a..124be4cd4aa1f 100644 --- a/data/metacrop/metacropbioschemas.jsonld +++ b/data/metacrop/metacropbioschemas.jsonld @@ -24,27 +24,27 @@ "sc:description": "Database that summarizes diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models.", "sc:featureList": [ { - "@id": "edam:operation_2429" + "@id": "edam:operation_3660" }, { "@id": "edam:operation_3561" }, { - "@id": "edam:operation_3282" + "@id": "edam:operation_2429" }, { - "@id": "edam:operation_3660" + "@id": "edam:operation_3715" }, { - "@id": "edam:operation_3715" + "@id": "edam:operation_3282" } ], "sc:license": "Unlicense", "sc:name": "MetaCrop", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://metacrop.ipk-gatersleben.de/" }, diff --git a/data/metacyc/metacycbioschemas.jsonld b/data/metacyc/metacycbioschemas.jsonld index f0854a09dfb52..1c5839b995a37 100644 --- a/data/metacyc/metacycbioschemas.jsonld +++ b/data/metacyc/metacycbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The MetaCyc database is a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations.", "sc:name": "MetaCyc", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://metacyc.org/" } \ No newline at end of file diff --git a/data/metacyto/metacytobioschemas.jsonld b/data/metacyto/metacytobioschemas.jsonld index 3dd9180ed30a2..830b5787cd311 100644 --- a/data/metacyto/metacytobioschemas.jsonld +++ b/data/metacyto/metacytobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Zicheng Hu", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database.", "sc:license": "GPL-2.0", "sc:name": "MetaCyto", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MetaCyto.html" } \ No newline at end of file diff --git a/data/metadbsite/metadbsitebioschemas.jsonld b/data/metadbsite/metadbsitebioschemas.jsonld index f2cf01ef726fb..ce5a20224dd69 100644 --- a/data/metadbsite/metadbsitebioschemas.jsonld +++ b/data/metadbsite/metadbsitebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "metaDBSite", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://projects.biotec.tu-dresden.de/metadbsite/" } \ No newline at end of file diff --git a/data/metadome/metadomebioschemas.jsonld b/data/metadome/metadomebioschemas.jsonld index 7988183329801..32fcc4f751e84 100644 --- a/data/metadome/metadomebioschemas.jsonld +++ b/data/metadome/metadomebioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "MIT", "sc:name": "MetaDome", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://stuart.radboudumc.nl/metadome" } \ No newline at end of file diff --git a/data/metadynminer/metadynminerbioschemas.jsonld b/data/metadynminer/metadynminerbioschemas.jsonld index 1f433786ede5d..19072d486cdc9 100644 --- a/data/metadynminer/metadynminerbioschemas.jsonld +++ b/data/metadynminer/metadynminerbioschemas.jsonld @@ -16,16 +16,16 @@ "sc:license": "GPL-3.0", "sc:name": "metadynminer", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.metadynamics.cz/metadynminer/", "sc:version": [ - "v0.1.4", "v0.1.0", - "v0.1.1", + "v0.1.3", "v0.1.2", - "v0.1.3" + "v0.1.4", + "v0.1.1" ] } \ No newline at end of file diff --git a/data/metagene/metagenebioschemas.jsonld b/data/metagene/metagenebioschemas.jsonld index 2703da180cca2..a29d514e0cee5 100644 --- a/data/metagene/metagenebioschemas.jsonld +++ b/data/metagene/metagenebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Charles Joly Beauparlant", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package produces metagenic plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Bam files are used to increase the resolution. Multiple combination of group of bam files and/or group of genomic regions can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles.", "sc:license": "Artistic-2.0", "sc:name": "metagene", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/metagene.html", "sc:version": "2.6.1" diff --git a/data/metageneannotator/metageneannotatorbioschemas.jsonld b/data/metageneannotator/metageneannotatorbioschemas.jsonld index 7e5a7fd199024..30d8c698d20b5 100644 --- a/data/metageneannotator/metageneannotatorbioschemas.jsonld +++ b/data/metageneannotator/metageneannotatorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MetaGeneAnnotator", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://metagene.cb.k.u-tokyo.ac.jp/" } \ No newline at end of file diff --git a/data/metagenesense/metagenesensebioschemas.jsonld b/data/metagenesense/metagenesensebioschemas.jsonld index 2a97ba20ec3ff..335e6e7e15373 100644 --- a/data/metagenesense/metagenesensebioschemas.jsonld +++ b/data/metagenesense/metagenesensebioschemas.jsonld @@ -17,15 +17,15 @@ "@id": "https://bio.tools/metagenesense", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Desktop application" + "Desktop application", + "Web application" ], "sc:citation": [ - "pubmed:28451381", "pmcid:PMC5405795", { "@id": "https://doi.org/10.12688/F1000RESEARCH.6139.3" - } + }, + "pubmed:28451381" ], "sc:description": "Managing and analytical bioinformatics framework that is engineered to run dedicated Galaxy workflows for the detection and eventually classification of pathogens.", "sc:featureList": [ @@ -33,10 +33,10 @@ "@id": "edam:operation_0310" }, { - "@id": "edam:operation_3460" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3460" } ], "sc:license": "GPL-2.0", diff --git a/data/metagenomefeatures/metagenomefeaturesbioschemas.jsonld b/data/metagenomefeatures/metagenomefeaturesbioschemas.jsonld index 2999cd3e90bf2..d96832f1ae8c9 100644 --- a/data/metagenomefeatures/metagenomefeaturesbioschemas.jsonld +++ b/data/metagenomefeatures/metagenomefeaturesbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nathan D. Olson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment.", "sc:license": "Artistic-2.0", "sc:name": "metagenomeFeatures", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html", "sc:version": "1.4.0" diff --git a/data/metagenomeseq/metagenomeseqbioschemas.jsonld b/data/metagenomeseq/metagenomeseqbioschemas.jsonld index 1addac3e15ba0..2dccd031f4f5d 100644 --- a/data/metagenomeseq/metagenomeseqbioschemas.jsonld +++ b/data/metagenomeseq/metagenomeseqbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "metagenomeSeq", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html", "sc:version": "1.16.0" diff --git a/data/metagenyo/metagenyobioschemas.jsonld b/data/metagenyo/metagenyobioschemas.jsonld index db163fac12d8b..c5ae5dcd837e6 100644 --- a/data/metagenyo/metagenyobioschemas.jsonld +++ b/data/metagenyo/metagenyobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Meta-analysis of genetic association studies.", "sc:name": "MetaGenyo", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioinfo.genyo.es/metagenyo/" } \ No newline at end of file diff --git a/data/metagxbreast/metagxbreastbioschemas.jsonld b/data/metagxbreast/metagxbreastbioschemas.jsonld index f821f6da9cc35..d0702918f7282 100644 --- a/data/metagxbreast/metagxbreastbioschemas.jsonld +++ b/data/metagxbreast/metagxbreastbioschemas.jsonld @@ -11,21 +11,21 @@ "@id": "https://bio.tools/MetaGxBreast", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Michael Zon", - "Benjamin Haibe-Kains" + "Benjamin Haibe-Kains", + "Michael Zon" ], "sc:additionalType": "Library", "sc:author": [ - "Deena M.A. Gen-doo", - "Benjamin Haibe-Kains" + "Benjamin Haibe-Kains", + "Deena M.A. Gen-doo" ], "sc:description": "A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium.", "sc:license": "Artistic-2.0", "sc:name": "MetaGxBreast", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://bioconductor.org/packages/release/data/experiment/html/MetaGxBreast.html" } \ No newline at end of file diff --git a/data/metaimprint/metaimprintbioschemas.jsonld b/data/metaimprint/metaimprintbioschemas.jsonld index 0c5d250876135..f24fe6627b032 100644 --- a/data/metaimprint/metaimprintbioschemas.jsonld +++ b/data/metaimprint/metaimprintbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An information repository of mammalian imprinted genes.", "sc:name": "MetaImprint", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://202.97.205.76:8080/MetaImprint/" } \ No newline at end of file diff --git a/data/metainter/metainterbioschemas.jsonld b/data/metainter/metainterbioschemas.jsonld index e67d4a73f369b..66a1f09da41b5 100644 --- a/data/metainter/metainterbioschemas.jsonld +++ b/data/metainter/metainterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool to perform meta-analysis of summary statistics obtained from a series of related studies. The special feature of it is the ability to meta-analyze the results of multiple linear and logistic regression models, broadly used in genome-wide association studies (GWAS).", "sc:name": "METAINTER", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://metainter.meb.uni-bonn.de/" } \ No newline at end of file diff --git a/data/metaldetector/metaldetectorbioschemas.jsonld b/data/metaldetector/metaldetectorbioschemas.jsonld index 8e39eaeb44413..03eca20eb9263 100644 --- a/data/metaldetector/metaldetectorbioschemas.jsonld +++ b/data/metaldetector/metaldetectorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "MetalDetector identifies CYS and HIS involved in transition metal protein binding sites beginning with protein sequence alone. The geometry of the metal binding site is also predicted.", "sc:name": "MetalDetector", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://metaldetector.dsi.unifi.it/v2.0/" } \ No newline at end of file diff --git a/data/metalionrna/metalionrnabioschemas.jsonld b/data/metalionrna/metalionrnabioschemas.jsonld index e6a81d7283222..6cbc1a64b0420 100644 --- a/data/metalionrna/metalionrnabioschemas.jsonld +++ b/data/metalionrna/metalionrnabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Novel bioinformatic method for predicting metal-binding sites in RNA structures.", "sc:name": "MetalionRNA", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://metalionrna.genesilico.pl/" } \ No newline at end of file diff --git a/data/metalpdb/metalpdbbioschemas.jsonld b/data/metalpdb/metalpdbbioschemas.jsonld index 4f09df2f9b97d..b23c1c0da952f 100644 --- a/data/metalpdb/metalpdbbioschemas.jsonld +++ b/data/metalpdb/metalpdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MetalPDB", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "CERM", "sc:url": "http://metalweb.cerm.unifi.it/" diff --git a/data/metals2/metals2bioschemas.jsonld b/data/metals2/metals2bioschemas.jsonld index df70a47684370..88d20cb53c3f8 100644 --- a/data/metals2/metals2bioschemas.jsonld +++ b/data/metals2/metals2bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Allows two metal-binding sites to be structurally aligned, independently of protein fold.", "sc:name": "MetalS2", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "CERM", "sc:url": "http://metalweb.cerm.unifi.it/tools/metals2/", diff --git a/data/metamhc/metamhcbioschemas.jsonld b/data/metamhc/metamhcbioschemas.jsonld index 1a1e91ec16ea2..69a03decadfc2 100644 --- a/data/metamhc/metamhcbioschemas.jsonld +++ b/data/metamhc/metamhcbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "MetaMHC", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://datamining-iip.fudan.edu.cn/MetaMHCpan/index.php/pages/view/info" } \ No newline at end of file diff --git a/data/metamicrobiomer/metamicrobiomerbioschemas.jsonld b/data/metamicrobiomer/metamicrobiomerbioschemas.jsonld index cca40ed5bd7af..d4e9321479186 100644 --- a/data/metamicrobiomer/metamicrobiomerbioschemas.jsonld +++ b/data/metamicrobiomer/metamicrobiomerbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Nhan Thi Ho", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:30991942", + "pmcid:PMC6469060", { "@id": "https://doi.org/10.1186/s12859-019-2744-2" - }, - "pubmed:30991942", - "pmcid:PMC6469060" + } ], "sc:description": "R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "metamicrobiomeR", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/nhanhocu/metamicrobiomeR" }, diff --git a/data/metamis/metamisbioschemas.jsonld b/data/metamis/metamisbioschemas.jsonld index b5718f1cb1820..b880c74fa8ec5 100644 --- a/data/metamis/metamisbioschemas.jsonld +++ b/data/metamis/metamisbioschemas.jsonld @@ -19,19 +19,19 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC5124289", + "pubmed:27887570", { "@id": "https://doi.org/10.1186/S12859-016-1359-0" - }, - "pmcid:PMC5124289", - "pubmed:27887570" + } ], "sc:description": "Metagenomic microbial interaction simulator based on microbial community profiles.", "sc:featureList": [ { - "@id": "edam:operation_3660" + "@id": "edam:operation_3562" }, { - "@id": "edam:operation_3562" + "@id": "edam:operation_3660" } ], "sc:name": "MetaMIS", diff --git a/data/metams/metamsbioschemas.jsonld b/data/metams/metamsbioschemas.jsonld index 479651690e275..f9f5821cd79e7 100644 --- a/data/metams/metamsbioschemas.jsonld +++ b/data/metams/metamsbioschemas.jsonld @@ -29,8 +29,8 @@ "sc:name": "metaMS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/metaMS.html", "sc:version": "1.10.0" diff --git a/data/metamylo/metamylobioschemas.jsonld b/data/metamylo/metamylobioschemas.jsonld index 1ecf78345f65c..8bdb327c49c6c 100644 --- a/data/metamylo/metamylobioschemas.jsonld +++ b/data/metamylo/metamylobioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Christian Delamarche", "sc:additionalType": "Web application", "sc:author": [ - "Anthony Talvas", "Mathieu Emily", - "Christian Delamarche" + "Christian Delamarche", + "Anthony Talvas" ], "sc:description": "Prediction of amyloid fragments.", "sc:name": "MetAmyl", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "GenOuest", diff --git a/data/metaneighbor/metaneighborbioschemas.jsonld b/data/metaneighbor/metaneighborbioschemas.jsonld index 4c204e97a4f48..d2cf472e03f02 100644 --- a/data/metaneighbor/metaneighborbioschemas.jsonld +++ b/data/metaneighbor/metaneighborbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MetaNeighbor", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MetaNeighbor.html", "sc:version": "1.0.0" diff --git a/data/metanet/metanetbioschemas.jsonld b/data/metanet/metanetbioschemas.jsonld index a5a1e32c7c03a..4e948a033a29a 100644 --- a/data/metanet/metanetbioschemas.jsonld +++ b/data/metanet/metanetbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Software tool in MATLAB for network construction and biologically significant module detection.", "sc:name": "MetaNet", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://biostatistics.csmc.edu/MetaNet/" } \ No newline at end of file diff --git a/data/metanetx/metanetxbioschemas.jsonld b/data/metanetx/metanetxbioschemas.jsonld index 97dc2b68ec807..cc80eba7d4fe9 100644 --- a/data/metanetx/metanetxbioschemas.jsonld +++ b/data/metanetx/metanetxbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "MetaNetX", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://metanetx.org/", "sc:version": "3.1" diff --git a/data/metano/metanobioschemas.jsonld b/data/metano/metanobioschemas.jsonld index cca0886f81df7..59d6e538b6aa1 100644 --- a/data/metano/metanobioschemas.jsonld +++ b/data/metano/metanobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "metano", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://metano.tu-bs.de/", "sc:version": "1.0" diff --git a/data/metaomgraph/metaomgraphbioschemas.jsonld b/data/metaomgraph/metaomgraphbioschemas.jsonld index 656ae1e6109f5..784e672435b9e 100644 --- a/data/metaomgraph/metaomgraphbioschemas.jsonld +++ b/data/metaomgraph/metaomgraphbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for plotting and analyzing large sets of data while using as little memory as possible. It was designed with biological experiment data in mind.", "sc:name": "MetaOmGraph", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.metnetdb.org/MetNet_MetaOmGraph.htm" } \ No newline at end of file diff --git a/data/metap/metapbioschemas.jsonld b/data/metap/metapbioschemas.jsonld index c8ce524cf449c..be113ddafbd0c 100644 --- a/data/metap/metapbioschemas.jsonld +++ b/data/metap/metapbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "The server automates data analysis for the processing of metabolomics experiments.", "sc:name": "metaP", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://metap.helmholtz-muenchen.de/metap2/", "sc:version": "2" diff --git a/data/metapath_online/metapath_onlinebioschemas.jsonld b/data/metapath_online/metapath_onlinebioschemas.jsonld index 92b3063efe766..e5f80e364ebae 100644 --- a/data/metapath_online/metapath_onlinebioschemas.jsonld +++ b/data/metapath_online/metapath_onlinebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MetaPath Online", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://scopes.biologie.hu-berlin.de/" } \ No newline at end of file diff --git a/data/metapathways/metapathwaysbioschemas.jsonld b/data/metapathways/metapathwaysbioschemas.jsonld index 54498b68b5eee..676bf0dd1aedf 100644 --- a/data/metapathways/metapathwaysbioschemas.jsonld +++ b/data/metapathways/metapathwaysbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Modular software pipeline for integrated analysis of environmental sequence information. The software performs a series of popular analyses for taxonomic profiling and functional potential with limited data handling, allowing researchers to spend their time analyzing their data instead of performing complicated data transformations.", "sc:name": "MetaPathways", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://hallam.microbiology.ubc.ca/MetaPathways/" diff --git a/data/metapepseq/metapepseqbioschemas.jsonld b/data/metapepseq/metapepseqbioschemas.jsonld index ff23248aa6b66..14e3cb0976ecf 100644 --- a/data/metapepseq/metapepseqbioschemas.jsonld +++ b/data/metapepseq/metapepseqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MetaPepSeq 0.8 Beta", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sourceforge.net/projects/metapepseq/" } \ No newline at end of file diff --git a/data/metaphlan/metaphlanbioschemas.jsonld b/data/metaphlan/metaphlanbioschemas.jsonld index 719b4e4c83a79..a95f9fbf4b64f 100644 --- a/data/metaphlan/metaphlanbioschemas.jsonld +++ b/data/metaphlan/metaphlanbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "MIT", "sc:name": "MetaPhlAn", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://huttenhower.sph.harvard.edu/metaphlan" } \ No newline at end of file diff --git a/data/metaphors/metaphorsbioschemas.jsonld b/data/metaphors/metaphorsbioschemas.jsonld index 725c74bb0b694..76fd845d16dc6 100644 --- a/data/metaphors/metaphorsbioschemas.jsonld +++ b/data/metaphors/metaphorsbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "MetaPhors", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://betaorthology.phylomedb.org/", "sc:version": "metaphors_201405" diff --git a/data/metaplab/metaplabbioschemas.jsonld b/data/metaplab/metaplabbioschemas.jsonld index 32477dc3356fb..b551d0d741cf3 100644 --- a/data/metaplab/metaplabbioschemas.jsonld +++ b/data/metaplab/metaplabbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Virtual laboratory which aims at assisting modellers both to understand the internal mechanisms of biological systems and to forecast, in silico, their response to external stimuli, environmental condition alterations or structural changes. Its framework is based on a core module which enables to design and manage biological models, and an extensible set of plugins by which MP models can be generated, optimized, simulated and analysed.", "sc:name": "MetaPlab", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://mplab.sci.univr.it/" } \ No newline at end of file diff --git a/data/metapop/metapopbioschemas.jsonld b/data/metapop/metapopbioschemas.jsonld index 2f9c4e72d4477..9cce8b5e8539b 100644 --- a/data/metapop/metapopbioschemas.jsonld +++ b/data/metapop/metapopbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/Metapop", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Armel Thöni", "Jean-Paul Soularue", - "Antoine Kremer", - "Armel Thöni" + "Antoine Kremer" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:30362291", diff --git a/data/metapred2cs/metapred2csbioschemas.jsonld b/data/metapred2cs/metapred2csbioschemas.jsonld index 65d3766d8b816..59bd3930b03c3 100644 --- a/data/metapred2cs/metapred2csbioschemas.jsonld +++ b/data/metapred2cs/metapred2csbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs).", "sc:name": "MetaPred2CS", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://metapred2cs.ibers.aber.ac.uk/" } \ No newline at end of file diff --git a/data/metapsicov/metapsicovbioschemas.jsonld b/data/metapsicov/metapsicovbioschemas.jsonld index 60dd1963602e6..af0035abff12e 100644 --- a/data/metapsicov/metapsicovbioschemas.jsonld +++ b/data/metapsicov/metapsicovbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Algorithm incorporating different approaches of contact predictions implemented with a neural network in order to improve the accuracies of the predicted contacts.", "sc:name": "MetaPSICOV", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioinf.cs.ucl.ac.uk/MetaPSICOV/" } \ No newline at end of file diff --git a/data/metaqc/metaqcbioschemas.jsonld b/data/metaqc/metaqcbioschemas.jsonld index 9b19f8ed6af32..cc0fb1af00adb 100644 --- a/data/metaqc/metaqcbioschemas.jsonld +++ b/data/metaqc/metaqcbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "MetaQC: A diagnosis tool for assessing quality of genomic studies for meta-analysis and determining inclusion/exclusion criteria.", "sc:name": "MetaQC", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.pitt.edu/~tsengweb/MetaOmicsHome.htm", diff --git a/data/metaqtl/metaqtlbioschemas.jsonld b/data/metaqtl/metaqtlbioschemas.jsonld index 5fd0ef659cd6d..6a73596fe47d3 100644 --- a/data/metaqtl/metaqtlbioschemas.jsonld +++ b/data/metaqtl/metaqtlbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MetaQTL is a Java package designed to perform the integration of data from the field of gene mapping experiments (e.g molecular markers, QTL, candidate genes, etc…). This package consists in a modular library and several programs written in pure Java. These programs can perform various tasks, including formatting, analyzing and visualizing data or results produced by MetaQTL.", "sc:name": "MetaQTL", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.bioinformatics.org/mqtl/wiki/", "sc:version": "1.2.0" diff --git a/data/metaquast/metaquastbioschemas.jsonld b/data/metaquast/metaquastbioschemas.jsonld index 874820f2b6937..59c320afefc23 100644 --- a/data/metaquast/metaquastbioschemas.jsonld +++ b/data/metaquast/metaquastbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-2.0", "sc:name": "MetaQUAST", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://quast.sourceforge.net/metaquast.html" } \ No newline at end of file diff --git a/data/metaquery/metaquerybioschemas.jsonld b/data/metaquery/metaquerybioschemas.jsonld index bdea7edbab119..5ce671541a778 100644 --- a/data/metaquery/metaquerybioschemas.jsonld +++ b/data/metaquery/metaquerybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web application for rapid and quantitative analysis of specific genes in the human gut microbiome.", "sc:name": "MetaQuery", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://metaquery.docpollard.org/" } \ No newline at end of file diff --git a/data/metaranker/metarankerbioschemas.jsonld b/data/metaranker/metarankerbioschemas.jsonld index 6be1361f61302..65f6f0522620c 100644 --- a/data/metaranker/metarankerbioschemas.jsonld +++ b/data/metaranker/metarankerbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0003-0207-4831", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/nar/gkt387", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/metaranker", @@ -24,46 +24,46 @@ }, "edam:has_output": [ { - "@id": "edam:data_0916" + "@id": "edam:data_2984" }, { - "@id": "edam:data_2984" + "@id": "edam:data_0916" } ], "sc:additionalType": "Web application", "sc:citation": [ "pubmed:23703204", - "pmcid:PMC3692047", { "@id": "https://doi.org/10.1093/nar/gkt387" - } + }, + "pmcid:PMC3692047" ], "sc:description": "Prioritization of the entire protein-coding part of the human genome based on heterogeneous user-specified data sets.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3197" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_2423" + "@id": "edam:operation_3233" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3233" + "@id": "edam:operation_2423" } ], "sc:license": "Other", "sc:name": "MetaRanker", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "CBS", @@ -71,8 +71,8 @@ "sc:version": "2.0" }, { - "@id": "https://doi.org/10.1093/nar/gkt387", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0003-0207-4831", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/metascape/metascapebioschemas.jsonld b/data/metascape/metascapebioschemas.jsonld index 3266877139fc0..11e369384ec92 100644 --- a/data/metascape/metascapebioschemas.jsonld +++ b/data/metascape/metascapebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/s41467-019-09234-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Metascape", "@type": "sc:SoftwareApplication", @@ -36,6 +32,10 @@ "Windows" ], "sc:url": "http://metascape.org/gp/index.html#/main/step1" + }, + { + "@id": "https://doi.org/10.1038/s41467-019-09234-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metasel/metaselbioschemas.jsonld b/data/metasel/metaselbioschemas.jsonld index 41862c4ec79be..5fb615fd23fbe 100644 --- a/data/metasel/metaselbioschemas.jsonld +++ b/data/metasel/metaselbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Sissades Tongsima", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:24564477", + "pmcid:PMC4015449", { "@id": "https://doi.org/10.1186/1471-2105-14-S16-S13" - }, - "pubmed:24564477", - "pmcid:PMC4015449" + } ], "sc:description": "Metaphase selection tool using a Gaussian-based classification technique.", "sc:featureList": { diff --git a/data/metaseq/bioconda_metaseq.yaml b/data/metaseq/bioconda_metaseq.yaml index 043dab458f4f5..409336456c6d2 100644 --- a/data/metaseq/bioconda_metaseq.yaml +++ b/data/metaseq/bioconda_metaseq.yaml @@ -4,7 +4,6 @@ description: The probabilities by one-sided NOISeq are combined by Fisher's meth home: https://bioconductor.org/packages/3.10/bioc/html/metaSeq.html identifiers: - biotools:metaseq -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-metaseq summary: Meta-analysis of RNA-Seq count data in multiple studies diff --git a/data/metaseq/metaseqbioschemas.jsonld b/data/metaseq/metaseqbioschemas.jsonld index 1401c37ff576f..8d9b8dace1951 100644 --- a/data/metaseq/metaseqbioschemas.jsonld +++ b/data/metaseq/metaseqbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Koki Tsuyuzaki", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.", "sc:license": "Artistic-2.0", diff --git a/data/metaseqr/metaseqrbioschemas.jsonld b/data/metaseqr/metaseqrbioschemas.jsonld index 1822f735f7c65..5279e43a3afb9 100644 --- a/data/metaseqr/metaseqrbioschemas.jsonld +++ b/data/metaseqr/metaseqrbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "metaseqR", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://www.bioconductor.org/packages/release/bioc/html/metaseqR.html", "sc:version": "1.16.0" diff --git a/data/metashot/metashotbioschemas.jsonld b/data/metashot/metashotbioschemas.jsonld index 2a23c6655ed13..83d2ca75b3c13 100644 --- a/data/metashot/metashotbioschemas.jsonld +++ b/data/metashot/metashotbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.", "sc:name": "MetaShot", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/bfosso/MetaShot" } \ No newline at end of file diff --git a/data/metasim/metasimbioschemas.jsonld b/data/metasim/metasimbioschemas.jsonld index 0966758354cee..47feb2fb4a93f 100644 --- a/data/metasim/metasimbioschemas.jsonld +++ b/data/metasim/metasimbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The software can be used to generate collections of synthetic reads.", "sc:name": "MetaSim", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www-ab.informatik.uni-tuebingen.de/software/metasim" } \ No newline at end of file diff --git a/data/metaskat/metaskatbioschemas.jsonld b/data/metaskat/metaskatbioschemas.jsonld index dcbecf908adc0..03eed69872baa 100644 --- a/data/metaskat/metaskatbioschemas.jsonld +++ b/data/metaskat/metaskatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MetaSKAT", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.hsph.harvard.edu/skat/metaskat/" } \ No newline at end of file diff --git a/data/metasnv/metasnvbioschemas.jsonld b/data/metasnv/metasnvbioschemas.jsonld index 0830e9a5a32d9..8685f83561995 100644 --- a/data/metasnv/metasnvbioschemas.jsonld +++ b/data/metasnv/metasnvbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0182392", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-1645-3947", "@type": "schema:Person" @@ -38,10 +34,14 @@ }, "sc:name": "metaSNV", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://metasnv.embl.de/" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0182392", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metaspades/metaspadesbioschemas.jsonld b/data/metaspades/metaspadesbioschemas.jsonld index 86dca6f96267d..4be9f8cc30f79 100644 --- a/data/metaspades/metaspadesbioschemas.jsonld +++ b/data/metaspades/metaspadesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Genome assembler for metagenomics datasets.", "sc:name": "metaspades", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cab.spbu.ru/software/spades/", "sc:version": "3.9.0" diff --git a/data/metaspark/metasparkbioschemas.jsonld b/data/metaspark/metasparkbioschemas.jsonld index 42da68fc7a976..53b2ee8309f62 100644 --- a/data/metaspark/metasparkbioschemas.jsonld +++ b/data/metaspark/metasparkbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Unlicense", "sc:name": "MetaSpark:", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/zhouweiyg/metaspark" } \ No newline at end of file diff --git a/data/metassimulo/metassimulobioschemas.jsonld b/data/metassimulo/metassimulobioschemas.jsonld index 3ce452520e1e9..c5d5f685e666b 100644 --- a/data/metassimulo/metassimulobioschemas.jsonld +++ b/data/metassimulo/metassimulobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "MATLAB-based package which simulates 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database.", "sc:name": "MetAssimulo", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://cisbic.bioinformatics.ic.ac.uk/metassimulo/" } \ No newline at end of file diff --git a/data/metastats/metastatsbioschemas.jsonld b/data/metastats/metastatsbioschemas.jsonld index f960fe9f08763..9a93fb490fe96 100644 --- a/data/metastats/metastatsbioschemas.jsonld +++ b/data/metastats/metastatsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher’s exact test.", "sc:name": "Metastats", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://metastats.cbcb.umd.edu/detection.html" diff --git a/data/metastudent/metastudentbioschemas.jsonld b/data/metastudent/metastudentbioschemas.jsonld index 5c065a61dc47c..f41daf6f27490 100644 --- a/data/metastudent/metastudentbioschemas.jsonld +++ b/data/metastudent/metastudentbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Metastudent predicts Gene Ontology (GO) terms from the Molecular Function Ontology (MFO) and Biological Process Ontology (BPO) for input protein sequences by homology-based inference from already annotated proteins.", "sc:name": "MetaStudent", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "tum.de", diff --git a/data/metatreemap/metatreemapbioschemas.jsonld b/data/metatreemap/metatreemapbioschemas.jsonld index de632fb6bb63f..4233b8e6f4b37 100644 --- a/data/metatreemap/metatreemapbioschemas.jsonld +++ b/data/metatreemap/metatreemapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Visualize phylogenic trees where each species (node) has a number of reads (quantity) that map on the reference genome of this species. Each species is represented by a rectangle and its area is proportional to the number of assigned reads. The final figure is nested rectangles representing tree branches.", "sc:name": "MetaTreeMap", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://metasystems.riken.jp/visualization/treemap/index.htm" } \ No newline at end of file diff --git a/data/metatrend/metatrendbioschemas.jsonld b/data/metatrend/metatrendbioschemas.jsonld index cc9a73266325a..04e4f5520eb1f 100644 --- a/data/metatrend/metatrendbioschemas.jsonld +++ b/data/metatrend/metatrendbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "metatrend", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.compgen.org/tools/metatrend" } \ No newline at end of file diff --git a/data/metavisitor/metavisitorbioschemas.jsonld b/data/metavisitor/metavisitorbioschemas.jsonld index 50b587e6b2d1c..d6c09311fb8b1 100644 --- a/data/metavisitor/metavisitorbioschemas.jsonld +++ b/data/metavisitor/metavisitorbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Software package that allows biologists and clinicians without specialized bioinformatics expertise to detect and assemble viral genomes from deep sequence datasets.", "sc:name": "Metavisitor", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/ARTbio/metavisitor" } \ No newline at end of file diff --git a/data/metaviz/metavizbioschemas.jsonld b/data/metaviz/metavizbioschemas.jsonld index 0083b15770cc5..d8428ee34e584 100644 --- a/data/metaviz/metavizbioschemas.jsonld +++ b/data/metaviz/metavizbioschemas.jsonld @@ -18,22 +18,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:29529268", "pmcid:PMC5887897", { "@id": "https://doi.org/10.1093/NAR/GKY136" - }, - "pubmed:29529268" + } ], "sc:description": "Interactive visualization and exploration of metagenomic sequencing data. Provides a novel navigation tool for exploring hierarchical feature data that is coupled with multiple data visualizations including heatmaps, stacked bar charts, and scatter plots. It supports a flexible plugin framework so users can add new d3 visualizations.", "sc:featureList": [ { - "@id": "edam:operation_3460" + "@id": "edam:operation_2940" }, { - "@id": "edam:operation_2939" + "@id": "edam:operation_3460" }, { - "@id": "edam:operation_2940" + "@id": "edam:operation_2939" } ], "sc:name": "Metaviz", diff --git a/data/metavizr/metavizrbioschemas.jsonld b/data/metavizr/metavizrbioschemas.jsonld index ca27782c07d35..a3ab9433f7c92 100644 --- a/data/metavizr/metavizrbioschemas.jsonld +++ b/data/metavizr/metavizrbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gky136", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/metavizr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hector Corrada Bravo", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:29529268", - "pmcid:PMC5887897", { "@id": "https://doi.org/10.1093/nar/gky136" - } + }, + "pubmed:29529268", + "pmcid:PMC5887897" ], "sc:description": "Websocket communication to the metaviz web app for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported, while providing an easy mechanism to support other data structures.", "sc:featureList": { @@ -38,6 +34,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/metavizr.html", "sc:version": "1.4.1" + }, + { + "@id": "https://doi.org/10.1093/nar/gky136", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metax/metaxbioschemas.jsonld b/data/metax/metaxbioschemas.jsonld index 524d05af3d543..3345b8415fa1a 100644 --- a/data/metax/metaxbioschemas.jsonld +++ b/data/metax/metaxbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1579-y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/metax", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bo Wen", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5361702", + "pubmed:28327092", { "@id": "https://doi.org/10.1186/s12859-017-1579-y" - }, - "pmcid:PMC5361702", - "pubmed:28327092" + } ], "sc:description": "An Automatic and Comprehensive Pipeline for Processing Untargeted Metabolomics Data.", "sc:featureList": { @@ -37,6 +33,10 @@ "Mac" ], "sc:url": "http://metax.genomics.cn/" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1579-y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metaxa/metaxabioschemas.jsonld b/data/metaxa/metaxabioschemas.jsonld index e972656b60981..f851f1ca2ce8a 100644 --- a/data/metaxa/metaxabioschemas.jsonld +++ b/data/metaxa/metaxabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Metaxa", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://microbiology.se/software/metaxa/" } \ No newline at end of file diff --git a/data/metaxa2/metaxa2bioschemas.jsonld b/data/metaxa2/metaxa2bioschemas.jsonld index 27a381e6a5471..d9ea44bc98de3 100644 --- a/data/metaxa2/metaxa2bioschemas.jsonld +++ b/data/metaxa2/metaxa2bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.", "sc:name": "Metaxa2", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://microbiology.se/software/metaxa2/" } \ No newline at end of file diff --git a/data/metccs/metccsbioschemas.jsonld b/data/metccs/metccsbioschemas.jsonld index 034ad323eda56..935197c96312a 100644 --- a/data/metccs/metccsbioschemas.jsonld +++ b/data/metccs/metccsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics.", "sc:name": "MetCCS", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.metabolomics-shanghai.org/MetCCS/" } \ No newline at end of file diff --git a/data/metcirc/metcircbioschemas.jsonld b/data/metcirc/metcircbioschemas.jsonld index 389395a01a22c..6ae920ce3797c 100644 --- a/data/metcirc/metcircbioschemas.jsonld +++ b/data/metcirc/metcircbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas Naake", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This tool comprises a workflow to interactively explore metabolomics data by creating MSP or calculating m/z values and the similarity between precursors.", "sc:license": "GPL-2.0", diff --git a/data/metdisease/metdiseasebioschemas.jsonld b/data/metdisease/metdiseasebioschemas.jsonld index 80c487aa54bd0..68ae85cc3bbd0 100644 --- a/data/metdisease/metdiseasebioschemas.jsonld +++ b/data/metdisease/metdiseasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "App for Cytoscape, the bioinformatics network visualization tool. The app is used to annotate a metabolic network with MeSH disease terms, explore related diseases within a network, and link to PubMed references corresponding to any network node and selection of MeSH terms.", "sc:name": "MetDisease", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://metdisease.ncibi.org/" } \ No newline at end of file diff --git a/data/metdraw/metdrawbioschemas.jsonld b/data/metdraw/metdrawbioschemas.jsonld index c6d89385e95d2..eaa6c6dcd8606 100644 --- a/data/metdraw/metdrawbioschemas.jsonld +++ b/data/metdraw/metdrawbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Creates visualizations of genome-scale, metabolic models. These “reaction maps” can be used to visualize high-throughput expression data using the companion program MetColor.", "sc:name": "MetDraw", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.metdraw.com/" } \ No newline at end of file diff --git a/data/metexplore/metexplorebioschemas.jsonld b/data/metexplore/metexplorebioschemas.jsonld index 1622fcfae8c95..b1f58439e8fa2 100644 --- a/data/metexplore/metexplorebioschemas.jsonld +++ b/data/metexplore/metexplorebioschemas.jsonld @@ -20,16 +20,16 @@ "@id": "https://orcid.org/0000-0001-9401-2894" }, "sc:additionalType": [ - "Web service", "Workbench", - "Web application" + "Web application", + "Web service" ], "sc:description": "Metabolic network curation, visualisation and omics data analysis. It is possible to curate and annotate metabolic networks in a collaborative environment. Several tools are available for metabolomics data mapping in networks and visualisation.", "sc:name": "MetExplore", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.metexplore.fr/", "sc:version": "2.23.14" diff --git a/data/metfamily/metfamilybioschemas.jsonld b/data/metfamily/metfamilybioschemas.jsonld index 735c565b3efcb..04a4f1ad2bfc2 100644 --- a/data/metfamily/metfamilybioschemas.jsonld +++ b/data/metfamily/metfamilybioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Freeware", "sc:name": "MetFamily", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://msbi.ipb-halle.de/MetFamily/", "sc:version": "1" diff --git a/data/metfrag/metfragbioschemas.jsonld b/data/metfrag/metfragbioschemas.jsonld index 0cf06ad87fd47..0452035df7297 100644 --- a/data/metfrag/metfragbioschemas.jsonld +++ b/data/metfrag/metfragbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It combines compound database searching and fragmentation prediction for small molecule identification from tandem mass spectrometry data. It supports candidate structure retrieval from the compound databases PubChem, ChemSpider and KEGG or user defined structure data file(SDF). After in silico fragmentation in a combinatorial manner, candidates get filtered and scored on criteria like: occurrence of certain elements/substructures, retention time information and reference information.", "sc:name": "MetFrag", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://msbi.ipb-halle.de/MetFragBeta/", "sc:version": "2.2" diff --git a/data/metfusion/metfusionbioschemas.jsonld b/data/metfusion/metfusionbioschemas.jsonld index 6142cdda9abb3..3c52ec5dee1be 100644 --- a/data/metfusion/metfusionbioschemas.jsonld +++ b/data/metfusion/metfusionbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Approach to combine the knowledge from spectral databases like MassBank with the multitude of candidates generated by fragmenters such as MetFrag.", "sc:name": "MetFusion", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://msbi.ipb-halle.de/MetFusion/" } \ No newline at end of file diff --git a/data/methbase/methbasebioschemas.jsonld b/data/methbase/methbasebioschemas.jsonld index 57203427dd82a..858b991f37c21 100644 --- a/data/methbase/methbasebioschemas.jsonld +++ b/data/methbase/methbasebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/MethBase", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "A reference methylome database for different organisms that is created from public BS-seq datasets.", "sc:license": "Unlicense", diff --git a/data/methdb/methdbbioschemas.jsonld b/data/methdb/methdbbioschemas.jsonld index b86d011e26331..1f61906e8e01f 100644 --- a/data/methdb/methdbbioschemas.jsonld +++ b/data/methdb/methdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The database contains information about the occurrence of methylated cytosines in the DNA.", "sc:name": "DNA Methylation Database", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.methdb.de/" } \ No newline at end of file diff --git a/data/methimpute/methimputebioschemas.jsonld b/data/methimpute/methimputebioschemas.jsonld index 72626c33ff904..310b286b2e22c 100644 --- a/data/methimpute/methimputebioschemas.jsonld +++ b/data/methimpute/methimputebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "methimpute", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/methimpute.html", "sc:version": "1.2.0" diff --git a/data/methinheritsim/methinheritsimbioschemas.jsonld b/data/methinheritsim/methinheritsimbioschemas.jsonld index fdb4f03a26df3..c457512c2acba 100644 --- a/data/methinheritsim/methinheritsimbioschemas.jsonld +++ b/data/methinheritsim/methinheritsimbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "methInheritSim", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/methInheritSim.html", "sc:version": "1.2.0" diff --git a/data/methk/methkbioschemas.jsonld b/data/methk/methkbioschemas.jsonld index 7892584cdb84c..bcdc5d994c211 100644 --- a/data/methk/methkbioschemas.jsonld +++ b/data/methk/methkbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server for identifying methylated lysines on histones and non-histone proteins.", "sc:name": "MethK", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://csb.cse.yzu.edu.tw/MethK/" } \ No newline at end of file diff --git a/data/methmarker/methmarkerbioschemas.jsonld b/data/methmarker/methmarkerbioschemas.jsonld index 801b647a74df4..f883becb948e6 100644 --- a/data/methmarker/methmarkerbioschemas.jsonld +++ b/data/methmarker/methmarkerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from a preselected differentially methylated region (DMR) and results in an optimized DNA methylation assay that is ready to be tested in a large-scale clinical trial.", "sc:name": "MethMarker", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://methmarker.mpi-inf.mpg.de/" } \ No newline at end of file diff --git a/data/methpat/methpatbioschemas.jsonld b/data/methpat/methpatbioschemas.jsonld index ee7a419fe4657..00a2480f34cf7 100644 --- a/data/methpat/methpatbioschemas.jsonld +++ b/data/methpat/methpatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Summarises the resultant DNA methylation pattern data from the output of Bismark bismark_methylation_extractor.", "sc:name": "Methpat", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bjpop.github.io/methpat/" diff --git a/data/methped/methpedbioschemas.jsonld b/data/methped/methpedbioschemas.jsonld index 40ad2b7762eef..57e05af219ea1 100644 --- a/data/methped/methpedbioschemas.jsonld +++ b/data/methped/methpedbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Helena Carén", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. We developed a diagnostic classifier based on DNA methylation profiles. This tool is a toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version can classify the following: DIPG, Ependymoma, ETMR, GBM, MB3 and 4, MB_WNT, MB_SHH, and PiloAstro.", "sc:license": "GPL-2.0", diff --git a/data/methpipe/methpipebioschemas.jsonld b/data/methpipe/methpipebioschemas.jsonld index 483754f816fe0..af0b8ad58915a 100644 --- a/data/methpipe/methpipebioschemas.jsonld +++ b/data/methpipe/methpipebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Methpipe", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://smithlabresearch.org/software/methpipe/" } \ No newline at end of file diff --git a/data/methtargetedngs/bioconda_methtargetedngs.yaml b/data/methtargetedngs/bioconda_methtargetedngs.yaml index 918b9330c29d5..4a68f2b696ec3 100644 --- a/data/methtargetedngs/bioconda_methtargetedngs.yaml +++ b/data/methtargetedngs/bioconda_methtargetedngs.yaml @@ -4,7 +4,6 @@ description: Perform step by step methylation analysis of Next Generation Sequen home: https://bioconductor.org/packages/3.10/bioc/html/MethTargetedNGS.html identifiers: - biotools:methtargetedngs -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-methtargetedngs summary: Perform Methylation Analysis on Next Generation Sequencing Data diff --git a/data/methtargetedngs/methtargetedngsbioschemas.jsonld b/data/methtargetedngs/methtargetedngsbioschemas.jsonld index 07836396ca77e..f672c1796e13d 100644 --- a/data/methtargetedngs/methtargetedngsbioschemas.jsonld +++ b/data/methtargetedngs/methtargetedngsbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "MethTargetedNGS", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MethTargetedNGS.html", "sc:version": "1.6.0" diff --git a/data/methvisual/methvisualbioschemas.jsonld b/data/methvisual/methvisualbioschemas.jsonld index fd3b924bf81dd..b84358599abf0 100644 --- a/data/methvisual/methvisualbioschemas.jsonld +++ b/data/methvisual/methvisualbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Arie Zackay", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package allows the visualization of DNA methylation data after bisulfite sequencing.", "sc:license": "GPL-2.0", "sc:name": "methVisual", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/methVisual.html", "sc:version": "1.26.0" diff --git a/data/methyanalysis/bioconda_methyanalysis.yaml b/data/methyanalysis/bioconda_methyanalysis.yaml index 49aa13b12662a..296975876ffb2 100644 --- a/data/methyanalysis/bioconda_methyanalysis.yaml +++ b/data/methyanalysis/bioconda_methyanalysis.yaml @@ -6,7 +6,6 @@ description: The methyAnalysis package aims for the DNA methylation data analysi home: https://bioconductor.org/packages/3.10/bioc/html/methyAnalysis.html identifiers: - biotools:methyanalysis -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-methyanalysis summary: DNA methylation data analysis and visualization diff --git a/data/methyanalysis/methyanalysisbioschemas.jsonld b/data/methyanalysis/methyanalysisbioschemas.jsonld index 3bd48c066466a..6fc078401f75d 100644 --- a/data/methyanalysis/methyanalysisbioschemas.jsonld +++ b/data/methyanalysis/methyanalysisbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "methyAnalysis", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/methyAnalysis.html", diff --git a/data/methylaction/methylactionbioschemas.jsonld b/data/methylaction/methylactionbioschemas.jsonld index 24e4d5e60a4bc..c3d3a46484c16 100644 --- a/data/methylaction/methylactionbioschemas.jsonld +++ b/data/methylaction/methylactionbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "R package for detecting differentially methylated regions (DMRs) from enrichment-based techniques for sequencing DNA methlyation genome-wide.", "sc:name": "MethylAction", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://jeffbhasin.github.io/methylaction/" } \ No newline at end of file diff --git a/data/methylaid/methylaidbioschemas.jsonld b/data/methylaid/methylaidbioschemas.jsonld index 4f639917cacc4..68664872e6dd0 100644 --- a/data/methylaid/methylaidbioschemas.jsonld +++ b/data/methylaid/methylaidbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "MethylAid", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MethylAid.html", "sc:version": "1.8.0" diff --git a/data/methylcal/methylcalbioschemas.jsonld b/data/methylcal/methylcalbioschemas.jsonld index 65325954ccb74..f816a7652f1b5 100644 --- a/data/methylcal/methylcalbioschemas.jsonld +++ b/data/methylcal/methylcalbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "MethylCal", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/lb664/MethylCal" } \ No newline at end of file diff --git a/data/methylcoder/methylcoderbioschemas.jsonld b/data/methylcoder/methylcoderbioschemas.jsonld index 9713d96323751..996ffe6549105 100644 --- a/data/methylcoder/methylcoderbioschemas.jsonld +++ b/data/methylcoder/methylcoderbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "MethylCoder", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/brentp/methylcode" } \ No newline at end of file diff --git a/data/methylextract/methylextractbioschemas.jsonld b/data/methylextract/methylextractbioschemas.jsonld index 5ba347dd0f72f..da091f9dbdc0f 100644 --- a/data/methylextract/methylextractbioschemas.jsonld +++ b/data/methylextract/methylextractbioschemas.jsonld @@ -13,8 +13,8 @@ "biotools:primaryContact": [ "Michael Hackenberg", "José L. Oliver", - "Ricardo Lebrón", - "Guillermo Barturen" + "Guillermo Barturen", + "Ricardo Lebrón" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:24627790", diff --git a/data/methylgsa/methylgsabioschemas.jsonld b/data/methylgsa/methylgsabioschemas.jsonld index a8296099e569a..d38743ca7a282 100644 --- a/data/methylgsa/methylgsabioschemas.jsonld +++ b/data/methylgsa/methylgsabioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "methylGSA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://bioconductor.org/packages/methylGSA" } \ No newline at end of file diff --git a/data/methylinheritance/methylinheritancebioschemas.jsonld b/data/methylinheritance/methylinheritancebioschemas.jsonld index caa56c216a97e..988d885697eba 100644 --- a/data/methylinheritance/methylinheritancebioschemas.jsonld +++ b/data/methylinheritance/methylinheritancebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "methylInheritance", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/methylInheritance.html", "sc:version": "1.4.0" diff --git a/data/methylkit/methylkitbioschemas.jsonld b/data/methylkit/methylkitbioschemas.jsonld index eb73162fb0a7d..a9abdd1011bd5 100644 --- a/data/methylkit/methylkitbioschemas.jsonld +++ b/data/methylkit/methylkitbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-0468-0117", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/gb-2012-13-10-r87", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/methylkit", "@type": "sc:SoftwareApplication", @@ -24,15 +16,15 @@ "@id": "http://orcid.org/0000-0002-0468-0117" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:23034086", - "pmcid:PMC3491415", { "@id": "https://doi.org/10.1186/gb-2012-13-10-r87" - } + }, + "pmcid:PMC3491415", + "pubmed:23034086" ], "sc:description": "R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.", "sc:featureList": { @@ -41,12 +33,20 @@ "sc:license": "Artistic-2.0", "sc:name": "methylKit", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/methylKit.html", "sc:version": "1.0.0" + }, + { + "@id": "http://orcid.org/0000-0002-0468-0117", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/gb-2012-13-10-r87", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/methylmnm/methylmnmbioschemas.jsonld b/data/methylmnm/methylmnmbioschemas.jsonld index e2b0b6a37adca..e7c75f009f62f 100644 --- a/data/methylmnm/methylmnmbioschemas.jsonld +++ b/data/methylmnm/methylmnmbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yan Zhou", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.", "sc:license": "GPL-3.0", diff --git a/data/methylomedb/methylomedbbioschemas.jsonld b/data/methylomedb/methylomedbbioschemas.jsonld index 9dd459db2110f..bf588c0695d4b 100644 --- a/data/methylomedb/methylomedbbioschemas.jsonld +++ b/data/methylomedb/methylomedbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of DNA methylation profiles of human and mouse brains.", "sc:name": "MethylomeDB", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.neuroepigenomics.org/methylomedb/index.html" } \ No newline at end of file diff --git a/data/methylpipe/methylpipebioschemas.jsonld b/data/methylpipe/methylpipebioschemas.jsonld index b171f412345d3..7c92c5799358e 100644 --- a/data/methylpipe/methylpipebioschemas.jsonld +++ b/data/methylpipe/methylpipebioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-4650-8745", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-015-0742-6", "@type": "sc:CreativeWork" }, + { + "@id": "http://orcid.org/0000-0002-4650-8745", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/methylpipe", "@type": "sc:SoftwareApplication", @@ -24,15 +24,15 @@ "@id": "http://orcid.org/0000-0002-4650-8745" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:26415965", { "@id": "https://doi.org/10.1186/s12859-015-0742-6" }, - "pmcid:PMC4587815" + "pmcid:PMC4587815", + "pubmed:26415965" ], "sc:description": "Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.", "sc:featureList": { @@ -41,8 +41,8 @@ "sc:license": "GPL-2.0", "sc:name": "methylPipe", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/methylPipe.html", diff --git a/data/methylseekr/methylseekrbioschemas.jsonld b/data/methylseekr/methylseekrbioschemas.jsonld index 739e84729a405..5c44d35916b65 100644 --- a/data/methylseekr/methylseekrbioschemas.jsonld +++ b/data/methylseekr/methylseekrbioschemas.jsonld @@ -18,11 +18,11 @@ "Library" ], "sc:citation": [ + "pmcid:PMC3763559", + "pubmed:23828043", { "@id": "https://doi.org/10.1093/nar/gkt599" - }, - "pmcid:PMC3763559", - "pubmed:23828043" + } ], "sc:description": "This is a package for the discovery of regulatory regions from Bis-seq data.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "MethylSeekR", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MethylSeekR.html", "sc:version": "1.14.0" diff --git a/data/methylseqdesign/methylseqdesignbioschemas.jsonld b/data/methylseqdesign/methylseqdesignbioschemas.jsonld index ebde73b73b08b..fa4b72dc6a9fb 100644 --- a/data/methylseqdesign/methylseqdesignbioschemas.jsonld +++ b/data/methylseqdesign/methylseqdesignbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "MethylSeqDesign", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/liupeng2117/MethylSeqDesign" } \ No newline at end of file diff --git a/data/methylsig/methylsigbioschemas.jsonld b/data/methylsig/methylsigbioschemas.jsonld index 16666452e3522..61b353d6deb59 100644 --- a/data/methylsig/methylsigbioschemas.jsonld +++ b/data/methylsig/methylsigbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced representation bisulfite sequencing (RRBS), or enhanced RRBS experiments.", "sc:name": "MethylSig", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://sartorlab.ccmb.med.umich.edu/node/17" } \ No newline at end of file diff --git a/data/methylumi/methylumibioschemas.jsonld b/data/methylumi/methylumibioschemas.jsonld index 510f0dab08b7e..6ed6a4910e3ae 100644 --- a/data/methylumi/methylumibioschemas.jsonld +++ b/data/methylumi/methylumibioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "methylumi", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/methylumi.html", "sc:version": "2.20.0" diff --git a/data/metitree/metitreebioschemas.jsonld b/data/metitree/metitreebioschemas.jsonld index 7e668dabcf52d..81076d69024a3 100644 --- a/data/metitree/metitreebioschemas.jsonld +++ b/data/metitree/metitreebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "MetiTree", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "ELIXIR-NL", diff --git a/data/metlab/metlabbioschemas.jsonld b/data/metlab/metlabbioschemas.jsonld index 559ab0d1b1b61..aa2d0c7069232 100644 --- a/data/metlab/metlabbioschemas.jsonld +++ b/data/metlab/metlabbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0160334", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/metlab", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Julliette Hayer", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC4968819", + "pubmed:27479078", { "@id": "https://doi.org/10.1371/journal.pone.0160334" }, - "pubmed:27479078" + "pmcid:PMC4968819" ], "sc:description": "MetLab is aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes.", "sc:featureList": { @@ -32,10 +28,14 @@ "sc:license": "GPL-3.0", "sc:name": "MetLab", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/norling/metlab" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0160334", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metmatch/metmatchbioschemas.jsonld b/data/metmatch/metmatchbioschemas.jsonld index abe42bc941abf..bf90140ca439d 100644 --- a/data/metmatch/metmatchbioschemas.jsonld +++ b/data/metmatch/metmatchbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3390/metabo6040039", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-7520-4943", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/metmatch", "@type": "sc:SoftwareApplication", @@ -39,6 +31,14 @@ "sc:name": "MetMatch", "sc:operatingSystem": "Windows", "sc:url": "https://metabolomics-ifa.boku.ac.at/MetMatch/index.html#" + }, + { + "@id": "https://doi.org/10.3390/metabo6040039", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-7520-4943", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/metpc/metpcbioschemas.jsonld b/data/metpc/metpcbioschemas.jsonld index 6300008bbaeaa..2c1f5f709ac3e 100644 --- a/data/metpc/metpcbioschemas.jsonld +++ b/data/metpc/metpcbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3390/METABO9050103", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/MetPC", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jaesik Jeong", "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC6572057", - "pubmed:31130635", { "@id": "https://doi.org/10.3390/METABO9050103" - } + }, + "pubmed:31130635", + "pmcid:PMC6572057" ], "sc:description": "Metabolite Pipeline Consisting of Metabolite Identification and Biomarker Discovery Under the Control of Two-Dimensional FDR.", "sc:featureList": [ @@ -31,20 +27,24 @@ "@id": "edam:operation_3803" }, { - "@id": "edam:operation_3891" + "@id": "edam:operation_3659" }, { - "@id": "edam:operation_3659" + "@id": "edam:operation_3891" } ], "sc:license": "Unlicense", "sc:name": "MetPC", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/jjs3098/CNU-Bioinformatics-Lab" + }, + { + "@id": "https://doi.org/10.3390/METABO9050103", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/metstat/metstatbioschemas.jsonld b/data/metstat/metstatbioschemas.jsonld index 59312e82279c8..7b4d716aa6c03 100644 --- a/data/metstat/metstatbioschemas.jsonld +++ b/data/metstat/metstatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Apache-2.0", "sc:name": "MetStat", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "ELIXIR-NL", "sc:url": "https://cran.r-project.org/web/packages/MetStaT/index.html", diff --git a/data/mettailor/mettailorbioschemas.jsonld b/data/mettailor/mettailorbioschemas.jsonld index 9ce79fd6e588f..a92d148d55fcb 100644 --- a/data/mettailor/mettailorbioschemas.jsonld +++ b/data/mettailor/mettailorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software package that performs post-extraction processing steps such as cross-sample realignment and data normalization that are specifically designed to account for the experimental factors from chromatographic separation and MS analysis.", "sc:name": "MetTailor", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sourceforge.net/projects/mettailor/" } \ No newline at end of file diff --git a/data/mev/mevbioschemas.jsonld b/data/mev/mevbioschemas.jsonld index ac426b1a4699b..b137179a6d3b7 100644 --- a/data/mev/mevbioschemas.jsonld +++ b/data/mev/mevbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "MeV", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://mev.tm4.org/#/welcome" } \ No newline at end of file diff --git a/data/mexpress/mexpressbioschemas.jsonld b/data/mexpress/mexpressbioschemas.jsonld index 5ccb3731389d7..2f083912e497a 100644 --- a/data/mexpress/mexpressbioschemas.jsonld +++ b/data/mexpress/mexpressbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "TCGA data mining tool.", "sc:name": "MEXPRESS", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "ugent.be", diff --git a/data/mfa/mfabioschemas.jsonld b/data/mfa/mfabioschemas.jsonld index 94549e8d0c547..9fa3864341803 100644 --- a/data/mfa/mfabioschemas.jsonld +++ b/data/mfa/mfabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "mfa", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mfa.html", diff --git a/data/mfdm/mfdmbioschemas.jsonld b/data/mfdm/mfdmbioschemas.jsonld index 493f611d308e1..29e11de704cac 100644 --- a/data/mfdm/mfdmbioschemas.jsonld +++ b/data/mfdm/mfdmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Designed to reliably detect recent positive selection in a varying size population, even if you only have polymorphism data from a single locus (i.e. a very short piece of DNA).", "sc:name": "MFDM", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.picb.ac.cn/evolgen/softwares/index.html" } \ No newline at end of file diff --git a/data/mfdp/mfdpbioschemas.jsonld b/data/mfdp/mfdpbioschemas.jsonld index df8e91b0ae039..1929f89892316 100644 --- a/data/mfdp/mfdpbioschemas.jsonld +++ b/data/mfdp/mfdpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Combines per-residue disorder probabilities predicted by MFDp with per-sequence disorder content predicted by DisCon, and applies novel post-processing filters to provide disorder predictions with improved predictive quality.", "sc:name": "MFDp", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://biomine-ws.ece.ualberta.ca/MFDp2/index.php" } \ No newline at end of file diff --git a/data/mflux/mfluxbioschemas.jsonld b/data/mflux/mfluxbioschemas.jsonld index 4699d18b74d1e..552a20386494f 100644 --- a/data/mflux/mfluxbioschemas.jsonld +++ b/data/mflux/mfluxbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/mflux", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Wu", + "Dr. Tang", "Dr. Bao", - "Dr. Tang" + "Dr. Wu" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:27092947", "sc:description": "Web-based platform that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms.", "sc:name": "MFlux", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://mflux.org/" diff --git a/data/mfmd/mfmdbioschemas.jsonld b/data/mfmd/mfmdbioschemas.jsonld index c031a2d8ce638..bf2f9406103d9 100644 --- a/data/mfmd/mfmdbioschemas.jsonld +++ b/data/mfmd/mfmdbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mfmd", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Abdelhamid Barakat", - "Hicham Charoute" + "Hicham Charoute", + "Abdelhamid Barakat" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:26173767", diff --git a/data/mfold/mfoldbioschemas.jsonld b/data/mfold/mfoldbioschemas.jsonld index f2c2d3aea8b7f..164859e4eb026 100644 --- a/data/mfold/mfoldbioschemas.jsonld +++ b/data/mfold/mfoldbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.", "sc:name": "Mfold", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mfold.rna.albany.edu/?q=mfold/download-mfold" } \ No newline at end of file diff --git a/data/mfpaq/mfpaqbioschemas.jsonld b/data/mfpaq/mfpaqbioschemas.jsonld index 9e7381a5ba476..19fe0efe00ee3 100644 --- a/data/mfpaq/mfpaqbioschemas.jsonld +++ b/data/mfpaq/mfpaqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Mascot file parsing and quantitation using ICAT and SILAC.", "sc:name": "MFPaQ", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://mfpaq.sourceforge.net" } \ No newline at end of file diff --git a/data/mfungd/mfungdbioschemas.jsonld b/data/mfungd/mfungdbioschemas.jsonld index c9b8fde2519a7..4f29d31c130ec 100644 --- a/data/mfungd/mfungdbioschemas.jsonld +++ b/data/mfungd/mfungdbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MIPS mouse functional genome database (MfunGD)", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bio2rdf.org/describe/?uri=http://bio2rdf.org/lsr:mfungd" } \ No newline at end of file diff --git a/data/mfuzz/mfuzzbioschemas.jsonld b/data/mfuzz/mfuzzbioschemas.jsonld index c0dabdf2846ba..afbc80659ce04 100644 --- a/data/mfuzz/mfuzzbioschemas.jsonld +++ b/data/mfuzz/mfuzzbioschemas.jsonld @@ -9,43 +9,43 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.6026/97320630002005", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mfuzz", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Matthias Futschik", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC2139991", - "pubmed:18084642", { "@id": "https://doi.org/10.6026/97320630002005" - } + }, + "pubmed:18084642" ], "sc:description": "Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_3432" }, { - "@id": "edam:operation_3432" + "@id": "edam:operation_0337" } ], "sc:license": "GPL-2.0", "sc:name": "Mfuzz", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Mfuzz.html", "sc:version": "2.34.0" - }, - { - "@id": "https://doi.org/10.6026/97320630002005", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mgcat/mgcatbioschemas.jsonld b/data/mgcat/mgcatbioschemas.jsonld index d79524ee3140b..bf37e765500a5 100644 --- a/data/mgcat/mgcatbioschemas.jsonld +++ b/data/mgcat/mgcatbioschemas.jsonld @@ -26,9 +26,9 @@ }, "sc:name": "M-GCAT 2.0 beta", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://alggen.lsi.upc.es/recerca/align/mgcat/" }, diff --git a/data/mgclus/mgclusbioschemas.jsonld b/data/mgclus/mgclusbioschemas.jsonld index 296ecddf84ffe..6f6b85a2b1660 100644 --- a/data/mgclus/mgclusbioschemas.jsonld +++ b/data/mgclus/mgclusbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MGclus", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sonnhammer.sbc.su.se/download/software/MGclus/Readme" } \ No newline at end of file diff --git a/data/mgd/mgdbioschemas.jsonld b/data/mgd/mgdbioschemas.jsonld index 506dff295712b..2c93454b06f44 100644 --- a/data/mgd/mgdbioschemas.jsonld +++ b/data/mgd/mgdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Community model organism database for the laboratory mouse and the source for phenotype and functional annotations of mouse genes. It includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information.", "sc:name": "Mouse Genome Database (MGD)", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.informatics.jax.org/" } \ No newline at end of file diff --git a/data/mgenomesubtractor/mgenomesubtractorbioschemas.jsonld b/data/mgenomesubtractor/mgenomesubtractorbioschemas.jsonld index 3c5d2c51f7ac5..4602a2bd00134 100644 --- a/data/mgenomesubtractor/mgenomesubtractorbioschemas.jsonld +++ b/data/mgenomesubtractor/mgenomesubtractorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "mGenomeSubtractor", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinfo-mml.sjtu.edu.cn/mGS/" } \ No newline at end of file diff --git a/data/mgert/mgertbioschemas.jsonld b/data/mgert/mgertbioschemas.jsonld index c57a0eb5da4dd..054f527cb7837 100644 --- a/data/mgert/mgertbioschemas.jsonld +++ b/data/mgert/mgertbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S13100-019-0163-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0002-6329-2421", "@type": "schema:Person" @@ -25,19 +21,19 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6515669", "pubmed:31114637", { "@id": "https://doi.org/10.1186/S13100-019-0163-6" - } + }, + "pmcid:PMC6515669" ], "sc:description": "Mobile Genetic Elements Retrieving Tool Pipeline (MGERT) for retrieving coding sequences of mobile genetic elements from genome assemblies.", "sc:featureList": [ { - "@id": "edam:operation_0525" + "@id": "edam:operation_0427" }, { - "@id": "edam:operation_0427" + "@id": "edam:operation_0525" }, { "@id": "edam:operation_2422" @@ -47,10 +43,14 @@ "sc:name": "MGERT", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/andrewgull/MGERT" + }, + { + "@id": "https://doi.org/10.1186/S13100-019-0163-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mgfm/mgfmbioschemas.jsonld b/data/mgfm/mgfmbioschemas.jsonld index 7eb38dc036caf..81e44222e794b 100644 --- a/data/mgfm/mgfmbioschemas.jsonld +++ b/data/mgfm/mgfmbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Khadija El Amrani", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package is designed to detect marker genes from Microarray gene expression data sets.", "sc:license": "GPL-3.0", "sc:name": "MGFM", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MGFM.html", "sc:version": "1.8.0" diff --git a/data/mgfr/mgfrbioschemas.jsonld b/data/mgfr/mgfrbioschemas.jsonld index a9b95a12b5590..e4c5df336bad2 100644 --- a/data/mgfr/mgfrbioschemas.jsonld +++ b/data/mgfr/mgfrbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Khadija El Amrani", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package is designed to detect marker genes from RNA-seq data.", "sc:license": "GPL-3.0", diff --git a/data/mgi/mgibioschemas.jsonld b/data/mgi/mgibioschemas.jsonld index dff81c21dfc2c..960fc550af966 100644 --- a/data/mgi/mgibioschemas.jsonld +++ b/data/mgi/mgibioschemas.jsonld @@ -36,8 +36,8 @@ "sc:name": "Mouse Genome Informatics (MGI)", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.informatics.jax.org/" }, diff --git a/data/mgip/mgipbioschemas.jsonld b/data/mgip/mgipbioschemas.jsonld index 4edc867facd94..ee69258045c09 100644 --- a/data/mgip/mgipbioschemas.jsonld +++ b/data/mgip/mgipbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.", "sc:name": "MGIP", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://mgip.biology.gatech.edu" } \ No newline at end of file diff --git a/data/mgmapper/mgmapperbioschemas.jsonld b/data/mgmapper/mgmapperbioschemas.jsonld index 77dc01cd92369..707973fe46b62 100644 --- a/data/mgmapper/mgmapperbioschemas.jsonld +++ b/data/mgmapper/mgmapperbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Reference based mapping and taxonomy annotation of metagenomics sequence reads.", "sc:name": "MGmapper", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://cge.cbs.dtu.dk/services/MGmapper/" } \ No newline at end of file diff --git a/data/mgsa/mgsabioschemas.jsonld b/data/mgsa/mgsabioschemas.jsonld index a868810e915ff..b5db6b6fb800d 100644 --- a/data/mgsa/mgsabioschemas.jsonld +++ b/data/mgsa/mgsabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sebastian Bauer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.", "sc:license": "Artistic-2.0", "sc:name": "mgsa", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mgsa.html", "sc:version": "1.22.0" diff --git a/data/mgsz/mgszbioschemas.jsonld b/data/mgsz/mgszbioschemas.jsonld index eaeacbfce1e1c..e67ccdb338060 100644 --- a/data/mgsz/mgszbioschemas.jsonld +++ b/data/mgsz/mgszbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Gene set analysis method based on GSZ (Gene Set Z-score) statistics and asymptotic p-value. It is different from the standard GSZ method in that it assigns asymptotic p-values to the gene set scores instead of empirical p-values.", "sc:name": "mGSZ", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://ekhidna.biocenter.helsinki.fi/downloads/pashupati/mGSZ.html" } \ No newline at end of file diff --git a/data/mgx/mgxbioschemas.jsonld b/data/mgx/mgxbioschemas.jsonld index 9a3dfd60088a6..ab7474cd90a9b 100644 --- a/data/mgx/mgxbioschemas.jsonld +++ b/data/mgx/mgxbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "AGPL-3.0", "sc:name": "MGX", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "bigi", "sc:url": "https://mgx-metagenomics.github.io/", diff --git a/data/mhc-np/mhc-npbioschemas.jsonld b/data/mhc-np/mhc-npbioschemas.jsonld index bffd2b7a9caa0..23725abd7a424 100644 --- a/data/mhc-np/mhc-npbioschemas.jsonld +++ b/data/mhc-np/mhc-npbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Python tool to identify peptides that are naturally processed by the MHC-I pathway.", "sc:name": "MHC-NP", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://tools.immuneepitope.org/mhcnp/" diff --git a/data/mhc2pred/mhc2predbioschemas.jsonld b/data/mhc2pred/mhc2predbioschemas.jsonld index b19ac3b7471c0..25055a9f7b1d4 100644 --- a/data/mhc2pred/mhc2predbioschemas.jsonld +++ b/data/mhc2pred/mhc2predbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SVM based method for prediction of promiscuous MHC class II binding peptides. The average accuracy of SVM based method for 42 alleles is ~80%. The performence of the method was poorer for few allele due to smaller size of dataset. The performence of the method was tested through 5-fold cross-validation.", "sc:name": "MHC2Pred", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/mhc2pred/" } \ No newline at end of file diff --git a/data/mhccluster/mhcclusterbioschemas.jsonld b/data/mhccluster/mhcclusterbioschemas.jsonld index 8adcc6bef69f7..4c3fe162ca9f2 100644 --- a/data/mhccluster/mhcclusterbioschemas.jsonld +++ b/data/mhccluster/mhcclusterbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1007/s00251-013-0714-9", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-7885-4311", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/mhccluster", "@type": "sc:SoftwareApplication", @@ -39,11 +31,11 @@ "@id": "edam:topic_2830" }, "sc:citation": [ + "pubmed:23775223", + "pmcid:PMC3750724", { "@id": "https://doi.org/10.1007/s00251-013-0714-9" - }, - "pmcid:PMC3750724", - "pubmed:23775223" + } ], "sc:description": "Functional cluster of MHC class I molecules (MHCI) based on their predicted binding specificity.", "sc:featureList": { @@ -63,6 +55,14 @@ }, "sc:url": "http://cbs.dtu.dk/services/MHCcluster/", "sc:version": "2.0" + }, + { + "@id": "http://orcid.org/0000-0001-7885-4311", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1007/s00251-013-0714-9", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mhcpred/mhcpredbioschemas.jsonld b/data/mhcpred/mhcpredbioschemas.jsonld index 51a799da5b71d..b1b9cbfaba785 100644 --- a/data/mhcpred/mhcpredbioschemas.jsonld +++ b/data/mhcpred/mhcpredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Uses the additive method to predict the binding affinity of major histocompatibility complex (MHC) class I and II molecules and also to the Transporter associated with Processing (TAP).", "sc:name": "MHCPred", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.ddg-pharmfac.net/mhcpred/MHCPred/" diff --git a/data/mhcseqnet/mhcseqnetbioschemas.jsonld b/data/mhcseqnet/mhcseqnetbioschemas.jsonld index cb91b86720075..ce2c359a7043e 100644 --- a/data/mhcseqnet/mhcseqnetbioschemas.jsonld +++ b/data/mhcseqnet/mhcseqnetbioschemas.jsonld @@ -22,26 +22,26 @@ { "@id": "https://doi.org/10.1186/s12859-019-2892-4" }, - "pmcid:PMC6540523", - "pubmed:31138107" + "pubmed:31138107", + "pmcid:PMC6540523" ], "sc:description": "Deep neural network model for universal Major Histocompatibility Complex (MHC) binding prediction.", "sc:featureList": [ { - "@id": "edam:operation_0252" + "@id": "edam:operation_3631" }, { "@id": "edam:operation_3227" }, { - "@id": "edam:operation_3631" + "@id": "edam:operation_0252" } ], "sc:license": "Apache-2.0", "sc:name": "MHCSeqNet", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/cmbcu/MHCSeqNet" } diff --git a/data/mi-sim/mi-simbioschemas.jsonld b/data/mi-sim/mi-simbioschemas.jsonld index e3d3a0a463377..b422449b01497 100644 --- a/data/mi-sim/mi-simbioschemas.jsonld +++ b/data/mi-sim/mi-simbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Mathematical analysis software specifically for use with mechanistically described microbial interactions described in terms of reactions, substrates/reactants and products. It provides a user-friendly environment in which microbiologists, microbial ecologists and biological mathematicians can rapidly and robustly characterize the dynamics of ecological motifs of up to three microbial species, without the requirement to develop their own code, programme models or rely on a detailed knowledge of the mathematics of dynamical systems analysis.", "sc:name": "MI-Sim", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://uk.mathworks.com/matlabcentral/fileexchange/55492-mi-sim-mi-sim-final" diff --git a/data/miarma-seq/miarma-seqbioschemas.jsonld b/data/miarma-seq/miarma-seqbioschemas.jsonld index 655e771a68f58..6c4192235c315 100644 --- a/data/miarma-seq/miarma-seqbioschemas.jsonld +++ b/data/miarma-seq/miarma-seqbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-0621-9914", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1038/srep25749", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/miarma-seq", "@type": "sc:SoftwareApplication", @@ -30,20 +38,12 @@ "sc:license": "CC-BY-2.0", "sc:name": "miARma-Seq", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://miarmaseq.idoproteins.com/", "sc:version": "1.7.2" - }, - { - "@id": "https://doi.org/10.1038/srep25749", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-0621-9914", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mib/mibbioschemas.jsonld b/data/mib/mibbioschemas.jsonld index 0afaac480c69a..756058cad41b7 100644 --- a/data/mib/mibbioschemas.jsonld +++ b/data/mib/mibbioschemas.jsonld @@ -17,10 +17,10 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:26727152", { "@id": "https://doi.org/10.1371/journal.pbio.1002340" }, - "pubmed:26727152", "pmcid:PMC4699692" ], "sc:description": "Microscopy image browser (MIB) is a software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data.", @@ -30,19 +30,19 @@ "sc:license": "GPL-2.0", "sc:name": "MIB", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://mib.helsinki.fi/index.html" }, - { - "@id": "https://doi.org/10.1371/journal.pbio.1002340", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-2190-4909", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1371/journal.pbio.1002340", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/micc/miccbioschemas.jsonld b/data/micc/miccbioschemas.jsonld index a4595cb2ffa1a..113a1640af798 100644 --- a/data/micc/miccbioschemas.jsonld +++ b/data/micc/miccbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/micc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Zhang MQ", - "Wang X" + "Wang X", + "Zhang MQ" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:26231426", diff --git a/data/micca/miccabioschemas.jsonld b/data/micca/miccabioschemas.jsonld index 84b8200e08a4d..24e98b36de93d 100644 --- a/data/micca/miccabioschemas.jsonld +++ b/data/micca/miccabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "MICCA", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ELIXIR-ITA-MACH", "sc:url": "http://micca.org", diff --git a/data/micelle_maker/micelle_makerbioschemas.jsonld b/data/micelle_maker/micelle_makerbioschemas.jsonld index fba1f3035a233..029f8c56524b3 100644 --- a/data/micelle_maker/micelle_makerbioschemas.jsonld +++ b/data/micelle_maker/micelle_makerbioschemas.jsonld @@ -36,9 +36,9 @@ ], "sc:name": "Micelle Maker", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://micelle.icm.uu.se/" } diff --git a/data/micheck/micheckbioschemas.jsonld b/data/micheck/micheckbioschemas.jsonld index d55de9b8e6451..829f701d4d46f 100644 --- a/data/micheck/micheckbioschemas.jsonld +++ b/data/micheck/micheckbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MICheck", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.genoscope.cns.fr/agc/tools/micheck/" } \ No newline at end of file diff --git a/data/michip/bioconda_michip.yaml b/data/michip/bioconda_michip.yaml index a510adcb174bd..fe9d200edbdbc 100644 --- a/data/michip/bioconda_michip.yaml +++ b/data/michip/bioconda_michip.yaml @@ -6,7 +6,6 @@ description: This package takes the MiChip miRNA microarray .grp scanner output home: https://bioconductor.org/packages/3.10/bioc/html/MiChip.html identifiers: - biotools:michip -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-michip diff --git a/data/michip/michipbioschemas.jsonld b/data/michip/michipbioschemas.jsonld index 41d61b41dab08..9a67df88a21a8 100644 --- a/data/michip/michipbioschemas.jsonld +++ b/data/michip/michipbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jonathon Blake", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package takes the miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.", "sc:license": "GPL-2.0", "sc:name": "MiChip", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MiChip.html", "sc:version": "1.28.0" diff --git a/data/mico/micobioschemas.jsonld b/data/mico/micobioschemas.jsonld index e87f6123a38fc..67319a0174b24 100644 --- a/data/mico/micobioschemas.jsonld +++ b/data/mico/micobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MICO", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mico.ggc.org/MICO/SearchEntry.jsp" } \ No newline at end of file diff --git a/data/microbegps/microbegpsbioschemas.jsonld b/data/microbegps/microbegpsbioschemas.jsonld index e9ab79213ba82..9d2c72471e7f1 100644 --- a/data/microbegps/microbegpsbioschemas.jsonld +++ b/data/microbegps/microbegpsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Bioinformatics tool for the analysis of metagenomic sequencing data. The goal is to profile the composition of metagenomic communities as accurately as possible and present the results to the user in a convenient manner.", "sc:name": "MicrobeGPS", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://sourceforge.net/projects/microbegps/" } \ No newline at end of file diff --git a/data/microbesonline/microbesonlinebioschemas.jsonld b/data/microbesonline/microbesonlinebioschemas.jsonld index 0146002292675..1294a4fc71478 100644 --- a/data/microbesonline/microbesonlinebioschemas.jsonld +++ b/data/microbesonline/microbesonlinebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms. It includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, it can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. It also includes fast phylogenetic profile searches and more.", "sc:name": "MicrobesOnline", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.MicrobesOnline.org" diff --git a/data/microbial_advanced_database_organisation_micado/microbial_advanced_database_organisation_micadobioschemas.jsonld b/data/microbial_advanced_database_organisation_micado/microbial_advanced_database_organisation_micadobioschemas.jsonld index f531792dc704e..2f216e823c28d 100644 --- a/data/microbial_advanced_database_organisation_micado/microbial_advanced_database_organisation_micadobioschemas.jsonld +++ b/data/microbial_advanced_database_organisation_micado/microbial_advanced_database_organisation_micadobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/microbial_advanced_database_organisation_micado", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hélène Chiapello", - "Annie Gendrault-Jacquemard" + "Annie Gendrault-Jacquemard", + "Hélène Chiapello" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:9283758", @@ -20,8 +20,8 @@ "sc:name": "Microbial advanced database organisation (Micado)", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi" } \ No newline at end of file diff --git a/data/microbial_genome_viewer/microbial_genome_viewerbioschemas.jsonld b/data/microbial_genome_viewer/microbial_genome_viewerbioschemas.jsonld index 3354c51d8b68b..27d9b47dce19a 100644 --- a/data/microbial_genome_viewer/microbial_genome_viewerbioschemas.jsonld +++ b/data/microbial_genome_viewer/microbial_genome_viewerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Microbial Genome Viewer", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cmbi.ru.nl/MGV/" } \ No newline at end of file diff --git a/data/microbiomer/microbiomerbioschemas.jsonld b/data/microbiomer/microbiomerbioschemas.jsonld index 83fc2bd1c7d77..17134f2003bd4 100644 --- a/data/microbiomer/microbiomerbioschemas.jsonld +++ b/data/microbiomer/microbiomerbioschemas.jsonld @@ -30,11 +30,11 @@ "sc:version": "0.6.1" }, { - "@id": "http://orcid.org/0000-0001-8096-0180", + "@id": "http://orcid.org/0000-0002-7687-0059", "@type": "schema:Person" }, { - "@id": "http://orcid.org/0000-0002-7687-0059", + "@id": "http://orcid.org/0000-0001-8096-0180", "@type": "schema:Person" } ] diff --git a/data/microclass/microclassbioschemas.jsonld b/data/microclass/microclassbioschemas.jsonld index d7f4bc6541ef6..a40289fd49c0d 100644 --- a/data/microclass/microclassbioschemas.jsonld +++ b/data/microclass/microclassbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "microclass", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/microclass/", diff --git a/data/microdor/microdorbioschemas.jsonld b/data/microdor/microdorbioschemas.jsonld index ae622d0b614b3..819e0592d6166 100644 --- a/data/microdor/microdorbioschemas.jsonld +++ b/data/microdor/microdorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "microDoR", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://reprod.njmu.edu.cn/cgi-bin/microdor/index.py" } \ No newline at end of file diff --git a/data/microerroranalyzer/microerroranalyzerbioschemas.jsonld b/data/microerroranalyzer/microerroranalyzerbioschemas.jsonld index 82548e59f5ed5..410be0593541b 100644 --- a/data/microerroranalyzer/microerroranalyzerbioschemas.jsonld +++ b/data/microerroranalyzer/microerroranalyzerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computer program  for analysing the genotyping errors of microsatellites in parentage exclusion analysis.", "sc:name": "MicroErrorAnalyzer", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.zsl.org/science/software/microerroranalyzer" } \ No newline at end of file diff --git a/data/microfootprinter/microfootprinterbioschemas.jsonld b/data/microfootprinter/microfootprinterbioschemas.jsonld index d60278339fa26..e68c5c1ed1270 100644 --- a/data/microfootprinter/microfootprinterbioschemas.jsonld +++ b/data/microfootprinter/microfootprinterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Identify the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.", "sc:name": "MicroFootPrinter", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bio.cs.washington.edu/MicroFootPrinter.html" } \ No newline at end of file diff --git a/data/micrographite/micrographitebioschemas.jsonld b/data/micrographite/micrographitebioschemas.jsonld index 92502342df7e0..366ee35baaf35 100644 --- a/data/micrographite/micrographitebioschemas.jsonld +++ b/data/micrographite/micrographitebioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gku354", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/micrographite", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chiara Romualdi", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC4066781", { "@id": "https://doi.org/10.1093/nar/gku354" }, - "pubmed:24803669", - "pmcid:PMC4066781" + "pubmed:24803669" ], "sc:description": "R package for topological pathway analysis integrating gene and miRNA expression profiles using validated and/or predicted miRNA-target interactions. It is based on updated versions of graphite and CliPPER Bioconductor packages dedicated to pathway analyses recently proposed by our group.", "sc:featureList": { @@ -32,13 +28,17 @@ "sc:license": "AGPL-3.0", "sc:name": "micrographite", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://romualdi.bio.unipd.it/micrographite", "sc:version": "4.0" + }, + { + "@id": "https://doi.org/10.1093/nar/gku354", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/microhibro/microhibrobioschemas.jsonld b/data/microhibro/microhibrobioschemas.jsonld index 9b1b8f4b8a214..45fd9df121e88 100644 --- a/data/microhibro/microhibrobioschemas.jsonld +++ b/data/microhibro/microhibrobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "MicroHibro", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.microhibro.com/" } \ No newline at end of file diff --git a/data/microkit/microkitbioschemas.jsonld b/data/microkit/microkitbioschemas.jsonld index 977a1a70b12a7..b3fa84f0a12bf 100644 --- a/data/microkit/microkitbioschemas.jsonld +++ b/data/microkit/microkitbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:description": "Database of proteins that localize in midbody, centrosome and/or kinetochore. The database contains experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification.", "sc:name": "MiCroKit", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://microkit.biocuckoo.org/" diff --git a/data/micromanager/micromanagerbioschemas.jsonld b/data/micromanager/micromanagerbioschemas.jsonld index efdb90e9e34a1..df37b590d6c78 100644 --- a/data/micromanager/micromanagerbioschemas.jsonld +++ b/data/micromanager/micromanagerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "microManager", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://valelab.ucsf.edu/~MM/MMwiki/" } \ No newline at end of file diff --git a/data/micromummie/micromummiebioschemas.jsonld b/data/micromummie/micromummiebioschemas.jsonld index cb2abcace0a74..e773e06c014ba 100644 --- a/data/micromummie/micromummiebioschemas.jsonld +++ b/data/micromummie/micromummiebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data.", "sc:name": "microMUMMIE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://ohlerlab.mdc-berlin.de/software/microMUMMIE_99/" } \ No newline at end of file diff --git a/data/microp/micropbioschemas.jsonld b/data/microp/micropbioschemas.jsonld index 730e92a3aa987..0e45f52719106 100644 --- a/data/microp/micropbioschemas.jsonld +++ b/data/microp/micropbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A new feature selection method called Biological Pathway-based Feature Selection (BPFS) for microarray data. Unlike most of the existing methods, the method integrates signaling and gene regulatory pathways with gene expression data to minimize the chance of overfitting of the method and to improve the test accuracy.", "sc:name": "microp", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioinformatics.cise.ufl.edu/microp.html" diff --git a/data/micropan/micropanbioschemas.jsonld b/data/micropan/micropanbioschemas.jsonld index d929b19dafa7c..e57446e5a611d 100644 --- a/data/micropan/micropanbioschemas.jsonld +++ b/data/micropan/micropanbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Lars Snipen", - "Kristian Hovde Liland" + "Kristian Hovde Liland", + "Lars Snipen" ], "sc:description": "R package for the study of prokaryotic pan-genomes. A pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species.", "sc:license": "GPL-2.0", "sc:name": "micropan", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "Norwegian University of Life Sciences", "sc:url": "https://cran.r-project.org/web/packages/micropan/index.html", diff --git a/data/micropattern/micropatternbioschemas.jsonld b/data/micropattern/micropatternbioschemas.jsonld index 33e385c1277ea..81ef2fbdb3637 100644 --- a/data/micropattern/micropatternbioschemas.jsonld +++ b/data/micropattern/micropatternbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "MicroPattern", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.cuilab.cn/micropattern" } \ No newline at end of file diff --git a/data/micropie/micropiebioschemas.jsonld b/data/micropie/micropiebioschemas.jsonld index 5c4c8fd6004c6..eb99ef3d11085 100644 --- a/data/micropie/micropiebioschemas.jsonld +++ b/data/micropie/micropiebioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-016-1396-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/micropie", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jin Mao", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5153691", + "pubmed:27955641", { "@id": "https://doi.org/10.1186/s12859-016-1396-8" - }, - "pmcid:PMC5153691", - "pubmed:27955641" + } ], "sc:description": "Microbial Phenomics Information Extractor (MicroPIE) is a natural language processing application that uses a robust supervised classification algorithm (Support Vector Machine) to identify characters from sentences in prokaryotic taxonomic descriptions, followed by a combination of algorithms applying linguistic rules with groups of known terms to extract characters as well as character states.", "sc:featureList": { @@ -32,12 +28,16 @@ "sc:license": "Other", "sc:name": "MicroPIE", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/biosemantics/micropie2/tree/0.1.0", "sc:version": "0.1.0" + }, + { + "@id": "https://doi.org/10.1186/s12859-016-1396-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/micropita/micropitabioschemas.jsonld b/data/micropita/micropitabioschemas.jsonld index c36f40c72115d..2af0a811a4335 100644 --- a/data/micropita/micropitabioschemas.jsonld +++ b/data/micropita/micropitabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Selects samples from abundance tables based on various selection schemes.", "sc:name": "micropita", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://huttenhower.sph.harvard.edu/micropita", diff --git a/data/microrna/bioconda_microrna.yaml b/data/microrna/bioconda_microrna.yaml index 6c11b41592106..4f817ee2db7df 100644 --- a/data/microrna/bioconda_microrna.yaml +++ b/data/microrna/bioconda_microrna.yaml @@ -4,7 +4,6 @@ description: Different data resources for microRNAs and some functions for manip home: https://bioconductor.org/packages/3.10/bioc/html/microRNA.html identifiers: - biotools:microrna -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-microrna summary: Data and functions for dealing with microRNAs diff --git a/data/microrna/micrornabioschemas.jsonld b/data/microrna/micrornabioschemas.jsonld index 2ee21f3604835..ceec3a1313756 100644 --- a/data/microrna/micrornabioschemas.jsonld +++ b/data/microrna/micrornabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "microRNA", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/microRNA.html", "sc:version": "1.32.0" diff --git a/data/microrpm/microrpmbioschemas.jsonld b/data/microrpm/microrpmbioschemas.jsonld index 325b6eb75f32b..9d309ed215d75 100644 --- a/data/microrpm/microrpmbioschemas.jsonld +++ b/data/microrpm/microrpmbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/microrpm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wen-Chi Chang", - "Na-Sheng Lin" + "Na-Sheng Lin", + "Wen-Chi Chang" ], "sc:additionalType": "Command-line tool", "sc:description": "MicroRNA prediction model based only on plant small RNA sequencing data.", "sc:name": "microRPM", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://microrpm.itps.ncku.edu.tw/" } \ No newline at end of file diff --git a/data/microscope/microscopebioschemas.jsonld b/data/microscope/microscopebioschemas.jsonld index 1358924ed6386..d940f3ce02aa4 100644 --- a/data/microscope/microscopebioschemas.jsonld +++ b/data/microscope/microscopebioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Bohdan B. Khomtchouk", "sc:additionalType": "Suite", "sc:citation": [ + "pmcid:PMC5034416", + "pubmed:27659774", { "@id": "https://doi.org/10.1186/s12859-016-1260-x" - }, - "pubmed:27659774", - "pmcid:PMC5034416" + } ], "sc:description": "MicroScope is a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data and includes integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network analysis.", "sc:featureList": { @@ -29,8 +29,8 @@ "sc:name": "MicroScope", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://microscopebioinformatics.org/" }, diff --git a/data/microscope_platform/microscope_platformbioschemas.jsonld b/data/microscope_platform/microscope_platformbioschemas.jsonld index dc3367e2f6a81..fb491709beab1 100644 --- a/data/microscope_platform/microscope_platformbioschemas.jsonld +++ b/data/microscope_platform/microscope_platformbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "LABGeM - CEA/Genosocope - UMR8030", "sc:additionalType": [ - "Bioinformatics portal", "Workbench", - "Web application" + "Web application", + "Bioinformatics portal" ], "sc:author": "LABGeM - CEA/Genosocope - UMR8030", "sc:description": "MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.", diff --git a/data/microsniper/microsniperbioschemas.jsonld b/data/microsniper/microsniperbioschemas.jsonld index e19bc2810c027..3f761114532aa 100644 --- a/data/microsniper/microsniperbioschemas.jsonld +++ b/data/microsniper/microsniperbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-based application which predicts the impact of a SNP on putative microRNA targets.", "sc:name": "MicroSNiPer", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://epicenter.ie-freiburg.mpg.de/services/microsniper/" } \ No newline at end of file diff --git a/data/microtaxi/microtaxibioschemas.jsonld b/data/microtaxi/microtaxibioschemas.jsonld index 41d2b129c1bb2..a6a05cb46174a 100644 --- a/data/microtaxi/microtaxibioschemas.jsonld +++ b/data/microtaxi/microtaxibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Uses an taxon-specific gene based approach and provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.", "sc:name": "Microtaxi", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://metagenomics.iiserb.ac.in/microtaxi/" } \ No newline at end of file diff --git a/data/midas/midasbioschemas.jsonld b/data/midas/midasbioschemas.jsonld index 19f3382d29252..59014995c7d7b 100644 --- a/data/midas/midasbioschemas.jsonld +++ b/data/midas/midasbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/midas", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Gelio Alves", - "Aleksey Ogurtsov" + "Aleksey Ogurtsov", + "Gelio Alves" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:24254576", diff --git a/data/mieaa/mieaabioschemas.jsonld b/data/mieaa/mieaabioschemas.jsonld index d91492b53851f..756f700386eb0 100644 --- a/data/mieaa/mieaabioschemas.jsonld +++ b/data/mieaa/mieaabioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKW345", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mieaa", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Backes C", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:27131362", - "pmcid:PMC4987907", { "@id": "https://doi.org/10.1093/NAR/GKW345" - } + }, + "pmcid:PMC4987907", + "pubmed:27131362" ], "sc:description": "MicroRNA enrichment analysis and annotation.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_0361" }, { - "@id": "edam:operation_0361" + "@id": "edam:operation_3501" } ], "sc:name": "miEAA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://ccb-compute2.cs.uni-saarland.de/mieaa_tool/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKW345", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/miframe/miframebioschemas.jsonld b/data/miframe/miframebioschemas.jsonld index e813597b40c89..4c7f71debe8c1 100644 --- a/data/miframe/miframebioschemas.jsonld +++ b/data/miframe/miframebioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12967-015-0594-X", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/miframe", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Keller A", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:26169944", "pmcid:PMC4501052", + "pubmed:26169944", { "@id": "https://doi.org/10.1186/S12967-015-0594-X" } @@ -28,19 +24,23 @@ "sc:description": "Analysis and visualization of miRNA sequencing data in neurological disorders.", "sc:featureList": [ { - "@id": "edam:operation_0564" + "@id": "edam:operation_3680" }, { - "@id": "edam:operation_3680" + "@id": "edam:operation_0564" } ], "sc:name": "miFRame", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://ccb-compute2.cs.uni-saarland.de/miframe/" + }, + { + "@id": "https://doi.org/10.1186/S12967-015-0594-X", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/migenas_toolkit/migenas_toolkitbioschemas.jsonld b/data/migenas_toolkit/migenas_toolkitbioschemas.jsonld index cfe9776397929..c662c41dc79fa 100644 --- a/data/migenas_toolkit/migenas_toolkitbioschemas.jsonld +++ b/data/migenas_toolkit/migenas_toolkitbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/migenas_toolkit", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Hermann Lederer", "Markus Rampp", - "MIGenAS support", - "Hermann Lederer" + "MIGenAS support" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:16844980", diff --git a/data/migraine/migrainebioschemas.jsonld b/data/migraine/migrainebioschemas.jsonld index 01d8105fbaba2..2aa54627fd600 100644 --- a/data/migraine/migrainebioschemas.jsonld +++ b/data/migraine/migrainebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Migraine", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://kimura.univ-montp2.fr/~rousset/Migraine.htm" } \ No newline at end of file diff --git a/data/miic/miicbioschemas.jsonld b/data/miic/miicbioschemas.jsonld index 556dbb836f83b..ffd0092470b89 100644 --- a/data/miic/miicbioschemas.jsonld +++ b/data/miic/miicbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Learn a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data.", "sc:name": "MIIC", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/miic/index.html" } \ No newline at end of file diff --git a/data/mim/mimbioschemas.jsonld b/data/mim/mimbioschemas.jsonld index 2fa78c6c552ea..42534cc087c61 100644 --- a/data/mim/mimbioschemas.jsonld +++ b/data/mim/mimbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Calculates a measure of sequence specificity called Motif Independent Metric.", "sc:name": "MIM", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bcb.dfci.harvard.edu/~gcyuan/software.html" diff --git a/data/mimager/mimagerbioschemas.jsonld b/data/mimager/mimagerbioschemas.jsonld index 8724c07742473..cb896f2f7ad83 100644 --- a/data/mimager/mimagerbioschemas.jsonld +++ b/data/mimager/mimagerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "mimager", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mimager.html", "sc:version": "1.4.0" diff --git a/data/mimeanto/mimeantobioschemas.jsonld b/data/mimeanto/mimeantobioschemas.jsonld index 0512032779e64..41bf2a0e6271b 100644 --- a/data/mimeanto/mimeantobioschemas.jsonld +++ b/data/mimeanto/mimeantobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Quantitative effects of each mutation at each position in the RNA can be recovered with statistical certainty using this herein developed user-friendly, cross-platform software.", "sc:name": "MIMEAnTo", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/maureensmith/MIMEAnTo" } \ No newline at end of file diff --git a/data/mimodb/mimodbbioschemas.jsonld b/data/mimodb/mimodbbioschemas.jsonld index 66a733bb6735f..428d8e2640f34 100644 --- a/data/mimodb/mimodbbioschemas.jsonld +++ b/data/mimodb/mimodbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A mimotope database. The MimoDB database also provides tools for simple and advanced searches, structure visualization, BLAST and alignment view on the fly.", "sc:name": "MimoDB", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://immunet.cn/mimodb/" } \ No newline at end of file diff --git a/data/mimosa/mimosabioschemas.jsonld b/data/mimosa/mimosabioschemas.jsonld index f49267f4b867d..d48f16427509e 100644 --- a/data/mimosa/mimosabioschemas.jsonld +++ b/data/mimosa/mimosabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-4341-9090", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/mimosa", "@type": "sc:SoftwareApplication", @@ -30,10 +34,10 @@ }, "sc:citation": [ "pmcid:PMC3862207", + "pubmed:23887981", { "@id": "https://doi.org/10.1093/biostatistics/kxt024" - }, - "pubmed:23887981" + } ], "sc:description": "Modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.", "sc:featureList": [ @@ -47,17 +51,13 @@ "sc:license": "Artistic-2.0", "sc:name": "MIMOSA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MIMOSA.html", "sc:version": "1.12.0" }, - { - "@id": "http://orcid.org/0000-0003-4341-9090", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1093/biostatistics/kxt024", "@type": "sc:CreativeWork" diff --git a/data/minactionpath/minactionpathbioschemas.jsonld b/data/minactionpath/minactionpathbioschemas.jsonld index 7e560cd8826c2..fbb4df27f93e5 100644 --- a/data/minactionpath/minactionpathbioschemas.jsonld +++ b/data/minactionpath/minactionpathbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "MinActionPath calculates the most-probable trajectory between two known structural states of a protein.", "sc:name": "MinActionPath", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://lorentz.immstr.pasteur.fr/joel/index.php" diff --git a/data/minas/minasbioschemas.jsonld b/data/minas/minasbioschemas.jsonld index 087226ca49920..5fd138727b385 100644 --- a/data/minas/minasbioschemas.jsonld +++ b/data/minas/minasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A database of metal ions in DNA and RNA. Complies info on innersphere, outsphere, and larger coordination environment of >70,000 metal ions of 36 elements fround in >2000 structures of nucleic acids.", "sc:name": "MINAS", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.minas.uzh.ch/" } \ No newline at end of file diff --git a/data/mindel/mindelbioschemas.jsonld b/data/mindel/mindelbioschemas.jsonld index fce79d7df820a..033be5a0163ab 100644 --- a/data/mindel/mindelbioschemas.jsonld +++ b/data/mindel/mindelbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12864-016-2614-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mindel", "@type": "sc:SoftwareApplication", @@ -22,24 +18,28 @@ }, "sc:additionalType": "Workflow", "sc:citation": [ - "pubmed:27079510", { "@id": "https://doi.org/10.1186/s12864-016-2614-5" }, + "pubmed:27079510", "pmcid:PMC4832496" ], "sc:description": "Next-generation variant caller specifically designed for InDel marker discovery. By taking in raw sequence reads and assembling them into contigs de novo, identifies InDel polymorphisms using a sliding window alignment from assembled contigs, rendering a unique advantage when a reference genome is unavailable.", "sc:featureList": [ { - "@id": "edam:operation_0452" + "@id": "edam:operation_3227" }, { - "@id": "edam:operation_3227" + "@id": "edam:operation_0452" } ], "sc:name": "mInDel", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/lyd0527/mInDel" + }, + { + "@id": "https://doi.org/10.1186/s12864-016-2614-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mindthegap/mindthegapbioschemas.jsonld b/data/mindthegap/mindthegapbioschemas.jsonld index 022197805debd..0a2598f10b140 100644 --- a/data/mindthegap/mindthegapbioschemas.jsonld +++ b/data/mindthegap/mindthegapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome.", "sc:name": "MindTheGap", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "GenOuest", "sc:url": "https://gatb.inria.fr/software/mind-the-gap/", diff --git a/data/mindy/mindybioschemas.jsonld b/data/mindy/mindybioschemas.jsonld index d040fd8e54068..12d8eb24c444d 100644 --- a/data/mindy/mindybioschemas.jsonld +++ b/data/mindy/mindybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A new information theoretic method to identify multivariate statistical dependencies between a transcription factor and one or more of its targets, conditional on the presence (or absence) of a candidate modulator gene.", "sc:name": "MINDY", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/MINDY2?" } \ No newline at end of file diff --git a/data/mineica/mineicabioschemas.jsonld b/data/mineica/mineicabioschemas.jsonld index 99334f65efb03..8f3168ccacb0c 100644 --- a/data/mineica/mineicabioschemas.jsonld +++ b/data/mineica/mineicabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "MineICA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MineICA.html", "sc:version": "1.14.0" diff --git a/data/minepath/minepathbioschemas.jsonld b/data/minepath/minepathbioschemas.jsonld index 1c0a25d1bc792..54132d139d17e 100644 --- a/data/minepath/minepathbioschemas.jsonld +++ b/data/minepath/minepathbioschemas.jsonld @@ -16,18 +16,18 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:27832067", - "pubmed:28431175", "pmcid:PMC5104320", { "@id": "https://doi.org/10.1371/journal.pcbi.1005187" - } + }, + "pubmed:28431175" ], "sc:description": "A pathway analysis tool.\nMinePath identifies of differentially expressed functional paths or sub-paths within a gene regulatory network (GRN) using gene expression data analysis. The analysis takes advantage of interactions among genes (e.g. activation/expression, inhibition) as nodes of a graph network, which are derived from expression data.", "sc:name": "MinePath", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.minepath.org/", "sc:version": "1.0" diff --git a/data/minerva/minervabioschemas.jsonld b/data/minerva/minervabioschemas.jsonld index 27a2be765daa2..9e77615208aba 100644 --- a/data/minerva/minervabioschemas.jsonld +++ b/data/minerva/minervabioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1101/gr.235499.118", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Minerva", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David C. Danko", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:30523036", + "pmcid:PMC6314158", { "@id": "https://doi.org/10.1101/gr.235499.118" - }, - "pubmed:30523036", - "pmcid:PMC6314158" + } ], "sc:description": "Alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics.", "sc:featureList": [ @@ -27,24 +31,20 @@ "@id": "edam:operation_3629" }, { - "@id": "edam:operation_3192" + "@id": "edam:operation_3200" }, { - "@id": "edam:operation_3200" + "@id": "edam:operation_3192" } ], "sc:license": "MIT", "sc:name": "Minerva", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/dcdanko/minerva_barcode_deconvolution" - }, - { - "@id": "https://doi.org/10.1101/gr.235499.118", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/minerva_platform/minerva_platformbioschemas.jsonld b/data/minerva_platform/minerva_platformbioschemas.jsonld index 5a96e21f9cf09..415b3f0a22da0 100644 --- a/data/minerva_platform/minerva_platformbioschemas.jsonld +++ b/data/minerva_platform/minerva_platformbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-1473-370X", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1038/npjsba.2016.20", "@type": "sc:CreativeWork" }, + { + "@id": "https://orcid.org/0000-0003-1473-370X", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/MINERVA_Platform", "@type": "sc:SoftwareApplication", @@ -27,37 +27,37 @@ "Piotr Gawron" ], "sc:additionalType": [ - "Web service", - "Web API" + "Web API", + "Web service" ], "sc:author": [ - "Piotr Gawron", - "David Hoksza" + "David Hoksza", + "Piotr Gawron" ], "sc:citation": [ { "@id": "https://doi.org/10.1038/npjsba.2016.20" }, + "pubmed:28725475", "pmcid:PMC5516855", - "pubmed:31074494", - "pubmed:28725475" + "pubmed:31074494" ], "sc:contributor": [ - "Rudi Balling", "Ewa Smula", - "Reinhard Schneider", { "@id": "https://orcid.org/0000-0003-1473-370X" }, - "Venkata Satagopam" + "Venkata Satagopam", + "Rudi Balling", + "Reinhard Schneider" ], "sc:description": "MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using CellDesigner or SBGN editors. Visualization of uploaded networks generated by the platform is accessible via a web browser to all viewers with the weblink to the resource.\n\nMINERVA is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java 8. The platform uses the Postgres SQL database for data storage and the Hibernate framework as a middle layer between web server and database. The user web-interface is generated using JSF and PrimeFaces. The displayed content is visualized by OpenLayers or Google Maps API, dedicated JavaScript and CSS.", "sc:license": "AGPL-3.0", "sc:name": "MINERVA Platform", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg", "sc:url": "https://minerva-web.lcsb.uni.lu", diff --git a/data/minet/minetbioschemas.jsonld b/data/minet/minetbioschemas.jsonld index 5d3cbcb46819c..c61119bbeace3 100644 --- a/data/minet/minetbioschemas.jsonld +++ b/data/minet/minetbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Patrick E. Meyer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package implements various algorithms for inferring mutual information networks from data.", "sc:name": "minet", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/minet.html", "sc:version": "3.32.0" diff --git a/data/minexpert/minexpertbioschemas.jsonld b/data/minexpert/minexpertbioschemas.jsonld index 6a8f49d7f3dc7..eafb09f67df41 100644 --- a/data/minexpert/minexpertbioschemas.jsonld +++ b/data/minexpert/minexpertbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/mineXpert", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Script", - "Desktop application" + "Desktop application", + "Script" ], "sc:description": "mineXpert is a graphical user interface software piece that allows the user to:\n- load mass spectrometry data files [ (x,y) text files or mzML standard format ] \n- visualize the TIC chromatogram and the intensity=(mz, dt) colormap in case of ion mobility mass spectrometry\n- integrate the mass data in many different ways and display them, effectively permitting the exploration of the mass data in their full depth\n- many other features", "sc:license": "GPL-3.0", "sc:name": "mineXpert", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://msxpertsuite.org" } \ No newline at end of file diff --git a/data/minfi/minfibioschemas.jsonld b/data/minfi/minfibioschemas.jsonld index 115497e55b8ae..a82213e5b16fd 100644 --- a/data/minfi/minfibioschemas.jsonld +++ b/data/minfi/minfibioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-0086-0687", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btw691", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/minfi", "@type": "sc:SoftwareApplication", @@ -24,34 +16,42 @@ "@id": "http://orcid.org/0000-0003-0086-0687" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pubmed:28035024", + "pmcid:PMC5408810", { "@id": "https://doi.org/10.1093/bioinformatics/btw691" - }, - "pmcid:PMC5408810" + } ], "sc:description": "Tools to analyze & visualize Illumina Infinium methylation arrays.", "sc:featureList": [ { - "@id": "edam:operation_2945" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_2945" } ], "sc:license": "Artistic-2.0", "sc:name": "minfi", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/minfi.html", "sc:version": "1.20.2" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btw691", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-0086-0687", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/minia/miniabioschemas.jsonld b/data/minia/miniabioschemas.jsonld index 1bef6966d2e59..6fa0ce943db17 100644 --- a/data/minia/miniabioschemas.jsonld +++ b/data/minia/miniabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/minia", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rayan Chikhi", - "Guillaume Rizk" + "Guillaume Rizk", + "Rayan Chikhi" ], "sc:additionalType": "Command-line tool", "sc:description": "Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.", diff --git a/data/minimumdistance/minimumdistancebioschemas.jsonld b/data/minimumdistance/minimumdistancebioschemas.jsonld index 94b19514b2492..94433e3c97fee 100644 --- a/data/minimumdistance/minimumdistancebioschemas.jsonld +++ b/data/minimumdistance/minimumdistancebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "MinimumDistance", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MinimumDistance.html", "sc:version": "1.18.0" diff --git a/data/minmotif_miner/minmotif_minerbioschemas.jsonld b/data/minmotif_miner/minmotif_minerbioschemas.jsonld index b3abc1ff681c2..ac0810467afb1 100644 --- a/data/minmotif_miner/minmotif_minerbioschemas.jsonld +++ b/data/minmotif_miner/minmotif_minerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Analyzes protein queries for the presence of short contiguous peptide motifs that have a known function in at least one other protein (Minimotifs), its functions include posttranslational modification of the minimotifs (PTM), binding to a target protein or molecule, and protein trafficking. MnM 3.0 uses a rich semantic model and trained algorithm to reduce false positive predictions.", "sc:name": "Minmotif Miner", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://minimotifminer.org" } \ No newline at end of file diff --git a/data/mint/mintbioschemas.jsonld b/data/mint/mintbioschemas.jsonld index ba6af78f706ec..d4c15713c4944 100644 --- a/data/mint/mintbioschemas.jsonld +++ b/data/mint/mintbioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkr930", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mint", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Daniele Peluso", "Luana Licata", - "Alberto Calderone" + "Alberto Calderone", + "Daniele Peluso" ], "edam:has_input": { "@id": "edam:data_2526" @@ -24,33 +28,33 @@ "@id": "edam:data_0906" }, "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:author": "Arnaud Ceol", "sc:citation": [ + "pmcid:PMC3244991", "pubmed:22096227", { "@id": "https://doi.org/10.1093/nar/gkr930" - }, - "pmcid:PMC3244991" + } ], "sc:contributor": [ - "Gianni Cesareni", + "Marta Iannuccelli", "Luana Licata", "Livia Perfetto", - "Marta Iannuccelli" + "Gianni Cesareni" ], "sc:description": "Molecular interaction Database (MINT) - public repository for protein-protein interactions (PPI) reported in peer-reviewed journals. The web interface allows the users to search, visualize and download interactions data", "sc:featureList": [ - { - "@id": "edam:operation_2497" - }, { "@id": "edam:operation_3431" }, { "@id": "edam:operation_2422" + }, + { + "@id": "edam:operation_2497" } ], "sc:name": "MINT", @@ -60,14 +64,10 @@ "Windows" ], "sc:provider": [ - "Dept. of Molecular Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome", - "ELIXIR-ITA-TORVERGATA" + "ELIXIR-ITA-TORVERGATA", + "Dept. of Molecular Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome" ], "sc:url": "https://mint.bio.uniroma2.it/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkr930", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mintmap/mintmapbioschemas.jsonld b/data/mintmap/mintmapbioschemas.jsonld index 009c52072e832..8dd0335a2b2f8 100644 --- a/data/mintmap/mintmapbioschemas.jsonld +++ b/data/mintmap/mintmapbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Isidore Rigoutsos", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:28220888", { "@id": "https://doi.org/10.1038/srep41184" }, - "pmcid:PMC5318995" + "pmcid:PMC5318995", + "pubmed:28220888" ], "sc:description": "Generate tRF profiles from short RNA-Seq datasets.", "sc:featureList": { diff --git a/data/miolite/miolitebioschemas.jsonld b/data/miolite/miolitebioschemas.jsonld index 106fc95902285..8e5da62a27205 100644 --- a/data/miolite/miolitebioschemas.jsonld +++ b/data/miolite/miolitebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems Biology Laboratory, Greece, appropriately filtered GOLM database peak information and Human Metabolome database information.", "sc:name": "MESBL GC-MS metabolite peak database", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://miolite2.iceht.forth.gr", diff --git a/data/mip_scaffolder/mip_scaffolderbioschemas.jsonld b/data/mip_scaffolder/mip_scaffolderbioschemas.jsonld index 5adb13e6139f5..cdaaf2bb84823 100644 --- a/data/mip_scaffolder/mip_scaffolderbioschemas.jsonld +++ b/data/mip_scaffolder/mip_scaffolderbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MIP Scaffolder", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/" } \ No newline at end of file diff --git a/data/mipav/mipavbioschemas.jsonld b/data/mipav/mipavbioschemas.jsonld index cb937a53bf3d2..e3c6cefc41560 100644 --- a/data/mipav/mipavbioschemas.jsonld +++ b/data/mipav/mipavbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/mipav", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Developers", + "Bugs", "Ideas for features", - "Bugs" + "Developers" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:17604116", diff --git a/data/mipgen/mipgenbioschemas.jsonld b/data/mipgen/mipgenbioschemas.jsonld index ef34d0892cc45..1893085b29615 100644 --- a/data/mipgen/mipgenbioschemas.jsonld +++ b/data/mipgen/mipgenbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mipgen", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jay Shendure", - "Evan Boyle" + "Evan Boyle", + "Jay Shendure" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:24867941", diff --git a/data/mipp/mippbioschemas.jsonld b/data/mipp/mippbioschemas.jsonld index 571a48ee0a73c..041153c708ff8 100644 --- a/data/mipp/mippbioschemas.jsonld +++ b/data/mipp/mippbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "MiPP", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MiPP.html", diff --git a/data/mir-at/mir-atbioschemas.jsonld b/data/mir-at/mir-atbioschemas.jsonld index 8e09d5053cb16..2f85f0dd0d06f 100644 --- a/data/mir-at/mir-atbioschemas.jsonld +++ b/data/mir-at/mir-atbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Computational tool for the identification of all transcripts that are targets of a list of input miRNAs.", "sc:name": "miR-AT", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://cptweb.cpt.wayne.edu/miR-AT/search.jsp" diff --git a/data/mir-prefer/mir-preferbioschemas.jsonld b/data/mir-prefer/mir-preferbioschemas.jsonld index ee726a44005ef..2ef364c256a3e 100644 --- a/data/mir-prefer/mir-preferbioschemas.jsonld +++ b/data/mir-prefer/mir-preferbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Uses expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.", "sc:name": "miR-PREFeR", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.cse.msu.edu/~leijikai/mir-prefer/" diff --git a/data/mir2gene/mir2genebioschemas.jsonld b/data/mir2gene/mir2genebioschemas.jsonld index ae1d341a383c5..6cafc865c7542 100644 --- a/data/mir2gene/mir2genebioschemas.jsonld +++ b/data/mir2gene/mir2genebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "miR2Gene", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cuilab.cn/mir2gene" } \ No newline at end of file diff --git a/data/mir2go/mir2gobioschemas.jsonld b/data/mir2go/mir2gobioschemas.jsonld index 4528f99714691..3c68a8c7ece77 100644 --- a/data/mir2go/mir2gobioschemas.jsonld +++ b/data/mir2go/mir2gobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO (Functional analysis of genetic and somatic mutations in microRNAs) and miRpair2GO (Comparative functional analysis for microRNA pairs).", "sc:name": "miR2GO", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://compbio.uthsc.edu/miR2GO/home.php" } \ No newline at end of file diff --git a/data/mira/mirabioschemas.jsonld b/data/mira/mirabioschemas.jsonld index 3da757083894a..f31b177f8c433 100644 --- a/data/mira/mirabioschemas.jsonld +++ b/data/mira/mirabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "MIRA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/p/mira-assembler/wiki/Home/" } \ No newline at end of file diff --git a/data/mirach/mirachbioschemas.jsonld b/data/mirach/mirachbioschemas.jsonld index e3058f70d8c6c..ddbe99488d955 100644 --- a/data/mirach/mirachbioschemas.jsonld +++ b/data/mirach/mirachbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A Statistical Online Model Checker for Biological Pathway Models, based on the PLTLs formalism for expressing the rules/properties to be checked. It can currently check pathways models written either in CSML or SBML.", "sc:name": "MIRACH", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://sourceforge.net/projects/mirach/" } \ No newline at end of file diff --git a/data/miracle/miraclebioschemas.jsonld b/data/miracle/miraclebioschemas.jsonld index 0eea03ac851ec..400bae928bf05 100644 --- a/data/miracle/miraclebioschemas.jsonld +++ b/data/miracle/miraclebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MIRACLE", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://nanocan.github.io/MIRACLE/" } \ No newline at end of file diff --git a/data/mirage/miragebioschemas.jsonld b/data/mirage/miragebioschemas.jsonld index 122f060ff9768..3a690070e3a36 100644 --- a/data/mirage/miragebioschemas.jsonld +++ b/data/mirage/miragebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-0867-8986", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/mirage", "@type": "sc:SoftwareApplication", @@ -20,15 +16,15 @@ "@id": "http://orcid.org/0000-0003-0867-8986" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC3257129", "pubmed:22272132", { "@id": "https://doi.org/10.3390/ijms12129265" - }, - "pmcid:PMC3257129" + } ], "sc:description": "The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.", "sc:featureList": { @@ -37,9 +33,9 @@ "sc:license": "GPL-3.0", "sc:name": "MiRaGE", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MiRaGE.html", "sc:version": "1.16.0" @@ -47,6 +43,10 @@ { "@id": "https://doi.org/10.3390/ijms12129265", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-0867-8986", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/miranalyzer/miranalyzerbioschemas.jsonld b/data/miranalyzer/miranalyzerbioschemas.jsonld index 81847fd425c87..ee39078417eae 100644 --- a/data/miranalyzer/miranalyzerbioschemas.jsonld +++ b/data/miranalyzer/miranalyzerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Web-server for identifying and analyzing miRNA in NGS sequencing experiments.", "sc:name": "MiRanalyzer", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php" } \ No newline at end of file diff --git a/data/mirbase/mirbasebioschemas.jsonld b/data/mirbase/mirbasebioschemas.jsonld index 36b2363585000..4c88b960f0268 100644 --- a/data/mirbase/mirbasebioschemas.jsonld +++ b/data/mirbase/mirbasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Repository for all microRNA sequences and annotation. It has mapped reads from short RNA deep-sequencing experiments to microRNAs and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression.", "sc:name": "miRBase", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.mirbase.org/" } \ No newline at end of file diff --git a/data/mirbaseconverter/mirbaseconverterbioschemas.jsonld b/data/mirbaseconverter/mirbaseconverterbioschemas.jsonld index 93af770906690..78e0dac4d9657 100644 --- a/data/mirbaseconverter/mirbaseconverterbioschemas.jsonld +++ b/data/mirbaseconverter/mirbaseconverterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "miRBaseConverter", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/miRBaseConverter.html", diff --git a/data/mircat/mircatbioschemas.jsonld b/data/mircat/mircatbioschemas.jsonld index 28add17425e2b..ddd32180a9527 100644 --- a/data/mircat/mircatbioschemas.jsonld +++ b/data/mircat/mircatbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predicts mature miRNAs and their precursors from an sRNA dataset and a genome.", "sc:name": "MiRCat", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://srna-workbench.cmp.uea.ac.uk" } \ No newline at end of file diff --git a/data/mircat2/mircat2bioschemas.jsonld b/data/mircat2/mircat2bioschemas.jsonld index 6e7eecb44cdef..fcd9bc6cb81d9 100644 --- a/data/mircat2/mircat2bioschemas.jsonld +++ b/data/mircat2/mircat2bioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "miRCat2", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://srna-workbench.cmp.uea.ac.uk/mircat-2/" } \ No newline at end of file diff --git a/data/mircomb/mircombbioschemas.jsonld b/data/mircomb/mircombbioschemas.jsonld index 773108a05af28..334b593abf7af 100644 --- a/data/mircomb/mircombbioschemas.jsonld +++ b/data/mircomb/mircombbioschemas.jsonld @@ -13,8 +13,8 @@ "@id": "https://bio.tools/mircomb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Juanjo Lozano", - "Maria Vila Casadesús" + "Maria Vila Casadesús", + "Juanjo Lozano" ], "sc:additionalType": "Library", "sc:citation": [ @@ -27,16 +27,16 @@ "sc:description": "Analyse miRNA-mRNA Interactions. Examples across Five Digestive Cancers.", "sc:featureList": [ { - "@id": "edam:operation_2478" + "@id": "edam:operation_2497" }, { - "@id": "edam:operation_2497" + "@id": "edam:operation_2478" } ], "sc:name": "MiRComb", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://mircomb.sourceforge.net/" diff --git a/data/mircomp-shiny/mircomp-shinybioschemas.jsonld b/data/mircomp-shiny/mircomp-shinybioschemas.jsonld index 385c206c0e226..88f3c0cef12e4 100644 --- a/data/mircomp-shiny/mircomp-shinybioschemas.jsonld +++ b/data/mircomp-shiny/mircomp-shinybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "miRcomp-Shiny", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://laurenkemperman.shinyapps.io/mircomp/", "sc:version": "1.10.0" diff --git a/data/mircomp/mircompbioschemas.jsonld b/data/mircomp/mircompbioschemas.jsonld index 819b64eca4ffb..fd153dc44a777 100644 --- a/data/mircomp/mircompbioschemas.jsonld +++ b/data/mircomp/mircompbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-016-0987-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mircomp", "@type": "sc:SoftwareApplication", @@ -29,16 +25,16 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0659" + "@id": "edam:topic_3572" }, { - "@id": "edam:topic_3572" + "@id": "edam:topic_3518" }, { "@id": "edam:topic_3519" }, { - "@id": "edam:topic_3518" + "@id": "edam:topic_0659" } ], "sc:citation": [ @@ -61,6 +57,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/miRcomp.html", "sc:version": "1.4.0" + }, + { + "@id": "https://doi.org/10.1186/s12859-016-0987-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mircompare/mircomparebioschemas.jsonld b/data/mircompare/mircomparebioschemas.jsonld index b73bfa4a50508..9f2a84d01d8d1 100644 --- a/data/mircompare/mircomparebioschemas.jsonld +++ b/data/mircompare/mircomparebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mircompare", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Stefano Pirro", - "Antonella Minutolo" + "Antonella Minutolo", + "Stefano Pirro" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:27428722", @@ -20,8 +20,8 @@ "sc:name": "MirCompare", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://160.80.35.140/MirCompare/" } \ No newline at end of file diff --git a/data/mirdentify/mirdentifybioschemas.jsonld b/data/mirdentify/mirdentifybioschemas.jsonld index 8d65b9bb2d717..fd5d4798332d6 100644 --- a/data/mirdentify/mirdentifybioschemas.jsonld +++ b/data/mirdentify/mirdentifybioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKU598", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mirdentify", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:25053842", { "@id": "https://doi.org/10.1093/NAR/GKU598" }, - "pmcid:PMC4176371", - "pubmed:25053842" + "pmcid:PMC4176371" ], "sc:description": "High stringency miRNA predictor identifies several novel animal miRNAs.", "sc:featureList": { @@ -28,14 +32,10 @@ "sc:name": "miRdentify", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ncrnalab.dk/#mirdentify/mirdentify.php" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKU598", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mirdrn/mirdrnbioschemas.jsonld b/data/mirdrn/mirdrnbioschemas.jsonld index 82c520123cc9e..f1bc0d7baf6ba 100644 --- a/data/mirdrn/mirdrnbioschemas.jsonld +++ b/data/mirdrn/mirdrnbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "miRDRN", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://mirdrn.ncu.edu.tw/mirdrn/" } \ No newline at end of file diff --git a/data/mirgen/mirgenbioschemas.jsonld b/data/mirgen/mirgenbioschemas.jsonld index d80fc61e20697..69a895ce3e39b 100644 --- a/data/mirgen/mirgenbioschemas.jsonld +++ b/data/mirgen/mirgenbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MirGeneDB", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "UiO", "sc:url": "http://mirgenedb.org/" diff --git a/data/miriam/miriambioschemas.jsonld b/data/miriam/miriambioschemas.jsonld index 975dd5394a036..0fdcdfdcdba59 100644 --- a/data/miriam/miriambioschemas.jsonld +++ b/data/miriam/miriambioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MIRIAM Resources", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ebi.ac.uk/miriam/", "sc:version": "1" diff --git a/data/miriam_ws/miriam_wsbioschemas.jsonld b/data/miriam_ws/miriam_wsbioschemas.jsonld index c491ef62f2b4d..e94c9251b3407 100644 --- a/data/miriam_ws/miriam_wsbioschemas.jsonld +++ b/data/miriam_ws/miriam_wsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Web Services which provide generation and resolving facilities for MIRIAM Annotations.", "sc:name": "MIRIAM WS", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/miriam/main/mdb?section=ws_help", "sc:version": "1" diff --git a/data/mirin/mirinbioschemas.jsonld b/data/mirin/mirinbioschemas.jsonld index 34692a8477943..36e00bc40b037 100644 --- a/data/mirin/mirinbioschemas.jsonld +++ b/data/mirin/mirinbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Mirin", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mirin.ym.edu.tw/tool.php" } \ No newline at end of file diff --git a/data/mirintegrator/mirintegratorbioschemas.jsonld b/data/mirintegrator/mirintegratorbioschemas.jsonld index a8449dda41e82..b910fbdc9c284 100644 --- a/data/mirintegrator/mirintegratorbioschemas.jsonld +++ b/data/mirintegrator/mirintegratorbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Diana Diaz", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.", "sc:license": "GPL-3.0", "sc:name": "mirIntegrator", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mirIntegrator.html", "sc:version": "1.4.0" diff --git a/data/mirlab/mirlabbioschemas.jsonld b/data/mirlab/mirlabbioschemas.jsonld index 3bf0c98807d5e..15f2131325f08 100644 --- a/data/mirlab/mirlabbioschemas.jsonld +++ b/data/mirlab/mirlabbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-9732-4313", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0145386", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mirlab", "@type": "sc:SoftwareApplication", @@ -24,16 +16,16 @@ "@id": "http://orcid.org/0000-0002-9732-4313" }, "sc:additionalType": [ - "Command-line tool", + "Library", "Plug-in", - "Library" + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4696828", + "pubmed:26716983", { "@id": "https://doi.org/10.1371/journal.pone.0145386" }, - "pubmed:26716983" + "pmcid:PMC4696828" ], "sc:description": "Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.", "sc:featureList": { @@ -42,12 +34,20 @@ "sc:license": "GPL-2.0", "sc:name": "miRLAB", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/miRLAB.html", "sc:version": "1.8.0" + }, + { + "@id": "http://orcid.org/0000-0002-9732-4313", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0145386", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mirlastic/mirlasticbioschemas.jsonld b/data/mirlastic/mirlasticbioschemas.jsonld index e3bdd17eba1bf..5d04cc94e6b28 100644 --- a/data/mirlastic/mirlasticbioschemas.jsonld +++ b/data/mirlastic/mirlasticbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Novel method  which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network.", "sc:name": "miRlastic", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.helmholtz-muenchen.de/icb/research/groups/computational-cell-maps/projects/mirlastic/index.html" } \ No newline at end of file diff --git a/data/mirmaid/mirmaidbioschemas.jsonld b/data/mirmaid/mirmaidbioschemas.jsonld index 6ac8a7dcadcea..fd2a0578b0176 100644 --- a/data/mirmaid/mirmaidbioschemas.jsonld +++ b/data/mirmaid/mirmaidbioschemas.jsonld @@ -11,14 +11,14 @@ "@id": "https://bio.tools/mirmaid", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Morten Lindow", - "Anders Jacobsen" + "Anders Jacobsen", + "Morten Lindow" ], "sc:additionalType": [ - "Web application", + "Library", "Database portal", "Web API", - "Library", + "Web application", "Command-line tool" ], "sc:description": "Intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.", diff --git a/data/mirmat/mirmatbioschemas.jsonld b/data/mirmat/mirmatbioschemas.jsonld index 25b1128ac8405..04033b14cf1db 100644 --- a/data/mirmat/mirmatbioschemas.jsonld +++ b/data/mirmat/mirmatbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/mirmat", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Prof. J.Wang (Other)", - "Chenfeng He (suggestions on online tool)" + "Chenfeng He (suggestions on online tool)", + "Prof. J.Wang (Other)" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:23300555", "sc:description": "MiRmat is a software designed to predict mature microRNA from pri-microRNA. This tool can be divided into two parts, one is for predicting Drosha processing site, which is based on energy distribution pattern along primary microRNA’s secondary structure; the other is for predicting Dicer processing site, which is based on precursor microRNA’s structure feature", "sc:name": "MiRmat", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mcube.nju.edu.cn/jwang/lab/soft/MiRmat/index.html" } \ No newline at end of file diff --git a/data/mirmine/mirminebioschemas.jsonld b/data/mirmine/mirminebioschemas.jsonld index d23c9dff99f89..cd1f68760ce07 100644 --- a/data/mirmine/mirminebioschemas.jsonld +++ b/data/mirmine/mirminebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "miRmine", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/miRmine.html", diff --git a/data/mirmmr/mirmmrbioschemas.jsonld b/data/mirmmr/mirmmrbioschemas.jsonld index 0a942aa12e7f6..dacfbfa6c7b27 100644 --- a/data/mirmmr/mirmmrbioschemas.jsonld +++ b/data/mirmmr/mirmmrbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/mirmmr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Li Ding", - "Steven M Foltz" + "Steven M Foltz", + "Li Ding" ], "sc:additionalType": "Command-line tool", "sc:description": "Binary classification of microsatellite instability using methylation and mutations.", "sc:name": "MIRMMR", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/ding-lab/MIRMMR" } \ No newline at end of file diff --git a/data/mirmod/mirmodbioschemas.jsonld b/data/mirmod/mirmodbioschemas.jsonld index b3f5b0861214b..83b4cbe2e004b 100644 --- a/data/mirmod/mirmodbioschemas.jsonld +++ b/data/mirmod/mirmodbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.7717/peerj.1332", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mirmod", "@type": "sc:SoftwareApplication", @@ -33,10 +37,6 @@ "sc:operatingSystem": "Windows", "sc:url": "http://bioinfo.icgeb.res.in/miRMOD/", "sc:version": "0.4" - }, - { - "@id": "https://doi.org/10.7717/peerj.1332", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mirna-dis/mirna-disbioschemas.jsonld b/data/mirna-dis/mirna-disbioschemas.jsonld index 140fb11a3bc6c..aecdf03151e1b 100644 --- a/data/mirna-dis/mirna-disbioschemas.jsonld +++ b/data/mirna-dis/mirna-disbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "MicroRNA precursor identification \nbased on distance structure status pairs.", "sc:name": "miRNA-dis", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinformatics.hitsz.edu.cn/miRNA-dis/" } \ No newline at end of file diff --git a/data/mirnafold/mirnafoldbioschemas.jsonld b/data/mirnafold/mirnafoldbioschemas.jsonld index 96456fdf82ec1..dd784da8119a4 100644 --- a/data/mirnafold/mirnafoldbioschemas.jsonld +++ b/data/mirnafold/mirnafoldbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Fast ab-initio algorithm for searching for pre-miRNA precursors in genomes.", "sc:name": "miRNAFold", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://evryrna.ibisc.univ-evry.fr/miRNAFold/" } \ No newline at end of file diff --git a/data/mirnakey/mirnakeybioschemas.jsonld b/data/mirnakey/mirnakeybioschemas.jsonld index 51361242616f2..cde5ebce74cd9 100644 --- a/data/mirnakey/mirnakeybioschemas.jsonld +++ b/data/mirnakey/mirnakeybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A software pipeline for the analysis of microRNA Deep Sequencing data", "sc:name": "MiRNAkey", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ibis.tau.ac.il/miRNAkey" } \ No newline at end of file diff --git a/data/mirnalasso/mirnalassobioschemas.jsonld b/data/mirnalasso/mirnalassobioschemas.jsonld index 5e5ecf62c0b8c..d20f29888e40c 100644 --- a/data/mirnalasso/mirnalassobioschemas.jsonld +++ b/data/mirnalasso/mirnalassobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Adaptive Lasso based method that integrates full spectrum of sequence features for microRNA target prediction.", "sc:name": "miRNALasso", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://nba.uth.tmc.edu/homepage/liu/miRNALasso/" } \ No newline at end of file diff --git a/data/mirnameconverter/mirnameconverterbioschemas.jsonld b/data/mirnameconverter/mirnameconverterbioschemas.jsonld index 4d8666d2af451..18790d4a0f670 100644 --- a/data/mirnameconverter/mirnameconverterbioschemas.jsonld +++ b/data/mirnameconverter/mirnameconverterbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "miRNAmeConverter", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/miRNAmeConverter.html", "sc:version": "1.2.0" diff --git a/data/mirnamotif/mirnamotifbioschemas.jsonld b/data/mirnamotif/mirnamotifbioschemas.jsonld index c3caba5b6cfd9..5852bfe3629a2 100644 --- a/data/mirnamotif/mirnamotifbioschemas.jsonld +++ b/data/mirnamotif/mirnamotifbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3390/ijms19124075", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/miRNAmotif", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:30562930", "pmcid:PMC6321451", { "@id": "https://doi.org/10.3390/ijms19124075" - } + }, + "pubmed:30562930" ], "sc:description": "Tool for the Prediction of Pre-miRNA⁻Protein Interactions.", "sc:featureList": [ @@ -39,11 +35,15 @@ "sc:license": "MIT", "sc:name": "miRNAmotif", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://mirnamotif.ibch.poznan.pl" + }, + { + "@id": "https://doi.org/10.3390/ijms19124075", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mirnapath/mirnapathbioschemas.jsonld b/data/mirnapath/mirnapathbioschemas.jsonld index a353bed9fffc2..343e529ab0ed8 100644 --- a/data/mirnapath/mirnapathbioschemas.jsonld +++ b/data/mirnapath/mirnapathbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3389/fncel.2015.00053", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mirnapath", "@type": "sc:SoftwareApplication", @@ -30,10 +26,10 @@ "@id": "edam:data_1772" }, { - "@id": "edam:data_1669" + "@id": "edam:data_1636" }, { - "@id": "edam:data_1636" + "@id": "edam:data_1669" } ], "sc:additionalType": [ @@ -52,8 +48,8 @@ { "@id": "https://doi.org/10.3389/fncel.2015.00053" }, - "pmcid:PMC4333818", - "pubmed:25745387" + "pubmed:25745387", + "pmcid:PMC4333818" ], "sc:description": "This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.", "sc:featureList": { @@ -62,12 +58,16 @@ "sc:license": "GPL-2.0", "sc:name": "miRNApath", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/miRNApath.html", "sc:version": "1.34.0" + }, + { + "@id": "https://doi.org/10.3389/fncel.2015.00053", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mirnatap/bioconda_mirnatap.yaml b/data/mirnatap/bioconda_mirnatap.yaml index 3f1d8860bf233..377b437ab7505 100644 --- a/data/mirnatap/bioconda_mirnatap.yaml +++ b/data/mirnatap/bioconda_mirnatap.yaml @@ -7,7 +7,6 @@ description: The package facilitates implementation of workflows requiring miRNA home: https://bioconductor.org/packages/3.10/bioc/html/miRNAtap.html identifiers: - biotools:mirnatap -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-mirnatap diff --git a/data/mirnatap/mirnatapbioschemas.jsonld b/data/mirnatap/mirnatapbioschemas.jsonld index 64578edcc844d..46075bd3cb871 100644 --- a/data/mirnatap/mirnatapbioschemas.jsonld +++ b/data/mirnatap/mirnatapbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Maciej Pajak", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation).", "sc:license": "GPL-2.0", "sc:name": "miRNAtap", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/miRNAtap.html", "sc:version": "1.8.0" diff --git a/data/mirnatip/mirnatipbioschemas.jsonld b/data/mirnatip/mirnatipbioschemas.jsonld index 43058948d981c..b7e106863fdfb 100644 --- a/data/mirnatip/mirnatipbioschemas.jsonld +++ b/data/mirnatip/mirnatipbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Antonino Fiannaca", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:28185545", - "pmcid:PMC5046196", { "@id": "https://doi.org/10.1186/S12859-016-1171-X" - } + }, + "pubmed:28185545", + "pmcid:PMC5046196" ], "sc:description": "A SOM-based miRNA-target interactions predictor.", "sc:featureList": { diff --git a/data/mirnest/mirnestbioschemas.jsonld b/data/mirnest/mirnestbioschemas.jsonld index 44226f39b9101..31a6ed43f01bd 100644 --- a/data/mirnest/mirnestbioschemas.jsonld +++ b/data/mirnest/mirnestbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "miRNEST", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://rhesus.amu.edu.pl/mirnest/copy/" } \ No newline at end of file diff --git a/data/mirnet/mirnetbioschemas.jsonld b/data/mirnet/mirnetbioschemas.jsonld index 4159d58ca6ffd..396d2f522279a 100644 --- a/data/mirnet/mirnetbioschemas.jsonld +++ b/data/mirnet/mirnetbioschemas.jsonld @@ -9,41 +9,41 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKW288", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mirnet", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jeff Xia", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC4987881", { "@id": "https://doi.org/10.1093/NAR/GKW288" }, - "pmcid:PMC4987881", "pubmed:27105848" ], "sc:description": "Tool with comprehensive support for statistical analysis and functional interpretation of data generated in miRNAs studies.", "sc:featureList": [ - { - "@id": "edam:operation_3792" - }, { "@id": "edam:operation_0463" }, { "@id": "edam:operation_2497" + }, + { + "@id": "edam:operation_3792" } ], "sc:name": "miRNet", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.mirnet.ca/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKW288", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mirortho/mirorthobioschemas.jsonld b/data/mirortho/mirorthobioschemas.jsonld index 6210aca13cbb4..54a4a538c46f8 100644 --- a/data/mirortho/mirorthobioschemas.jsonld +++ b/data/mirortho/mirorthobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "miROrtho contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline.", "sc:name": "miROrtho", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://cegg.unige.ch/mirortho" diff --git a/data/mirpipe/mirpipebioschemas.jsonld b/data/mirpipe/mirpipebioschemas.jsonld index c3dca3ca7a21d..b13d613317f77 100644 --- a/data/mirpipe/mirpipebioschemas.jsonld +++ b/data/mirpipe/mirpipebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MIRPIPE", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://bioinformatics.mpi-bn.mpg.de/" } \ No newline at end of file diff --git a/data/mirplant/mirplantbioschemas.jsonld b/data/mirplant/mirplantbioschemas.jsonld index fed8436d351dc..1c15109bf6045 100644 --- a/data/mirplant/mirplantbioschemas.jsonld +++ b/data/mirplant/mirplantbioschemas.jsonld @@ -27,9 +27,9 @@ }, "sc:name": "miRPlant", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.australianprostatecentre.org/research/software/mirplant", "sc:version": "v4" diff --git a/data/mirplex/mirplexbioschemas.jsonld b/data/mirplex/mirplexbioschemas.jsonld index 35660778cf431..638c6d32b59c5 100644 --- a/data/mirplex/mirplexbioschemas.jsonld +++ b/data/mirplex/mirplexbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/mirplex", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Simon Moxon,", - "Dr. Daniel Mapleson" + "Dr. Daniel Mapleson", + "Dr. Simon Moxon," ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:23184675", "sc:description": "Tool for microRNA prediction from high-throughput sequencing data that requires only small RNA datasets as input.", "sc:name": "MiRPlex", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.uea.ac.uk/computing/mirplex" } \ No newline at end of file diff --git a/data/mirpub/mirpubbioschemas.jsonld b/data/mirpub/mirpubbioschemas.jsonld index d9792f2d8e202..f52a66cfe3013 100644 --- a/data/mirpub/mirpubbioschemas.jsonld +++ b/data/mirpub/mirpubbioschemas.jsonld @@ -17,15 +17,15 @@ "@id": "https://bio.tools/mirpub", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ - "pmcid:PMC4410649", - "pubmed:25527833", { "@id": "https://doi.org/10.1093/bioinformatics/btu819" - } + }, + "pmcid:PMC4410649", + "pubmed:25527833" ], "sc:description": "Database and a related web application which provides a powerful and intuitive interface to the researchers that want to search for publications related to particular microRNA molecules. It also provides useful information about the correlation of these microRNAs to any diseases, tissues and genes. It facilitates publication search by considering microRNA families and the history of the microRNA nomenclature.", "sc:featureList": { @@ -33,8 +33,8 @@ }, "sc:name": "mirPub", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mirpub/index" diff --git a/data/mirpursuit/mirpursuitbioschemas.jsonld b/data/mirpursuit/mirpursuitbioschemas.jsonld index 7762142e058a7..d1acefb41bda0 100644 --- a/data/mirpursuit/mirpursuitbioschemas.jsonld +++ b/data/mirpursuit/mirpursuitbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-3794-4262", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/mirpursuit", "@type": "sc:SoftwareApplication", @@ -25,10 +29,6 @@ ], "sc:url": "https://github.com/forestbiotech-lab/miRPursuit", "sc:version": "v1.0" - }, - { - "@id": "http://orcid.org/0000-0002-3794-4262", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mirscan/mirscanbioschemas.jsonld b/data/mirscan/mirscanbioschemas.jsonld index bf3b47082bf34..245286829e825 100644 --- a/data/mirscan/mirscanbioschemas.jsonld +++ b/data/mirscan/mirscanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computational procedure to identify miRNA genes conserved in more than one genome.", "sc:name": "MiRScan", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bartellab.wi.mit.edu/softwareDocs/MiRscan3/Introduction.html" } \ No newline at end of file diff --git a/data/mirsponge/mirspongebioschemas.jsonld b/data/mirsponge/mirspongebioschemas.jsonld index 4996b0c2f2ea3..c447f17d448a4 100644 --- a/data/mirsponge/mirspongebioschemas.jsonld +++ b/data/mirsponge/mirspongebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "miRsponge", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/miRsponge.html", "sc:version": "1.6.0" diff --git a/data/mirsponger/mirspongerbioschemas.jsonld b/data/mirsponger/mirspongerbioschemas.jsonld index df48d46104537..c163695c80e0a 100644 --- a/data/mirsponger/mirspongerbioschemas.jsonld +++ b/data/mirsponger/mirspongerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "miRspongeR", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/miRspongeR.html", "sc:version": "1.10.1" diff --git a/data/mirsynergy/mirsynergybioschemas.jsonld b/data/mirsynergy/mirsynergybioschemas.jsonld index 53feb67993eac..5e8a7b6af2d17 100644 --- a/data/mirsynergy/mirsynergybioschemas.jsonld +++ b/data/mirsynergy/mirsynergybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yue Li", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:24894504", "sc:description": "Detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion.", "sc:license": "GPL-2.0", "sc:name": "Mirsynergy", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Mirsynergy.html", diff --git a/data/mirsystem/mirsystembioschemas.jsonld b/data/mirsystem/mirsystembioschemas.jsonld index 1fb008c452885..02ba52dcb3843 100644 --- a/data/mirsystem/mirsystembioschemas.jsonld +++ b/data/mirsystem/mirsystembioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. miRSystem integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan.", "sc:name": "miRSystem", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://mirsystem.cgm.ntu.edu.tw/", "sc:version": "20150312" diff --git a/data/mirtar2go/mirtar2gobioschemas.jsonld b/data/mirtar2go/mirtar2gobioschemas.jsonld index 2a7bcfa9fbb36..6a88d95d306d2 100644 --- a/data/mirtar2go/mirtar2gobioschemas.jsonld +++ b/data/mirtar2go/mirtar2gobioschemas.jsonld @@ -9,21 +9,25 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKW1185", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mirtar2go", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Support", - "Gyorgy Hutvagner", - "Gaurav Sablok" + "Gaurav Sablok", + "Gyorgy Hutvagner" ], "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5389546", "pubmed:27903911", { "@id": "https://doi.org/10.1093/NAR/GKW1185" - } + }, + "pmcid:PMC5389546" ], "sc:description": "Novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA–target interaction data.", "sc:featureList": { @@ -31,15 +35,11 @@ }, "sc:name": "miRTar2GO", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://academic.oup.com/nar/article/45/6/e42/2605966" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKW1185", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mirtarvis/mirtarvisbioschemas.jsonld b/data/mirtarvis/mirtarvisbioschemas.jsonld index 554684a4b5b4c..00dc5fabb2412 100644 --- a/data/mirtarvis/mirtarvisbioschemas.jsonld +++ b/data/mirtarvis/mirtarvisbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Visual analysis tool for miRNA-mRNA expression profile data.", "sc:name": "mirTarVis", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://hcil.snu.ac.kr/~rati/miRTarVis/index.html" diff --git a/data/mirtex/mirtexbioschemas.jsonld b/data/mirtex/mirtexbioschemas.jsonld index 0378743ddec50..361498a01e761 100644 --- a/data/mirtex/mirtexbioschemas.jsonld +++ b/data/mirtex/mirtexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature.", "sc:name": "miRTex", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://research.bioinformatics.udel.edu/miRTex/" diff --git a/data/mirtif/mirtifbioschemas.jsonld b/data/mirtif/mirtifbioschemas.jsonld index 8dc71f7f298dc..9741e627d1b5d 100644 --- a/data/mirtif/mirtifbioschemas.jsonld +++ b/data/mirtif/mirtifbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MiRTif", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://mirtif.bii.a-star.edu.sg/" } \ No newline at end of file diff --git a/data/mirtime/mirtimebioschemas.jsonld b/data/mirtime/mirtimebioschemas.jsonld index 861515ba0cc15..d2309d1b3dcb6 100644 --- a/data/mirtime/mirtimebioschemas.jsonld +++ b/data/mirtime/mirtimebioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "mirTime", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/mirTime/mirtime" } \ No newline at end of file diff --git a/data/mirtissue/mirtissuebioschemas.jsonld b/data/mirtissue/mirtissuebioschemas.jsonld index 6ff778f58106a..897e090ebcbef 100644 --- a/data/mirtissue/mirtissuebioschemas.jsonld +++ b/data/mirtissue/mirtissuebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2418-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/miRTissue", "@type": "sc:SoftwareApplication", @@ -23,10 +19,10 @@ ], "sc:citation": [ "pubmed:30497361", + "pmcid:PMC6266954", { "@id": "https://doi.org/10.1186/s12859-018-2418-5" - }, - "pmcid:PMC6266954" + } ], "sc:description": "Web application for the analysis of miRNA-target interactions in human tissues.", "sc:featureList": [ @@ -34,20 +30,24 @@ "@id": "edam:operation_3792" }, { - "@id": "edam:operation_0463" + "@id": "edam:operation_2497" }, { - "@id": "edam:operation_2497" + "@id": "edam:operation_0463" } ], "sc:license": "Unlicense", "sc:name": "miRTissue", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://150.145.111.118:3838/mirTissue/" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2418-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mirtools/mirtoolsbioschemas.jsonld b/data/mirtools/mirtoolsbioschemas.jsonld index c57465e6be51c..7258e95582909 100644 --- a/data/mirtools/mirtoolsbioschemas.jsonld +++ b/data/mirtools/mirtoolsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Web server for microRNA data analysis, profiling and discovery based on high-throughput sequencing.", "sc:name": "MirTools", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://centre.bioinformatics.zj.cn/mirtools/" } \ No newline at end of file diff --git a/data/mirtrace/mirtracebioschemas.jsonld b/data/mirtrace/mirtracebioschemas.jsonld index c09b6224de874..8e6f0fd29f03a 100644 --- a/data/mirtrace/mirtracebioschemas.jsonld +++ b/data/mirtrace/mirtracebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "miRTrace", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/friedlanderlab/mirtrace" } \ No newline at end of file diff --git a/data/mirtrail/mirtrailbioschemas.jsonld b/data/mirtrail/mirtrailbioschemas.jsonld index b29cbd9883356..b55880d269512 100644 --- a/data/mirtrail/mirtrailbioschemas.jsonld +++ b/data/mirtrail/mirtrailbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web-based application to analyse the interactions between miRNAs and predicated target genes via their transcripts (mRNAs).", "sc:name": "miRTrail", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://mirtrail.bioinf.uni-sb.de/" diff --git a/data/mirtrios/mirtriosbioschemas.jsonld b/data/mirtrios/mirtriosbioschemas.jsonld index 176bccd5288bb..3f148601c4bbf 100644 --- a/data/mirtrios/mirtriosbioschemas.jsonld +++ b/data/mirtrios/mirtriosbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/mirtrios", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Qing Xie", "Yi Jiang", "Jinchen Li", + "Huiqian Chen", "Tao Wang", - "Huiqian Chen" + "Qing Xie" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:25596308", "sc:description": "Web server to accurately detect de novo mutations (DNMs) based on Expectation-maximization (EM) model. mirTrios also surports identification of rare inherited mutations, known diagnostic variants, as well as the prioritisation of novel and promising candidate genes.", "sc:name": "MirTrios", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://centre.bioinformatics.zj.cn/mirTrios/" } \ No newline at end of file diff --git a/data/miru-profiler/miru-profilerbioschemas.jsonld b/data/miru-profiler/miru-profilerbioschemas.jsonld index 93d1d2f2332f7..dedef3c9dd0ad 100644 --- a/data/miru-profiler/miru-profilerbioschemas.jsonld +++ b/data/miru-profiler/miru-profilerbioschemas.jsonld @@ -13,16 +13,16 @@ "@id": "https://bio.tools/miru-profiler", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rahim Rajwani", - "Gilman Kit Hang Siu" + "Gilman Kit Hang Siu", + "Rahim Rajwani" ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6045920", { "@id": "https://doi.org/10.7717/peerj.5090" }, - "pubmed:30018852", - "pmcid:PMC6045920" + "pubmed:30018852" ], "sc:description": "Performs digital 24-loci MIRU-VNTR typing for Mycobacterium tuberculosis.", "sc:featureList": { @@ -31,8 +31,8 @@ "sc:license": "GPL-3.0", "sc:name": "MIRU-profiler", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/rahimrajwani/MIRU-profiler" diff --git a/data/miru-vntrplus/miru-vntrplusbioschemas.jsonld b/data/miru-vntrplus/miru-vntrplusbioschemas.jsonld index fffca6de79b48..e9629f0908cb2 100644 --- a/data/miru-vntrplus/miru-vntrplusbioschemas.jsonld +++ b/data/miru-vntrplus/miru-vntrplusbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MIRU-VNTRplus", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.miru-vntrplus.org" } \ No newline at end of file diff --git a/data/miru/mirubioschemas.jsonld b/data/miru/mirubioschemas.jsonld index a1f4055cec0c1..dfe22a6bf0c07 100644 --- a/data/miru/mirubioschemas.jsonld +++ b/data/miru/mirubioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "miRU", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinfo.noble.org/gateway/index.php?option=com_content&task=view&id=53&Itemid=44" } \ No newline at end of file diff --git a/data/mirumir/mirumirbioschemas.jsonld b/data/mirumir/mirumirbioschemas.jsonld index 965874baadf4f..843f92a260272 100644 --- a/data/mirumir/mirumirbioschemas.jsonld +++ b/data/mirumir/mirumirbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MIRUMIR", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.chemoprofiling.org/cgi-bin/GEO/MIRUMIR/web_run_MIRUMIR.V1.pl" } \ No newline at end of file diff --git a/data/mirvestigator/mirvestigatorbioschemas.jsonld b/data/mirvestigator/mirvestigatorbioschemas.jsonld index ba88e1ac1c770..d56899709e22e 100644 --- a/data/mirvestigator/mirvestigatorbioschemas.jsonld +++ b/data/mirvestigator/mirvestigatorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "miRvestigator is a web based tool to identify miRNAs mediating co-regulation of gene expression patterns observed in transcriptome profilng data. The miRvestigator takes as input a list of co-expressed genes and returns the most likely miRNA regulating the genes. It searches for an over-represented sequence motif in the 3' UTRs of the genes using Weeder and compares the motif to all unique miRNA seed sequences in miRBase using our custom built miRvestigator hidden Markov model (HMM).", "sc:name": "miRvestigator", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://mirvestigator.systemsbiology.net" diff --git a/data/mirvial/mirvialbioschemas.jsonld b/data/mirvial/mirvialbioschemas.jsonld index d6b4db5433f48..a4f07252737c4 100644 --- a/data/mirvial/mirvialbioschemas.jsonld +++ b/data/mirvial/mirvialbioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.1093/nar/gkx834" }, - "pubmed:29036674", - "pmcid:PMC5716067" + "pmcid:PMC5716067", + "pubmed:29036674" ], "sc:description": "Robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs.", "sc:featureList": { diff --git a/data/misis/misisbioschemas.jsonld b/data/misis/misisbioschemas.jsonld index dc86e12c02546..31554e58d154d 100644 --- a/data/misis/misisbioschemas.jsonld +++ b/data/misis/misisbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool to view and analyze sRNA maps of genomic loci and viruses which spawn multiple sRNAs.", "sc:name": "MISIS", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.fasteris.com/apps/" diff --git a/data/miso_r/miso_rbioschemas.jsonld b/data/miso_r/miso_rbioschemas.jsonld index 0e5b5fc98c675..984b8be8d9f14 100644 --- a/data/miso_r/miso_rbioschemas.jsonld +++ b/data/miso_r/miso_rbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Miso", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://cran.r-project.org/package=Miso", diff --git a/data/missequel/missequelbioschemas.jsonld b/data/missequel/missequelbioschemas.jsonld index a4445acc18f0e..3efa1f00a6a97 100644 --- a/data/missequel/missequelbioschemas.jsonld +++ b/data/missequel/missequelbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "misSEQuel", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.cs.colostate.edu/seq/missequel/" } \ No newline at end of file diff --git a/data/missmethyl/missmethylbioschemas.jsonld b/data/missmethyl/missmethylbioschemas.jsonld index 3d039bc9c935a..1515261a8b6a0 100644 --- a/data/missmethyl/missmethylbioschemas.jsonld +++ b/data/missmethyl/missmethylbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-1711-7454", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/missmethyl", "@type": "sc:SoftwareApplication", @@ -33,8 +29,8 @@ "sc:license": "GPL-2.0", "sc:name": "missMethyl", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/missMethyl.html", @@ -43,6 +39,10 @@ { "@id": "http://orcid.org/0000-0002-9458-3061", "@type": "schema:Person" + }, + { + "@id": "http://orcid.org/0000-0002-1711-7454", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/missrows/missrowsbioschemas.jsonld b/data/missrows/missrowsbioschemas.jsonld index 41ead409296a2..b0dab8c36b0ca 100644 --- a/data/missrows/missrowsbioschemas.jsonld +++ b/data/missrows/missrowsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-016-1273-5", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/missrows", "@type": "sc:SoftwareApplication", @@ -17,10 +21,10 @@ }, "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5048483", { "@id": "https://doi.org/10.1186/s12859-016-1273-5" }, - "pmcid:PMC5048483", "pubmed:27716030" ], "sc:description": "The missRows package implements the MI-MFA method to deal with missing individuals ('biological units') in multi-omics data integration. The package provides functions for estimating coordinates of individuals and variables, imputing missing individuals, and various diagnostic plots to inspect the pattern of missingness and visualize the uncertainty due to missing values.", @@ -30,9 +34,9 @@ "sc:license": "Artistic-2.0", "sc:name": "missRows", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/missRows.html", "sc:version": "1.0.0" @@ -40,10 +44,6 @@ { "@id": "http://orcid.org/0000-0003-3432-6909", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1273-5", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mist/mistbioschemas.jsonld b/data/mist/mistbioschemas.jsonld index 6248cd0883529..645094925f3d9 100644 --- a/data/mist/mistbioschemas.jsonld +++ b/data/mist/mistbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/mist", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": "pubmed:19900966", "sc:description": "Identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. It contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; among others.", "sc:name": "MiST", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://mistdb.com/" } \ No newline at end of file diff --git a/data/mistic-tumour/mistic-tumourbioschemas.jsonld b/data/mistic-tumour/mistic-tumourbioschemas.jsonld index 73e8209779783..efdb02ce282a1 100644 --- a/data/mistic-tumour/mistic-tumourbioschemas.jsonld +++ b/data/mistic-tumour/mistic-tumourbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Sylvie Mader", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5570030", - "pubmed:28472340", { "@id": "https://doi.org/10.1093/nar/gkx338" - } + }, + "pubmed:28472340", + "pmcid:PMC5570030" ], "sc:description": "Integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:license": "GPL-3.0", "sc:name": "MiSTIC", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/iric-soft/MiSTIC" }, diff --git a/data/mistic/misticbioschemas.jsonld b/data/mistic/misticbioschemas.jsonld index 86e2715e0950c..9000f5fce59c3 100644 --- a/data/mistic/misticbioschemas.jsonld +++ b/data/mistic/misticbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "MISTIC (Mutual Information Server to Infer Coevolution) is a web server for graphical representation of the information contained in a multiple sequence alignment and a complete analysis tool for mutual information networks in proteins.", "sc:name": "MISTIC", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://mistic.leloir.org.ar" diff --git a/data/mistimm/mistimmbioschemas.jsonld b/data/mistimm/mistimmbioschemas.jsonld index 864afc46386a7..563f94f25b4a5 100644 --- a/data/mistimm/mistimmbioschemas.jsonld +++ b/data/mistimm/mistimmbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1186/S12976-019-0105-5", "@type": "sc:CreativeWork" }, + { + "@id": "https://orcid.org/0000-0001-9541-246X", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/MiStImm", "@type": "sc:SoftwareApplication", @@ -21,32 +25,28 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:31046789", + "pmcid:PMC6498635", { "@id": "https://doi.org/10.1186/S12976-019-0105-5" - }, - "pubmed:31046789", - "pmcid:PMC6498635" + } ], "sc:description": "Agent-based simulation tool to study the self-nonself discrimination of the adaptive immune response.", "sc:featureList": [ { - "@id": "edam:operation_2426" + "@id": "edam:operation_0478" }, { - "@id": "edam:operation_0478" + "@id": "edam:operation_2426" } ], "sc:license": "GPL-2.0", "sc:name": "MiStImm", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/kerepesi/mistimm" - }, - { - "@id": "https://orcid.org/0000-0001-9541-246X", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mitea/miteabioschemas.jsonld b/data/mitea/miteabioschemas.jsonld index 3cd972a239fb0..77f90ec6824db 100644 --- a/data/mitea/miteabioschemas.jsonld +++ b/data/mitea/miteabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for identifying and visualizing enriched miRNA targets in ranked lists of genes.", "sc:name": "miTEA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://cbl-gorilla.cs.technion.ac.il/miTEA/" } \ No newline at end of file diff --git a/data/mitk-modelfit/mitk-modelfitbioschemas.jsonld b/data/mitk-modelfit/mitk-modelfitbioschemas.jsonld index 6b2c73d14841d..49ee727dc23a2 100644 --- a/data/mitk-modelfit/mitk-modelfitbioschemas.jsonld +++ b/data/mitk-modelfit/mitk-modelfitbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC6335810", + "pubmed:30651067", { "@id": "https://doi.org/10.1186/s12859-018-2588-1" }, - "pubmed:30651067" + "pmcid:PMC6335810" ], "sc:description": "Generic open-source framework for model fits and their exploration in medical imaging - design, implementation and application on the example of DCE-MRI.", "sc:featureList": { @@ -31,8 +31,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "MITK-ModelFit", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://mitk.org/wiki/MITK-ModelFit" diff --git a/data/mitobank/mitobankbioschemas.jsonld b/data/mitobank/mitobankbioschemas.jsonld index 240d0dcc9210f..e999b29039201 100644 --- a/data/mitobank/mitobankbioschemas.jsonld +++ b/data/mitobank/mitobankbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MitoBank is a simple perl script to obtain from GeneBank mitochondrial genomes, parse them, and store the different genes in separate files. It can be used to retrieve both coding genes and RNA genes. Coding genes might be obtained in their amino acid or nucleotide sequence.", "sc:name": "MitoBank", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://darwin.uvigo.es/software/mitobank.html", "sc:version": "2.1" diff --git a/data/mitobreak/mitobreakbioschemas.jsonld b/data/mitobreak/mitobreakbioschemas.jsonld index e57df756452af..c0091f7cac0b4 100644 --- a/data/mitobreak/mitobreakbioschemas.jsonld +++ b/data/mitobreak/mitobreakbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:24170808", { "@id": "https://doi.org/10.1093/nar/gkt982" }, - "pmcid:PMC3965124", - "pubmed:24170808" + "pmcid:PMC3965124" ], "sc:description": "Comprehensive on-line resource with curated datasets of mitochondrial DNA (mtDNA) rearrangements. MitoBreak provides a complete, quality checked and regularly updated list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially-duplicated (duplications) and linear mtDNAs.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "MITOBREAK", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://mitobreak.portugene.com/" }, diff --git a/data/mitofish/mitofishbioschemas.jsonld b/data/mitofish/mitofishbioschemas.jsonld index 0cd8e4ffcc4bd..fbd0ddeb6c0b8 100644 --- a/data/mitofish/mitofishbioschemas.jsonld +++ b/data/mitofish/mitofishbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/MOLBEV/MST141", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mitofish", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Wataru Iwasaki", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:23955518", - "pmcid:PMC3808866", { "@id": "https://doi.org/10.1093/MOLBEV/MST141" - } + }, + "pubmed:23955518", + "pmcid:PMC3808866" ], "sc:description": "Mitochondrial genome database of fish with an accurate and automatic annotation pipeline.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "MitoFish", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://mitofish.aori.u-tokyo.ac.jp/" - }, - { - "@id": "https://doi.org/10.1093/MOLBEV/MST141", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mitofy/mitofybioschemas.jsonld b/data/mitofy/mitofybioschemas.jsonld index 82a8e4eb8a80e..51c7b4d44a8a4 100644 --- a/data/mitofy/mitofybioschemas.jsonld +++ b/data/mitofy/mitofybioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/mitofy", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:20118192", "sc:description": "Developed to assist in the annotation of genes and tRNAs in seed plant mitochondrial genomes.", "sc:name": "MITOFY", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://dogma.ccbb.utexas.edu/mitofy/" } \ No newline at end of file diff --git a/data/mitogenesisdb/mitogenesisdbbioschemas.jsonld b/data/mitogenesisdb/mitogenesisdbbioschemas.jsonld index 7e3e28cb8d9f3..0af2c1faee89d 100644 --- a/data/mitogenesisdb/mitogenesisdbbioschemas.jsonld +++ b/data/mitogenesisdb/mitogenesisdbbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/mitogenesisdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Claude JACQ", "Mickael ORGEUR", "Jean-Christophe GELLY", - "Claude JACQ", "Gaelle LELANDAIS" ], "sc:additionalType": "Database portal", @@ -21,9 +21,9 @@ "sc:description": "Dynamic of mitochondrial protein formation through global mRNA analyses. Three main parameters confer a global view of mitochondrial biogenesis: (i) time-course of mRNA production in highly synchronized yeast cell cultures, (ii) microarray analyses of mRNA localization that define translation sites and (iii) mRNA transcription rate and stability. It integrates and establishes cross-comparisons between these data.", "sc:name": "MitoGenesisDB", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.dsimb.inserm.fr/dsimb_tools/mitgene/" } \ No newline at end of file diff --git a/data/mitoimpute/mitoimputebioschemas.jsonld b/data/mitoimpute/mitoimputebioschemas.jsonld index d6edd8f0b0f67..1812edc72ac92 100644 --- a/data/mitoimpute/mitoimputebioschemas.jsonld +++ b/data/mitoimpute/mitoimputebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "MitoImpute", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/sjfandrews/MitoImpute" } \ No newline at end of file diff --git a/data/mitominer/mitominerbioschemas.jsonld b/data/mitominer/mitominerbioschemas.jsonld index 3a1ed5a6d2529..c31bfa72af99c 100644 --- a/data/mitominer/mitominerbioschemas.jsonld +++ b/data/mitominer/mitominerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "MitoMiner integrates mitochondrial proteomics data for a range of organisms. You can run flexible queries, export results and analyse lists of data.", "sc:name": "MitoMiner", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://mitominer.mrc-mbu.cam.ac.uk/release-2.0/begin.do" diff --git a/data/mitoode/mitoodebioschemas.jsonld b/data/mitoode/mitoodebioschemas.jsonld index 8eff981a57fb7..ececcb2595efa 100644 --- a/data/mitoode/mitoodebioschemas.jsonld +++ b/data/mitoode/mitoodebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-0474-2218", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1186/1471-2105-14-308", "@type": "sc:CreativeWork" @@ -27,10 +31,10 @@ }, "edam:has_output": [ { - "@id": "edam:data_2884" + "@id": "edam:data_1772" }, { - "@id": "edam:data_1772" + "@id": "edam:data_2884" } ], "sc:additionalType": [ @@ -39,16 +43,16 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0625" + "@id": "edam:topic_2229" }, { - "@id": "edam:topic_3523" + "@id": "edam:topic_3383" }, { - "@id": "edam:topic_2229" + "@id": "edam:topic_0625" }, { - "@id": "edam:topic_3383" + "@id": "edam:topic_3523" } ], "sc:citation": [ @@ -66,15 +70,11 @@ "sc:name": "mitoODE", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mitoODE.html", "sc:version": "1.12.0" - }, - { - "@id": "http://orcid.org/0000-0002-0474-2218", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mitoprot_ii/mitoprot_iibioschemas.jsonld b/data/mitoprot_ii/mitoprot_iibioschemas.jsonld index cf4ace4b675e1..61c6e7c8b74c6 100644 --- a/data/mitoprot_ii/mitoprot_iibioschemas.jsonld +++ b/data/mitoprot_ii/mitoprot_iibioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mitoprot_ii", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Manuel G. Claros", - "Pierre Vincens" + "Pierre Vincens", + "Manuel G. Claros" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:8944766", diff --git a/data/mitotip/mitotipbioschemas.jsonld b/data/mitotip/mitotipbioschemas.jsonld index 8893500588611..8b8d2dbe9ca54 100644 --- a/data/mitotip/mitotipbioschemas.jsonld +++ b/data/mitotip/mitotipbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MitoTIP", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.mitomap.org/MITOMAP" } \ No newline at end of file diff --git a/data/mitotool/mitotoolbioschemas.jsonld b/data/mitotool/mitotoolbioschemas.jsonld index e42fb58895efe..7379ca1c1c88a 100644 --- a/data/mitotool/mitotoolbioschemas.jsonld +++ b/data/mitotool/mitotoolbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-based bioinformatics platform, provides a convenient, user-friendly interface for handling human mtDNA sequence data.", "sc:name": "MitoTool", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.mitotool.org/" } \ No newline at end of file diff --git a/data/mitotoolpy/mitotoolpybioschemas.jsonld b/data/mitotoolpy/mitotoolpybioschemas.jsonld index 7509ad9e43d15..7e749b86612c6 100644 --- a/data/mitotoolpy/mitotoolpybioschemas.jsonld +++ b/data/mitotoolpy/mitotoolpybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Designed for data analysis of mitochondrial DNA of eight domestic animals, including cattle, chicken, dog, horse, goat, pig, sheep and yak.", "sc:name": "MitoToolPy", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.mitotool.org/mp.html#intro" } \ No newline at end of file diff --git a/data/mitoxplorer/mitoxplorerbioschemas.jsonld b/data/mitoxplorer/mitoxplorerbioschemas.jsonld index 475338cf5c11f..6c5c7b59605b6 100644 --- a/data/mitoxplorer/mitoxplorerbioschemas.jsonld +++ b/data/mitoxplorer/mitoxplorerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "mitoXplorer", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://mitoxplorer.ibdm.univ-mrs.fr" } \ No newline at end of file diff --git a/data/mitrata/mitratabioschemas.jsonld b/data/mitrata/mitratabioschemas.jsonld index fa8d45f0e425f..3e5d61ca32a01 100644 --- a/data/mitrata/mitratabioschemas.jsonld +++ b/data/mitrata/mitratabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "miTRATA", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://wasabi.ddpsc.org/~apps/ta/" diff --git a/data/mitsu/mitsubioschemas.jsonld b/data/mitsu/mitsubioschemas.jsonld index f99f695e65f7e..e18cb2a919588 100644 --- a/data/mitsu/mitsubioschemas.jsonld +++ b/data/mitsu/mitsubioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Command line application for the discovery of transcription factor binding site (TFBS) motifs.", "sc:name": "MITSU", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://sourceforge.net/projects/mitsu-motif/" } \ No newline at end of file diff --git a/data/mix/mixbioschemas.jsonld b/data/mix/mixbioschemas.jsonld index a3ae2ac63c792..bd3dc0086de7e 100644 --- a/data/mix/mixbioschemas.jsonld +++ b/data/mix/mixbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Macha Nikolski", - "Alexis Groppi", "Heissam Soueidan", - "Florence Maurier" + "Florence Maurier", + "Alexis Groppi", + "Macha Nikolski" ], "sc:description": "Tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.", "sc:license": "MIT", @@ -23,8 +23,8 @@ "sc:operatingSystem": "Linux", "sc:provider": [ "CNRS / LaBRI, Universite Bordeaux 1, 351 cours de la Liberation, 33405 Talence Cedex, France", - "NKI-AVL, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands", - "CBiB - Universite Victor Segalen Bordeaux, 146, rue Leo Saignat, 33076 Bordeaux, France" + "CBiB - Universite Victor Segalen Bordeaux, 146, rue Leo Saignat, 33076 Bordeaux, France", + "NKI-AVL, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands" ], "sc:url": "https://github.com/cbib/MIX", "sc:version": "1" diff --git a/data/mix99/mix99bioschemas.jsonld b/data/mix99/mix99bioschemas.jsonld index 1b71c27448de1..19ca2b2759faa 100644 --- a/data/mix99/mix99bioschemas.jsonld +++ b/data/mix99/mix99bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Proprietary", "sc:name": "Mix99", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://portal.mtt.fi/portal/page/portal/mtt_en/mtt/about/researchunits/bel/biometricalgenetics/software/MiX99" } \ No newline at end of file diff --git a/data/mixchip/mixchipbioschemas.jsonld b/data/mixchip/mixchipbioschemas.jsonld index a00e2ababd524..6375b5b024f3b 100644 --- a/data/mixchip/mixchipbioschemas.jsonld +++ b/data/mixchip/mixchipbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/mixchip", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Harri Lähdesmäki", - "Sini Rautio" + "Sini Rautio", + "Harri Lähdesmäki" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:26703974", "sc:description": "Probabilistic method for identifying cell type specific TF binding sites from heterogeneous chromatin immunoprecipitation sequencing (ChIP-seq) data.", "sc:name": "MixChIP", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://research.ics.aalto.fi/csb/software/" } \ No newline at end of file diff --git a/data/mixclone/mixclonebioschemas.jsonld b/data/mixclone/mixclonebioschemas.jsonld index f2bdc36f127df..9ebd91d5f827a 100644 --- a/data/mixclone/mixclonebioschemas.jsonld +++ b/data/mixclone/mixclonebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Comprehensive software package to study the subclonal structures of tumor genomes, including subclonal cellular prevalences estimation, allelic configuration estimation, absolute copy number estimation and a few visualization tools.", "sc:name": "MixClone", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/uci-cbcl/MixClone", diff --git a/data/mixcr/mixcrbioschemas.jsonld b/data/mixcr/mixcrbioschemas.jsonld index 6274eda41fb6b..62f9a8c1309c5 100644 --- a/data/mixcr/mixcrbioschemas.jsonld +++ b/data/mixcr/mixcrbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "MiXCR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://milaboratory.com/software/mixcr/" } \ No newline at end of file diff --git a/data/mixomics/mixomicsbioschemas.jsonld b/data/mixomics/mixomicsbioschemas.jsonld index 457efea92828d..58bea8a0942ff 100644 --- a/data/mixomics/mixomicsbioschemas.jsonld +++ b/data/mixomics/mixomicsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "mixomics", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "unimelb.edu.au", "sc:url": "http://mixomics.org/" diff --git a/data/mixr/mixrbioschemas.jsonld b/data/mixr/mixrbioschemas.jsonld index 3a6c06f719240..579fd84cead48 100644 --- a/data/mixr/mixrbioschemas.jsonld +++ b/data/mixr/mixrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1073/PNAS.1814995116", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/MIXR", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ ], "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6561249", { "@id": "https://doi.org/10.1073/PNAS.1814995116" }, - "pubmed:31113885", - "pmcid:PMC6561249" + "pubmed:31113885" ], "sc:description": "Mismatching Isoform eXon Remover.", "sc:featureList": [ @@ -30,24 +34,20 @@ "@id": "edam:operation_0499" }, { - "@id": "edam:operation_0544" + "@id": "edam:operation_3258" }, { - "@id": "edam:operation_3258" + "@id": "edam:operation_0544" } ], "sc:license": "Unlicense", "sc:name": "MIXR", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://github.com/hawkjo/mixr" - }, - { - "@id": "https://doi.org/10.1073/PNAS.1814995116", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mixscore/mixscorebioschemas.jsonld b/data/mixscore/mixscorebioschemas.jsonld index d6cb6366b5346..472c17eb84541 100644 --- a/data/mixscore/mixscorebioschemas.jsonld +++ b/data/mixscore/mixscorebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mixscore", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alkes L. Price", - "Bogdan Pasaniuc" + "Bogdan Pasaniuc", + "Alkes L. Price" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:21541012", diff --git a/data/mizbee/mizbeebioschemas.jsonld b/data/mizbee/mizbeebioschemas.jsonld index b01b9269efdc0..00277a43bacb7 100644 --- a/data/mizbee/mizbeebioschemas.jsonld +++ b/data/mizbee/mizbeebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "MizBee", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.cs.utah.edu/~miriah/mizbee/Overview.html" } \ No newline at end of file diff --git a/data/mizutama/mizutamabioschemas.jsonld b/data/mizutama/mizutamabioschemas.jsonld index 925e3053c099b..ed02658aa341f 100644 --- a/data/mizutama/mizutamabioschemas.jsonld +++ b/data/mizutama/mizutamabioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Mizutama", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://datadryad.org/resource/doi:10.5061/dryad.bk2690n?show=full" } \ No newline at end of file diff --git a/data/mkesa/mkesabioschemas.jsonld b/data/mkesa/mkesabioschemas.jsonld index 997d3958df42d..8cfc86dda9a9d 100644 --- a/data/mkesa/mkesabioschemas.jsonld +++ b/data/mkesa/mkesabioschemas.jsonld @@ -16,13 +16,13 @@ "sc:license": "GPL-2.0", "sc:name": "mkESA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "BiBiServ", - "Bielefeld University", - "CeBiTec" + "CeBiTec", + "Bielefeld University" ], "sc:url": "http://bibiserv.cebitec.uni-bielefeld.de/mkesa", "sc:version": "1" diff --git a/data/mkt/mktbioschemas.jsonld b/data/mkt/mktbioschemas.jsonld index 21e12e5b0a61c..c9f3a249545c4 100644 --- a/data/mkt/mktbioschemas.jsonld +++ b/data/mkt/mktbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Sonia Casillas", - "Antonio Barbadilla", - "Raquel Egea" + "Raquel Egea", + "Antonio Barbadilla" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:18515345", "sc:description": "Standard and Generalized McDonald-Kreitman Test (MKT) is a web tool for the molecular level detection of signatures of natural selection.", "sc:name": "MKT", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mkt.uab.es" } \ No newline at end of file diff --git a/data/ml_repo/ml_repobioschemas.jsonld b/data/ml_repo/ml_repobioschemas.jsonld index 1d826e07a3b56..20657ee0194f5 100644 --- a/data/ml_repo/ml_repobioschemas.jsonld +++ b/data/ml_repo/ml_repobioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ042", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0002-8205-2511", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/ML_Repo", "@type": "sc:SoftwareApplication", @@ -25,8 +17,8 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6493971", "pubmed:31042284", + "pmcid:PMC6493971", { "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ042" } @@ -34,23 +26,31 @@ "sc:description": "Microbiome Learning Repo (ML Repo) - public repository of microbiome regression and classification tasks", "sc:featureList": [ { - "@id": "edam:operation_3192" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3659" + "@id": "edam:operation_3192" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_3659" } ], "sc:license": "MIT", "sc:name": "ML Repo", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://knights-lab.github.io/MLRepo/" + }, + { + "@id": "https://orcid.org/0000-0002-8205-2511", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ042", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mlasso-hum/mlasso-humbioschemas.jsonld b/data/mlasso-hum/mlasso-humbioschemas.jsonld index 43aa355838767..ec7d24ce5c7d8 100644 --- a/data/mlasso-hum/mlasso-humbioschemas.jsonld +++ b/data/mlasso-hum/mlasso-humbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/mlasso-hum", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Man-Wai Mak", - "Shibiao Wan" + "Shibiao Wan", + "Man-Wai Mak" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:26164062", "sc:description": "A LASSO-based interpretable human-protein subcellular localization predictor.", "sc:name": "mLASSO-Hum", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioinfo.eie.polyu.edu.hk/mLASSOHumServer/index.html" diff --git a/data/mlbias/mlbiasbioschemas.jsonld b/data/mlbias/mlbiasbioschemas.jsonld index 2ac21aaf4124e..28781018290b8 100644 --- a/data/mlbias/mlbiasbioschemas.jsonld +++ b/data/mlbias/mlbiasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "R package to correct for machine learning bias when many classifiers are compared and the best is selected.", "sc:name": "MLbias", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://tsenglab.biostat.pitt.edu/software.htm#MLbias" } \ No newline at end of file diff --git a/data/mlc/mlcbioschemas.jsonld b/data/mlc/mlcbioschemas.jsonld index ba6a0f384af99..5c55c61b0d721 100644 --- a/data/mlc/mlcbioschemas.jsonld +++ b/data/mlc/mlcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "MLC", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.github.com/stamakro/MLC" diff --git a/data/mlegp/mlegpbioschemas.jsonld b/data/mlegp/mlegpbioschemas.jsonld index cb97ebcea8886..4919f405a12d5 100644 --- a/data/mlegp/mlegpbioschemas.jsonld +++ b/data/mlegp/mlegpbioschemas.jsonld @@ -14,10 +14,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC2732217", { "@id": "https://doi.org/10.1093/bioinformatics/btn329" }, + "pmcid:PMC2732217", "pubmed:18635570" ], "sc:description": "An R package to analyze computer models of complex systems.", @@ -26,9 +26,9 @@ }, "sc:name": "mlegp", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://gdancik.github.io/bioinformatics/software.html", "sc:version": "3.1.4" diff --git a/data/mlibrary/mlibrarybioschemas.jsonld b/data/mlibrary/mlibrarybioschemas.jsonld index cb2c07b75ecca..90db955a58094 100644 --- a/data/mlibrary/mlibrarybioschemas.jsonld +++ b/data/mlibrary/mlibrarybioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Database search engine developed to assist the user in the detection and identification of small compounds, such as anabolic androgenic steroids, using the soft ionisation technique Matrix Assisted Laser Desorption/Ionisation (MALDI) coupled with mass spectrometry. It compares the results of the experimental data with theoretic values included in the database. It simplifies the interpretation of the mass spectrometry data and reduces the amount of time required to analyze the results manually.", "sc:name": "MLibrary", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.sing-group.org/MLibrary/", "sc:version": "1.0.0" diff --git a/data/mlinterfaces/bioconda_mlinterfaces.yaml b/data/mlinterfaces/bioconda_mlinterfaces.yaml index b342af9f591fd..c66e772062a23 100644 --- a/data/mlinterfaces/bioconda_mlinterfaces.yaml +++ b/data/mlinterfaces/bioconda_mlinterfaces.yaml @@ -4,7 +4,6 @@ description: This package provides uniform interfaces to machine learning code f home: https://bioconductor.org/packages/3.10/bioc/html/MLInterfaces.html identifiers: - biotools:mlinterfaces -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-mlinterfaces diff --git a/data/mlinterfaces/mlinterfacesbioschemas.jsonld b/data/mlinterfaces/mlinterfacesbioschemas.jsonld index b49b82c0e1441..6f09e09e6cb66 100644 --- a/data/mlinterfaces/mlinterfacesbioschemas.jsonld +++ b/data/mlinterfaces/mlinterfacesbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "MLInterfaces", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MLInterfaces.html", diff --git a/data/mlm/mlmbioschemas.jsonld b/data/mlm/mlmbioschemas.jsonld index 55e86609c4b9c..3ac0cc3b13bd9 100644 --- a/data/mlm/mlmbioschemas.jsonld +++ b/data/mlm/mlmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "MLM", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://figshare.com/articles/MLM_Algorithm/7393517/1" } \ No newline at end of file diff --git a/data/mlml2r/mlml2rbioschemas.jsonld b/data/mlml2r/mlml2rbioschemas.jsonld index 321b91695eeb8..728b62a15b7cc 100644 --- a/data/mlml2r/mlml2rbioschemas.jsonld +++ b/data/mlml2r/mlml2rbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "MIT", "sc:name": "MLML2R", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://cran.r-project.org/package=MLML2R", diff --git a/data/mlp/mlpbioschemas.jsonld b/data/mlp/mlpbioschemas.jsonld index 75c2c7feed192..57aad69c0083d 100644 --- a/data/mlp/mlpbioschemas.jsonld +++ b/data/mlp/mlpbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Tobias Verbeke", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Mean Log P Analysis.", "sc:license": "GPL-3.0", "sc:name": "MLP", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MLP.html", "sc:version": "1.22.0" diff --git a/data/mlphaser/mlphaserbioschemas.jsonld b/data/mlphaser/mlphaserbioschemas.jsonld index 140f6c88e465e..568b6e0bdead5 100644 --- a/data/mlphaser/mlphaserbioschemas.jsonld +++ b/data/mlphaser/mlphaserbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "mlPhaser is an R package for phase haplotypes from genotypes based on a list of known haplotypes. Suited to highly diverse loci such as HLA.", "sc:name": "mlPhaser", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://cran.r-project.org/web/packages/mlPhaser/index.html", "sc:version": "0.01" diff --git a/data/mlseq/bioconda_mlseq.yaml b/data/mlseq/bioconda_mlseq.yaml index 6578955c57454..1aa98b74b3574 100644 --- a/data/mlseq/bioconda_mlseq.yaml +++ b/data/mlseq/bioconda_mlseq.yaml @@ -4,7 +4,6 @@ description: This package applies several machine learning methods, including SV home: https://bioconductor.org/packages/3.10/bioc/html/MLSeq.html identifiers: - biotools:mlseq -- doi:10.1038/nmeth.3252 license: GPL(>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-mlseq diff --git a/data/mlseq/mlseqbioschemas.jsonld b/data/mlseq/mlseqbioschemas.jsonld index 595a775203f2b..b163e62eac747 100644 --- a/data/mlseq/mlseqbioschemas.jsonld +++ b/data/mlseq/mlseqbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "MLSeq", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MLSeq.html", diff --git a/data/mlst-db/mlst-dbbioschemas.jsonld b/data/mlst-db/mlst-dbbioschemas.jsonld index aff4965ead2db..a47f947eb120c 100644 --- a/data/mlst-db/mlst-dbbioschemas.jsonld +++ b/data/mlst-db/mlst-dbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MLST-DB", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://mlstdb.bmc.uu.se/" diff --git a/data/mlst/mlstbioschemas.jsonld b/data/mlst/mlstbioschemas.jsonld index 4ca759d8b86dd..7bcc4c711a265 100644 --- a/data/mlst/mlstbioschemas.jsonld +++ b/data/mlst/mlstbioschemas.jsonld @@ -24,8 +24,8 @@ "@id": "edam:topic_2830" }, "sc:citation": [ - "pubmed:22238442", "pmcid:PMC3318499", + "pubmed:22238442", { "@id": "https://doi.org/10.1128/JCM.06094-11" } diff --git a/data/mlsta/mlstabioschemas.jsonld b/data/mlsta/mlstabioschemas.jsonld index 09a5262ff457a..e5f4ae3840db3 100644 --- a/data/mlsta/mlstabioschemas.jsonld +++ b/data/mlsta/mlstabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Machine learning integration for predicting the effect of single amino acid substitutions on protein stability.", "sc:name": "MLSTA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.prc.boun.edu.tr/appserv/prc/mlsta/" } \ No newline at end of file diff --git a/data/mltree/mltreebioschemas.jsonld b/data/mltree/mltreebioschemas.jsonld index f4ff18c0e515e..5092feabb15a8 100644 --- a/data/mltree/mltreebioschemas.jsonld +++ b/data/mltree/mltreebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "MLtree is a software to compute maximum likelihood optimization of models of character evolution (either DNA or phenotypic ones) along the branches of a phylogenetic tree. It is assuming that the phylogenetic tree is known.", "sc:name": "MLtree", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://www2.unil.ch/phylo/bioinformatics/mltree.html" diff --git a/data/mltreemap/mltreemapbioschemas.jsonld b/data/mltreemap/mltreemapbioschemas.jsonld index 4ba998de97c3d..20ee225d7f905 100644 --- a/data/mltreemap/mltreemapbioschemas.jsonld +++ b/data/mltreemap/mltreemapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool that employs full maximum likelihood to give insights into phylogenetic and functional properties of metagenomes and the underlying microbial communities. It does so by detecting and phylotyping a series of relevant marker genes on the submitted DNA fragments.", "sc:name": "MLTreeMap", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://mltreemap.org/" } \ No newline at end of file diff --git a/data/mmappr/mmapprbioschemas.jsonld b/data/mmappr/mmapprbioschemas.jsonld index 45075c26c60e8..ae7e5d1e883ae 100644 --- a/data/mmappr/mmapprbioschemas.jsonld +++ b/data/mmappr/mmapprbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "An analysis pipeline for mapping mutations using RNA-seq. It works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome.", "sc:name": "MMAPPR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://yost.genetics.utah.edu/software.php", "sc:version": "0.83" diff --git a/data/mmb/mmbbioschemas.jsonld b/data/mmb/mmbbioschemas.jsonld index b9151cf0c20e7..ee24205f91e62 100644 --- a/data/mmb/mmbbioschemas.jsonld +++ b/data/mmb/mmbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein as well as RNA. Aside from the renaming, MMB 2.3 differs from RNABuilder 2.2 in two important ways. Release 2.3 has fully overhauled guts. It uses the BiopolymerClassContainer, a much cleaner programming construct which will make future upgrades and extensions more efficient.", "sc:name": "MMB", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://simtk.org/home/rnatoolbox" } \ No newline at end of file diff --git a/data/mmbgx/mmbgxbioschemas.jsonld b/data/mmbgx/mmbgxbioschemas.jsonld index 7f33e21641512..3c8abc6e98371 100644 --- a/data/mmbgx/mmbgxbioschemas.jsonld +++ b/data/mmbgx/mmbgxbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays.", "sc:name": "MMBGX", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bgx.org.uk/software/mmbgx.html" } \ No newline at end of file diff --git a/data/mmbpred/mmbpredbioschemas.jsonld b/data/mmbpred/mmbpredbioschemas.jsonld index c3e90778d10ba..f9b20b6b12bce 100644 --- a/data/mmbpred/mmbpredbioschemas.jsonld +++ b/data/mmbpred/mmbpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server of prediction of of MHC class I binders which can bind to wide range of MHC alleles with high affinity. This server has potential to develop sub-unit vaccine for large population.", "sc:name": "MMBPred", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/mmbpred/" } \ No newline at end of file diff --git a/data/mmdb/mmdbbioschemas.jsonld b/data/mmdb/mmdbbioschemas.jsonld index 1c18ab3349bee..a02b1538d37ca 100644 --- a/data/mmdb/mmdbbioschemas.jsonld +++ b/data/mmdb/mmdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Database of molecular modelling of 3-D structures; experimentally determined structures only.", "sc:name": "MMDB", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml" diff --git a/data/mmdiff2/bioconda_mmdiff2.yaml b/data/mmdiff2/bioconda_mmdiff2.yaml index 98cdb17d07c74..cb7720d2b69d1 100644 --- a/data/mmdiff2/bioconda_mmdiff2.yaml +++ b/data/mmdiff2/bioconda_mmdiff2.yaml @@ -5,7 +5,6 @@ description: This package detects statistically significant differences between home: https://bioconductor.org/packages/3.10/bioc/html/MMDiff2.html identifiers: - biotools:mmdiff2 -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-mmdiff2 summary: Statistical Testing for ChIP-Seq data sets diff --git a/data/mmdiff2/mmdiff2bioschemas.jsonld b/data/mmdiff2/mmdiff2bioschemas.jsonld index 9166454be2a7b..b632f2629252c 100644 --- a/data/mmdiff2/mmdiff2bioschemas.jsonld +++ b/data/mmdiff2/mmdiff2bioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Gabriele Schweikert", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).", "sc:license": "Artistic-2.0", "sc:name": "MMDiff2", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MMDiff2.html", diff --git a/data/mmeta/mmetabioschemas.jsonld b/data/mmeta/mmetabioschemas.jsonld index 5be1b55c1c74d..e36e9870a7b8d 100644 --- a/data/mmeta/mmetabioschemas.jsonld +++ b/data/mmeta/mmetabioschemas.jsonld @@ -20,13 +20,13 @@ "sc:license": "GPL-3.0", "sc:name": "mmeta", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ - "crg.eu", - "Lab Roderic Guigo Group" + "Lab Roderic Guigo Group", + "crg.eu" ], "sc:url": "http://big.crg.cat/services/mmeta", "sc:version": "1" diff --git a/data/mmnet/mmnetbioschemas.jsonld b/data/mmnet/mmnetbioschemas.jsonld index 6c7a41323a719..8b93ef7d444a9 100644 --- a/data/mmnet/mmnetbioschemas.jsonld +++ b/data/mmnet/mmnetbioschemas.jsonld @@ -15,8 +15,8 @@ "Yang Cao" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package gives the implementations microbiome metabolic network constructing and analyzing. It introduces a unique metagenomic systems biology approach, mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. The system-level network and the next topological analysis will be of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome.", "sc:license": "GPL-2.0", diff --git a/data/mmp/mmpbioschemas.jsonld b/data/mmp/mmpbioschemas.jsonld index fc0b59608deed..0476076a82d21 100644 --- a/data/mmp/mmpbioschemas.jsonld +++ b/data/mmp/mmpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-NC-3.0", "sc:name": "Marine Metagenomics Portal", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://mmp.sfb.uit.no/" } \ No newline at end of file diff --git a/data/mmquant/mmquantbioschemas.jsonld b/data/mmquant/mmquantbioschemas.jsonld index f1aeb04642a49..4d08acb054958 100644 --- a/data/mmquant/mmquantbioschemas.jsonld +++ b/data/mmquant/mmquantbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool for computing gene expression, included duplicated genes. If a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes.", "sc:name": "mmquant", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bitbucket.org/mzytnicki/multi-mapping-counter" } \ No newline at end of file diff --git a/data/mmr/mmrbioschemas.jsonld b/data/mmr/mmrbioschemas.jsonld index ffc47d78e1130..33814ea8f10fc 100644 --- a/data/mmr/mmrbioschemas.jsonld +++ b/data/mmr/mmrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Infers optimal mapping locations from the coverage densities of other mapped reads in vicinity.", "sc:name": "MMR", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://raetschlab.org/suppl/MMR" } \ No newline at end of file diff --git a/data/mmsdusty/mmsdustybioschemas.jsonld b/data/mmsdusty/mmsdustybioschemas.jsonld index 3376443238d44..34df31eb806c5 100644 --- a/data/mmsdusty/mmsdustybioschemas.jsonld +++ b/data/mmsdusty/mmsdustybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Alternative web-oriented InChI-based normalization tool developed with the specific aim to efficiently analyze and remove chemical redundancy, minimizing all problems that might affect the performance and the usability of any chemical database.", "sc:name": "MMsDusty", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://mms.dsfarm.unipd.it/MMsDusty/", diff --git a/data/mmseq/mmseqbioschemas.jsonld b/data/mmseq/mmseqbioschemas.jsonld index bbe8506fe2a52..98b259f2a15c2 100644 --- a/data/mmseq/mmseqbioschemas.jsonld +++ b/data/mmseq/mmseqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data.", "sc:name": "MMSEQ", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/eturro/mmseq" } \ No newline at end of file diff --git a/data/mmssimilarity/mmssimilaritybioschemas.jsonld b/data/mmssimilarity/mmssimilaritybioschemas.jsonld index 897d63dabba4a..85b9cab40c1b5 100644 --- a/data/mmssimilarity/mmssimilaritybioschemas.jsonld +++ b/data/mmssimilarity/mmssimilaritybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web-oriented tool developed with the specific aim to calculate chemical similarity indexes between a query structure and a chemical database.", "sc:name": "MMsSimilarity", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", diff --git a/data/mmtsb_toolset/mmtsb_toolsetbioschemas.jsonld b/data/mmtsb_toolset/mmtsb_toolsetbioschemas.jsonld index acf2884a391c4..8faf9b66e56bf 100644 --- a/data/mmtsb_toolset/mmtsb_toolsetbioschemas.jsonld +++ b/data/mmtsb_toolset/mmtsb_toolsetbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Can be used for replica exchange calculations with sander. This package also facilitates other Amber tasks, such as dealing in a consistent way with an ensemble of conformations, massaging PDB files, and carrying out some common types of structural analysis.", "sc:name": "MMTSB toolset", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://blue11.bch.msu.edu/mmtsb/Main_Page" diff --git a/data/mmx-i/mmx-ibioschemas.jsonld b/data/mmx-i/mmx-ibioschemas.jsonld index e2d45d09d8c22..0ed88b176b5f2 100644 --- a/data/mmx-i/mmx-ibioschemas.jsonld +++ b/data/mmx-i/mmx-ibioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1107/S1600577516003052", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mmx-i", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Antoine Bergamaschi", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC4853872", "pubmed:27140159", { "@id": "https://doi.org/10.1107/S1600577516003052" - } + }, + "pmcid:PMC4853872" ], "sc:description": "MMX-I is a data-processing software for multimodal X-ray imaging and tomography.", "sc:featureList": { @@ -33,6 +29,10 @@ "sc:name": "MMX-I", "sc:operatingSystem": "Windows", "sc:url": "https://bitbucket.org/antoinebergamaschi/mmx-i/overview" + }, + { + "@id": "https://doi.org/10.1107/S1600577516003052", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mni/mnibioschemas.jsonld b/data/mni/mnibioschemas.jsonld index 5cc0dafccc0bb..18e2969da5832 100644 --- a/data/mni/mnibioschemas.jsonld +++ b/data/mni/mnibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Algorithm to identify the gene targets of a drug treatment based on gene-expression data. In a typical use of the algorithm, a single expression profile, say obtained as a result of a treatment under study, is used as the test profile while a set of hundreds of expression profiles is used as the training set.", "sc:name": "MNI", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://dibernardo.tigem.it/softwares/mode-of-action-by-network-inference-mni" } \ No newline at end of file diff --git a/data/moad/moadbioschemas.jsonld b/data/moad/moadbioschemas.jsonld index b865c8ab8565b..3d1167d84cd2c 100644 --- a/data/moad/moadbioschemas.jsonld +++ b/data/moad/moadbioschemas.jsonld @@ -19,19 +19,19 @@ "biotools:primaryContact": "Heather A. Carlson", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC6589129", { "@id": "https://doi.org/10.1016/J.JMB.2019.05.024" }, - "pmcid:PMC6589129", "pubmed:31125569" ], "sc:description": "Mother of All Databases (MOAD) - Polypharmacology Tools and Their Utility in Drug Repurposing.", "sc:featureList": [ { - "@id": "edam:operation_2575" + "@id": "edam:operation_0482" }, { - "@id": "edam:operation_0482" + "@id": "edam:operation_2575" }, { "@id": "edam:operation_2950" diff --git a/data/moan/moanbioschemas.jsonld b/data/moan/moanbioschemas.jsonld index fccc55a8e288c..60f8fbd1690b8 100644 --- a/data/moan/moanbioschemas.jsonld +++ b/data/moan/moanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Discriminative pattern finder capable of using a very large negative set to greatly improve its predictive power. It is capable of handling sequences that are not repeat masked given that the negative set is a representative sample of promoters from the organism examined.", "sc:name": "MoAn", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "binf.ku.dk", "sc:url": "http://moan.binf.ku.dk/", diff --git a/data/moat/moatbioschemas.jsonld b/data/moat/moatbioschemas.jsonld index 844b6f387a084..caa5d3e322e82 100644 --- a/data/moat/moatbioschemas.jsonld +++ b/data/moat/moatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "MOAT", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://moat.gersteinlab.org/" } \ No newline at end of file diff --git a/data/mobcal-mpi/mobcal-mpibioschemas.jsonld b/data/mobcal-mpi/mobcal-mpibioschemas.jsonld index 0d4bed1b7e8d2..5088f702701bc 100644 --- a/data/mobcal-mpi/mobcal-mpibioschemas.jsonld +++ b/data/mobcal-mpi/mobcal-mpibioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/MobCal-MPI", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "C. Ieritano", - "W. S. Hopkins" + "W. S. Hopkins", + "C. Ieritano" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:30649115", diff --git a/data/mobi/mobibioschemas.jsonld b/data/mobi/mobibioschemas.jsonld index 2633648430ac5..ec60f0f233635 100644 --- a/data/mobi/mobibioschemas.jsonld +++ b/data/mobi/mobibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server to detect and visualise flexible regions in NMR solved structures.", "sc:name": "Mobi", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/mobi/", diff --git a/data/mobidb/mobidbbioschemas.jsonld b/data/mobidb/mobidbbioschemas.jsonld index 98efd41b919c9..10ee274a37685 100644 --- a/data/mobidb/mobidbbioschemas.jsonld +++ b/data/mobidb/mobidbbioschemas.jsonld @@ -28,9 +28,9 @@ "sc:license": "CC-BY-NC-1.0", "sc:name": "MobiDB", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", "sc:url": "http://mobidb.bio.unipd.it", diff --git a/data/mobilomefinder/mobilomefinderbioschemas.jsonld b/data/mobilomefinder/mobilomefinderbioschemas.jsonld index 0637ca03f92de..97ee1daa8d106 100644 --- a/data/mobilomefinder/mobilomefinderbioschemas.jsonld +++ b/data/mobilomefinder/mobilomefinderbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/mobilomefinder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hong-Yu Ou", + "Kumar Rajakumar", "Zixin Deng", - "Kumar Rajakumar" + "Hong-Yu Ou" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:17537813", @@ -21,9 +21,9 @@ "sc:license": "Unlicense", "sc:name": "MobilomeFINDER", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://db-mml.sjtu.edu.cn/MobilomeFINDER/" } \ No newline at end of file diff --git a/data/mocapy_plus_plus/mocapy_plus_plusbioschemas.jsonld b/data/mocapy_plus_plus/mocapy_plus_plusbioschemas.jsonld index 7217e4645cb8e..462f8fabbfc5f 100644 --- a/data/mocapy_plus_plus/mocapy_plus_plusbioschemas.jsonld +++ b/data/mocapy_plus_plus/mocapy_plus_plusbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Dynamic Bayesian Network toolkit, implemented in C++. It supports discrete, multinomial, Gaussian, Kent, Von Mises and Poisson nodes. Inference and learning is done by Gibbs sampling/Stochastic-EM.", "sc:name": "Mocapy plus plus", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "binf.ku.dk", "sc:url": "http://sourceforge.net/projects/mocapy/", diff --git a/data/moccs/moccsbioschemas.jsonld b/data/moccs/moccsbioschemas.jsonld index d41823cfea05c..ae095358e1975 100644 --- a/data/moccs/moccsbioschemas.jsonld +++ b/data/moccs/moccsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Method for for clarifying DNA-binding motif ambiguity.", "sc:name": "MOCCS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/yuifu/moccs" } \ No newline at end of file diff --git a/data/mochiview/mochiviewbioschemas.jsonld b/data/mochiview/mochiviewbioschemas.jsonld index 69913c1ff1f5d..80786c5cc454c 100644 --- a/data/mochiview/mochiviewbioschemas.jsonld +++ b/data/mochiview/mochiviewbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Hybrid genome browser and motif visualization/analysis/management desktop software.", "sc:name": "MochiView", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://johnsonlab.ucsf.edu/sj/mochiview-start/" diff --git a/data/mocsphaser/mocsphaserbioschemas.jsonld b/data/mocsphaser/mocsphaserbioschemas.jsonld index ef7a2917c9221..070736288f209 100644 --- a/data/mocsphaser/mocsphaserbioschemas.jsonld +++ b/data/mocsphaser/mocsphaserbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.", "sc:name": "MOCSphaser", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://emu.src.riken.jp/index_kato.html" } \ No newline at end of file diff --git a/data/mod_bio/mod_biobioschemas.jsonld b/data/mod_bio/mod_biobioschemas.jsonld index 521d9e20fc985..26a731fff8a0c 100644 --- a/data/mod_bio/mod_biobioschemas.jsonld +++ b/data/mod_bio/mod_biobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Set of Apache modules for Bioinformatics based on the htslib C library.", "sc:name": "mod_bio", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/lindenb/mod_bio" } \ No newline at end of file diff --git a/data/mod_tools/mod_toolsbioschemas.jsonld b/data/mod_tools/mod_toolsbioschemas.jsonld index 34a5cd7e2a72d..8e1bf52648fdf 100644 --- a/data/mod_tools/mod_toolsbioschemas.jsonld +++ b/data/mod_tools/mod_toolsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes, WeederH, a tool for detecting TFBS and regulatory regions from homologous genes, and RNA profile, a tool for secondary structure motif discovery in RNA sequences.", "sc:name": "MoD Tools", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://159.149.160.51/modtools/" diff --git a/data/moda/modabioschemas.jsonld b/data/moda/modabioschemas.jsonld index 301c5d287426a..ddbe90c603949 100644 --- a/data/moda/modabioschemas.jsonld +++ b/data/moda/modabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "MODA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MODA.html", diff --git a/data/modbase/modbasebioschemas.jsonld b/data/modbase/modbasebioschemas.jsonld index a80d3b7acc7b0..30e706c1d022f 100644 --- a/data/modbase/modbasebioschemas.jsonld +++ b/data/modbase/modbasebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Three-dimensional protein models calculated by comparative modelling.", "sc:name": "ModBase", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi" } \ No newline at end of file diff --git a/data/modcell2/modcell2bioschemas.jsonld b/data/modcell2/modcell2bioschemas.jsonld index 311ef1506eb0e..60dbdbb5edc3d 100644 --- a/data/modcell2/modcell2bioschemas.jsonld +++ b/data/modcell2/modcell2bioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "ModCell2", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://modcell2.readthedocs.io/en/latest/" } \ No newline at end of file diff --git a/data/mode-task/mode-taskbioschemas.jsonld b/data/mode-task/mode-taskbioschemas.jsonld index dd51cae7243b7..f2f5d9441de5f 100644 --- a/data/mode-task/mode-taskbioschemas.jsonld +++ b/data/mode-task/mode-taskbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "PCA and normal mode analysis of protein.", "sc:name": "MODE-TASK", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/RUBi-ZA/MODE-TASK" } \ No newline at end of file diff --git a/data/model/modelbioschemas.jsonld b/data/model/modelbioschemas.jsonld index 04a5dc22240f6..430f01f216dcf 100644 --- a/data/model/modelbioschemas.jsonld +++ b/data/model/modelbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Database of protein Molecular Dynamics simulations, with 1800 trajectories representing different structural clusters of the PDB.", "sc:name": "MoDEL", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mmb.irbbarcelona.org/MoDEL", "sc:version": "1.0" diff --git a/data/modelestimator/modelestimatorbioschemas.jsonld b/data/modelestimator/modelestimatorbioschemas.jsonld index 9f584f114aa4f..86bae8119a237 100644 --- a/data/modelestimator/modelestimatorbioschemas.jsonld +++ b/data/modelestimator/modelestimatorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Estimates amino acid replacement rates from an input of aligned sequences.", "sc:name": "MODELESTIMATOR", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.csc.kth.se/~arve/code/modelestimator/" diff --git a/data/modelexplorer/modelexplorerbioschemas.jsonld b/data/modelexplorer/modelexplorerbioschemas.jsonld index be56e451d0274..b89d2306776f3 100644 --- a/data/modelexplorer/modelexplorerbioschemas.jsonld +++ b/data/modelexplorer/modelexplorerbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2615-x", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ModelExplorer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Eivind Almaas", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:30691403", - "pmcid:PMC6348647", { "@id": "https://doi.org/10.1186/s12859-019-2615-x" - } + }, + "pmcid:PMC6348647", + "pubmed:30691403" ], "sc:description": "Software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions.", "sc:featureList": { @@ -28,16 +32,12 @@ "sc:license": "CC-BY-4.0", "sc:name": "ModelExplorer", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://almaaslab.nt.ntnu.no/index.php/resources/metabolic-modeling/", "sc:version": "2.0" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2615-x", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/modeller/modellerbioschemas.jsonld b/data/modeller/modellerbioschemas.jsonld index ff29560985eb7..6103c9e4a9bca 100644 --- a/data/modeller/modellerbioschemas.jsonld +++ b/data/modeller/modellerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.", "sc:name": "MODELLER", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://salilab.org/modeller/" diff --git a/data/modenrichr/modenrichrbioschemas.jsonld b/data/modenrichr/modenrichrbioschemas.jsonld index a970a39ff9fc9..77f5e721a2697 100644 --- a/data/modenrichr/modenrichrbioschemas.jsonld +++ b/data/modenrichr/modenrichrbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://orcid.org/0000-0002-6904-1017", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ347", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/modEnrichr", "@type": "sc:SoftwareApplication", @@ -24,12 +20,12 @@ "@id": "https://orcid.org/0000-0002-6904-1017" }, "sc:additionalType": [ - "Web application", - "Suite" + "Suite", + "Web application" ], "sc:citation": [ - "pmcid:PMC6602483", "pubmed:31069376", + "pmcid:PMC6602483", { "@id": "https://doi.org/10.1093/NAR/GKZ347" } @@ -37,10 +33,10 @@ "sc:description": "Suite of gene set enrichment analysis tools for model organisms.", "sc:featureList": [ { - "@id": "edam:operation_3439" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3439" }, { "@id": "edam:operation_3501" @@ -49,11 +45,15 @@ "sc:license": "Unlicense", "sc:name": "modEnrichr", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://amp.pharm.mssm.edu/modEnrichr/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ347", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/modent/modentbioschemas.jsonld b/data/modent/modentbioschemas.jsonld index 8dad24caafea6..62bd6f6614f5a 100644 --- a/data/modent/modentbioschemas.jsonld +++ b/data/modent/modentbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Computational tool that reconstructs gene regulatory networks from high throughput experimental data.", "sc:name": "ModEnt", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://acgt.cs.tau.ac.il/modent/" } \ No newline at end of file diff --git a/data/moderna/modernabioschemas.jsonld b/data/moderna/modernabioschemas.jsonld index 479c9f6a63e10..5f081836d4505 100644 --- a/data/moderna/modernabioschemas.jsonld +++ b/data/moderna/modernabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-1.0", "sc:name": "ModeRNA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://genesilico.pl/moderna/", diff --git a/data/modest/modestbioschemas.jsonld b/data/modest/modestbioschemas.jsonld index 3269c9e21f67e..deac43794483f 100644 --- a/data/modest/modestbioschemas.jsonld +++ b/data/modest/modestbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "MODEST: A web-based tool for rapid and effective design of optimal multiplex automated genome engineering (MAGE) oligos based on simple input, to achieve any mutation possible with MAGE. The tool is useful in oligonucleotide-mediated genome engineering and recombineering.", "sc:name": "MODEST", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://modest.biosustain.dtu.dk" } \ No newline at end of file diff --git a/data/modexplorer/modexplorerbioschemas.jsonld b/data/modexplorer/modexplorerbioschemas.jsonld index 707ce24e44baa..bc908285fdfd0 100644 --- a/data/modexplorer/modexplorerbioschemas.jsonld +++ b/data/modexplorer/modexplorerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general.", "sc:name": "MODexplorer", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://modorama.org/modexplorer/index/" } \ No newline at end of file diff --git a/data/modfold/modfoldbioschemas.jsonld b/data/modfold/modfoldbioschemas.jsonld index 82ac57e4a0259..9fdc2065ad6a5 100644 --- a/data/modfold/modfoldbioschemas.jsonld +++ b/data/modfold/modfoldbioschemas.jsonld @@ -9,44 +9,44 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkx332", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/modfold", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr Liam J. McGuffin", "edam:has_input": [ { - "@id": "edam:data_0950" + "@id": "edam:data_2974" }, { - "@id": "edam:data_2974" + "@id": "edam:data_0950" } ], "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:28460136", { "@id": "https://doi.org/10.1093/nar/gkx332" }, - "pubmed:28460136", "pmcid:PMC5570241" ], "sc:description": "Global and local quality estimation of 3D protein models. It integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores.", "sc:featureList": [ { - "@id": "edam:operation_0303" + "@id": "edam:operation_0321" }, { "@id": "edam:operation_0267" }, { - "@id": "edam:operation_0321" + "@id": "edam:operation_0303" } ], "sc:name": "ModFOLD6", "sc:url": "http://www.reading.ac.uk/bioinf/ModFOLD/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkx332", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/modfold4/modfold4bioschemas.jsonld b/data/modfold4/modfold4bioschemas.jsonld index 9a5af99b4330b..0cd9bc44aef21 100644 --- a/data/modfold4/modfold4bioschemas.jsonld +++ b/data/modfold4/modfold4bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Webserver for the estimation of both global and local (per-residue) quality of 3D protein models. It produces both machine readable and graphical output.", "sc:name": "ModFOLD4", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.reading.ac.uk/bioinf/ModFOLD/" } \ No newline at end of file diff --git a/data/modifygenomiccoordinates/modifygenomiccoordinatesbioschemas.jsonld b/data/modifygenomiccoordinates/modifygenomiccoordinatesbioschemas.jsonld index 6c895a2fed870..48ede96460f8e 100644 --- a/data/modifygenomiccoordinates/modifygenomiccoordinatesbioschemas.jsonld +++ b/data/modifygenomiccoordinates/modifygenomiccoordinatesbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Extend or shrink a list of genomic coordinates.", "sc:name": "modifygenomiccoordinates", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", diff --git a/data/modil/modilbioschemas.jsonld b/data/modil/modilbioschemas.jsonld index a2b44af48b590..d5b52b2a221d4 100644 --- a/data/modil/modilbioschemas.jsonld +++ b/data/modil/modilbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Mixture of Distributions Indel Locator, a novel method for finding medium sized indels from high throughput sequencing datasets.", "sc:name": "MoDIL", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://compbio.cs.toronto.edu/modil/" } \ No newline at end of file diff --git a/data/modlamp/modlampbioschemas.jsonld b/data/modlamp/modlampbioschemas.jsonld index 9a2a282adb567..cc9fd85037b50 100644 --- a/data/modlamp/modlampbioschemas.jsonld +++ b/data/modlamp/modlampbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Package for the design, classification and visual representation of peptide data.", "sc:name": "modlAMP", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://rossa-prod-ap11.ethz.ch/delivery/DeliveryManagerServlet?dps_pid=IE4903447" diff --git a/data/modlink/modlinkbioschemas.jsonld b/data/modlink/modlinkbioschemas.jsonld index b31c2969f967b..459934271ceaa 100644 --- a/data/modlink/modlinkbioschemas.jsonld +++ b/data/modlink/modlinkbioschemas.jsonld @@ -9,39 +9,39 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btp238", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/modlink", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web API", "sc:author": [ - "Oriol Fornes", { "@id": "http://orcid.org/0000-0002-0128-8363" - } + }, + "Oriol Fornes" ], "sc:citation": [ - "pubmed:19357100", - "pubmed:15883372", { "@id": "https://doi.org/10.1093/bioinformatics/btp238" }, - "pmcid:PMC2687990" + "pubmed:15883372", + "pmcid:PMC2687990", + "pubmed:19357100" ], "sc:description": "A tool predicts protein fold domain and family by means of sequence similarity and a relevant number of similar interactions (the same partners or is potential homologs).", "sc:name": "ModLink+", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "upf.edu", "sc:url": "http://sbi.imim.es/modlink/", "sc:version": "1" }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btp238", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0002-0128-8363", "@type": "schema:Person" diff --git a/data/modmap/modmapbioschemas.jsonld b/data/modmap/modmapbioschemas.jsonld index 106c976c0368f..3e51e9b49aecb 100644 --- a/data/modmap/modmapbioschemas.jsonld +++ b/data/modmap/modmapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for advanced analysis of biological networks. Given two biological networks, it seeks a set of modules, each representing strongly connected nodes in the first network, that are also strongly interconnected in the second network.", "sc:name": "ModMap", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://acgt.cs.tau.ac.il/modmap/" } \ No newline at end of file diff --git a/data/modmatcher/modmatcherbioschemas.jsonld b/data/modmatcher/modmatcherbioschemas.jsonld index e20444edf6570..13574436a8560 100644 --- a/data/modmatcher/modmatcherbioschemas.jsonld +++ b/data/modmatcher/modmatcherbioschemas.jsonld @@ -14,10 +14,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:25122495", { "@id": "https://doi.org/10.1371/journal.pcbi.1003790" }, - "pubmed:25122495", "pmcid:PMC4133046" ], "sc:description": "MODMatcher is a multi-omics data matcher for integrative genomic analysis.", diff --git a/data/modpepint/modpepintbioschemas.jsonld b/data/modpepint/modpepintbioschemas.jsonld index ee698bb493e32..517c310dc69ef 100644 --- a/data/modpepint/modpepintbioschemas.jsonld +++ b/data/modpepint/modpepintbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "New, easy-to-use webserver for the prediction of binding partners for modular protein domains. The server comprises three different tools, i.e. SH2PepInt, SH3PepInt and PDZPepInt, for predicting the binding partners of three different modular protein domains, i.e. SH2, SH3 and PDZ domains, respectively.", "sc:name": "MoDPepInt", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://modpepint.informatik.uni-freiburg.de/" diff --git a/data/modpred/modpredbioschemas.jsonld b/data/modpred/modpredbioschemas.jsonld index 532acd2f331de..52e00c661a02b 100644 --- a/data/modpred/modpredbioschemas.jsonld +++ b/data/modpred/modpredbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ModPred", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://montana.informatics.indiana.edu/ModPred/" } \ No newline at end of file diff --git a/data/modsara-variant/modsara-variantbioschemas.jsonld b/data/modsara-variant/modsara-variantbioschemas.jsonld index f1c759b0201bc..e3e1c711f8830 100644 --- a/data/modsara-variant/modsara-variantbioschemas.jsonld +++ b/data/modsara-variant/modsara-variantbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btx212", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/modsara-variant", "@type": "sc:SoftwareApplication", @@ -18,8 +22,8 @@ { "@id": "https://doi.org/10.1093/bioinformatics/btx212" }, - "pubmed:28453611", - "pmcid:PMC5860124" + "pmcid:PMC5860124", + "pubmed:28453611" ], "sc:description": "modSaRa is an R package designed to perform copy number variants identification.", "sc:featureList": { @@ -29,15 +33,11 @@ "sc:name": "modSaRa", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://publichealth.yale.edu/c2s2/software/modSaRa/", "sc:version": "1.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btx212", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/modsubnetbiomident/modsubnetbiomidentbioschemas.jsonld b/data/modsubnetbiomident/modsubnetbiomidentbioschemas.jsonld index f168e4ab3f2b3..8a5f5c7cedf60 100644 --- a/data/modsubnetbiomident/modsubnetbiomidentbioschemas.jsonld +++ b/data/modsubnetbiomident/modsubnetbiomidentbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Modular Subnetwork Biomarker Identification", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.cs.utoronto.ca/~juris/data/GB10/" } \ No newline at end of file diff --git a/data/modulemaster/modulemasterbioschemas.jsonld b/data/modulemaster/modulemasterbioschemas.jsonld index d6abfe4a1a74d..ddc56815fd573 100644 --- a/data/modulemaster/modulemasterbioschemas.jsonld +++ b/data/modulemaster/modulemasterbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/modulemaster", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Klaus Harter", - "Andreas Zell" + "Andreas Zell", + "Klaus Harter" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:19819296", "sc:description": "Novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs.", "sc:name": "ModuleMaster", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/welcome_e.html" } \ No newline at end of file diff --git a/data/modulesearch/modulesearchbioschemas.jsonld b/data/modulesearch/modulesearchbioschemas.jsonld index 87650bf6dd1d6..4c7663ba9f408 100644 --- a/data/modulesearch/modulesearchbioschemas.jsonld +++ b/data/modulesearch/modulesearchbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software for finding cliques and near-cliques in a protein-protein interaction network.", "sc:name": "ModuleSearch", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bclab.inha.ac.kr/ModuleSearch/" } \ No newline at end of file diff --git a/data/moff/moffbioschemas.jsonld b/data/moff/moffbioschemas.jsonld index 5d58ff45a5bd0..375ce8d870bb9 100644 --- a/data/moff/moffbioschemas.jsonld +++ b/data/moff/moffbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MoFF", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/compomics/moFF", diff --git a/data/mogsa/mogsabioschemas.jsonld b/data/mogsa/mogsabioschemas.jsonld index 375159af0bca7..a794954b62f5a 100644 --- a/data/mogsa/mogsabioschemas.jsonld +++ b/data/mogsa/mogsabioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chen Meng", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provide a method for doing gene set analysis based on multiple omics data.", "sc:license": "GPL-2.0", diff --git a/data/molaxis/molaxisbioschemas.jsonld b/data/molaxis/molaxisbioschemas.jsonld index 5bb54a55de7be..e6d2eb750f733 100644 --- a/data/molaxis/molaxisbioschemas.jsonld +++ b/data/molaxis/molaxisbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The MolAxis web server allows users to identify transmembrane channels in proteins and channels in macromolecules that connect buried cavities to the external surface. Gating residues, channel lining residues and a 3D graphical representation of the channel surface are output.", "sc:name": "MolAxis", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/MolAxis" } \ No newline at end of file diff --git a/data/molden/moldenbioschemas.jsonld b/data/molden/moldenbioschemas.jsonld index fe92d11c3c0f6..25d44bf5a85a6 100644 --- a/data/molden/moldenbioschemas.jsonld +++ b/data/molden/moldenbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.", "sc:name": "MOLDEN", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cmbi.ru.nl/molden/molden.html" } \ No newline at end of file diff --git a/data/mole/molebioschemas.jsonld b/data/mole/molebioschemas.jsonld index 10ad7e7ac26b5..6578c35b80c60 100644 --- a/data/mole/molebioschemas.jsonld +++ b/data/mole/molebioschemas.jsonld @@ -25,8 +25,8 @@ "sc:name": "MOLE", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "Masaryk University, Brno, Czech Republic", diff --git a/data/mole_pymol_plugin/mole_pymol_pluginbioschemas.jsonld b/data/mole_pymol_plugin/mole_pymol_pluginbioschemas.jsonld index 5acc6acf44f71..db85f3ffd0a98 100644 --- a/data/mole_pymol_plugin/mole_pymol_pluginbioschemas.jsonld +++ b/data/mole_pymol_plugin/mole_pymol_pluginbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "MOLE PyMOL plugin", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "Masaryk University Brno, Czech Republic", diff --git a/data/molecular_clock/molecular_clockbioschemas.jsonld b/data/molecular_clock/molecular_clockbioschemas.jsonld index 10e804cdd2742..5acc45baf778c 100644 --- a/data/molecular_clock/molecular_clockbioschemas.jsonld +++ b/data/molecular_clock/molecular_clockbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "MIT", "sc:name": "Molecular clock", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/ugobas/Molecular_clock" diff --git a/data/moleonline/moleonlinebioschemas.jsonld b/data/moleonline/moleonlinebioschemas.jsonld index f0cbf8a3b8de6..02aa59a0bfb00 100644 --- a/data/moleonline/moleonlinebioschemas.jsonld +++ b/data/moleonline/moleonlinebioschemas.jsonld @@ -12,26 +12,26 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:author": [ - "Karel Berka", - "Ondřej Hanák", "Michal Otyepka", - "David Sehnal" + "Ondřej Hanák", + "David Sehnal", + "Karel Berka" ], "sc:contributor": [ - "Crina-Maria Ionescu", - "Radka Svobodová Vařeková", "Jaroslav Koča", - "Pavel Banáš", + "Veronika Navrátilová", + "Radka Svobodová Vařeková", + "Crina-Maria Ionescu", "Deepti Jaiswal", - "Veronika Navrátilová" + "Pavel Banáš" ], "sc:description": "Provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis.", "sc:license": "CC-BY-NC-3.0", "sc:name": "MOLEonline", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "Palacký University Olomouc, Czech Republic", diff --git a/data/molgenis-impute/molgenis-imputebioschemas.jsonld b/data/molgenis-impute/molgenis-imputebioschemas.jsonld index e40b953c457fc..c5b03e09af6e3 100644 --- a/data/molgenis-impute/molgenis-imputebioschemas.jsonld +++ b/data/molgenis-impute/molgenis-imputebioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Alexandros Kanterakis", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4541731", - "pubmed:26286716", { "@id": "https://doi.org/10.1186/S13104-015-1309-3" - } + }, + "pmcid:PMC4541731", + "pubmed:26286716" ], "sc:description": "Rapid generation of genetic imputation scripts for grid/cluster/local environments.", "sc:featureList": { @@ -27,8 +27,8 @@ }, "sc:name": "Molgenis-impute", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/molgenis/molgenis-imputation" }, diff --git a/data/molligen/molligenbioschemas.jsonld b/data/molligen/molligenbioschemas.jsonld index 64b487e884f49..38934b5be546c 100644 --- a/data/molligen/molligenbioschemas.jsonld +++ b/data/molligen/molligenbioschemas.jsonld @@ -19,17 +19,17 @@ "sc:additionalType": "Database portal", "sc:author": "Aurelien Barré", "sc:contributor": [ + "Pascal Sirand-Pugnet", { "@id": "http://orcid.org/0000-0003-4223-5185" - }, - "Pascal Sirand-Pugnet" + } ], "sc:description": "Database dedicated to the comparative genomics of bacteria belonging to the class Mollicutes. It provides annotated sequence data and analysis for 72 genomes belonging to 51 species. The database provides genome and genetic element pages, homology relationship defined by various methods, pre-computed statistics, metabolic pathways, and a huge collection of tools for exploring and comparing genomes.", "sc:name": "Molligen", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "Centre de Bioinformatique de Bordeaux (CBiB)", "sc:url": "http://services.cbib.u-bordeaux2.fr/molligen/" diff --git a/data/molmedb/molmedbbioschemas.jsonld b/data/molmedb/molmedbbioschemas.jsonld index d2add8eccf499..34a1b1aa3e2e8 100644 --- a/data/molmedb/molmedbbioschemas.jsonld +++ b/data/molmedb/molmedbbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-9472-2589", + "@type": "schema:Person" + }, { "@id": "http://orcid.org/0000-0003-3393-3010", "@type": "schema:Person" @@ -27,10 +31,10 @@ } ], "sc:contributor": [ + "Michaela Melíková", { "@id": "http://orcid.org/0000-0001-9556-2978" }, - "Michaela Melíková", { "@id": "http://orcid.org/0000-0001-9472-2589" } @@ -44,10 +48,6 @@ { "@id": "http://orcid.org/0000-0001-9556-2978", "@type": "schema:Person" - }, - { - "@id": "http://orcid.org/0000-0001-9472-2589", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/molmeth/molmethbioschemas.jsonld b/data/molmeth/molmethbioschemas.jsonld index 7fb76c6dc223b..9f8447816d163 100644 --- a/data/molmeth/molmethbioschemas.jsonld +++ b/data/molmeth/molmethbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A structured database that provides best practice-based protocols for molecular analyses.", "sc:name": "MolMeth", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "bils.se", diff --git a/data/molmovdb/molmovdbbioschemas.jsonld b/data/molmovdb/molmovdbbioschemas.jsonld index a46d071fede3d..dc078b10649da 100644 --- a/data/molmovdb/molmovdbbioschemas.jsonld +++ b/data/molmovdb/molmovdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.", "sc:name": "MolMovDB", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://molmovdb.org/" } \ No newline at end of file diff --git a/data/molprobity/molprobitybioschemas.jsonld b/data/molprobity/molprobitybioschemas.jsonld index a64cf48411946..e7b1629009780 100644 --- a/data/molprobity/molprobitybioschemas.jsonld +++ b/data/molprobity/molprobitybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.", "sc:name": "MolProbity", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://molprobity.biochem.duke.edu/" diff --git a/data/molrep/molrepbioschemas.jsonld b/data/molrep/molrepbioschemas.jsonld index 2d92c22896648..1a0c3762a5959 100644 --- a/data/molrep/molrepbioschemas.jsonld +++ b/data/molrep/molrepbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A program for automated molecular replacement in the case where a homologous structure has already been identified.", "sc:name": "MolRep", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://www.ccp4.ac.uk/html/molrep.html", diff --git a/data/molsurfer/molsurferbioschemas.jsonld b/data/molsurfer/molsurferbioschemas.jsonld index 99d167c8ddb34..3f9ee8ea19451 100644 --- a/data/molsurfer/molsurferbioschemas.jsonld +++ b/data/molsurfer/molsurferbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "MolSurfer", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://projects.h-its.org/dbase/molsurfer/index.html" } \ No newline at end of file diff --git a/data/mom/mombioschemas.jsonld b/data/mom/mombioschemas.jsonld index 29f1dd06eed57..48dde0e0ff454 100644 --- a/data/mom/mombioschemas.jsonld +++ b/data/mom/mombioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Short-read mapping", "sc:name": "MOM", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/hugheaves/MOM" diff --git a/data/moma/momabioschemas.jsonld b/data/moma/momabioschemas.jsonld index f8a4f8d974dbd..5cba97c3e2f9d 100644 --- a/data/moma/momabioschemas.jsonld +++ b/data/moma/momabioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Florian Jug", "sc:additionalType": [ - "Desktop application", - "Plug-in" + "Plug-in", + "Desktop application" ], "sc:description": "Takes specific advantage of the geometry of the device to accurately segment and track cells using only phase-contrast images, and further provides a curation user interface with leveraged-editing, meaning that a set of related errors are often fixed with a single click.", "sc:name": "MoMA", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/fjug/MoMA" } \ No newline at end of file diff --git a/data/monet/monetbioschemas.jsonld b/data/monet/monetbioschemas.jsonld index ebbc5991bf429..aacffde714719 100644 --- a/data/monet/monetbioschemas.jsonld +++ b/data/monet/monetbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/MONET", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mattia Tomasoni", - "Sven Bergmann" + "Sven Bergmann", + "Mattia Tomasoni" ], "sc:additionalType": "Command-line tool", "sc:description": "Toolbox integrating top-performing methods for NEtwork MOdularisation.", diff --git a/data/monetfamily/monetfamilybioschemas.jsonld b/data/monetfamily/monetfamilybioschemas.jsonld index 0f86c4fe30f2a..8d0a0f756213d 100644 --- a/data/monetfamily/monetfamilybioschemas.jsonld +++ b/data/monetfamily/monetfamilybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server that can identify the modules, homologous modules (called module family), and MMI networks across multiple species for the query protein(s).", "sc:name": "MoNetFamily", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://monetfamily.life.nctu.edu.tw/" } \ No newline at end of file diff --git a/data/mongkie/mongkiebioschemas.jsonld b/data/mongkie/mongkiebioschemas.jsonld index b0e03fdb02fac..87556392937ee 100644 --- a/data/mongkie/mongkiebioschemas.jsonld +++ b/data/mongkie/mongkiebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13062-016-0112-y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mongkie", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pubmed:26987515", - "pmcid:PMC4797132", { "@id": "https://doi.org/10.1186/s13062-016-0112-y" - } + }, + "pmcid:PMC4797132" ], "sc:description": "Modular Network Generation and Visualization Platform with Knowledge Integration Environments (MONGKIE) is a software platform that integrates network visualization with omics data analysis tools.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "AGPL-3.0", "sc:name": "MONGKIE", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://yjjang.github.io/mongkie/" + }, + { + "@id": "https://doi.org/10.1186/s13062-016-0112-y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/monoallelic_gene_inference_from_chromatin/monoallelic_gene_inference_from_chromatinbioschemas.jsonld b/data/monoallelic_gene_inference_from_chromatin/monoallelic_gene_inference_from_chromatinbioschemas.jsonld index ca5295741368f..113facfccaa55 100644 --- a/data/monoallelic_gene_inference_from_chromatin/monoallelic_gene_inference_from_chromatinbioschemas.jsonld +++ b/data/monoallelic_gene_inference_from_chromatin/monoallelic_gene_inference_from_chromatinbioschemas.jsonld @@ -9,27 +9,23 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2679-7", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Monoallelic_Gene_Inference_from_Chromatin", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Henry Ward", + "Svetlana Vinogradova", "Alexander Gimelbrant", "Sachit Saksena", - "Svetlana Vinogradova", - "Sébastien Vigneau", - "Henry Ward" + "Sébastien Vigneau" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:30819107", "pmcid:PMC6394031", + "pubmed:30819107", { "@id": "https://doi.org/10.1186/s12859-019-2679-7" } @@ -37,10 +33,10 @@ "sc:description": "Monoallelic Gene Inference from Chromatin (MaGIC) - tool to classify genes into monoallelically expressed (MAE) and biallelically expressed (BAE) using chromatin mark enrichment data.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_3227" }, { - "@id": "edam:operation_3227" + "@id": "edam:operation_3501" } ], "sc:license": "MIT", @@ -51,6 +47,10 @@ "Mac" ], "sc:url": "https://github.com/gimelbrantlab/magic" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2679-7", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/monoallelic_gene_inference_from_chromatin_magic/monoallelic_gene_inference_from_chromatin_magicbioschemas.jsonld b/data/monoallelic_gene_inference_from_chromatin_magic/monoallelic_gene_inference_from_chromatin_magicbioschemas.jsonld index 62234aa759260..9e76de5d63ac3 100644 --- a/data/monoallelic_gene_inference_from_chromatin_magic/monoallelic_gene_inference_from_chromatin_magicbioschemas.jsonld +++ b/data/monoallelic_gene_inference_from_chromatin_magic/monoallelic_gene_inference_from_chromatin_magicbioschemas.jsonld @@ -9,27 +9,23 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2679-7", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Monoallelic_gene_inference_from_chromatin_MaGIC", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Svetlana Vinogradova", - "Henry Ward", - "Sébastien Vigneau", "Sachit Saksena", - "Alexander Gimelbrant" + "Alexander Gimelbrant", + "Sébastien Vigneau", + "Henry Ward" ], "sc:additionalType": "Library", "sc:citation": [ + "pubmed:30819107", "pmcid:PMC6394031", { "@id": "https://doi.org/10.1186/s12859-019-2679-7" - }, - "pubmed:30819107" + } ], "sc:description": "Machine learning tool set and web application for monoallelic gene inference from chromatin. Classifies genes into monoallelically expressed (MAE) and biallelically expressed (BAE) using chromatin mark enrichment data.", "sc:featureList": [ @@ -47,6 +43,10 @@ "Linux" ], "sc:url": "https://github.com/gimelbrantlab/magic" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2679-7", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/monoclad/monocladbioschemas.jsonld b/data/monoclad/monocladbioschemas.jsonld index 05b3e5f816c4a..2e3ae87b5e1ec 100644 --- a/data/monoclad/monocladbioschemas.jsonld +++ b/data/monoclad/monocladbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Finds meaningful partitions using semi-supervised class discovery.", "sc:name": "MonoClad", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioinfo.cs.technion.ac.il/people/zohar/MonoClad/software.html" diff --git a/data/monocle/monoclebioschemas.jsonld b/data/monocle/monoclebioschemas.jsonld index 757cfdf7eb9b9..7658ead5688e3 100644 --- a/data/monocle/monoclebioschemas.jsonld +++ b/data/monocle/monoclebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/nmeth.4150", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/monocle", "@type": "sc:SoftwareApplication", @@ -16,23 +20,23 @@ "@id": "http://orcid.org/0000-0002-8105-4347" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC5330805", "pubmed:28114287", { "@id": "https://doi.org/10.1038/nmeth.4150" - }, - "pmcid:PMC5330805" + } ], "sc:description": "This tool performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. It also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.", "sc:license": "Artistic-2.0", "sc:name": "monocle", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/monocle.html", "sc:version": "2.2.0" @@ -40,10 +44,6 @@ { "@id": "http://orcid.org/0000-0002-8105-4347", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1038/nmeth.4150", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/monosaccharidedb/monosaccharidedbbioschemas.jsonld b/data/monosaccharidedb/monosaccharidedbbioschemas.jsonld index 5095bdbf7589b..43d6867dc26aa 100644 --- a/data/monosaccharidedb/monosaccharidedbbioschemas.jsonld +++ b/data/monosaccharidedb/monosaccharidedbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Information on the residues used in glycan databases.", "sc:name": "Monosaccharide database", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.monosaccharidedb.org/" diff --git a/data/monster/monsterbioschemas.jsonld b/data/monster/monsterbioschemas.jsonld index 88d97a5e040c5..c271400e28370 100644 --- a/data/monster/monsterbioschemas.jsonld +++ b/data/monster/monsterbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Not licensed", "sc:name": "MONSTER", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://monster.northwestern.edu/" } \ No newline at end of file diff --git a/data/moonlightr/moonlightrbioschemas.jsonld b/data/moonlightr/moonlightrbioschemas.jsonld index b7c1b22fc42db..44c8ed79acb58 100644 --- a/data/moonlightr/moonlightrbioschemas.jsonld +++ b/data/moonlightr/moonlightrbioschemas.jsonld @@ -15,8 +15,8 @@ "Catharina Olsen" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:28456671", "sc:description": "The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role. We present an R/bioconductor package which returns a list of candidate driver genes for specific cancer types based on TCGA expression data. First infers gene regulatory networks and then carries out a functional enrichment analysis to score the importance of well-known biological processes with respect to the studied cancer type.", @@ -24,8 +24,8 @@ "sc:name": "MoonlightR", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MoonlightR.html", "sc:version": "1.0.0" diff --git a/data/mops/mopsbioschemas.jsonld b/data/mops/mopsbioschemas.jsonld index c0d604c880e61..bb3ac0c2af793 100644 --- a/data/mops/mopsbioschemas.jsonld +++ b/data/mops/mopsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "MoPS", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MoPS.html", "sc:version": "1.8.0" diff --git a/data/morca/morcabioschemas.jsonld b/data/morca/morcabioschemas.jsonld index e35f0fc7f74c0..fccc7a3d4ef13 100644 --- a/data/morca/morcabioschemas.jsonld +++ b/data/morca/morcabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "mORCA", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "uma.es", "sc:url": "http://bitlab-es.com/morca/", diff --git a/data/mordred/mordredbioschemas.jsonld b/data/mordred/mordredbioschemas.jsonld index 5956bb71afbf4..a7fb99912c134 100644 --- a/data/mordred/mordredbioschemas.jsonld +++ b/data/mordred/mordredbioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13321-018-0258-y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mordred", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Moriwaki H", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:29411163", "pmcid:PMC5801138", + "pubmed:29411163", { "@id": "https://doi.org/10.1186/s13321-018-0258-y" } @@ -32,10 +28,14 @@ "sc:license": "BSD-3-Clause", "sc:name": "Mordred", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/mordred-descriptor/mordred" + }, + { + "@id": "https://doi.org/10.1186/s13321-018-0258-y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/morfeus/morfeusbioschemas.jsonld b/data/morfeus/morfeusbioschemas.jsonld index 86acb4dc0aced..ecc425a0523d0 100644 --- a/data/morfeus/morfeusbioschemas.jsonld +++ b/data/morfeus/morfeusbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-15-263", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/morfeus", "@type": "sc:SoftwareApplication", @@ -25,8 +21,8 @@ { "@id": "https://doi.org/10.1186/1471-2105-15-263" }, - "pubmed:25096057", - "pmcid:PMC4137093" + "pmcid:PMC4137093", + "pubmed:25096057" ], "sc:description": "Meta-analysis based orthology finder using symmetrical best hits.", "sc:featureList": { @@ -34,11 +30,15 @@ }, "sc:name": "morFeus", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bio.biochem.mpg.de/morfeus/" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-15-263", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/morph/morphbioschemas.jsonld b/data/morph/morphbioschemas.jsonld index c4b3776ab250e..8f04430af50fc 100644 --- a/data/morph/morphbioschemas.jsonld +++ b/data/morph/morphbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-7096-8063", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/morph", "@type": "sc:SoftwareApplication", @@ -24,12 +20,16 @@ "sc:description": "Algorithm to associate candidate genes with a given target pathway. Unlike any other algorithm in plant sciences, this algorithm tests multiple combinations by learning how to choose among various forms of evidence (large scale data sets) to link genes to a specific target pathway.", "sc:name": "MORPH", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioinformatics.psb.ugent.be/webtools/morph/", "sc:version": "1" + }, + { + "@id": "http://orcid.org/0000-0002-7096-8063", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/morphin/morphinbioschemas.jsonld b/data/morphin/morphinbioschemas.jsonld index a01df5f27c94e..67b000913866b 100644 --- a/data/morphin/morphinbioschemas.jsonld +++ b/data/morphin/morphinbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-based bioinformatics tool to study human diseases using model organism genes.", "sc:name": "MORPHIN", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.inetbio.org/morphin/" } \ No newline at end of file diff --git a/data/morphocatcher/morphocatcherbioschemas.jsonld b/data/morphocatcher/morphocatcherbioschemas.jsonld index 32ef183dbb891..5dc84397033bc 100644 --- a/data/morphocatcher/morphocatcherbioschemas.jsonld +++ b/data/morphocatcher/morphocatcherbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.7717/PEERJ.6801", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/MorphoCatcher", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:31086739", + "pmcid:PMC6487805", { "@id": "https://doi.org/10.7717/PEERJ.6801" - }, - "pmcid:PMC6487805" + } ], "sc:description": "Multiple-alignment based web tool for target selection and designing taxon-specific primers in the loop-mediated isothermal amplification method.", "sc:featureList": [ @@ -41,10 +37,14 @@ "sc:name": "MorphoCatcher", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://morphocatcher.ru" + }, + { + "@id": "https://doi.org/10.7717/PEERJ.6801", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/morpholibj/morpholibjbioschemas.jsonld b/data/morpholibj/morpholibjbioschemas.jsonld index 4397a5beab889..c5dbd44fa6ca3 100644 --- a/data/morpholibj/morpholibjbioschemas.jsonld +++ b/data/morpholibj/morpholibjbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Library that proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins.", "sc:name": "MorphoLibJ", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://ijpb.github.io/MorphoLibJ/" } \ No newline at end of file diff --git a/data/mosaic/mosaicbioschemas.jsonld b/data/mosaic/mosaicbioschemas.jsonld index 1f17ba92b0ff3..a121875932ebf 100644 --- a/data/mosaic/mosaicbioschemas.jsonld +++ b/data/mosaic/mosaicbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Software which calculates the ‘mosaicity’ of a one dimensional hybrid zone. This package uses likelihood to fit step-wise models to one dimensional hybrid zone data, and to estimate the ‘mosaicity’ of the hybrid zone.", "sc:name": "mosaic", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.zoology.ubc.ca/prog/mosaic/" diff --git a/data/mosaic_vaccine_designer/mosaic_vaccine_designerbioschemas.jsonld b/data/mosaic_vaccine_designer/mosaic_vaccine_designerbioschemas.jsonld index 72efc13d58d31..520ca9afeb174 100644 --- a/data/mosaic_vaccine_designer/mosaic_vaccine_designerbioschemas.jsonld +++ b/data/mosaic_vaccine_designer/mosaic_vaccine_designerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Mosaic Vaccine Designer", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.hiv.lanl.gov/content/sequence/MOSAIC/makeVaccine.html" } \ No newline at end of file diff --git a/data/mosaics/mosaicsbioschemas.jsonld b/data/mosaics/mosaicsbioschemas.jsonld index 25e23bd7a8126..6326619619b1c 100644 --- a/data/mosaics/mosaicsbioschemas.jsonld +++ b/data/mosaics/mosaicsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dongjun Chung", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides functions for fitting MOSAiCS-HMM, an statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.", "sc:license": "GPL-2.0", "sc:name": "mosaics", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mosaics.html", "sc:version": "2.12.0" diff --git a/data/mosaik/mosaikbioschemas.jsonld b/data/mosaik/mosaikbioschemas.jsonld index c560cad106ad0..3d11cbce5c46c 100644 --- a/data/mosaik/mosaikbioschemas.jsonld +++ b/data/mosaik/mosaikbioschemas.jsonld @@ -19,16 +19,16 @@ "biotools:primaryContact": "Wan Ping Lee", "sc:additionalType": "Suite", "sc:citation": [ + "pmcid:PMC4051166", "pubmed:24599324", { - "@id": "https://doi.org/10.1371/journal.pone.0090581" + "@id": "https://doi.org/10.1186/1471-2164-15-264" }, - "pmcid:PMC3944147", { - "@id": "https://doi.org/10.1186/1471-2164-15-264" + "@id": "https://doi.org/10.1371/journal.pone.0090581" }, - "pmcid:PMC4051166", - "pubmed:24708189" + "pubmed:24708189", + "pmcid:PMC3944147" ], "sc:description": "Reference guided aligner/assembler.", "sc:featureList": { diff --git a/data/mosclip/mosclipbioschemas.jsonld b/data/mosclip/mosclipbioschemas.jsonld index 31b625d506137..aa5c732e619a4 100644 --- a/data/mosclip/mosclipbioschemas.jsonld +++ b/data/mosclip/mosclipbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "AGPL-3.0", "sc:name": "MOSClip", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/cavei/MOSClip" } \ No newline at end of file diff --git a/data/mosdi/mosdibioschemas.jsonld b/data/mosdi/mosdibioschemas.jsonld index f09432cacfb97..e017a3be8b2b4 100644 --- a/data/mosdi/mosdibioschemas.jsonld +++ b/data/mosdi/mosdibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Contains a lot of sequence analysis algorithms, including methods for motif statistics, exact motif discovery, analysis of pattern matching algorithms, etc.", "sc:name": "MoSDi", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://bitbucket.org/tobiasmarschall/mosdi" } \ No newline at end of file diff --git a/data/mosflm/mosflmbioschemas.jsonld b/data/mosflm/mosflmbioschemas.jsonld index 670d937777cc1..d92d997f3b5ba 100644 --- a/data/mosflm/mosflmbioschemas.jsonld +++ b/data/mosflm/mosflmbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Andrew G.W. Leslie", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "Program for integrating single crystal diffraction data from area detectors. It is assumed that the experiment was conducted using the Arndt-Wonacott oscillation method, and also that monochromatic radiation was used.", "sc:name": "Mosflm", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://www.mrc-lmb.cam.ac.uk/harry/mosflm/index.html", diff --git a/data/motan/motanbioschemas.jsonld b/data/motan/motanbioschemas.jsonld index d33682dcd0ed9..3c9a1f7728ed1 100644 --- a/data/motan/motanbioschemas.jsonld +++ b/data/motan/motanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Detects structural motifs containing β-strands.", "sc:name": "MotAn", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=motan" } \ No newline at end of file diff --git a/data/motif-x/motif-xbioschemas.jsonld b/data/motif-x/motif-xbioschemas.jsonld index ede378011f2e1..6230e74606ec2 100644 --- a/data/motif-x/motif-xbioschemas.jsonld +++ b/data/motif-x/motif-xbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.", "sc:name": "motif-x", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://motif-x.med.harvard.edu/motif-x.html" diff --git a/data/motifbreakr/motifbreakrbioschemas.jsonld b/data/motifbreakr/motifbreakrbioschemas.jsonld index de667835b2545..001d8123e7bc3 100644 --- a/data/motifbreakr/motifbreakrbioschemas.jsonld +++ b/data/motifbreakr/motifbreakrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btv470", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/motifbreakr", "@type": "sc:SoftwareApplication", @@ -31,16 +35,12 @@ "sc:license": "GPL-2.0", "sc:name": "motifbreakR", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/motifbreakR.html", "sc:version": "1.4.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btv470", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/motifcounter/motifcounterbioschemas.jsonld b/data/motifcounter/motifcounterbioschemas.jsonld index 23aadbb5284ef..8b9dff742de49 100644 --- a/data/motifcounter/motifcounterbioschemas.jsonld +++ b/data/motifcounter/motifcounterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "motifcounter", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/motifcounter.html", "sc:version": "1.4.0" diff --git a/data/motifcut/motifcutbioschemas.jsonld b/data/motifcut/motifcutbioschemas.jsonld index 8574b9cede796..91b2acc12970f 100644 --- a/data/motifcut/motifcutbioschemas.jsonld +++ b/data/motifcut/motifcutbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "DNA motif-finding algorithm using a Maximum Density Subgraph.", "sc:name": "MotifCut 0.1 beta", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://motifcut.stanford.edu/" } \ No newline at end of file diff --git a/data/motifdb/bioconda_motifdb.yaml b/data/motifdb/bioconda_motifdb.yaml index a85c91052bdca..cb43cfb01c2b7 100644 --- a/data/motifdb/bioconda_motifdb.yaml +++ b/data/motifdb/bioconda_motifdb.yaml @@ -4,7 +4,6 @@ description: More than 9900 annotated position frequency matrices from 14 public home: https://bioconductor.org/packages/3.10/bioc/html/MotifDb.html identifiers: - biotools:motifdb -- doi:10.1038/nmeth.3252 license: Artistic-2.0 | file LICENSE license_file: LICENSE name: bioconductor-motifdb diff --git a/data/motifdb/motifdbbioschemas.jsonld b/data/motifdb/motifdbbioschemas.jsonld index 80c1f720ced23..43bca1f8cec65 100644 --- a/data/motifdb/motifdbbioschemas.jsonld +++ b/data/motifdb/motifdbbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "MotifDb", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MotifDb.html", "sc:version": "1.16.0" diff --git a/data/motiflab/motiflabbioschemas.jsonld b/data/motiflab/motiflabbioschemas.jsonld index 04373e576c72b..745d46aae7821 100644 --- a/data/motiflab/motiflabbioschemas.jsonld +++ b/data/motiflab/motiflabbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:description": "General workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. It can improve performance of binding site predictions by allowing users to integrate several motif discovery tools, as well as different types of data: phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, TF-TF interactions, TF-expression and target gene expression.", "sc:name": "MotifLab", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.motiflab.org", "sc:version": "1.8" diff --git a/data/motifmatchr/motifmatchrbioschemas.jsonld b/data/motifmatchr/motifmatchrbioschemas.jsonld index ec122ddc2cd72..a1ff29af1ac74 100644 --- a/data/motifmatchr/motifmatchrbioschemas.jsonld +++ b/data/motifmatchr/motifmatchrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "motifmatchr", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/motifmatchr.html", "sc:version": "1.2.0" diff --git a/data/motifregressor/motifregressorbioschemas.jsonld b/data/motifregressor/motifregressorbioschemas.jsonld index ccb766fd3a87b..d42c0e48f8ab0 100644 --- a/data/motifregressor/motifregressorbioschemas.jsonld +++ b/data/motifregressor/motifregressorbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MOTIFREGRESSOR for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. MOTIF REGRESSOR is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions.", "sc:name": "MotifRegressor", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.math.umass.edu/~conlon/mr.html" } \ No newline at end of file diff --git a/data/motifsampler/motifsamplerbioschemas.jsonld b/data/motifsampler/motifsamplerbioschemas.jsonld index d5601bdf7584e..c130a41fe4ecb 100644 --- a/data/motifsampler/motifsamplerbioschemas.jsonld +++ b/data/motifsampler/motifsamplerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MotifSampler tries to find over-represented motifs in the upstream region of a set of co-regulated genes. This motif finding algorithm uses Gibbs sampling to find the position probability matrix that represents the motif. In this implementation we focus on the use of higher-order background models to improve the robustness of the motif finding. At the moment the MotifSampler comes with background models for several organisms .", "sc:name": "MotifSampler", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://homes.esat.kuleuven.be/~sistawww/bioi/thijs/Work/MotifSampler.html", "sc:version": "3.2" diff --git a/data/motifscan/motifscanbioschemas.jsonld b/data/motifscan/motifscanbioschemas.jsonld index 459e46d029d7f..19e87b30dac18 100644 --- a/data/motifscan/motifscanbioschemas.jsonld +++ b/data/motifscan/motifscanbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MotifScan is a non-parametric DNA motif scanning algorithm.", "sc:name": "MotifScan", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://motifscan.stanford.edu/" } \ No newline at end of file diff --git a/data/motifsim/motifsimbioschemas.jsonld b/data/motifsim/motifsimbioschemas.jsonld index cbd8d0b700cd8..4aa42df517c56 100644 --- a/data/motifsim/motifsimbioschemas.jsonld +++ b/data/motifsim/motifsimbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Contact form", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5610392", - "pubmed:28632401", { "@id": "https://doi.org/10.1089/cmb.2017.0005" - } + }, + "pmcid:PMC5610392", + "pubmed:28632401" ], "sc:description": "Detecting similarity in a single or multiple DNA motif datasets.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "MOTIFSIM", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://motifsim.org/" }, diff --git a/data/motifstack/bioconda_motifstack.yaml b/data/motifstack/bioconda_motifstack.yaml index 0c71a5f9dd136..bc5a15e666ac0 100644 --- a/data/motifstack/bioconda_motifstack.yaml +++ b/data/motifstack/bioconda_motifstack.yaml @@ -6,7 +6,6 @@ description: The motifStack package is designed for graphic representation of mu home: https://bioconductor.org/packages/3.10/bioc/html/motifStack.html identifiers: - biotools:motifstack -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-motifstack diff --git a/data/motifstack/motifstackbioschemas.jsonld b/data/motifstack/motifstackbioschemas.jsonld index 693fd086e1caa..6e92abf16a288 100644 --- a/data/motifstack/motifstackbioschemas.jsonld +++ b/data/motifstack/motifstackbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jianhong Ou", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.", "sc:license": "GPL-2.0", "sc:name": "motifStack", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/motifStack.html", "sc:version": "1.18.0" diff --git a/data/motifsuite/motifsuitebioschemas.jsonld b/data/motifsuite/motifsuitebioschemas.jsonld index 2c16b16bbde9f..30bb06c08b59e 100644 --- a/data/motifsuite/motifsuitebioschemas.jsonld +++ b/data/motifsuite/motifsuitebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Probabilistic motif detection.", "sc:name": "MotifSuite", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/MotifSuite/Index.htm", diff --git a/data/motifviz/motifvizbioschemas.jsonld b/data/motifviz/motifvizbioschemas.jsonld index 4f83779a7f6be..efa94a43c1aea 100644 --- a/data/motifviz/motifvizbioschemas.jsonld +++ b/data/motifviz/motifvizbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum.", "sc:name": "MotifViz", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://biowulf.bu.edu/MotifViz/" } \ No newline at end of file diff --git a/data/motiv/bioconda_motiv.yaml b/data/motiv/bioconda_motiv.yaml index f6ae5daa0276a..35705f8a6172b 100644 --- a/data/motiv/bioconda_motiv.yaml +++ b/data/motiv/bioconda_motiv.yaml @@ -5,7 +5,6 @@ description: This package makes use of STAMP for comparing a set of motifs to a home: https://bioconductor.org/packages/3.10/bioc/html/MotIV.html identifiers: - biotools:motiv -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-motiv diff --git a/data/motiv/motivbioschemas.jsonld b/data/motiv/motivbioschemas.jsonld index a3c7f21a8d185..e5e87fb49f75e 100644 --- a/data/motiv/motivbioschemas.jsonld +++ b/data/motiv/motivbioschemas.jsonld @@ -15,16 +15,16 @@ "Raphael Gottardo" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.", "sc:license": "GPL-2.0", "sc:name": "MotIV", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MotIV.html", "sc:version": "1.30.0" diff --git a/data/motivevalidator/motivevalidatorbioschemas.jsonld b/data/motivevalidator/motivevalidatorbioschemas.jsonld index d929870db1628..7e2be582aba19 100644 --- a/data/motivevalidator/motivevalidatorbioschemas.jsonld +++ b/data/motivevalidator/motivevalidatorbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/motivevalidator", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": "David Sehnal", "sc:contributor": [ "Deepti Jaiswal", - "Lukáš Pravda", + "Crina-Maria Ionescu", "Radka Svobodová Vařeková", - "Crina-Maria Ionescu" + "Lukáš Pravda" ], "sc:description": "A web application for validation of annotation of ligands and \nresidues.", "sc:name": "MotiveValidator", diff --git a/data/motus/motusbioschemas.jsonld b/data/motus/motusbioschemas.jsonld index f42db5155852e..339657812c7ea 100644 --- a/data/motus/motusbioschemas.jsonld +++ b/data/motus/motusbioschemas.jsonld @@ -25,12 +25,12 @@ "sc:license": "GPL-3.0", "sc:name": "Metagenomic operational taxonomic units (mOTUs)", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "European Molecular Biology Laboratory (EMBL)", - "HD-HuB" + "HD-HuB", + "European Molecular Biology Laboratory (EMBL)" ], "sc:url": "http://www.bork.embl.de/software/mOTU/", "sc:version": "1.0" diff --git a/data/mouse_atlas/mouse_atlasbioschemas.jsonld b/data/mouse_atlas/mouse_atlasbioschemas.jsonld index ae80193054d5d..3afe0cb2395a4 100644 --- a/data/mouse_atlas/mouse_atlasbioschemas.jsonld +++ b/data/mouse_atlas/mouse_atlasbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A quantitative and comprehensive atlas of gene expression in mouse development. The project has a goal of producing 150 publically available SAGE libraries.", "sc:name": "Mouse Atlas of Gene Expression", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.mouseatlas.org/mouseatlas_index_html" } \ No newline at end of file diff --git a/data/mousebook/mousebookbioschemas.jsonld b/data/mousebook/mousebookbioschemas.jsonld index 2fe5c3fdb6923..02082fda4bc13 100644 --- a/data/mousebook/mousebookbioschemas.jsonld +++ b/data/mousebook/mousebookbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The database and web portal provide access to information about mutant mouse lines held as live or cryopreserved stocks at MRC Harwell. It portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide value-added information.", "sc:name": "Mousebook", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.mousebook.org/" } \ No newline at end of file diff --git a/data/mousedivgeno/mousedivgenobioschemas.jsonld b/data/mousedivgeno/mousedivgenobioschemas.jsonld index 2979c9dd1c4c3..422d6a86cf390 100644 --- a/data/mousedivgeno/mousedivgenobioschemas.jsonld +++ b/data/mousedivgeno/mousedivgenobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "R package specifically designed to genotype the Mouse Diversity Genotyping Array, an Affymetrix mouse genotyping array similar to the human SNP 6.0. It contains functions which allow you to perform genotyping, identify probe sets potentially harboring a new mutation (Variable INtensity Oligonucleotide or VINO, here we call it a vinotyping) and perform CNV analysis.", "sc:name": "MouseDivGeno", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://cgd.jax.org/tools/mousedivgeno/" } \ No newline at end of file diff --git a/data/mousemine/mouseminebioschemas.jsonld b/data/mousemine/mouseminebioschemas.jsonld index fa26ca0008623..d4f1befe2587b 100644 --- a/data/mousemine/mouseminebioschemas.jsonld +++ b/data/mousemine/mouseminebioschemas.jsonld @@ -13,15 +13,15 @@ "@id": "https://bio.tools/mousemine", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:citation": [ - "pubmed:26092688", - "pmcid:PMC4534495", { "@id": "https://doi.org/10.1007/s00335-015-9573-z" - } + }, + "pubmed:26092688", + "pmcid:PMC4534495" ], "sc:description": "Data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer.", "sc:featureList": { diff --git a/data/moviemaker/moviemakerbioschemas.jsonld b/data/moviemaker/moviemakerbioschemas.jsonld index 074c24766275b..5921ae12270cf 100644 --- a/data/moviemaker/moviemakerbioschemas.jsonld +++ b/data/moviemaker/moviemakerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MovieMaker", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://wishart.biology.ualberta.ca/moviemaker/" } \ No newline at end of file diff --git a/data/mowserv/mowservbioschemas.jsonld b/data/mowserv/mowservbioschemas.jsonld index e390dfc8caa20..70713b5fa2465 100644 --- a/data/mowserv/mowservbioschemas.jsonld +++ b/data/mowserv/mowservbioschemas.jsonld @@ -13,18 +13,18 @@ "@id": "https://bio.tools/mowserv", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Esteban Pérez-Wohlfeil", { "@id": "https://orcid.org/0000-0003-1554-8987" - }, - "Esteban Pérez-Wohlfeil" + } ], "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:20525794", + "pmcid:PMC2896175", { "@id": "https://doi.org/10.1093/nar/gkq497" - }, - "pubmed:20525794", - "pmcid:PMC2896175" + } ], "sc:description": "Versatile web client to access BioMOBY compatible services for interaction with multiple sources of biological data. .", "sc:featureList": [ @@ -32,18 +32,18 @@ "@id": "edam:operation_3760" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_0335" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_2422" } ], "sc:license": "GPL-3.0", "sc:name": "MOWServ", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "uma.es", "sc:url": "http://bitlab-es.com/gnv5/", diff --git a/data/mpa/mpabioschemas.jsonld b/data/mpa/mpabioschemas.jsonld index 272c141acdec3..59650cd32f8ba 100644 --- a/data/mpa/mpabioschemas.jsonld +++ b/data/mpa/mpabioschemas.jsonld @@ -21,9 +21,9 @@ "sc:license": "Other", "sc:name": "MPA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://www.medcomp.medicina.unipd.it/stefano/mpa/", diff --git a/data/mpblast/mpblastbioschemas.jsonld b/data/mpblast/mpblastbioschemas.jsonld index 5695b662c3e49..554064f5cce7e 100644 --- a/data/mpblast/mpblastbioschemas.jsonld +++ b/data/mpblast/mpblastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software that increases the throughput of batch BLASTN searches by multiplexing (concatenating) query sequences and thereby reducing the number of actual database searches performed.", "sc:name": "MPBLAST", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://korflab.ucdavis.edu/software.html" } \ No newline at end of file diff --git a/data/mpd-primer/mpd-primerbioschemas.jsonld b/data/mpd-primer/mpd-primerbioschemas.jsonld index 10b72b0b35465..16cb2f4a48756 100644 --- a/data/mpd-primer/mpd-primerbioschemas.jsonld +++ b/data/mpd-primer/mpd-primerbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-016-1453-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mpd-primer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28056760", { "@id": "https://doi.org/10.1186/s12859-016-1453-3" }, + "pubmed:28056760", "pmcid:PMC5217220" ], "sc:description": "Multiplex primer design for next-generation targeted sequencing.", @@ -32,10 +28,14 @@ "sc:license": "GPL-3.0", "sc:name": "MPD", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://wingolab-org.github.io/mpd-c/" + }, + { + "@id": "https://doi.org/10.1186/s12859-016-1453-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mpd/mpdbioschemas.jsonld b/data/mpd/mpdbioschemas.jsonld index 8deef034ca0e4..2ccb87c03e0ee 100644 --- a/data/mpd/mpdbioschemas.jsonld +++ b/data/mpd/mpdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Mouse Phenome Database: houses a wealth of strain characteristics data to facilitate the use of the laboratory mouse in translational research for human health and disease. Data sets are voluntarily contributed by researchers from a variety of institutions. MPD maintains a growing collection of standardized reference data that assists investigators in selecting mouse strains for research applications.", "sc:name": "MPD", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://phenome.jax.org/" } \ No newline at end of file diff --git a/data/mpex/mpexbioschemas.jsonld b/data/mpex/mpexbioschemas.jsonld index 956021d2ead33..a78efc6eb5409 100644 --- a/data/mpex/mpexbioschemas.jsonld +++ b/data/mpex/mpexbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MPEx", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://blanco.biomol.uci.edu/mpex/" } \ No newline at end of file diff --git a/data/mpfe/mpfebioschemas.jsonld b/data/mpfe/mpfebioschemas.jsonld index 243be610800d2..a32bed973b36f 100644 --- a/data/mpfe/mpfebioschemas.jsonld +++ b/data/mpfe/mpfebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "MPFE", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MPFE.html", diff --git a/data/mpi_toolkit/mpi_toolkitbioschemas.jsonld b/data/mpi_toolkit/mpi_toolkitbioschemas.jsonld index d17c98e4fb346..8e82fb3b11e7e 100644 --- a/data/mpi_toolkit/mpi_toolkitbioschemas.jsonld +++ b/data/mpi_toolkit/mpi_toolkitbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.", "sc:name": "MPI Toolkit", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://toolkit.tuebingen.mpg.de" } \ No newline at end of file diff --git a/data/mpileup/mpileupbioschemas.jsonld b/data/mpileup/mpileupbioschemas.jsonld index 1e51dbab63f4a..8c80584a7833c 100644 --- a/data/mpileup/mpileupbioschemas.jsonld +++ b/data/mpileup/mpileupbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Filter bam file using mpileup on coverage and SNPs.", "sc:name": "mpileup", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.htslib.org/", "sc:version": "0.1.19" diff --git a/data/mpileup_vcf/mpileup_vcfbioschemas.jsonld b/data/mpileup_vcf/mpileup_vcfbioschemas.jsonld index f470f2dff5cab..fe37889f423ec 100644 --- a/data/mpileup_vcf/mpileup_vcfbioschemas.jsonld +++ b/data/mpileup_vcf/mpileup_vcfbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "On coverage and SNPs and output a vcf file.", "sc:name": "mpileup_vcf", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.htslib.org/", "sc:version": "1.0.2" diff --git a/data/mpiutils/mpiutilsbioschemas.jsonld b/data/mpiutils/mpiutilsbioschemas.jsonld index 7f9cce8e4291b..6d583f6e3dcca 100644 --- a/data/mpiutils/mpiutilsbioschemas.jsonld +++ b/data/mpiutils/mpiutilsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Do you have thousands of files that you need to run the same program on? Are xargs, GNU parallel, and any of the million workflow management systems not working out for you? This package may be of assistance. It provides a command line tool for parallel execution of many command line tasks on any architecture that supports MPI. It also includes parallel implementations of the Python :func:`map` and :func:`imap` functions and a few handy bits and pieces for logging.", "sc:name": "mpiutils", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "unimelb.edu.au", "sc:url": "https://bitbucket.org/bkaehler/mpiutils", diff --git a/data/mpp/mppbioschemas.jsonld b/data/mpp/mppbioschemas.jsonld index b55f72ff8228e..6e38a7d10d96f 100644 --- a/data/mpp/mppbioschemas.jsonld +++ b/data/mpp/mppbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Microarray-to-Phylogeny-Pipeline encompasses both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. It analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. It can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network.", "sc:name": "MPP", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://cbr.jic.ac.uk/dicks/software/mpp/index.html", "sc:version": "2.0" diff --git a/data/mpra/mprabioschemas.jsonld b/data/mpra/mprabioschemas.jsonld index f987c37e5c3b0..0742cfaca43a9 100644 --- a/data/mpra/mprabioschemas.jsonld +++ b/data/mpra/mprabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "mpra", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mpra.html", diff --git a/data/mpra_design_tools/mpra_design_toolsbioschemas.jsonld b/data/mpra_design_tools/mpra_design_toolsbioschemas.jsonld index dd7b603814c0b..c58a09535e159 100644 --- a/data/mpra_design_tools/mpra_design_toolsbioschemas.jsonld +++ b/data/mpra_design_tools/mpra_design_toolsbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chad A Shaw", "sc:additionalType": [ - "Web application", - "Library" + "Library", + "Web application" ], "sc:description": "Interactive MPRA experimental design encompassing both power analysis and design of constructs.", "sc:name": "MPRA design tools", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://andrewghazi.shinyapps.io/designmpra/" } \ No newline at end of file diff --git a/data/mpranator/mpranatorbioschemas.jsonld b/data/mpranator/mpranatorbioschemas.jsonld index d94e5501e745b..9ebc3733f340c 100644 --- a/data/mpranator/mpranatorbioschemas.jsonld +++ b/data/mpranator/mpranatorbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/MPRAnator", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ilias Georgakopoulos-Soares", - "Martin Hemberg" + "Martin Hemberg", + "Ilias Georgakopoulos-Soares" ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Web-based tool for the design of massively parallel reporter assay experiments.", "sc:license": "MIT", "sc:name": "MPRAnator", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.sanger.ac.uk/science/tools/mpranator" } \ No newline at end of file diff --git a/data/mpromdb/mpromdbbioschemas.jsonld b/data/mpromdb/mpromdbbioschemas.jsonld index 5cea2592fc5d4..f16aaf836f0e1 100644 --- a/data/mpromdb/mpromdbbioschemas.jsonld +++ b/data/mpromdb/mpromdbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Mammalian Promoter Database (MPromDb)", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinformatics.wistar.upenn.edu/MPromDb/" } \ No newline at end of file diff --git a/data/mpscan/mpscanbioschemas.jsonld b/data/mpscan/mpscanbioschemas.jsonld index 66c0b3b36bd58..eea4a549966d8 100644 --- a/data/mpscan/mpscanbioschemas.jsonld +++ b/data/mpscan/mpscanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "MPscan (multi-pattern scan) is a program for mapping short reads (<30bp) exactly on a set of reference sequences (eg, a genome) without indexing the reference. MPscan performs only exact mapping (no substitution, nor indels), is fast (optimal complexity), and easy to use.", "sc:name": "MPscan", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.atgc-montpellier.fr/mpscan/" } \ No newline at end of file diff --git a/data/mptheory/mptheorybioschemas.jsonld b/data/mptheory/mptheorybioschemas.jsonld index c54d87f608e24..73e8454b18b25 100644 --- a/data/mptheory/mptheorybioschemas.jsonld +++ b/data/mptheory/mptheorybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Collects a set of Java objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a discrete mathematical theory based on P systems, introduced by Prof. Vincenzo Manca in 2004 for modeling biological dynamics. By means of the library, it is possible to model dynamical systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations.", "sc:name": "MpTheory", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://mptheory.scienze.univr.it/" diff --git a/data/mptopoquerier/mptopoquerierbioschemas.jsonld b/data/mptopoquerier/mptopoquerierbioschemas.jsonld index 12c1e33b73a5c..00efea50042fc 100644 --- a/data/mptopoquerier/mptopoquerierbioschemas.jsonld +++ b/data/mptopoquerier/mptopoquerierbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Java applet developed for searching MPtopo, a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. Retrieved sequences can be examined automatically by MPEx, a java-based hydropathy-plot tool.", "sc:name": "MPtopoQuerier", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://blanco.biomol.uci.edu/mptopo/" diff --git a/data/mptp/mptpbioschemas.jsonld b/data/mptp/mptpbioschemas.jsonld index 0dd2431a34988..b6f1976aebcba 100644 --- a/data/mptp/mptpbioschemas.jsonld +++ b/data/mptp/mptpbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/mptp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Tomas Flouri", "Alexandros Stamatakis", - "Paschalia Kapli", - "Tomas Flouri" + "Paschalia Kapli" ], "sc:additionalType": "Web application", "sc:description": "Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.", "sc:name": "mPTP", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://mptp.h-its.org/#/tree" diff --git a/data/mqc/mqcbioschemas.jsonld b/data/mqc/mqcbioschemas.jsonld index 608168518abad..5b95d58695f4f 100644 --- a/data/mqc/mqcbioschemas.jsonld +++ b/data/mqc/mqcbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-9441-9539", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0002-7575-2085", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/mQC", "@type": "sc:SoftwareApplication", @@ -24,19 +32,11 @@ "sc:license": "GPL-3.0", "sc:name": "mQC", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/Biobix/mQC", "sc:version": "1.10" - }, - { - "@id": "https://orcid.org/0000-0001-9441-9539", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0002-7575-2085", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mqscore/mqscorebioschemas.jsonld b/data/mqscore/mqscorebioschemas.jsonld index 16584e98c83f4..30e33040f7684 100644 --- a/data/mqscore/mqscorebioschemas.jsonld +++ b/data/mqscore/mqscorebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MQscore", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mga.bionet.nsc.ru/soft/mqscore/" } \ No newline at end of file diff --git a/data/mr-mega/mr-megabioschemas.jsonld b/data/mr-mega/mr-megabioschemas.jsonld index b5f74d7c45565..877c7060c1374 100644 --- a/data/mr-mega/mr-megabioschemas.jsonld +++ b/data/mr-mega/mr-megabioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/MR-MEGA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Andrew P Morris", - "Reedik Magi" + "Reedik Magi", + "Andrew P Morris" ], "sc:additionalType": "Command-line tool", "sc:description": "MR-MEGA (Meta-Regression of Multi-Ethnic Genetic Association) - tool to detect and fine-map complex trait association signals via trans-ethnic meta-regression.", "sc:license": "Unlicense", "sc:name": "MR-MEGA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://www.geenivaramu.ee/en/tools/mr-mega", diff --git a/data/mr-microt/mr-microtbioschemas.jsonld b/data/mr-microt/mr-microtbioschemas.jsonld index 48c16fc0fbda2..6d9fece877fbb 100644 --- a/data/mr-microt/mr-microtbioschemas.jsonld +++ b/data/mr-microt/mr-microtbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MR-microT", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mrmicrot/index" } \ No newline at end of file diff --git a/data/mrbayes/mrbayesbioschemas.jsonld b/data/mrbayes/mrbayesbioschemas.jsonld index db2ff3cb655e6..e8666f2b1f440 100644 --- a/data/mrbayes/mrbayesbioschemas.jsonld +++ b/data/mrbayes/mrbayesbioschemas.jsonld @@ -14,15 +14,15 @@ "sc:author": "Fredrik Ronquist", "sc:citation": "pubmed:11524383", "sc:contributor": [ - "Donald Simon", + "Maxim Teslenko", "NSF", - "NIH", + "John Huelsenbeck", + "Bret Larget", + "Donald Simon", "Chi Zhang", "Paul van der Mark", - "Vetenskapsrådet", - "Bret Larget", - "Maxim Teslenko", - "John Huelsenbeck" + "NIH", + "Vetenskapsrådet" ], "sc:description": "Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.", "sc:funder": [ @@ -33,9 +33,9 @@ "sc:license": "GPL-3.0", "sc:name": "MrBayes", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ "icm.uu.se", diff --git a/data/mrbump/mrbumpbioschemas.jsonld b/data/mrbump/mrbumpbioschemas.jsonld index ace14429a503d..d75facf0f99fd 100644 --- a/data/mrbump/mrbumpbioschemas.jsonld +++ b/data/mrbump/mrbumpbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A set of scripts for molecular replacement. It searches for homologous structures, creates a set of suitable search models from template structures, does molecular replacement and tests the solutions.", "sc:name": "MrBUMP", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://www.ccp4.ac.uk/MrBUMP/", diff --git a/data/mrbws/mrbwsbioschemas.jsonld b/data/mrbws/mrbwsbioschemas.jsonld index 9c0212209d99a..b399e428aa43c 100644 --- a/data/mrbws/mrbwsbioschemas.jsonld +++ b/data/mrbws/mrbwsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Resource management project that provides a dynamic and interactive view of world wide available mouse resources.", "sc:name": "Mrbws", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioit.fleming.gr/mrb/data.jsp", "sc:version": "1" diff --git a/data/mrc_image_processing_package/mrc_image_processing_packagebioschemas.jsonld b/data/mrc_image_processing_package/mrc_image_processing_packagebioschemas.jsonld index f7ec5a3be2b84..dbd32ec40699c 100644 --- a/data/mrc_image_processing_package/mrc_image_processing_packagebioschemas.jsonld +++ b/data/mrc_image_processing_package/mrc_image_processing_packagebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Software for image processing of 2D and 3D crystals.", "sc:name": "MRC Image Processing Package", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://www2.mrc-lmb.cam.ac.uk/image2000.html", diff --git a/data/mrcfile/mrcfilebioschemas.jsonld b/data/mrcfile/mrcfilebioschemas.jsonld index f6643bc41f517..1565168a8ac74 100644 --- a/data/mrcfile/mrcfilebioschemas.jsonld +++ b/data/mrcfile/mrcfilebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "mrcfile", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://mrcfile.readthedocs.io/en/latest/readme.html", diff --git a/data/mredictor/mredictorbioschemas.jsonld b/data/mredictor/mredictorbioschemas.jsonld index 2ae36188c4915..01e6a1f3b8c55 100644 --- a/data/mredictor/mredictorbioschemas.jsonld +++ b/data/mredictor/mredictorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Highly accurate method for the identification of bona-fide microRNAs targets within mammalian genes.", "sc:name": "MREdictor", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://mredictor.hugef-research.org/" } \ No newline at end of file diff --git a/data/mreps/mrepsbioschemas.jsonld b/data/mreps/mrepsbioschemas.jsonld index 915b227930e41..d1a9e89836508 100644 --- a/data/mreps/mrepsbioschemas.jsonld +++ b/data/mreps/mrepsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "mreps is a tool for identifing tandemn repeats in DNA sequences.", "sc:name": "mreps", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioinfo.lifl.fr/mreps/" diff --git a/data/mres2x/mres2xbioschemas.jsonld b/data/mres2x/mres2xbioschemas.jsonld index 74fe692f82a60..f1cde63358889 100644 --- a/data/mres2x/mres2xbioschemas.jsonld +++ b/data/mres2x/mres2xbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool to process MASCOT results.", "sc:name": "mres2x", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/protms/files/mres2x/" } \ No newline at end of file diff --git a/data/mrhmms/mrhmmsbioschemas.jsonld b/data/mrhmms/mrhmmsbioschemas.jsonld index 20af0ef15321c..3733898650f9e 100644 --- a/data/mrhmms/mrhmmsbioschemas.jsonld +++ b/data/mrhmms/mrhmmsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Accommodates a variety of HMMs that can be flexibly applied to many biological studies and beyond.", "sc:name": "MRHMMs", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://sourceforge.net/projects/mrhmms/" } \ No newline at end of file diff --git a/data/mricloud/mricloudbioschemas.jsonld b/data/mricloud/mricloudbioschemas.jsonld index 00d8cf20cde5a..6b5332781c920 100644 --- a/data/mricloud/mricloudbioschemas.jsonld +++ b/data/mricloud/mricloudbioschemas.jsonld @@ -17,16 +17,16 @@ "@id": "https://bio.tools/MRICloud", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kumiko Oishi", - "Kenichi Oishi" + "Kenichi Oishi", + "Kumiko Oishi" ], "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC6609486", - "pubmed:31037800", { "@id": "https://doi.org/10.1111/JON.12623" - } + }, + "pubmed:31037800" ], "sc:description": "Multi‐Atlas Label Fusion Tool for Neonatal Brain MRI Parcellation and Quantification.", "sc:featureList": { @@ -36,8 +36,8 @@ "sc:name": "MRICloud", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://braingps.mricloud.org" } diff --git a/data/mrmre/mrmrebioschemas.jsonld b/data/mrmre/mrmrebioschemas.jsonld index 6aef233d3aefa..8add56dc576c1 100644 --- a/data/mrmre/mrmrebioschemas.jsonld +++ b/data/mrmre/mrmrebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "mRMRe", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.pmgenomics.ca/bhklab/software/mrmre" } \ No newline at end of file diff --git a/data/mrna_optimiser/mrna_optimiserbioschemas.jsonld b/data/mrna_optimiser/mrna_optimiserbioschemas.jsonld index 48e5b2979b915..534075300fbd9 100644 --- a/data/mrna_optimiser/mrna_optimiserbioschemas.jsonld +++ b/data/mrna_optimiser/mrna_optimiserbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "mRNA optimiser", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioinformatics.ua.pt/software/mrna-optimiser/" } \ No newline at end of file diff --git a/data/mrprimerw/mrprimerwbioschemas.jsonld b/data/mrprimerw/mrprimerwbioschemas.jsonld index 9b2afdfff66e5..7178f6e059002 100644 --- a/data/mrprimerw/mrprimerwbioschemas.jsonld +++ b/data/mrprimerw/mrprimerwbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Server that performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, and ranks the resulting primers to return the top-1 best primers to the user.", "sc:name": "MRPrimerW", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://mrprimerw.com/" } \ No newline at end of file diff --git a/data/mrprimerw2/mrprimerw2bioschemas.jsonld b/data/mrprimerw2/mrprimerw2bioschemas.jsonld index 6adbc02918938..f4531223aefaf 100644 --- a/data/mrprimerw2/mrprimerw2bioschemas.jsonld +++ b/data/mrprimerw2/mrprimerw2bioschemas.jsonld @@ -17,10 +17,10 @@ "@id": "https://bio.tools/MRPrimerW2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Min-Soo Kim", { "@id": "https://orcid.org/0000-0003-4962-8272" - }, - "Min-Soo Kim" + } ], "sc:additionalType": "Web application", "sc:description": "Tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments.", @@ -28,8 +28,8 @@ "sc:name": "MRPrimerW2", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://MRPrimerW2.com" } diff --git a/data/mrs/mrsbioschemas.jsonld b/data/mrs/mrsbioschemas.jsonld index b18ff2098a2f9..0b021d4ffbe86 100644 --- a/data/mrs/mrsbioschemas.jsonld +++ b/data/mrs/mrsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MRS", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mrs.cmbi.ru.nl/" } \ No newline at end of file diff --git a/data/mrsfast/mrsfastbioschemas.jsonld b/data/mrsfast/mrsfastbioschemas.jsonld index 1dafd2b1c24ff..31874b38c4292 100644 --- a/data/mrsfast/mrsfastbioschemas.jsonld +++ b/data/mrsfast/mrsfastbioschemas.jsonld @@ -18,16 +18,16 @@ ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC3115707", "pubmed:20676076", { - "@id": "https://doi.org/10.1186/1471-2105-14-184" + "@id": "https://doi.org/10.1038/nmeth0810-576" }, - "pmcid:PMC3694458", - "pmcid:PMC3115707", { - "@id": "https://doi.org/10.1038/nmeth0810-576" + "@id": "https://doi.org/10.1186/1471-2105-14-184" }, - "pubmed:23758764" + "pubmed:23758764", + "pmcid:PMC3694458" ], "sc:description": "micro-read substitution-only Fast Alignment Search Tool. Short read mapper that optimizes cache usage to get higher performance.", "sc:featureList": [ diff --git a/data/mruninovo/mruninovobioschemas.jsonld b/data/mruninovo/mruninovobioschemas.jsonld index ff14c552007ce..de4a60132f6d6 100644 --- a/data/mruninovo/mruninovobioschemas.jsonld +++ b/data/mruninovo/mruninovobioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/MRUniNovo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kenli Li", - "Tao Chen" + "Tao Chen", + "Kenli Li" ], "sc:description": "Tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.", "sc:license": "Unlicense", "sc:name": "MRUniNovo", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioinfo.hupo.org.cn/MRUniNovo/index.php" } \ No newline at end of file diff --git a/data/ms-blast/ms-blastbioschemas.jsonld b/data/ms-blast/ms-blastbioschemas.jsonld index 7d741ae02c7a1..a6ad3560673b1 100644 --- a/data/ms-blast/ms-blastbioschemas.jsonld +++ b/data/ms-blast/ms-blastbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Specialised BLAST –based protocol developed for identification of proteins by sequence similarity searches using peptide sequences produced by the interpretation of tandem mass spectra.", "sc:name": "MS-BLAST", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genetics.bwh.harvard.edu/msblast/" } \ No newline at end of file diff --git a/data/ms-deconv/ms-deconvbioschemas.jsonld b/data/ms-deconv/ms-deconvbioschemas.jsonld index b2bfd701713b1..a8b00346c13de 100644 --- a/data/ms-deconv/ms-deconvbioschemas.jsonld +++ b/data/ms-deconv/ms-deconvbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MS-Deconv is a combinatorial algorithm for spectral deconvolution. The algorithm first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest scoring subset of envelopes as a heaviest path in the graph.", "sc:name": "MS-Deconv", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://proteomics.ucsd.edu/software-tools/ms-deconv/", "sc:version": "0.8.0.7370" diff --git a/data/ms-digest/ms-digestbioschemas.jsonld b/data/ms-digest/ms-digestbioschemas.jsonld index bf7eda742b625..ac892af1af5e4 100644 --- a/data/ms-digest/ms-digestbioschemas.jsonld +++ b/data/ms-digest/ms-digestbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/ms-digest", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Digests a protein sequence.", "sc:name": "MS-Digest", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msdigest" } \ No newline at end of file diff --git a/data/ms-fit/ms-fitbioschemas.jsonld b/data/ms-fit/ms-fitbioschemas.jsonld index 530c5efe57d3c..015aedbd7f72f 100644 --- a/data/ms-fit/ms-fitbioschemas.jsonld +++ b/data/ms-fit/ms-fitbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/ms-fit", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Peptide mass fingerpriting tool in the ProteinProspector suite.", "sc:name": "MS-Fit", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msfitstandard" } \ No newline at end of file diff --git a/data/ms-gfdb/ms-gfdbbioschemas.jsonld b/data/ms-gfdb/ms-gfdbbioschemas.jsonld index 1ee4748cedc12..c3f1bd140df97 100644 --- a/data/ms-gfdb/ms-gfdbbioschemas.jsonld +++ b/data/ms-gfdb/ms-gfdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MS-GFDB", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://proteomics.ucsd.edu/ProteoSAFe/" } \ No newline at end of file diff --git a/data/ms-helios/ms-heliosbioschemas.jsonld b/data/ms-helios/ms-heliosbioschemas.jsonld index 47c63296b6652..d579acc11b033 100644 --- a/data/ms-helios/ms-heliosbioschemas.jsonld +++ b/data/ms-helios/ms-heliosbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-018-2564-9", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/MS-Helios", "@type": "sc:SoftwareApplication", @@ -18,34 +22,30 @@ { "@id": "https://doi.org/10.1186/s12859-018-2564-9" }, - "pmcid:PMC6330434", - "pubmed:30634897" + "pubmed:30634897", + "pmcid:PMC6330434" ], "sc:description": "Tool with multiple built-in data processing functions, allowing non-expert users to construct circular proteome maps (CPMs) or in general terms circular plots with a non-genomic basis.", "sc:featureList": [ { - "@id": "edam:operation_2939" + "@id": "edam:operation_0417" }, { - "@id": "edam:operation_2940" + "@id": "edam:operation_2939" }, { - "@id": "edam:operation_0417" + "@id": "edam:operation_2940" } ], "sc:license": "Apache-2.0", "sc:name": "MS-Helios", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://sourceforge.net/projects/ms-helios/", "sc:version": "1.1.8" - }, - { - "@id": "https://doi.org/10.1186/s12859-018-2564-9", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ms-isotope/ms-isotopebioschemas.jsonld b/data/ms-isotope/ms-isotopebioschemas.jsonld index 57be0879775e8..ca2479b868d2a 100644 --- a/data/ms-isotope/ms-isotopebioschemas.jsonld +++ b/data/ms-isotope/ms-isotopebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/ms-isotope", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Calculates the isotopic distribution from a peptide sequence.", "sc:name": "MS-Isotope", diff --git a/data/ms-lims/ms-limsbioschemas.jsonld b/data/ms-lims/ms-limsbioschemas.jsonld index 2af8b244be255..913f8cd547f80 100644 --- a/data/ms-lims/ms-limsbioschemas.jsonld +++ b/data/ms-lims/ms-limsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Project that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.", "sc:name": "Ms-lims", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "ugent.be", diff --git a/data/ms2pip_server/ms2pip_serverbioschemas.jsonld b/data/ms2pip_server/ms2pip_serverbioschemas.jsonld index 333be4eb52745..f85b1e303faaf 100644 --- a/data/ms2pip_server/ms2pip_serverbioschemas.jsonld +++ b/data/ms2pip_server/ms2pip_serverbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/MS2PIP_Server", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web API", - "Web application" + "Web application", + "Web API" ], "sc:description": "MS²PIP is a tool to predict MS² peak intensities from peptide sequences. This makes it possible to generate in silico predicted spectral libraries for full proteomes. MS²PIP employs the XGBoost machine learning algorithm and is written in Python.", "sc:license": "Apache-2.0", diff --git a/data/ms_align/ms_alignbioschemas.jsonld b/data/ms_align/ms_alignbioschemas.jsonld index 865163f20ff68..95d1901cd6f9b 100644 --- a/data/ms_align/ms_alignbioschemas.jsonld +++ b/data/ms_align/ms_alignbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "MS_Align", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.atgc-montpellier.fr/ms_align/" } \ No newline at end of file diff --git a/data/msa/msabioschemas.jsonld b/data/msa/msabioschemas.jsonld index 83b475af94e54..8140fa17ed58a 100644 --- a/data/msa/msabioschemas.jsonld +++ b/data/msa/msabioschemas.jsonld @@ -17,11 +17,11 @@ ], "sc:author": "Sebastian Wilzbach", "sc:contributor": [ - "Google Summer of Code (GSoC) 2014", - "Benedikt Rauscher", - "Ian Sillitoe", "Tatyana Goldberg", - "Guy Yachdav" + "Benedikt Rauscher", + "Guy Yachdav", + "Google Summer of Code (GSoC) 2014", + "Ian Sillitoe" ], "sc:description": "Display multiple-sequence alignment. The tool is also available as R/BioConductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms.", "sc:funder": "Google Summer of Code (GSoC) 2014", @@ -33,8 +33,8 @@ "Linux" ], "sc:provider": [ - "BioJS", - "Technische Universität München" + "Technische Universität München", + "BioJS" ], "sc:url": "http://msa.biojs.net", "sc:version": "1.0.0" diff --git a/data/msacquisitionsimulator/msacquisitionsimulatorbioschemas.jsonld b/data/msacquisitionsimulator/msacquisitionsimulatorbioschemas.jsonld index 7d3bcb104e84b..b9259d1d225c5 100644 --- a/data/msacquisitionsimulator/msacquisitionsimulatorbioschemas.jsonld +++ b/data/msacquisitionsimulator/msacquisitionsimulatorbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/msacquisitionsimulator", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wang W", - "Major MB" + "Major MB", + "Wang W" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:26685308", diff --git a/data/msaprobs/msaprobsbioschemas.jsonld b/data/msaprobs/msaprobsbioschemas.jsonld index 7a705bb71d0eb..6b5a68648576e 100644 --- a/data/msaprobs/msaprobsbioschemas.jsonld +++ b/data/msaprobs/msaprobsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Multiple alignment algorithm for protein sequences.", "sc:name": "MSAprobs", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://msaprobs.sourceforge.net/homepage.htm#latest", "sc:version": "1" diff --git a/data/msaviewer/msaviewerbioschemas.jsonld b/data/msaviewer/msaviewerbioschemas.jsonld index 9b8f3c770df04..d942f51f19c5c 100644 --- a/data/msaviewer/msaviewerbioschemas.jsonld +++ b/data/msaviewer/msaviewerbioschemas.jsonld @@ -13,20 +13,20 @@ "sc:additionalType": "Library", "sc:author": "Sebastian Wilzbach", "sc:contributor": [ - "Benedikt Rauscher", - "Google Summer of Code (GSoC) 2014", - "Guy Yachdav", "Ian Sillitoe", - "Tatyana Goldberg" + "Guy Yachdav", + "Tatyana Goldberg", + "Benedikt Rauscher", + "Google Summer of Code (GSoC) 2014" ], "sc:description": "Large MSAs visualization interactively on the web.", "sc:funder": "Google Summer of Code (GSoC) 2014", "sc:license": "Apache-2.0", "sc:name": "MSAViewer", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "BioJS", diff --git a/data/msbar/msbarbioschemas.jsonld b/data/msbar/msbarbioschemas.jsonld index dfbe1a97e23c5..7b8646b655a42 100644 --- a/data/msbar/msbarbioschemas.jsonld +++ b/data/msbar/msbarbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK BBSRC", "UK MRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "Wellcome Trust" ], "sc:description": "Mutate a sequence.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "msbar", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/msbar.html", "sc:version": "r6" diff --git a/data/msbe/msbebioschemas.jsonld b/data/msbe/msbebioschemas.jsonld index e2b3e8334da13..ad4cad85f375d 100644 --- a/data/msbe/msbebioschemas.jsonld +++ b/data/msbe/msbebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for the analysis of gene expression data using a new bi-clustering method. It can find constant bi-clusters and additive bi-clusters.", "sc:name": "MSBE", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.cs.cityu.edu.hk/~lwang/software/msbe/" } \ No newline at end of file diff --git a/data/mscentipede/mscentipedebioschemas.jsonld b/data/mscentipede/mscentipedebioschemas.jsonld index 7533d8cb1fbed..99040a8fe046d 100644 --- a/data/mscentipede/mscentipedebioschemas.jsonld +++ b/data/mscentipede/mscentipedebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "msCentipede", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/rajanil/msCentipede" } \ No newline at end of file diff --git a/data/mscltoolbox/mscltoolboxbioschemas.jsonld b/data/mscltoolbox/mscltoolboxbioschemas.jsonld index 377e6096cb00e..c07bb4cbc7c65 100644 --- a/data/mscltoolbox/mscltoolboxbioschemas.jsonld +++ b/data/mscltoolbox/mscltoolboxbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MSCLtoolbox", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://abs.cit.nih.gov/MSCLtoolbox/", "sc:version": "200902" diff --git a/data/msclust/msclustbioschemas.jsonld b/data/msclust/msclustbioschemas.jsonld index 6fe7d9d95a4bc..906e110e90229 100644 --- a/data/msclust/msclustbioschemas.jsonld +++ b/data/msclust/msclustbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MSClust", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://zhaocenter.org/software/#Genomic_Protein_Sequence_Analysis", "sc:version": "20130708" diff --git a/data/msconvert/msconvertbioschemas.jsonld b/data/msconvert/msconvertbioschemas.jsonld index 69e212c528411..dc6d6c7fe22dd 100644 --- a/data/msconvert/msconvertbioschemas.jsonld +++ b/data/msconvert/msconvertbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/nbt.2377", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/msconvert", "@type": "sc:SoftwareApplication", @@ -29,26 +25,26 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0121" + "@id": "edam:topic_3520" }, { - "@id": "edam:topic_3520" + "@id": "edam:topic_0121" } ], "sc:citation": [ - "pmcid:PMC3471674", { "@id": "https://doi.org/10.1038/nbt.2377" }, + "pmcid:PMC3471674", "pubmed:23051804" ], "sc:description": "msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.", "sc:featureList": [ { - "@id": "edam:operation_3695" + "@id": "edam:operation_0335" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_3695" } ], "sc:isAccessibleForFree": true, @@ -61,6 +57,10 @@ }, "sc:url": "http://proteowizard.sourceforge.net/tools.shtml", "sc:version": "3.0" + }, + { + "@id": "https://doi.org/10.1038/nbt.2377", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/msd_file_reader/msd_file_readerbioschemas.jsonld b/data/msd_file_reader/msd_file_readerbioschemas.jsonld index c21b0e7751f7f..9a096b22e75a6 100644 --- a/data/msd_file_reader/msd_file_readerbioschemas.jsonld +++ b/data/msd_file_reader/msd_file_readerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Read, display and save data from the original HP MSD based on the HP Pascal Chemstation.", "sc:name": "MSD File Reader", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.quadtechassociates.com/freeware.html" } \ No newline at end of file diff --git a/data/msea/mseabioschemas.jsonld b/data/msea/mseabioschemas.jsonld index c2abadaf843c9..96bc6fac71e5e 100644 --- a/data/msea/mseabioschemas.jsonld +++ b/data/msea/mseabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Performs enrichment analyses for (primarily human) metabolomic studies. It identifies patterns of metabolite concentration changes in a biologically meaningful context. It uses a library of ~6300 predefined metabolite sets from pathways, disease signatures, genetic traits, and cellular/tissue locations. It also facilitates conversion between metabolite common names, synonyms and other database identifies.", "sc:name": "MSEA", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.msea.ca" } \ No newline at end of file diff --git a/data/msfilereader_python_bindings/msfilereader_python_bindingsbioschemas.jsonld b/data/msfilereader_python_bindings/msfilereader_python_bindingsbioschemas.jsonld index e59d81ae01c64..7dc5a322a2d5a 100644 --- a/data/msfilereader_python_bindings/msfilereader_python_bindingsbioschemas.jsonld +++ b/data/msfilereader_python_bindings/msfilereader_python_bindingsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Python bindings for the (non-free) ThermoFisher Scientific MSFileReader.", "sc:name": "MSFileReader_Python_bindings", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/frallain/MSFileReader_Python_bindings" } \ No newline at end of file diff --git a/data/msgbsr/msgbsrbioschemas.jsonld b/data/msgbsr/msgbsrbioschemas.jsonld index 2b060b82be367..28f920cd54c1b 100644 --- a/data/msgbsr/msgbsrbioschemas.jsonld +++ b/data/msgbsr/msgbsrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "msgbsR", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://bioconductor.org/packages/release/bioc/html/msgbsR.html", diff --git a/data/msgfdb2pepxml/msgfdb2pepxmlbioschemas.jsonld b/data/msgfdb2pepxml/msgfdb2pepxmlbioschemas.jsonld index cf2870a590a17..5952ec8ed6831 100644 --- a/data/msgfdb2pepxml/msgfdb2pepxmlbioschemas.jsonld +++ b/data/msgfdb2pepxml/msgfdb2pepxmlbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "msgfdb2pepxml", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://ms-utils.org/msgfdb2pepxml/index.html" } \ No newline at end of file diff --git a/data/msgfgui/msgfguibioschemas.jsonld b/data/msgfgui/msgfguibioschemas.jsonld index 03112ff59a75b..2ad36fbf903a6 100644 --- a/data/msgfgui/msgfguibioschemas.jsonld +++ b/data/msgfgui/msgfguibioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas Lin Pedersen", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package makes it possible to perform analyses using the MSGFplus package in a GUI environment. Furthermore it enables the user to investigate the results using interactive plots, summary statistics and filtering. Lastly it exposes the current results to another R session so the user can seamlessly integrate the gui into other workflows.", "sc:license": "GPL-2.0", "sc:name": "MSGFgui", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MSGFgui.html", diff --git a/data/msgfplus/msgfplusbioschemas.jsonld b/data/msgfplus/msgfplusbioschemas.jsonld index f7d2acfb38754..75bf558f186e5 100644 --- a/data/msgfplus/msgfplusbioschemas.jsonld +++ b/data/msgfplus/msgfplusbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas Lin Pedersen", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package contains function to perform peptide identification using MS-GF+.", "sc:license": "GPL-2.0", "sc:name": "MSGFplus", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MSGFplus.html", diff --git a/data/msgl/msglbioschemas.jsonld b/data/msgl/msglbioschemas.jsonld index 8e7fd8dc60848..2f9abc13bdf68 100644 --- a/data/msgl/msglbioschemas.jsonld +++ b/data/msgl/msglbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "This R package (multinomial sparse group lasso) fits multinomial models for e.g. multiclass classification with a sparse group lasso penalty.", "sc:name": "msgl", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.math.ku.dk/~richard/msgl/" diff --git a/data/mshot/mshotbioschemas.jsonld b/data/mshot/mshotbioschemas.jsonld index 083bfa1119ab3..12c3a1fdecf73 100644 --- a/data/mshot/mshotbioschemas.jsonld +++ b/data/mshot/mshotbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Not licensed", "sc:name": "msHOT", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://uchicago.app.box.com/s/l3e5uf13tikfjm7e1il1eujitlsjdx13" } \ No newline at end of file diff --git a/data/msimageview/msimageviewbioschemas.jsonld b/data/msimageview/msimageviewbioschemas.jsonld index be937d40c03b8..e567225819c7b 100644 --- a/data/msimageview/msimageviewbioschemas.jsonld +++ b/data/msimageview/msimageviewbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "MSImageView", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://ms-imaging.org/wp/msimageview/" } \ No newline at end of file diff --git a/data/msireader/msireaderbioschemas.jsonld b/data/msireader/msireaderbioschemas.jsonld index 59f60cd6b9663..2beba77f58877 100644 --- a/data/msireader/msireaderbioschemas.jsonld +++ b/data/msireader/msireaderbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MSiReader", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www4.ncsu.edu/~dcmuddim/msireader.html" } \ No newline at end of file diff --git a/data/msisensor/msisensorbioschemas.jsonld b/data/msisensor/msisensorbioschemas.jsonld index fede90f440a73..51ed37475044e 100644 --- a/data/msisensor/msisensorbioschemas.jsonld +++ b/data/msisensor/msisensorbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/msisensor", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Beifang Niu", - "Kai Ye" + "Kai Ye", + "Beifang Niu" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:24371154", diff --git a/data/msmbuilder/msmbuilderbioschemas.jsonld b/data/msmbuilder/msmbuilderbioschemas.jsonld index d30f61e1bd01a..495613eca876a 100644 --- a/data/msmbuilder/msmbuilderbioschemas.jsonld +++ b/data/msmbuilder/msmbuilderbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1016/j.bpj.2016.10.042", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/msmbuilder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Robert T. McGibbon", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5232355", - "pubmed:28076801", { "@id": "https://doi.org/10.1016/j.bpj.2016.10.042" - } + }, + "pubmed:28076801", + "pmcid:PMC5232355" ], "sc:description": "Statistical Models for Biomolecular Dynamics.", "sc:featureList": { @@ -29,10 +33,6 @@ "sc:name": "MSMBuilder", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/msmbuilder/msmbuilder" - }, - { - "@id": "https://doi.org/10.1016/j.bpj.2016.10.042", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/msms/msmsbioschemas.jsonld b/data/msms/msmsbioschemas.jsonld index 23b7cb0886f30..b3d1b949eef7c 100644 --- a/data/msms/msmsbioschemas.jsonld +++ b/data/msms/msmsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "LGPL-3.0", "sc:name": "msms", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.mabs.at/ewing/msms/index.shtml" } \ No newline at end of file diff --git a/data/msmseda/bioconda_msmseda.yaml b/data/msmseda/bioconda_msmseda.yaml index bb46a577003cb..51a54376cba66 100644 --- a/data/msmseda/bioconda_msmseda.yaml +++ b/data/msmseda/bioconda_msmseda.yaml @@ -4,7 +4,6 @@ description: Exploratory data analysis to assess the quality of a set of LC-MS/M home: https://bioconductor.org/packages/3.10/bioc/html/msmsEDA.html identifiers: - biotools:msmseda -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-msmseda diff --git a/data/msmseda/msmsedabioschemas.jsonld b/data/msmseda/msmsedabioschemas.jsonld index 038d81f906764..9eef0d8a6a0b2 100644 --- a/data/msmseda/msmsedabioschemas.jsonld +++ b/data/msmseda/msmsedabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Josep Gregori", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.", "sc:license": "GPL-2.0", "sc:name": "msmsEDA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/msmsEDA.html", "sc:version": "1.12.0" diff --git a/data/msmstests/msmstestsbioschemas.jsonld b/data/msmstests/msmstestsbioschemas.jsonld index 09d0833e28835..d6a26a58aa537 100644 --- a/data/msmstests/msmstestsbioschemas.jsonld +++ b/data/msmstests/msmstestsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "msmsTests", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/msmsTests.html", "sc:version": "1.12.0" diff --git a/data/msnbase/msnbasebioschemas.jsonld b/data/msnbase/msnbasebioschemas.jsonld index 54e1af5d13ea4..e1b2b96ca93ec 100644 --- a/data/msnbase/msnbasebioschemas.jsonld +++ b/data/msnbase/msnbasebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-1520-2268", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/msnbase", "@type": "sc:SoftwareApplication", @@ -28,12 +24,16 @@ "sc:license": "Artistic-2.0", "sc:name": "MSnbase", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MSnbase.html", "sc:version": "2.0.1" + }, + { + "@id": "http://orcid.org/0000-0002-1520-2268", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/msnid/bioconda_msnid.yaml b/data/msnid/bioconda_msnid.yaml index b78336db6aacf..e4716620ee665 100644 --- a/data/msnid/bioconda_msnid.yaml +++ b/data/msnid/bioconda_msnid.yaml @@ -8,7 +8,6 @@ description: Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or home: https://bioconductor.org/packages/3.10/bioc/html/MSnID.html identifiers: - biotools:msnid -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-msnid summary: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics diff --git a/data/msnid/msnidbioschemas.jsonld b/data/msnid/msnidbioschemas.jsonld index 7a228fdcb8446..2bd0e60c44a8a 100644 --- a/data/msnid/msnidbioschemas.jsonld +++ b/data/msnid/msnidbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "MSnID", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MSnID.html", "sc:version": "1.8.0" diff --git a/data/msp-htprimer/msp-htprimerbioschemas.jsonld b/data/msp-htprimer/msp-htprimerbioschemas.jsonld index 9f69cd64be851..adeaa1253145d 100644 --- a/data/msp-htprimer/msp-htprimerbioschemas.jsonld +++ b/data/msp-htprimer/msp-htprimerbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Ram Vinay Pandey", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:27688817", { "@id": "https://doi.org/10.1186/S13148-016-0269-3" }, - "pmcid:PMC5031341", - "pubmed:27688817" + "pmcid:PMC5031341" ], "sc:description": "A high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "MSP-HTPrimer", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/msp-htprimer/" } diff --git a/data/mspc-morpheus/mspc-morpheusbioschemas.jsonld b/data/mspc-morpheus/mspc-morpheusbioschemas.jsonld index 2c757213adc1c..1d427aa54210f 100644 --- a/data/mspc-morpheus/mspc-morpheusbioschemas.jsonld +++ b/data/mspc-morpheus/mspc-morpheusbioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5089804", + "pubmed:26791624", { "@id": "https://doi.org/10.1002/pmic.201500420" - }, - "pubmed:26791624" + } ], "sc:description": "Morpheus Spectral Counter (MSpC) as the first computational tool that directly calculates Normalized Spectral Abundance Factor (NSAF) values from output obtained from Morpheus, a fast, open-source, peptide-MS/MS matching engine compatible with high-resolution accurate-mass instruments.", "sc:featureList": { diff --git a/data/mspc/mspcbioschemas.jsonld b/data/mspc/mspcbioschemas.jsonld index 1050e607aab04..511e1008fe4d6 100644 --- a/data/mspc/mspcbioschemas.jsonld +++ b/data/mspc/mspcbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MSPC", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.bioinformatics.deib.polimi.it/genomic_computing/MSPC/" } \ No newline at end of file diff --git a/data/mspire/mspirebioschemas.jsonld b/data/mspire/mspirebioschemas.jsonld index eeebdfeafd175..714c15b769d36 100644 --- a/data/mspire/mspirebioschemas.jsonld +++ b/data/mspire/mspirebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Full featured library for working with mass spectrometry data, particularly proteomic, metabolomic and lipidomic data sets. It aims to be fast, robust, and beautiful.", "sc:name": "mspire", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/princelab/mspire" } \ No newline at end of file diff --git a/data/msplit/msplitbioschemas.jsonld b/data/msplit/msplitbioschemas.jsonld index bfd47c56d7ddb..85de48ba5875e 100644 --- a/data/msplit/msplitbioschemas.jsonld +++ b/data/msplit/msplitbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "M-SPLIT is a spectral-library search tool for identification of mixture spectra of up to two peptides.", "sc:name": "MSPLIT", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://proteomics.ucsd.edu/software-tools/msplit/", "sc:version": "1.0" diff --git a/data/msprogene/msprogenebioschemas.jsonld b/data/msprogene/msprogenebioschemas.jsonld index 36f7733b899d1..8924d7c7dbe49 100644 --- a/data/msprogene/msprogenebioschemas.jsonld +++ b/data/msprogene/msprogenebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MSProGene", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sourceforge.net/projects/msprogene/" } \ No newline at end of file diff --git a/data/msqrob/msqrobbioschemas.jsonld b/data/msqrob/msqrobbioschemas.jsonld index 623cb765e01ce..aa44af5831f75 100644 --- a/data/msqrob/msqrobbioschemas.jsonld +++ b/data/msqrob/msqrobbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-8285-7766", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/msqrob", "@type": "sc:SoftwareApplication", @@ -24,11 +20,15 @@ "sc:license": "GPL-3.0", "sc:name": "MSqRob", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/ludgergoeminne/MSqRob" + }, + { + "@id": "http://orcid.org/0000-0002-8285-7766", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/msqt/msqtbioschemas.jsonld b/data/msqt/msqtbioschemas.jsonld index 15cfe1068ac46..dc9fe1f86cb0d 100644 --- a/data/msqt/msqtbioschemas.jsonld +++ b/data/msqt/msqtbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "MSQT is a SNP Query Tool.It was developed to make polymorphism information readily accessible and to assist researchers in selecting distinct sequence changes and developing SNP detection assays.", "sc:name": "MSQT", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://msqt.weigelworld.org/", "sc:version": "0.7.3" diff --git a/data/msstats/msstatsbioschemas.jsonld b/data/msstats/msstatsbioschemas.jsonld index cbc8c80086097..cbd1569c8fa9b 100644 --- a/data/msstats/msstatsbioschemas.jsonld +++ b/data/msstats/msstatsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Statistical tool for quantitative mass spectrometry-based proteomics.", "sc:name": "MSstats", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.msstats.org/" } \ No newline at end of file diff --git a/data/msstatsqc/msstatsqcbioschemas.jsonld b/data/msstatsqc/msstatsqcbioschemas.jsonld index aac5be513a3f5..6e60c77f41e86 100644 --- a/data/msstatsqc/msstatsqcbioschemas.jsonld +++ b/data/msstatsqc/msstatsqcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "MSstatsQC", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MSstatsQC.html", diff --git a/data/msstatsqcgui/msstatsqcguibioschemas.jsonld b/data/msstatsqcgui/msstatsqcguibioschemas.jsonld index cd0f532287486..9f66eb684851b 100644 --- a/data/msstatsqcgui/msstatsqcguibioschemas.jsonld +++ b/data/msstatsqcgui/msstatsqcguibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "MSstatsQCgui", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MSstatsQCgui.html", diff --git a/data/msv3d/msv3dbioschemas.jsonld b/data/msv3d/msv3dbioschemas.jsonld index 2110fa826ef5f..8e6b5964e294b 100644 --- a/data/msv3d/msv3dbioschemas.jsonld +++ b/data/msv3d/msv3dbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Database of human missense variants mapped to 3D protein structures.", "sc:name": "MSV3d", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://decrypthon.igbmc.fr/msv3d/cgi-bin/home", "sc:version": "1" diff --git a/data/msviz/msvizbioschemas.jsonld b/data/msviz/msvizbioschemas.jsonld index 24ba4b7f09ac8..0e4d97a76e60f 100644 --- a/data/msviz/msvizbioschemas.jsonld +++ b/data/msviz/msvizbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Roman Mylonas", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:citation": "pubmed:28636386", "sc:description": "Supports manual validation of post-translational modifications (PTMs) and their relative quantitation in small- and medium-size experiments. Thanks to its interactive interface MsViz can display peptide spectrum matches, sequence coverage information, or tandem mass spectrometry (MS/MS) spectra and extracted ion chromatograms. It allows easy and comprehensive visualization of small and medium bottom-up proteomics datasets.", "sc:license": "GPL-2.0", "sc:name": "MsViz", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://msviz-public.vital-it.ch", "sc:version": "1.0.1" diff --git a/data/mtctscan/mtctscanbioschemas.jsonld b/data/mtctscan/mtctscanbioschemas.jsonld index b7f2ba5afd00a..ff25f4b620dc0 100644 --- a/data/mtctscan/mtctscanbioschemas.jsonld +++ b/data/mtctscan/mtctscanbioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC5793836", + "pubmed:28482068", { "@id": "https://doi.org/10.1093/nar/gkx400" - }, - "pmcid:PMC5793836", - "pubmed:28482068" + } ], "sc:description": "Mutation To Cancer Therapy Scan. Systematically analyze mutations affecting cancer drug sensitivity based on individual genomic profiles. It was developed by leveraging the latest knowledge on mutation-cancer drug sensitivity associations and the results from large-scale chemical screening using human cancer cell lines.", "sc:featureList": { diff --git a/data/mtdna-server/mtdna-serverbioschemas.jsonld b/data/mtdna-server/mtdna-serverbioschemas.jsonld index 97cbef37e781c..5e241069132ac 100644 --- a/data/mtdna-server/mtdna-serverbioschemas.jsonld +++ b/data/mtdna-server/mtdna-serverbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/mtdna-server", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hansi Weissensteiner", - "Sebastian Schoenherr" + "Sebastian Schoenherr", + "Hansi Weissensteiner" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:27084948", "sc:description": "Free mtDNA NGS analysis pipeline including heteroplasmy detection and haplogroup-based contamination deconvolution.", "sc:name": "mtDNA-Server", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://mtdna-server.uibk.ac.at/" diff --git a/data/mtg2/mtg2bioschemas.jsonld b/data/mtg2/mtg2bioschemas.jsonld index c2c66acf7c719..ce5ad720a90f7 100644 --- a/data/mtg2/mtg2bioschemas.jsonld +++ b/data/mtg2/mtg2bioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MTG2", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://sites.google.com/site/honglee0707/mtg2" } \ No newline at end of file diff --git a/data/mtmdat-haddock/mtmdat-haddockbioschemas.jsonld b/data/mtmdat-haddock/mtmdat-haddockbioschemas.jsonld index 9feb0d93849fb..49d419396b47b 100644 --- a/data/mtmdat-haddock/mtmdat-haddockbioschemas.jsonld +++ b/data/mtmdat-haddock/mtmdat-haddockbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Facilitates fast and detailed evaluation of mass spectrometry data of limited proteolysis experiments to probe the tertiary structure of proteins and even complex formation with other proteins, ligands, and surfaces.", "sc:name": "MTMDAT-HADDOCK", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ifm.liu.se/chemistry/molbiotech/maria_sunnerhagens_group/mtmdat/" } \ No newline at end of file diff --git a/data/mtoolbox/mtoolboxbioschemas.jsonld b/data/mtoolbox/mtoolboxbioschemas.jsonld index 4406b24f25285..e1d876fa08d56 100644 --- a/data/mtoolbox/mtoolboxbioschemas.jsonld +++ b/data/mtoolbox/mtoolboxbioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:25028726", "pmcid:PMC4201154", { "@id": "https://doi.org/10.1093/bioinformatics/btu483" - }, - "pubmed:25028726" + } ], "sc:description": "A highly automated bioinformatics pipeline to reconstruct and analyse human mitochondrial DNA from NGS data, also provides mitochondrial haplogroups predictions.", "sc:featureList": { diff --git a/data/mtprotevol/mtprotevolbioschemas.jsonld b/data/mtprotevol/mtprotevolbioschemas.jsonld index b83a0316b2433..53a70c8d06ace 100644 --- a/data/mtprotevol/mtprotevolbioschemas.jsonld +++ b/data/mtprotevol/mtprotevolbioschemas.jsonld @@ -9,41 +9,41 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12862-019-1371-x", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mtProtEvol", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Konstantin Gunbin", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6391778", - "pubmed:30813887", { "@id": "https://doi.org/10.1186/s12862-019-1371-x" - } + }, + "pmcid:PMC6391778", + "pubmed:30813887" ], "sc:description": "Resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.", "sc:featureList": [ - { - "@id": "edam:operation_3431" - }, { "@id": "edam:operation_3478" }, { "@id": "edam:operation_0384" + }, + { + "@id": "edam:operation_3431" } ], "sc:name": "mtProtEvol", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioinfodbs.kantiana.ru/mtProtEvol/" - }, - { - "@id": "https://doi.org/10.1186/s12862-019-1371-x", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mu2a/mu2abioschemas.jsonld b/data/mu2a/mu2abioschemas.jsonld index 852cc1ee671b8..951ba2ddd5ba3 100644 --- a/data/mu2a/mu2abioschemas.jsonld +++ b/data/mu2a/mu2abioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Genomic variant annotation tool", "sc:name": "MU2A", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://code.google.com/archive/p/mu2a/" diff --git a/data/mucor/mucorbioschemas.jsonld b/data/mucor/mucorbioschemas.jsonld index 738b9041ce58c..ad5a4f2aec7da 100644 --- a/data/mucor/mucorbioschemas.jsonld +++ b/data/mucor/mucorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MuCor", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/blachlylab/mucor" } \ No newline at end of file diff --git a/data/mud/mudbioschemas.jsonld b/data/mud/mudbioschemas.jsonld index 2c222dea3f3b1..7065547dd5f27 100644 --- a/data/mud/mudbioschemas.jsonld +++ b/data/mud/mudbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A server for predicting the affect of missense mutations on protein function using sequence and structural features.", "sc:name": "MuD", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://mud.tau.ac.il/", diff --git a/data/mude/mudebioschemas.jsonld b/data/mude/mudebioschemas.jsonld index a6b2c8d61233e..3d8dd4289cc9c 100644 --- a/data/mude/mudebioschemas.jsonld +++ b/data/mude/mudebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "A set of programs implementing the framework to assess MS/MS spectra assignments", "sc:name": "MUDE", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://sourceforge.net/projects/mude/" diff --git a/data/mulan/mulanbioschemas.jsonld b/data/mulan/mulanbioschemas.jsonld index 4d3feb9afb987..29f4cf4aff5f1 100644 --- a/data/mulan/mulanbioschemas.jsonld +++ b/data/mulan/mulanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Performs local multiple DNA sequence alignments of finished and draft-quality sequences. It identifies transcription factor binding sites evolutionarily conserved across multiple species.", "sc:name": "Mulan", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mulan.dcode.org/" } \ No newline at end of file diff --git a/data/mulcom/mulcombioschemas.jsonld b/data/mulcom/mulcombioschemas.jsonld index 6665fb670d9a5..b0dafe6b230ab 100644 --- a/data/mulcom/mulcombioschemas.jsonld +++ b/data/mulcom/mulcombioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "Mulcom", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Mulcom.html", "sc:version": "1.24.0" diff --git a/data/mulpba/mulpbabioschemas.jsonld b/data/mulpba/mulpbabioschemas.jsonld index 8e810bd393361..395b4c604889a 100644 --- a/data/mulpba/mulpbabioschemas.jsonld +++ b/data/mulpba/mulpbabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mulpba", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Agnel Praveen Joseph", - "Sylvain Léonard" + "Sylvain Léonard", + "Agnel Praveen Joseph" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:23659291", diff --git a/data/mulrf/mulrfbioschemas.jsonld b/data/mulrf/mulrfbioschemas.jsonld index 34ad146684405..9a64ff3511bcd 100644 --- a/data/mulrf/mulrfbioschemas.jsonld +++ b/data/mulrf/mulrfbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Platform-independent software program designed to infer species trees from incongruent multi-copy gene trees using a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees.", "sc:name": "MulRF", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://genome.cs.iastate.edu/CBL/MulRF/" diff --git a/data/multeesum/multeesumbioschemas.jsonld b/data/multeesum/multeesumbioschemas.jsonld index 2ce2e34be2a42..0f5e7cc3d7b70 100644 --- a/data/multeesum/multeesumbioschemas.jsonld +++ b/data/multeesum/multeesumbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Visualization system that supports inspection and curation of data sets showing gene expression over time, in conjunction with the spatial location of the cells where the genes are expressed — it is the first tool to support comparisons across multiple such datasets.", "sc:name": "MulteeSum", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.cs.utah.edu/~miriah/multeesum/" } \ No newline at end of file diff --git a/data/multi-car/multi-carbioschemas.jsonld b/data/multi-car/multi-carbioschemas.jsonld index f097c5b24657b..eced49d9b05fb 100644 --- a/data/multi-car/multi-carbioschemas.jsonld +++ b/data/multi-car/multi-carbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Chin Lung Lu", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28155633", "pmcid:PMC5260120", { "@id": "https://doi.org/10.1186/S12859-016-1328-7" - } + }, + "pubmed:28155633" ], "sc:description": "Tool of contig scaffolding using multiple references.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "Multi-CAR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://140.114.85.168/Multi-CAR/index.php" } diff --git a/data/multi-dice/multi-dicebioschemas.jsonld b/data/multi-dice/multi-dicebioschemas.jsonld index 25bba52a1bcfd..6877e32f96bea 100644 --- a/data/multi-dice/multi-dicebioschemas.jsonld +++ b/data/multi-dice/multi-dicebioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC5724483", - "pubmed:28449263", { "@id": "https://doi.org/10.1111/1755-0998.12686" - } + }, + "pubmed:28449263" ], "sc:description": "Comparative population genomic inference under hierarchical co‐demographic models of independent single‐population size changes.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "multi-dice", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/xanderxue/Multi-DICE", "sc:version": "1.0.2" diff --git a/data/multi-fingerprint_browser/multi-fingerprint_browserbioschemas.jsonld b/data/multi-fingerprint_browser/multi-fingerprint_browserbioschemas.jsonld index 05df81cc2c2f9..420ab7cb9777f 100644 --- a/data/multi-fingerprint_browser/multi-fingerprint_browserbioschemas.jsonld +++ b/data/multi-fingerprint_browser/multi-fingerprint_browserbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Multi-fingerprint Browser", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://dcb-reymond23.unibe.ch:8080/MCSS/" } \ No newline at end of file diff --git a/data/multi-harmony/multi-harmonybioschemas.jsonld b/data/multi-harmony/multi-harmonybioschemas.jsonld index 8a443882dab53..68ddabc219353 100644 --- a/data/multi-harmony/multi-harmonybioschemas.jsonld +++ b/data/multi-harmony/multi-harmonybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.", "sc:name": "Multi-Harmony", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://ibi.vu.nl/programs/shmrwww/" } \ No newline at end of file diff --git a/data/multi_experiment_matrix/multi_experiment_matrixbioschemas.jsonld b/data/multi_experiment_matrix/multi_experiment_matrixbioschemas.jsonld index 0bb8586355097..0f738adf55434 100644 --- a/data/multi_experiment_matrix/multi_experiment_matrixbioschemas.jsonld +++ b/data/multi_experiment_matrix/multi_experiment_matrixbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web based tool for performing co-expression queries over large collections of gene expression experiments. It provides access to several hundreds of publicly available gene expression datasets of different tissues, diseases and conditions, arranged by the species and microarray platform types. The main user input is the name or ID of a query gene (various syononyms are accepted) and the choice of the collection of microarray experiments to be used in the co-expression query.", "sc:name": "Multi Experiment Matrix", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://biit.cs.ut.ee/mem", diff --git a/data/multiassayexperiment/multiassayexperimentbioschemas.jsonld b/data/multiassayexperiment/multiassayexperimentbioschemas.jsonld index f48bcdc279899..2c3344c02a035 100644 --- a/data/multiassayexperiment/multiassayexperimentbioschemas.jsonld +++ b/data/multiassayexperiment/multiassayexperimentbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Marcel Ramos", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Develop an integrative environment where multiple assays are managed and preprocessed for genomic data analysis.", "sc:license": "Artistic-2.0", "sc:name": "MultiAssayExperiment", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MultiAssayExperiment.html", "sc:version": "1.0.0" diff --git a/data/multibind/multibindbioschemas.jsonld b/data/multibind/multibindbioschemas.jsonld index 8282c9740ea41..ae3d6928bc002 100644 --- a/data/multibind/multibindbioschemas.jsonld +++ b/data/multibind/multibindbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Multiple Alignment of Protein Binding Sites (MultiBind) is a prediction tool for protein binding sites. Users input a set of protein-small molecule complexes and MultiBind predicts the common physio-chemical patterns responsible for protein binding.", "sc:name": "MultiBind", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/MultiBind" } \ No newline at end of file diff --git a/data/multibreak-sv/multibreak-svbioschemas.jsonld b/data/multibreak-sv/multibreak-svbioschemas.jsonld index d72aec8986a96..50e23943aaa28 100644 --- a/data/multibreak-sv/multibreak-svbioschemas.jsonld +++ b/data/multibreak-sv/multibreak-svbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.", "sc:name": "MultiBreak-SV", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://compbio.cs.brown.edu/projects/multibreaksv/" } \ No newline at end of file diff --git a/data/multiclust/multiclustbioschemas.jsonld b/data/multiclust/multiclustbioschemas.jsonld index 73144c55d2040..38ce32e0c7e60 100644 --- a/data/multiclust/multiclustbioschemas.jsonld +++ b/data/multiclust/multiclustbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "multiClust", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/multiClust.html", "sc:version": "1.4.0" diff --git a/data/multicoil/multicoilbioschemas.jsonld b/data/multicoil/multicoilbioschemas.jsonld index 5c52711d1c33d..64aae754b9c01 100644 --- a/data/multicoil/multicoilbioschemas.jsonld +++ b/data/multicoil/multicoilbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The MultiCoil program predicts the location of coiled-coil regions in amino acid sequences and classifies the predictions as dimeric or trimeric.", "sc:name": "Multicoil2", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://groups.csail.mit.edu/cb/multicoil" } \ No newline at end of file diff --git a/data/multidataset/multidatasetbioschemas.jsonld b/data/multidataset/multidatasetbioschemas.jsonld index fed8a6f8a1459..86fcd8c5e9133 100644 --- a/data/multidataset/multidatasetbioschemas.jsonld +++ b/data/multidataset/multidatasetbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-016-1455-1", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-6014-3498", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/multidataset", "@type": "sc:SoftwareApplication", @@ -20,11 +28,11 @@ "Command-line tool" ], "sc:citation": [ + "pmcid:PMC5240259", "pubmed:28095799", { "@id": "https://doi.org/10.1186/s12859-016-1455-1" - }, - "pmcid:PMC5240259" + } ], "sc:description": "Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) dataset and MethylationSet. It is designed for integrating multi omics data sets and MethylationSet to contain normalized methylation data. These package contains base classes for MEAL and rexposome packages.", "sc:featureList": { @@ -32,20 +40,12 @@ }, "sc:name": "MultiDataSet", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MultiDataSet.html", "sc:version": "1.2.0" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1455-1", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-6014-3498", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/multidcox/multidcoxbioschemas.jsonld b/data/multidcox/multidcoxbioschemas.jsonld index ebb7e98efd0ba..b1b28062ac91a 100644 --- a/data/multidcox/multidcoxbioschemas.jsonld +++ b/data/multidcox/multidcoxbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Space and time efficient procedure to identify differentially co-expressed gene sets and successfully identify influence of individual factors on differential co-expression.", "sc:name": "MultiDCoX", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/lianyh/MultiDCoX" } \ No newline at end of file diff --git a/data/multidisp/multidispbioschemas.jsonld b/data/multidisp/multidispbioschemas.jsonld index bc94862c693f9..e120b6ac17231 100644 --- a/data/multidisp/multidispbioschemas.jsonld +++ b/data/multidisp/multidispbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A tool for analysing and visualising multiple sequence alignments (MSAs).", "sc:name": "MultiDisp", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://structure.bmc.lu.se/MultiDisp/index.html", diff --git a/data/multifastamix/multifastamixbioschemas.jsonld b/data/multifastamix/multifastamixbioschemas.jsonld index 57bd00ba43043..f66c4d98980d8 100644 --- a/data/multifastamix/multifastamixbioschemas.jsonld +++ b/data/multifastamix/multifastamixbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Mix Multi-Fasta for each sequence in a multi-fasta file.", "sc:name": "multifastamix", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/MultiFastaMix/0.1%20beta", "sc:version": "0.1 beta" diff --git a/data/multifit/multifitbioschemas.jsonld b/data/multifit/multifitbioschemas.jsonld index 01d0c6ceddfe4..844cc2cc6c597 100644 --- a/data/multifit/multifitbioschemas.jsonld +++ b/data/multifit/multifitbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "MultiFit is a web server for fitting multiple protein structures into their electron microscopy density map. The server takes as input a set of protein structures in the PDB format and an EM density map in the MRC format. The output is an ensemble of models ranked by their quality-of-fit to the density map.", "sc:name": "Multifit", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://modbase.compbio.ucsf.edu/multifit/" } \ No newline at end of file diff --git a/data/multiglycan/multiglycanbioschemas.jsonld b/data/multiglycan/multiglycanbioschemas.jsonld index b2c44e6020dc4..84cb36a3abf87 100644 --- a/data/multiglycan/multiglycanbioschemas.jsonld +++ b/data/multiglycan/multiglycanbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/multiglycan", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Haixu Tang", - "Chuan-Yih Yu" + "Chuan-Yih Yu", + "Haixu Tang" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:23610369", diff --git a/data/multimap/multimapbioschemas.jsonld b/data/multimap/multimapbioschemas.jsonld index 752dbd96c0b1c..9dc509e0db974 100644 --- a/data/multimap/multimapbioschemas.jsonld +++ b/data/multimap/multimapbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/multimap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rasheeda Williams", - "Tara C. Matise" + "Tara C. Matise", + "Rasheeda Williams" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:8054979", diff --git a/data/multimed/multimedbioschemas.jsonld b/data/multimed/multimedbioschemas.jsonld index e17765096286d..91e9e44502ff0 100644 --- a/data/multimed/multimedbioschemas.jsonld +++ b/data/multimed/multimedbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Simina M. Boca", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Implements permutation method with joint correction for testing multiple mediators.", "sc:license": "GPL-2.0", diff --git a/data/multimeta/multimetabioschemas.jsonld b/data/multimeta/multimetabioschemas.jsonld index e4a033ca089f8..86e436dfa78e7 100644 --- a/data/multimeta/multimetabioschemas.jsonld +++ b/data/multimeta/multimetabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This R package provides an implementation of the inverse-variance based method for meta-analysis, generalized to an n-dimensional setting.", "sc:name": "MultiMeta", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://cran.r-project.org/web/packages/MultiMeta/index.html" } \ No newline at end of file diff --git a/data/multiomicsviz/multiomicsvizbioschemas.jsonld b/data/multiomicsviz/multiomicsvizbioschemas.jsonld index 3c2388caf7991..dc3989e4c5b88 100644 --- a/data/multiomicsviz/multiomicsvizbioschemas.jsonld +++ b/data/multiomicsviz/multiomicsvizbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "LGPL-2.0", "sc:name": "multiOmicsViz", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/multiOmicsViz.html", "sc:version": "1.4.0" diff --git a/data/multiphate/multiphatebioschemas.jsonld b/data/multiphate/multiphatebioschemas.jsonld index 5e14508d2c48a..8ad0573b0a085 100644 --- a/data/multiphate/multiphatebioschemas.jsonld +++ b/data/multiphate/multiphatebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Carol L. Ecale Zhou", "sc:additionalType": [ - "Script", - "Command-line tool" + "Command-line tool", + "Script" ], "sc:citation": "pubmed:31086982", "sc:description": "Bioinformatics pipeline for functional annotation of phage isolates.", "sc:license": "BSD-3-Clause", "sc:name": "multiPhATE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/carolzhou/multiPhATE" } \ No newline at end of file diff --git a/data/multiphen/multiphenbioschemas.jsonld b/data/multiphen/multiphenbioschemas.jsonld index dc981ac069129..bca5d5fe78161 100644 --- a/data/multiphen/multiphenbioschemas.jsonld +++ b/data/multiphen/multiphenbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MultiPhen", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/MultiPhen/index.html" } \ No newline at end of file diff --git a/data/multiplx/multiplxbioschemas.jsonld b/data/multiplx/multiplxbioschemas.jsonld index e9bfb409df40a..bd28b76f292d4 100644 --- a/data/multiplx/multiplxbioschemas.jsonld +++ b/data/multiplx/multiplxbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool that uses state-of-the-art nearest neighbour DNA binding thermodynamics to estimate possible unwanted pairings between PCR samples and calculates automatically optimal multiplexing (grouping) solution.", "sc:name": "MultiPLX", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://bioinfo.ut.ee/multiplx", diff --git a/data/multipow/multipowbioschemas.jsonld b/data/multipow/multipowbioschemas.jsonld index 88d52dff78cf2..3b863bd8579fd 100644 --- a/data/multipow/multipowbioschemas.jsonld +++ b/data/multipow/multipowbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Calculates the power for both joint and replication-based analysis of general multi-stage genetic association studies.", "sc:name": "MULTIPOW", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.hsph.harvard.edu/peter-kraft/software/" } \ No newline at end of file diff --git a/data/multipred2/multipred2bioschemas.jsonld b/data/multipred2/multipred2bioschemas.jsonld index 1e5db691aa194..53fa1b542bcaa 100644 --- a/data/multipred2/multipred2bioschemas.jsonld +++ b/data/multipred2/multipred2bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Computational system for large-scale screening of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR supertypes as well as to alleles belonging to an individual’s genotype.", "sc:name": "MULTIPRED2", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://cvc.dfci.harvard.edu/multipred2/index.php" } \ No newline at end of file diff --git a/data/multiprot/multiprotbioschemas.jsonld b/data/multiprot/multiprotbioschemas.jsonld index 4f1429eda8feb..ebd47172654ad 100644 --- a/data/multiprot/multiprotbioschemas.jsonld +++ b/data/multiprot/multiprotbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/multiprot", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:15162494", "sc:description": "Fully automated highly efficient technique which detects the multiple structural alignments of protein structures. It finds the common geometrical cores between the input molecules.", "sc:name": "MultiProt", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/MultiProt/" } \ No newline at end of file diff --git a/data/multipsq/multipsqbioschemas.jsonld b/data/multipsq/multipsqbioschemas.jsonld index 965f8422e59a3..5d23f079a69bf 100644 --- a/data/multipsq/multipsqbioschemas.jsonld +++ b/data/multipsq/multipsqbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "LGPL-3.0", "sc:name": "MultiPSQ", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sourceforge.net/projects/multipsq/" } \ No newline at end of file diff --git a/data/multiqc/multiqcbioschemas.jsonld b/data/multiqc/multiqcbioschemas.jsonld index af68b0c177630..dd4502e53c742 100644 --- a/data/multiqc/multiqcbioschemas.jsonld +++ b/data/multiqc/multiqcbioschemas.jsonld @@ -25,10 +25,10 @@ }, "sc:citation": [ "pubmed:27312411", - "pmcid:PMC5039924", { "@id": "https://doi.org/10.1093/bioinformatics/btw354" - } + }, + "pmcid:PMC5039924" ], "sc:description": "MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.", "sc:featureList": { diff --git a/data/multirnafold/multirnafoldbioschemas.jsonld b/data/multirnafold/multirnafoldbioschemas.jsonld index c7d91de9a0807..29c5385750aa5 100644 --- a/data/multirnafold/multirnafoldbioschemas.jsonld +++ b/data/multirnafold/multirnafoldbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Contains software for secondary structure prediction of one, two, or many interacting RNA or DNA molecules. It is composed of three pieces of software: SimFold, PairFold and MultiFold.", "sc:name": "MultiRNAFold", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.rnasoft.ca/download/README.html" } \ No newline at end of file diff --git a/data/multiscan/bioconda_multiscan.yaml b/data/multiscan/bioconda_multiscan.yaml index ff346b658eb9f..f48f5f767e87f 100644 --- a/data/multiscan/bioconda_multiscan.yaml +++ b/data/multiscan/bioconda_multiscan.yaml @@ -3,7 +3,6 @@ description: Estimates gene expressions from several laser scans of the same mic home: https://bioconductor.org/packages/3.10/bioc/html/multiscan.html identifiers: - biotools:multiscan -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-multiscan diff --git a/data/multiscan/multiscanbioschemas.jsonld b/data/multiscan/multiscanbioschemas.jsonld index 53eda94dffebd..4089dc2e5ba02 100644 --- a/data/multiscan/multiscanbioschemas.jsonld +++ b/data/multiscan/multiscanbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mizanur Khondoker", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Estimates gene expressions from several laser scans of the same microarray.", "sc:license": "GPL-2.0", "sc:name": "multiscan", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/multiscan.html", "sc:version": "1.34.0" diff --git a/data/multiview/multiviewbioschemas.jsonld b/data/multiview/multiviewbioschemas.jsonld index 901dabf75a57e..64b3637241a76 100644 --- a/data/multiview/multiviewbioschemas.jsonld +++ b/data/multiview/multiviewbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-4-Clause", "sc:name": "multiview", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://b2slab.upc.edu/software-and-tutorials/multiview-package-multiview-clustering-dimensionality-reduction-methods/" } \ No newline at end of file diff --git a/data/multiwaver/multiwaverbioschemas.jsonld b/data/multiwaver/multiwaverbioschemas.jsonld index 793ad8989cff8..98227ca1c7ffa 100644 --- a/data/multiwaver/multiwaverbioschemas.jsonld +++ b/data/multiwaver/multiwaverbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Models discrete and continuous gene flow to reconstruct complex population admixtures.", "sc:name": "MultiWaver", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.picb.ac.cn/PGG/resource.php", "sc:version": "2.0" diff --git a/data/multixcan/multixcanbioschemas.jsonld b/data/multixcan/multixcanbioschemas.jsonld index fedad7c01495c..4c447a2291e9f 100644 --- a/data/multixcan/multixcanbioschemas.jsonld +++ b/data/multixcan/multixcanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "MultiXcan", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/hakyimlab/MetaXcan" } \ No newline at end of file diff --git a/data/multovl/multovlbioschemas.jsonld b/data/multovl/multovlbioschemas.jsonld index 8bd98a8e9126a..12f3ebf921aa4 100644 --- a/data/multovl/multovlbioschemas.jsonld +++ b/data/multovl/multovlbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "MULTOVL", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.interquadrat.eu/aa/software.php", "sc:version": "1.3" diff --git a/data/multtest/multtestbioschemas.jsonld b/data/multtest/multtestbioschemas.jsonld index 13af388e5e7b9..f10935f07e34f 100644 --- a/data/multtest/multtestbioschemas.jsonld +++ b/data/multtest/multtestbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Katherine S. Pollard", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This extension includes non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed).", "sc:license": "GPL-3.0", "sc:name": "multtest", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/multtest.html", "sc:version": "2.30.0" diff --git a/data/mumrescuelite/mumrescuelitebioschemas.jsonld b/data/mumrescuelite/mumrescuelitebioschemas.jsonld index 7d982617f0c28..44a2fee7117c8 100644 --- a/data/mumrescuelite/mumrescuelitebioschemas.jsonld +++ b/data/mumrescuelite/mumrescuelitebioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "MuMRescueLite", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://genome.gsc.riken.jp/osc/english/software/" } \ No newline at end of file diff --git a/data/mupet/mupetbioschemas.jsonld b/data/mupet/mupetbioschemas.jsonld index 7ab3f8d40411f..7ace8a085695d 100644 --- a/data/mupet/mupetbioschemas.jsonld +++ b/data/mupet/mupetbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/j.neuron.2017.04.005", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mupet", "@type": "sc:SoftwareApplication", @@ -32,11 +28,15 @@ "sc:license": "Apache-2.0", "sc:name": "MUPET", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://sail.usc.edu/mupet/" + }, + { + "@id": "https://doi.org/10.1016/j.neuron.2017.04.005", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mupred/mupredbioschemas.jsonld b/data/mupred/mupredbioschemas.jsonld index 9a3aa83403032..ba0b8f15cbc3f 100644 --- a/data/mupred/mupredbioschemas.jsonld +++ b/data/mupred/mupredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Protein secondary structure and solvent accessibility prediction server based on a novel framework.", "sc:name": "MUPRED", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://digbio.missouri.edu/mupred/" } \ No newline at end of file diff --git a/data/mupro/muprobioschemas.jsonld b/data/mupro/muprobioschemas.jsonld index 5bbafea83bcab..83e8120832661 100644 --- a/data/mupro/muprobioschemas.jsonld +++ b/data/mupro/muprobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mupro", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Paul Rigor", "Jianlin Cheng", + "Paul Rigor", "Pierre Baldi" ], "sc:additionalType": "Web application", @@ -20,9 +20,9 @@ "sc:description": "Set of machine learning programs to predict how single-site amino acid mutation affects protein stability. We developed two machine learning methods: Support Vector Machines and Neural Networks.", "sc:name": "MUpro", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://mupro.proteomics.ics.uci.edu/" } \ No newline at end of file diff --git a/data/muscle/musclebioschemas.jsonld b/data/muscle/musclebioschemas.jsonld index 5e444d5f91bb5..c7500c4e4668b 100644 --- a/data/muscle/musclebioschemas.jsonld +++ b/data/muscle/musclebioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "Other", "sc:name": "MUSCLE", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://www.drive5.com/muscle/", "sc:version": "3.16.0" diff --git a/data/muscle_ebi/muscle_ebibioschemas.jsonld b/data/muscle_ebi/muscle_ebibioschemas.jsonld index 9e0d7628c7496..64819b3ee3ed6 100644 --- a/data/muscle_ebi/muscle_ebibioschemas.jsonld +++ b/data/muscle_ebi/muscle_ebibioschemas.jsonld @@ -13,8 +13,8 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "Robert Edgar", - "Web Production" + "Web Production", + "Robert Edgar" ], "sc:description": "Sequence alignment using the Multiple Sequence Comparison by Log-Expectation (MUSCLE) method", "sc:name": "MUSCLE (EBI)", diff --git a/data/muscle_gene_sets/muscle_gene_setsbioschemas.jsonld b/data/muscle_gene_sets/muscle_gene_setsbioschemas.jsonld index 9809283e602fe..cf1f8542f6dde 100644 --- a/data/muscle_gene_sets/muscle_gene_setsbioschemas.jsonld +++ b/data/muscle_gene_sets/muscle_gene_setsbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-2239-9094", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/S13395-019-0196-Z", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Muscle_Gene_Sets", "@type": "sc:SoftwareApplication", @@ -20,16 +28,16 @@ { "@id": "https://doi.org/10.1186/S13395-019-0196-Z" }, - "pubmed:31053169", - "pmcid:PMC6498474" + "pmcid:PMC6498474", + "pubmed:31053169" ], "sc:description": "Versatile methodological aid to functional genomics in the neuromuscular field.", "sc:featureList": [ { - "@id": "edam:operation_0571" + "@id": "edam:operation_2436" }, { - "@id": "edam:operation_2436" + "@id": "edam:operation_0571" }, { "@id": "edam:operation_3223" @@ -38,19 +46,11 @@ "sc:license": "Unlicense", "sc:name": "Muscle Gene Sets", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.sys-myo.com/muscle_gene_sets" - }, - { - "@id": "https://doi.org/10.1186/S13395-019-0196-Z", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0003-2239-9094", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/muscle_ws_jabaws/muscle_ws_jabawsbioschemas.jsonld b/data/muscle_ws_jabaws/muscle_ws_jabawsbioschemas.jsonld index bfd8164790c6f..c3fd6c7a7beef 100644 --- a/data/muscle_ws_jabaws/muscle_ws_jabawsbioschemas.jsonld +++ b/data/muscle_ws_jabaws/muscle_ws_jabawsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Multiple sequence algnment tool.", "sc:name": "Muscle WS (jabaws)", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.compbio.dundee.ac.uk/jabaws", diff --git a/data/musi-bind/musi-bindbioschemas.jsonld b/data/musi-bind/musi-bindbioschemas.jsonld index a2e699135d67b..7019e7cc78b82 100644 --- a/data/musi-bind/musi-bindbioschemas.jsonld +++ b/data/musi-bind/musi-bindbioschemas.jsonld @@ -11,10 +11,10 @@ "@id": "https://bio.tools/musi-bind", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "TaeHyung Simon Kim", - "Philip M. Kim", + "Marc Tyndel", "David Gfeller", - "Marc Tyndel" + "TaeHyung Simon Kim", + "Philip M. Kim" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:22210894", diff --git a/data/musi/musibioschemas.jsonld b/data/musi/musibioschemas.jsonld index 2320e0ca414f3..964ee25c9de32 100644 --- a/data/musi/musibioschemas.jsonld +++ b/data/musi/musibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Designed to analyze (aligned) gene libraries, in particular in case that codon directed mutagenesis was applied to them. The program generates several tables providing information about trinucleotide characteristics, deletions, substitutions and amino acids distributions.", "sc:name": "MuSi", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://gobics.de/ingo/musi/musi.html" } \ No newline at end of file diff --git a/data/music2/music2bioschemas.jsonld b/data/music2/music2bioschemas.jsonld index df20c09e36394..3f859bf2313c6 100644 --- a/data/music2/music2bioschemas.jsonld +++ b/data/music2/music2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-1517-2975", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/MuSiC2", "@type": "sc:SoftwareApplication", @@ -25,10 +29,6 @@ "sc:operatingSystem": "Linux", "sc:url": "http://gmt.genome.wustl.edu/packages/genome-music/index.html", "sc:version": "0.2" - }, - { - "@id": "https://orcid.org/0000-0003-1517-2975", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/musica/musicabioschemas.jsonld b/data/musica/musicabioschemas.jsonld index dd9c856b74110..deb6a4e1b50aa 100644 --- a/data/musica/musicabioschemas.jsonld +++ b/data/musica/musicabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "MuSiCa", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioinfo.ciberehd.org/GPtoCRC/en/tools.html" } \ No newline at end of file diff --git a/data/musica_2/musica_2bioschemas.jsonld b/data/musica_2/musica_2bioschemas.jsonld index dec4479da008a..a7acb9b6ca052 100644 --- a/data/musica_2/musica_2bioschemas.jsonld +++ b/data/musica_2/musica_2bioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/musica_2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Shin-ichi Morishita", "Reginaldo Kuroshu", "Masahiro Kasahara", - "Shin-ichi Morishita", "Yutaka Suzuki" ], "sc:additionalType": "Workflow", @@ -21,8 +21,8 @@ "sc:description": "Assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ~800 human full-length cDNA clones.", "sc:name": "MuSICA 2", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://musica.gi.k.u-tokyo.ac.jp/" } \ No newline at end of file diff --git a/data/must/mustbioschemas.jsonld b/data/must/mustbioschemas.jsonld index 676889d9233a2..73a280ceefc85 100644 --- a/data/must/mustbioschemas.jsonld +++ b/data/must/mustbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Improved de novo detection program for recently active miniature inverted repeat transposable elements (MITEs).", "sc:name": "MUST", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.healthinformaticslab.org/supp/" } \ No newline at end of file diff --git a/data/mustguseal/mustgusealbioschemas.jsonld b/data/mustguseal/mustgusealbioschemas.jsonld index dcd46f8878094..b2ad26d09747b 100644 --- a/data/mustguseal/mustgusealbioschemas.jsonld +++ b/data/mustguseal/mustgusealbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Multiple structure-guided sequence alignment of protein families.", "sc:name": "Mustguseal", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://biokinet.belozersky.msu.ru/mustguseal" diff --git a/data/mutaid/mutaidbioschemas.jsonld b/data/mutaid/mutaidbioschemas.jsonld index 4b3e5de48201b..5716c38a39bd2 100644 --- a/data/mutaid/mutaidbioschemas.jsonld +++ b/data/mutaid/mutaidbioschemas.jsonld @@ -19,25 +19,25 @@ "biotools:primaryContact": "Ram Vinay Pandey", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:26840129", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0147697" }, - "pubmed:26840129", "pmcid:PMC4739551" ], "sc:description": "Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.", "sc:featureList": [ { - "@id": "edam:operation_3202" + "@id": "edam:operation_0361" }, { - "@id": "edam:operation_0361" + "@id": "edam:operation_3202" } ], "sc:name": "MutAid", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/mutaid/" } diff --git a/data/mutalisk/mutaliskbioschemas.jsonld b/data/mutalisk/mutaliskbioschemas.jsonld index 2fd548ab6776c..249c84cfdcc74 100644 --- a/data/mutalisk/mutaliskbioschemas.jsonld +++ b/data/mutalisk/mutaliskbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-7816-1299", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/mutalisk", "@type": "sc:SoftwareApplication", @@ -25,10 +29,6 @@ "Windows" ], "sc:url": "http://mutalisk.org" - }, - { - "@id": "https://orcid.org/0000-0002-7816-1299", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mutanalyst/mutanalystbioschemas.jsonld b/data/mutanalyst/mutanalystbioschemas.jsonld index baa8ff195fdf0..828e05a26df58 100644 --- a/data/mutanalyst/mutanalystbioschemas.jsonld +++ b/data/mutanalyst/mutanalystbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Mutanalyst", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.mutanalyst.com/" } \ No newline at end of file diff --git a/data/mutanet/mutanetbioschemas.jsonld b/data/mutanet/mutanetbioschemas.jsonld index d53d2f8bd713e..7ed433013fb18 100644 --- a/data/mutanet/mutanetbioschemas.jsonld +++ b/data/mutanet/mutanetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "MutaNET", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://service.bioinformatik.uni-saarland.de/mutanet/" } \ No newline at end of file diff --git a/data/mutation3d/mutation3dbioschemas.jsonld b/data/mutation3d/mutation3dbioschemas.jsonld index eca7db7bba139..8e75be8a9ef4a 100644 --- a/data/mutation3d/mutation3dbioschemas.jsonld +++ b/data/mutation3d/mutation3dbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1002/HUMU.22963", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mutation3d", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Haiyuan Yu", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4833594", + "pubmed:26841357", { "@id": "https://doi.org/10.1002/HUMU.22963" }, - "pubmed:26841357" + "pmcid:PMC4833594" ], "sc:description": "A functional prediction and visualization tool for studying the spatial arrangement of amino acid substitutions on protein models and structures.", "sc:featureList": { @@ -28,14 +32,10 @@ "sc:name": "mutation3D", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mutation3d.org/" - }, - { - "@id": "https://doi.org/10.1002/HUMU.22963", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mutation_taster/mutation_tasterbioschemas.jsonld b/data/mutation_taster/mutation_tasterbioschemas.jsonld index 694f6842f001d..a443efc228f9c 100644 --- a/data/mutation_taster/mutation_tasterbioschemas.jsonld +++ b/data/mutation_taster/mutation_tasterbioschemas.jsonld @@ -15,8 +15,8 @@ "Dominik Seelow" ], "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:citation": "pubmed:24681721", "sc:description": "It evaluates the pathogenic potential of DNA sequence alterations. It is designed to predict the functional consequences of amino acid substitutions as well as intronic and synonymous alterations, short insertion and/or deletion mutations and variants spanning intron-exon borders.", diff --git a/data/mutationaligner/mutationalignerbioschemas.jsonld b/data/mutationaligner/mutationalignerbioschemas.jsonld index 63154158774f0..1f60333d6ce1c 100644 --- a/data/mutationaligner/mutationalignerbioschemas.jsonld +++ b/data/mutationaligner/mutationalignerbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKV1132", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/mutationaligner", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": [ - "Database portal", - "Web API" + "Web API", + "Database portal" ], "sc:citation": [ - "pubmed:26590264", "pmcid:PMC4702822", + "pubmed:26590264", { "@id": "https://doi.org/10.1093/NAR/GKV1132" } @@ -34,11 +30,15 @@ }, "sc:name": "MutationAligner", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.mutationaligner.org/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKV1132", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mutationalpatterns/mutationalpatternsbioschemas.jsonld b/data/mutationalpatterns/mutationalpatternsbioschemas.jsonld index 2bb3678c789b1..86c38e8e58ce8 100644 --- a/data/mutationalpatterns/mutationalpatternsbioschemas.jsonld +++ b/data/mutationalpatterns/mutationalpatternsbioschemas.jsonld @@ -15,16 +15,16 @@ "Roel Janssen" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.", "sc:license": "MIT", "sc:name": "MutationalPatterns", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MutationalPatterns.html", "sc:version": "1.0.0" diff --git a/data/mutationdistiller/mutationdistillerbioschemas.jsonld b/data/mutationdistiller/mutationdistillerbioschemas.jsonld index 73e5c9767e93c..6e23f553281ab 100644 --- a/data/mutationdistiller/mutationdistillerbioschemas.jsonld +++ b/data/mutationdistiller/mutationdistillerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Make the analysis of Next-Generation Sequencing data simple. Depending on your background and interest, it offers various modes with optimised settings: Clinical (HPO), Clinical (Gene Panels), Gene Function and Basic Search.", "sc:name": "MutationDistiller", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://www.mutationdistiller.org/" } \ No newline at end of file diff --git a/data/mutationinfo/mutationinfobioschemas.jsonld b/data/mutationinfo/mutationinfobioschemas.jsonld index bef19661f4992..9e4cf1dc9484f 100644 --- a/data/mutationinfo/mutationinfobioschemas.jsonld +++ b/data/mutationinfo/mutationinfobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alexandros Kanterakis", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "MutationInfo is a python package to extract the position, the reference and the alternative sequence of a genomic variant. It accepts variants in dbSNP rs format or in HGVS format.", "sc:license": "MIT", "sc:name": "MutationInfo", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.epga.gr/MutationInfo/", "sc:version": "1.3" diff --git a/data/mutationmotif/mutationmotifbioschemas.jsonld b/data/mutationmotif/mutationmotifbioschemas.jsonld index c8ab42778bb9d..3bd4eb3fe7891 100644 --- a/data/mutationmotif/mutationmotifbioschemas.jsonld +++ b/data/mutationmotif/mutationmotifbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This library provides capabilities for analysis of mutation properties. Two different analysis approaches are supported: (1) log-linear analysis of neighbourhood base influences on mutation coupled with a sequence logo like representation of influences; (2) log-linear analysis of mutation spectra, the relative proportions of different mutation directioons from a starting base. A logo-like visualisation of the latter is also supported.", "sc:name": "MutationMotif", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "unimelb.edu.au", "sc:url": "https://bitbucket.org/pycogent3/mutationmotif", diff --git a/data/mutations-meta-analyser/mutations-meta-analyserbioschemas.jsonld b/data/mutations-meta-analyser/mutations-meta-analyserbioschemas.jsonld index a842f48e0fdca..1d9efa8254062 100644 --- a/data/mutations-meta-analyser/mutations-meta-analyserbioschemas.jsonld +++ b/data/mutations-meta-analyser/mutations-meta-analyserbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "Mutations-Meta-Analyser", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/BioDAG/Mutations-Meta-Analyser", "sc:version": "1.0" diff --git a/data/mutationtaster/mutationtasterbioschemas.jsonld b/data/mutationtaster/mutationtasterbioschemas.jsonld index 0656107009523..dd5eec3e6e63c 100644 --- a/data/mutationtaster/mutationtasterbioschemas.jsonld +++ b/data/mutationtaster/mutationtasterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Not licensed", "sc:name": "MutationTaster", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.mutationtaster.org/" } \ No newline at end of file diff --git a/data/mutdb/mutdbbioschemas.jsonld b/data/mutdb/mutdbbioschemas.jsonld index d22a2bb5999d9..3f32515bbc2f5 100644 --- a/data/mutdb/mutdbbioschemas.jsonld +++ b/data/mutdb/mutdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.", "sc:name": "MutDB", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.mutdb.org/" diff --git a/data/mutect/mutectbioschemas.jsonld b/data/mutect/mutectbioschemas.jsonld index bb7ee25f2a3f0..e0e26a3e4e500 100644 --- a/data/mutect/mutectbioschemas.jsonld +++ b/data/mutect/mutectbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A method for identification of somatic point mutations in next generation sequencing data of cancer genomes.", "sc:name": "MuTect", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.broadinstitute.org/cancer/cga/mutect" diff --git a/data/mutexsl/mutexslbioschemas.jsonld b/data/mutexsl/mutexslbioschemas.jsonld index b16ca0e41d6f4..8818882e08bff 100644 --- a/data/mutexsl/mutexslbioschemas.jsonld +++ b/data/mutexsl/mutexslbioschemas.jsonld @@ -17,11 +17,11 @@ }, "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:26427375", - "pmcid:PMC4590705", { "@id": "https://doi.org/10.1186/s13062-015-0086-1" - } + }, + "pmcid:PMC4590705", + "pubmed:26427375" ], "sc:description": "Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Australia.", "sc:featureList": { @@ -29,20 +29,20 @@ }, "sc:name": "MutExSL", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://sites.google.com/site/mutexsl/", "sc:version": "v1" }, - { - "@id": "https://doi.org/10.1186/s13062-015-0086-1", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-0713-6723", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/s13062-015-0086-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mutlbsgenedb/mutlbsgenedbbioschemas.jsonld b/data/mutlbsgenedb/mutlbsgenedbbioschemas.jsonld index ab9898945b47c..60e89ea30f67e 100644 --- a/data/mutlbsgenedb/mutlbsgenedbbioschemas.jsonld +++ b/data/mutlbsgenedb/mutlbsgenedbbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Zhongming Zha", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:27907895", { "@id": "https://doi.org/10.1093/NAR/GKW905" }, - "pmcid:PMC5210621" + "pmcid:PMC5210621", + "pubmed:27907895" ], "sc:description": "Mutated ligand binding site gene DataBase.", "sc:featureList": { diff --git a/data/mutplot/mutplotbioschemas.jsonld b/data/mutplot/mutplotbioschemas.jsonld index fc0ba34f3f904..ab1add76c8f50 100644 --- a/data/mutplot/mutplotbioschemas.jsonld +++ b/data/mutplot/mutplotbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-6123-8034", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/Mutplot", "@type": "sc:SoftwareApplication", @@ -21,11 +17,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31091262", - "pmcid:PMC6519802", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0215838" - } + }, + "pubmed:31091262", + "pmcid:PMC6519802" ], "sc:description": "Tool for plotting complex mutation data with flexibility.", "sc:featureList": [ @@ -39,15 +35,19 @@ "sc:license": "Unlicense", "sc:name": "Mutplot", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://bioinformaticstools.shinyapps.io/lollipop/" }, { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0215838", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-6123-8034", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mutpred/mutpredbioschemas.jsonld b/data/mutpred/mutpredbioschemas.jsonld index 990a542144031..2cc3cf9a47664 100644 --- a/data/mutpred/mutpredbioschemas.jsonld +++ b/data/mutpred/mutpredbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MutPred is a web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. In addition, it predicts molecular cause of disease.", "sc:name": "MutPred", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://mutpred.mutdb.org/", "sc:version": "1.2" diff --git a/data/muts-needle-plot/muts-needle-plotbioschemas.jsonld b/data/muts-needle-plot/muts-needle-plotbioschemas.jsonld index a661678e00a4e..3c743ec56b8f3 100644 --- a/data/muts-needle-plot/muts-needle-plotbioschemas.jsonld +++ b/data/muts-needle-plot/muts-needle-plotbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Draws a Needle-Plot for mutation data (stacked).", "sc:name": "muts-needle-plot", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "BioJS", "sc:url": "https://github.com/bbglab/muts-needle-plot", diff --git a/data/mvbiodatasim/mvbiodatasimbioschemas.jsonld b/data/mvbiodatasim/mvbiodatasimbioschemas.jsonld index 38626dbc81474..4e56e2c441645 100644 --- a/data/mvbiodatasim/mvbiodatasimbioschemas.jsonld +++ b/data/mvbiodatasim/mvbiodatasimbioschemas.jsonld @@ -13,23 +13,27 @@ "@id": "http://orcid.org/0000-0002-3374-1492", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/s12859-015-0577-1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mvbiodatasim", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Roberto Tagliaferri", - "Paola Galdi", { "@id": "http://orcid.org/0000-0002-3374-1492" - } + }, + "Paola Galdi", + "Roberto Tagliaferri" ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4448275", { "@id": "https://doi.org/10.1186/s12859-015-0577-1" }, - "pubmed:25962835", - "pmcid:PMC4448275" + "pubmed:25962835" ], "sc:description": "R package for multi-view genomic data simulator. It is a tool in R to generate synthetic datasets from ordinary differential equations (ODE)-based models with known parameters.", "sc:featureList": { @@ -38,16 +42,12 @@ "sc:name": "MVBioDataSim", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ELIXIR-ITA-SALERNO", "sc:url": "http://elixir-italy.org/salerno/en/archives/servizi/mvbiodatasim", "sc:version": "1" - }, - { - "@id": "https://doi.org/10.1186/s12859-015-0577-1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mvcclass/bioconda_mvcclass.yaml b/data/mvcclass/bioconda_mvcclass.yaml index 0077632fb1fcb..be71dbde69d92 100644 --- a/data/mvcclass/bioconda_mvcclass.yaml +++ b/data/mvcclass/bioconda_mvcclass.yaml @@ -3,7 +3,6 @@ description: Creates classes used in model-view-controller (MVC) design home: https://bioconductor.org/packages/3.10/bioc/html/MVCClass.html identifiers: - biotools:mvcclass -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-mvcclass diff --git a/data/mvcclass/mvcclassbioschemas.jsonld b/data/mvcclass/mvcclassbioschemas.jsonld index e8378f12806b7..1866813bd2a7b 100644 --- a/data/mvcclass/mvcclassbioschemas.jsonld +++ b/data/mvcclass/mvcclassbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Elizabeth Whalen", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Creates classes used in model-view-controller (MVC) design.", "sc:license": "GPL-3.0", "sc:name": "MVCClass", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/MVCClass.html", diff --git a/data/mvda/mvdabioschemas.jsonld b/data/mvda/mvdabioschemas.jsonld index b8e827137b41a..f0d13fa3f778d 100644 --- a/data/mvda/mvdabioschemas.jsonld +++ b/data/mvda/mvdabioschemas.jsonld @@ -18,10 +18,10 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Paola Galdi", + "Roberto Tagliaferri", { "@id": "http://orcid.org/0000-0002-3374-1492" - }, - "Roberto Tagliaferri" + } ], "sc:additionalType": "Command-line tool", "sc:author": "Angela Serra", diff --git a/data/mvgst/mvgstbioschemas.jsonld b/data/mvgst/mvgstbioschemas.jsonld index 1e3bff4692499..fb14a9d489dfe 100644 --- a/data/mvgst/mvgstbioschemas.jsonld +++ b/data/mvgst/mvgstbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "John R. Stevens", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Platform-independent tools to identify GO terms that are differentially active in multiple contrasts of interest. Given a matrix of one-sided p-values, it uses meta-analytic methods to combine p-values for all genes annotated to each gene set, and then classify them as significantly more active, less active, or not significantly differentially active in each contrast of interest. With multiple contrasts of interest, each gene set is assigned to a profile of differential activity.", "sc:license": "GPL-3.0", "sc:name": "mvGST", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mvGST.html", "sc:version": "1.8.0" diff --git a/data/mview_api_ebi/mview_api_ebibioschemas.jsonld b/data/mview_api_ebi/mview_api_ebibioschemas.jsonld index 8745eb32160f5..e04c4a4f63991 100644 --- a/data/mview_api_ebi/mview_api_ebibioschemas.jsonld +++ b/data/mview_api_ebi/mview_api_ebibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Re-format the results of a sequence database search (BLAST, FASTA, etc) or a multiple alignment (MSF, PIR, CLUSTAL, etc) adding optional HTML markup to control colouring and web page layout.", "sc:name": "Mview API (EBI)", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/msa/mview_rest", "sc:version": "1" diff --git a/data/mview_ebi/mview_ebibioschemas.jsonld b/data/mview_ebi/mview_ebibioschemas.jsonld index 872650ba7695c..7fbdfda8c61d3 100644 --- a/data/mview_ebi/mview_ebibioschemas.jsonld +++ b/data/mview_ebi/mview_ebibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Reformat the results of a sequence database search (BLAST, FASTA) or a multiple alignment adding optional HTML markup to control colouring and web page layout.", "sc:name": "MView (EBI)", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/msa/mview/", diff --git a/data/mvqtlcim/mvqtlcimbioschemas.jsonld b/data/mvqtlcim/mvqtlcimbioschemas.jsonld index 6ffdabddb951f..162f74257bd82 100644 --- a/data/mvqtlcim/mvqtlcimbioschemas.jsonld +++ b/data/mvqtlcim/mvqtlcimbioschemas.jsonld @@ -22,10 +22,10 @@ ], "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5701343", { "@id": "https://doi.org/10.1186/s12859-017-1908-1" }, - "pmcid:PMC5701343", "pubmed:29169342" ], "sc:description": "CIM QTL mapping via multivariate statistical method in an outbred full-sib family.", diff --git a/data/mwastools/mwastoolsbioschemas.jsonld b/data/mwastools/mwastoolsbioschemas.jsonld index 68cabe333e2ef..e7145e5a061b1 100644 --- a/data/mwastools/mwastoolsbioschemas.jsonld +++ b/data/mwastools/mwastoolsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/mwastools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Andrea Rodriguez-Martinez", - "Rafael Ayala" + "Rafael Ayala", + "Andrea Rodriguez-Martinez" ], "sc:additionalType": "Library", "sc:description": "It provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.", diff --git a/data/mwcontam/mwcontambioschemas.jsonld b/data/mwcontam/mwcontambioschemas.jsonld index d695832687bc0..d36dae84075b2 100644 --- a/data/mwcontam/mwcontambioschemas.jsonld +++ b/data/mwcontam/mwcontambioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "EMBOSS Contributors", + "UK BBSRC", "UK MRC", - "UK BBSRC" + "EMBOSS Contributors", + "Wellcome Trust" ], "sc:description": "Find weights common to multiple molecular weights files.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "mwcontam", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/mwcontam.html", "sc:version": "r6" diff --git a/data/mwfilter/mwfilterbioschemas.jsonld b/data/mwfilter/mwfilterbioschemas.jsonld index 6cd36de55218d..c754558572d9f 100644 --- a/data/mwfilter/mwfilterbioschemas.jsonld +++ b/data/mwfilter/mwfilterbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", "EMBOSS Contributors", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC", + "UK BBSRC" ], "sc:description": "Filter noisy data from molecular weights file.", "sc:funder": [ - "Wellcome Trust", "UK MRC", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "mwfilter", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/mwt/mwtbioschemas.jsonld b/data/mwt/mwtbioschemas.jsonld index 632c638d72b74..6aa8a77a7fdec 100644 --- a/data/mwt/mwtbioschemas.jsonld +++ b/data/mwt/mwtbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MWT computes FDR based on a moderated version of the Welch test. It’s particularly suited for small samples comparisons exprecially with unequal variances", "sc:name": "MWT", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://fafner.meb.ki.se/personal/yudpaw/?page_id=13", "sc:version": "0.2.7" diff --git a/data/mxm/mxmbioschemas.jsonld b/data/mxm/mxmbioschemas.jsonld index 1b8cd704085e1..a28d66a050fa3 100644 --- a/data/mxm/mxmbioschemas.jsonld +++ b/data/mxm/mxmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MXM", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/MXM/index.html", "sc:version": "1.3.9" diff --git a/data/my_forensic_loci_queries/my_forensic_loci_queriesbioschemas.jsonld b/data/my_forensic_loci_queries/my_forensic_loci_queriesbioschemas.jsonld index 91b33d46735e3..6156991c2e54b 100644 --- a/data/my_forensic_loci_queries/my_forensic_loci_queriesbioschemas.jsonld +++ b/data/my_forensic_loci_queries/my_forensic_loci_queriesbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Analysis of forensic DNA profiles.", "sc:name": "My Forensic Loci queries", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/beukueb/myflq", diff --git a/data/mybs/mybsbioschemas.jsonld b/data/mybs/mybsbioschemas.jsonld index 731f04650bd8a..21b045ca17100 100644 --- a/data/mybs/mybsbioschemas.jsonld +++ b/data/mybs/mybsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.", "sc:name": "MYBS", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bits.iis.sinica.edu.tw/~mybs/" } \ No newline at end of file diff --git a/data/mycomemsvm/mycomemsvmbioschemas.jsonld b/data/mycomemsvm/mycomemsvmbioschemas.jsonld index 744ac89fd49fe..0a9efcdf4bd7d 100644 --- a/data/mycomemsvm/mycomemsvmbioschemas.jsonld +++ b/data/mycomemsvm/mycomemsvmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A sequence-based predictor for identifying mycobacterial membrane proteins and their types.", "sc:name": "MycoMemSVM", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://lin.uestc.edu.cn/server/MycoMemSVM" } \ No newline at end of file diff --git a/data/mydgr/mydgrbioschemas.jsonld b/data/mydgr/mydgrbioschemas.jsonld index 06c99dc12f380..d1cc3dcc4ee2f 100644 --- a/data/mydgr/mydgrbioschemas.jsonld +++ b/data/mydgr/mydgrbioschemas.jsonld @@ -14,15 +14,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yuzhen Ye", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": [ - "pmcid:PMC6602519", + "pubmed:31049585", { "@id": "https://doi.org/10.1093/NAR/GKZ329" }, - "pubmed:31049585" + "pmcid:PMC6602519" ], "sc:description": "Server for identification and characterization of diversity-generating retroelements.", "sc:featureList": [ @@ -39,9 +39,9 @@ "sc:license": "Unlicense", "sc:name": "myDGR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://omics.informatics.indiana.edu/myDGR" }, diff --git a/data/myelinj/myelinjbioschemas.jsonld b/data/myelinj/myelinjbioschemas.jsonld index a6e4daedcf046..84e6aeef13693 100644 --- a/data/myelinj/myelinjbioschemas.jsonld +++ b/data/myelinj/myelinjbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Unlicense", "sc:name": "MyelinJ", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/BarnettLab/MyelinJ" } \ No newline at end of file diff --git a/data/myexperiment/myexperimentbioschemas.jsonld b/data/myexperiment/myexperimentbioschemas.jsonld index 7e80d4bae562a..7d4c5a4209272 100644 --- a/data/myexperiment/myexperimentbioschemas.jsonld +++ b/data/myexperiment/myexperimentbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "myExperiment", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.myexperiment.org" } \ No newline at end of file diff --git a/data/mygenomebrowser/mygenomebrowserbioschemas.jsonld b/data/mygenomebrowser/mygenomebrowserbioschemas.jsonld index d843e78605990..e0401c3f0b5b4 100644 --- a/data/mygenomebrowser/mygenomebrowserbioschemas.jsonld +++ b/data/mygenomebrowser/mygenomebrowserbioschemas.jsonld @@ -29,10 +29,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC5408841", + "pubmed:28011789", { "@id": "https://doi.org/10.1093/bioinformatics/btw800" - }, - "pubmed:28011789" + } ], "sc:description": "Web-based environment that provides biologists with a way to build, query and share their genome browsers.", "sc:featureList": { @@ -42,8 +42,8 @@ "sc:name": "myGenomeBrowser", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://bbric-pipelines.toulouse.inra.fr/myGenomeBrowser" } diff --git a/data/myminer/myminerbioschemas.jsonld b/data/myminer/myminerbioschemas.jsonld index 2124de5d16b23..c2322f7d44dc1 100644 --- a/data/myminer/myminerbioschemas.jsonld +++ b/data/myminer/myminerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MyMiner is a free and user-friendly text annotation tool aimed to assist in carrying out the main biocuration tasks and to provide labelled data for the development of text mining systems.", "sc:name": "MyMiner", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://myminer.armi.monash.edu.au/" } \ No newline at end of file diff --git a/data/myphylodb/myphylodbbioschemas.jsonld b/data/myphylodb/myphylodbbioschemas.jsonld index c713510e57739..de8cafafcc47f 100644 --- a/data/myphylodb/myphylodbbioschemas.jsonld +++ b/data/myphylodb/myphylodbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Open-source software package aimed at developing a user-friendly web-interface for accessing and analyzing all of your laboratory’s microbial ecology data.", "sc:name": "myPhyloDB", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.myphylodb.org/" } \ No newline at end of file diff --git a/data/myproteinnet/myproteinnetbioschemas.jsonld b/data/myproteinnet/myproteinnetbioschemas.jsonld index c0494c73047dd..98cda7905a680 100644 --- a/data/myproteinnet/myproteinnetbioschemas.jsonld +++ b/data/myproteinnet/myproteinnetbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Esti Yeger-Lotem", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:25990735", { "@id": "https://doi.org/10.1093/nar/gkv515" }, - "pubmed:25990735", "pmcid:PMC4489290" ], "sc:description": "The tool enables to create context-sensitive protein interaction networks for organisms, tissues and user-defined contexts.", @@ -27,10 +27,10 @@ "@id": "edam:operation_3439" }, { - "@id": "edam:operation_0276" + "@id": "edam:operation_2949" }, { - "@id": "edam:operation_2949" + "@id": "edam:operation_0276" }, { "@id": "edam:operation_3083" @@ -38,9 +38,9 @@ ], "sc:name": "MyproteinNet", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://netbio.bgu.ac.il/myproteinnet/" }, diff --git a/data/myrialign/myrialignbioschemas.jsonld b/data/myrialign/myrialignbioschemas.jsonld index e27cb8b4b0b70..baa44e82f0424 100644 --- a/data/myrialign/myrialignbioschemas.jsonld +++ b/data/myrialign/myrialignbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software to align short reads produced by a short read genome sequencer to a reference genome. It performs brute force alignment using a variant on the \"bitap\" algorithm that aligns several thousand reads to a reference in parallel. It uses bit-parallelism, multiple processors, and Cell SPUs if available.\nIt will find alignments with any number of errors up to a user specified cutoff. The emphasis is on doing a 100% accurate search as fast as is possible.", "sc:name": "Myrialign", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://savannah.nongnu.org/projects/myrialign" } \ No newline at end of file diff --git a/data/myvariant/myvariantbioschemas.jsonld b/data/myvariant/myvariantbioschemas.jsonld index b3e73b3cf1bcb..81f01b6ab6342 100644 --- a/data/myvariant/myvariantbioschemas.jsonld +++ b/data/myvariant/myvariantbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "myvariant", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/myvariant.html", "sc:version": "1.4.0" diff --git a/data/myvcf/myvcfbioschemas.jsonld b/data/myvcf/myvcfbioschemas.jsonld index 91ba8228e0dc6..63fbfe54bfc7e 100644 --- a/data/myvcf/myvcfbioschemas.jsonld +++ b/data/myvcf/myvcfbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Desktop application for high-throughput mutations data management.", "sc:name": "myVCF", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://apietrelli.github.io/myVCF/" } \ No newline at end of file diff --git a/data/mz2mgf/mz2mgfbioschemas.jsonld b/data/mz2mgf/mz2mgfbioschemas.jsonld index f545f0968048a..d409c5eb2cdb6 100644 --- a/data/mz2mgf/mz2mgfbioschemas.jsonld +++ b/data/mz2mgf/mz2mgfbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "mz2mgf", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ce4csb.org/software.shtml" } \ No newline at end of file diff --git a/data/mzid/bioconda_mzid.yaml b/data/mzid/bioconda_mzid.yaml index ceafd7ec57f85..230e9e3f75638 100644 --- a/data/mzid/bioconda_mzid.yaml +++ b/data/mzid/bioconda_mzid.yaml @@ -7,7 +7,6 @@ description: A parser for mzIdentML files implemented using the XML package. The home: https://bioconductor.org/packages/3.10/bioc/html/mzID.html identifiers: - biotools:mzid -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-mzid diff --git a/data/mzid/mzidbioschemas.jsonld b/data/mzid/mzidbioschemas.jsonld index e5eb8a37f5c5d..786c9ce203e1b 100644 --- a/data/mzid/mzidbioschemas.jsonld +++ b/data/mzid/mzidbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "mzID", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mzID.html", diff --git a/data/mzjava/mzjavabioschemas.jsonld b/data/mzjava/mzjavabioschemas.jsonld index 436fa450dd660..40441f2fb6215 100644 --- a/data/mzjava/mzjavabioschemas.jsonld +++ b/data/mzjava/mzjavabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Library for the analysis of mass spectrometry data from large scale proteomics and glycomics experiments.", "sc:name": "MzJava", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mzjava.expasy.org/" } \ No newline at end of file diff --git a/data/mzmatch/mzmatchbioschemas.jsonld b/data/mzmatch/mzmatchbioschemas.jsonld index d320e508941a9..a3c369b339029 100644 --- a/data/mzmatch/mzmatchbioschemas.jsonld +++ b/data/mzmatch/mzmatchbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Modular, open source and platform independent data processing pipeline for metabolomics LC/MS data written in the Java language. It was designed to provide small tools for the common processing tasks for LC/MS data.", "sc:name": "mzMatch", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://mzmatch.sourceforge.net/" diff --git a/data/mzmine/mzminebioschemas.jsonld b/data/mzmine/mzminebioschemas.jsonld index 9377012b354ca..6d0feeac917c5 100644 --- a/data/mzmine/mzminebioschemas.jsonld +++ b/data/mzmine/mzminebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "MZmine", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mzmine.sourceforge.net" } \ No newline at end of file diff --git a/data/mzr/mzrbioschemas.jsonld b/data/mzr/mzrbioschemas.jsonld index e2109f86f9efb..5ed8682581a35 100644 --- a/data/mzr/mzrbioschemas.jsonld +++ b/data/mzr/mzrbioschemas.jsonld @@ -9,18 +9,22 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btn323", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/mzr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Bernd Fischer", - "Steffen Neumann", + "Qiang Kou", "Laurent Gatto", - "Qiang Kou" + "Steffen Neumann", + "Bernd Fischer" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pubmed:18606607", @@ -36,16 +40,12 @@ "sc:license": "Artistic-2.0", "sc:name": "mzR", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/mzR.html", "sc:version": "2.8.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btn323", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/mzvar/mzvarbioschemas.jsonld b/data/mzvar/mzvarbioschemas.jsonld index 8688e01140607..d582489556d8d 100644 --- a/data/mzvar/mzvarbioschemas.jsonld +++ b/data/mzvar/mzvarbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-6548-709X", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/mzvar", "@type": "sc:SoftwareApplication", @@ -22,15 +26,11 @@ "sc:description": "MzVar is a Java tool allowing the compilation of customized variant protein and peptide databases in the FASTA format for database searching of MS/MS data, using a VCF file as variant input and a FASTA file as transcript input. The tool is compatible with transcript sequences retrieved from either Ensembl or the UCSC Table Browser.", "sc:name": "MzVar", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://bitbucket.org/sib-pig/mzvar-public/src/master/" - }, - { - "@id": "https://orcid.org/0000-0001-6548-709X", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/mzxml_viewer/mzxml_viewerbioschemas.jsonld b/data/mzxml_viewer/mzxml_viewerbioschemas.jsonld index 83625077e8580..285007470c2a8 100644 --- a/data/mzxml_viewer/mzxml_viewerbioschemas.jsonld +++ b/data/mzxml_viewer/mzxml_viewerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "MzXML viewer from Seattle Proteome Center.", "sc:name": "mzXML Viewer", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://tools.proteomecenter.org/mzXMLViewer.php" } \ No newline at end of file diff --git a/data/mzxmlplot/mzxmlplotbioschemas.jsonld b/data/mzxmlplot/mzxmlplotbioschemas.jsonld index 163c34ec0f9b8..afc07348a9f6d 100644 --- a/data/mzxmlplot/mzxmlplotbioschemas.jsonld +++ b/data/mzxmlplot/mzxmlplotbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Plots mzXML LC-MS data as virtual gels or heat maps.", "sc:name": "mzXMLplot", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ms-utils.org/mzXMLplot/index.html" } \ No newline at end of file diff --git a/data/n-glyco/n-glycobioschemas.jsonld b/data/n-glyco/n-glycobioschemas.jsonld index e0af57a07924c..18c5d97175613 100644 --- a/data/n-glyco/n-glycobioschemas.jsonld +++ b/data/n-glyco/n-glycobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "HIV N-linked Glycosylation Site Analyzer", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://hivtools.publichealth.uga.edu/N-Glyco/" } \ No newline at end of file diff --git a/data/n-score/n-scorebioschemas.jsonld b/data/n-score/n-scorebioschemas.jsonld index 8b2b4aaa8d19f..c95d23ffcf895 100644 --- a/data/n-score/n-scorebioschemas.jsonld +++ b/data/n-score/n-scorebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "N-score", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bcb.dfci.harvard.edu/~gcyuan/software.html" } \ No newline at end of file diff --git a/data/n1pas/n1pasbioschemas.jsonld b/data/n1pas/n1pasbioschemas.jsonld index bc9349961383a..5096267f3f51e 100644 --- a/data/n1pas/n1pasbioschemas.jsonld +++ b/data/n1pas/n1pasbioschemas.jsonld @@ -9,45 +9,45 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3389/FGENE.2019.00414", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/N1PAS", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yves A. Lussier", - "Alfred Grant Schissler" + "Alfred Grant Schissler", + "Yves A. Lussier" ], "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6521780", + "pubmed:31143202", { "@id": "https://doi.org/10.3389/FGENE.2019.00414" - }, - "pmcid:PMC6521780", - "pubmed:31143202" + } ], "sc:description": "Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes.", "sc:featureList": [ - { - "@id": "edam:operation_3501" - }, { "@id": "edam:operation_0533" }, { "@id": "edam:operation_3800" + }, + { + "@id": "edam:operation_3501" } ], "sc:license": "MIT", "sc:name": "N1PAS", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/grizant/n1pas/tree/master" - }, - { - "@id": "https://doi.org/10.3389/FGENE.2019.00414", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nadbinder/nadbinderbioschemas.jsonld b/data/nadbinder/nadbinderbioschemas.jsonld index 9e0f45813fc3d..1a1c58f37f6a7 100644 --- a/data/nadbinder/nadbinderbioschemas.jsonld +++ b/data/nadbinder/nadbinderbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "NADbinder server discriminate the NAD interacting residues and non-interacting residues from a given sequence. The NADbinder server uses the SVM based method by using the Position Specific Scoring Matrix (PSSM) generated from the query sequence(s).", "sc:name": "NADbinder", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/nadbinder/" diff --git a/data/nadfinder/nadfinderbioschemas.jsonld b/data/nadfinder/nadfinderbioschemas.jsonld index 563f273e3059e..7e42461cbb981 100644 --- a/data/nadfinder/nadfinderbioschemas.jsonld +++ b/data/nadfinder/nadfinderbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/nadfinder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jianhong Ou", - "Lihua Julie Zhu" + "Lihua Julie Zhu", + "Jianhong Ou" ], "sc:additionalType": "Library", "sc:description": "This Bioconductor package has been developed for bioinformatic analysis of the NAD-seq data, including normalization, smoothing, peak calling, peak trimming and annotation.", "sc:license": "GPL-2.0", "sc:name": "NADfinder", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NADfinder.html", "sc:version": "1.4.0" diff --git a/data/nail/nailbioschemas.jsonld b/data/nail/nailbioschemas.jsonld index 31d2100df7054..93dfd34765b6e 100644 --- a/data/nail/nailbioschemas.jsonld +++ b/data/nail/nailbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Set of tools for solving problems in the life sciences using network (graph) approaches. It includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results.", "sc:name": "NAIL", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://sourceforge.net/projects/nailsystemsbiology/" } \ No newline at end of file diff --git a/data/nam/nambioschemas.jsonld b/data/nam/nambioschemas.jsonld index 416d51c5293b9..fb6217ef2df67 100644 --- a/data/nam/nambioschemas.jsonld +++ b/data/nam/nambioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "R package that allows user to take into account prior information regarding population stratification to relax the linkage phase assumption of current methods.", "sc:name": "NAM", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/NAM/index.html" } \ No newline at end of file diff --git a/data/nannochloropsis/nannochloropsisbioschemas.jsonld b/data/nannochloropsis/nannochloropsisbioschemas.jsonld index a2444f5748b9f..7394ce4f182a0 100644 --- a/data/nannochloropsis/nannochloropsisbioschemas.jsonld +++ b/data/nannochloropsis/nannochloropsisbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Nannocholopsis gaditana Database", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://www.nannochloropsis.org/" diff --git a/data/nanodj/nanodjbioschemas.jsonld b/data/nanodj/nanodjbioschemas.jsonld index 75307a1c70b76..a9a97a905b155 100644 --- a/data/nanodj/nanodjbioschemas.jsonld +++ b/data/nanodj/nanodjbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-5352-069X", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/S12859-019-2860-Z", "@type": "sc:CreativeWork" @@ -29,10 +25,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:31072312", + "pmcid:PMC6509807", { "@id": "https://doi.org/10.1186/S12859-019-2860-Z" - }, - "pmcid:PMC6509807" + } ], "sc:description": "Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly.", "sc:featureList": [ @@ -40,20 +36,24 @@ "@id": "edam:operation_0525" }, { - "@id": "edam:operation_3192" + "@id": "edam:operation_3185" }, { - "@id": "edam:operation_3185" + "@id": "edam:operation_3192" } ], "sc:license": "GPL-3.0", "sc:name": "NanoDJ", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/genomicsITER/NanoDJ" + }, + { + "@id": "https://orcid.org/0000-0001-5352-069X", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/nanomod/nanomodbioschemas.jsonld b/data/nanomod/nanomodbioschemas.jsonld index de3df4cc1049b..45a899afcd52b 100644 --- a/data/nanomod/nanomodbioschemas.jsonld +++ b/data/nanomod/nanomodbioschemas.jsonld @@ -9,25 +9,29 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12864-018-5372-8", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/NanoMod", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Wang Genomics Lab", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:30712508", - "pmcid:PMC6360650", { "@id": "https://doi.org/10.1186/s12864-018-5372-8" - } + }, + "pubmed:30712508", + "pmcid:PMC6360650" ], "sc:description": "Computational tool to detect DNA modifications using Nanopore long-read sequencing data.", "sc:featureList": [ { - "@id": "edam:operation_3185" + "@id": "edam:operation_0417" }, { - "@id": "edam:operation_0417" + "@id": "edam:operation_3185" }, { "@id": "edam:operation_0452" @@ -41,10 +45,6 @@ ], "sc:url": "https://github.com/WGLab/NanoMod", "sc:version": "0.1.0" - }, - { - "@id": "https://doi.org/10.1186/s12864-018-5372-8", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nanook/nanookbioschemas.jsonld b/data/nanook/nanookbioschemas.jsonld index 4117699129339..3b6117668a47d 100644 --- a/data/nanook/nanookbioschemas.jsonld +++ b/data/nanook/nanookbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btv540", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-3044-4297", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/nanook", "@type": "sc:SoftwareApplication", @@ -25,11 +17,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:26382197", + "pmcid:PMC4681994", { "@id": "https://doi.org/10.1093/bioinformatics/btv540" }, - "pmcid:PMC4681994" + "pubmed:26382197" ], "sc:description": "A tool for comprehensive analysis of Oxford Nanopore MinION sequence data.", "sc:featureList": [ @@ -44,6 +36,14 @@ "sc:name": "NanoOK", "sc:operatingSystem": "Linux", "sc:url": "http://www.earlham.ac.uk/nanook" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv540", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-3044-4297", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/nanopack/nanopackbioschemas.jsonld b/data/nanopack/nanopackbioschemas.jsonld index 8dabdae0400e8..f94b138106962 100644 --- a/data/nanopack/nanopackbioschemas.jsonld +++ b/data/nanopack/nanopackbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Visualizing and processing long-read sequencing data.", "sc:name": "NanoPack", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/wdecoster/nanopack" } \ No newline at end of file diff --git a/data/nanopipe/nanopipebioschemas.jsonld b/data/nanopipe/nanopipebioschemas.jsonld index b34a10832fb65..bcf28d90e05cc 100644 --- a/data/nanopipe/nanopipebioschemas.jsonld +++ b/data/nanopipe/nanopipebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "NanoPipe", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://nanopipe.readthedocs.io/en/latest/" } \ No newline at end of file diff --git a/data/nanor/nanorbioschemas.jsonld b/data/nanor/nanorbioschemas.jsonld index 975fd09c756b0..be92891b2a167 100644 --- a/data/nanor/nanorbioschemas.jsonld +++ b/data/nanor/nanorbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "NanoR", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/davidebolo1993/NanoR", "sc:version": "2.0" diff --git a/data/nanostringdiff/nanostringdiffbioschemas.jsonld b/data/nanostringdiff/nanostringdiffbioschemas.jsonld index 7a94ca0bc8fe2..368bfb754f9f8 100644 --- a/data/nanostringdiff/nanostringdiffbioschemas.jsonld +++ b/data/nanostringdiff/nanostringdiffbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "NanoStringDiff", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NanoStringDiff.html", diff --git a/data/nanostringnormcnv/nanostringnormcnvbioschemas.jsonld b/data/nanostringnormcnv/nanostringnormcnvbioschemas.jsonld index 51bc085556a88..1c271ace5d9bb 100644 --- a/data/nanostringnormcnv/nanostringnormcnvbioschemas.jsonld +++ b/data/nanostringnormcnv/nanostringnormcnvbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "NanoStringNormCNV", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://labs.oicr.on.ca/boutros-lab/software/nanostringnormcnv" } \ No newline at end of file diff --git a/data/nanotiler/nanotilerbioschemas.jsonld b/data/nanotiler/nanotilerbioschemas.jsonld index 6195468e93c4c..0d60ece52573b 100644 --- a/data/nanotiler/nanotilerbioschemas.jsonld +++ b/data/nanotiler/nanotilerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Java application for the design of RNA nanostructures. Among other things, it can accomplish the following: 1) Detection, extraction and annotation of RNA structural elements, 2) Use of RNA building blocks for assemblying larger structures, 3) Combinatorial search of building blocks 4) Optimization of building block positions 5) Topology classification 6) Sequence Optimization (i.e. sequence design for self-assembly into the given topology).", "sc:name": "NanoTiler", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://binkley2.ncifcrf.gov/users/bshapiro/software.html" diff --git a/data/nap/napbioschemas.jsonld b/data/nap/napbioschemas.jsonld index 60a4431b6644d..6ee2b8a361c4e 100644 --- a/data/nap/napbioschemas.jsonld +++ b/data/nap/napbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Nucleotide Amino Acid Alignment is a Java interface to the nap C program. The NAP program computes an optimal global alignment of a DNA sequence and a protein sequence without penalizing terminal gaps. NAP handles frameshifts and long introns in the DNA sequence. It delivers the alignment in linear space, so long sequences can be aligned. The experimental results demonstrate that NAP is a sensitive and powerful tool for finding genes by DNA-protein sequence homology.", "sc:name": "NAP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://athena.bioc.uvic.ca/virology-ca-tools/nap/" } \ No newline at end of file diff --git a/data/napp/nappbioschemas.jsonld b/data/napp/nappbioschemas.jsonld index 95fd222b89450..7537af54e47fa 100644 --- a/data/napp/nappbioschemas.jsonld +++ b/data/napp/nappbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Nucleic Acid Phylogenetic Profile Database: classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes.", "sc:name": "NAPP", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://napp.u-psud.fr/" } \ No newline at end of file diff --git a/data/narrowpeaks/narrowpeaksbioschemas.jsonld b/data/narrowpeaks/narrowpeaksbioschemas.jsonld index a62a498e7467a..126ca3ea066e0 100644 --- a/data/narrowpeaks/narrowpeaksbioschemas.jsonld +++ b/data/narrowpeaks/narrowpeaksbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13059-015-0597-1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/narrowpeaks", "@type": "sc:SoftwareApplication", @@ -20,8 +24,8 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4378019", "pubmed:25853185", + "pmcid:PMC4378019", { "@id": "https://doi.org/10.1186/s13059-015-0597-1" } @@ -34,16 +38,12 @@ "sc:name": "NarrowPeaks", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NarrowPeaks.html", "sc:version": "1.18.0" }, - { - "@id": "https://doi.org/10.1186/s13059-015-0597-1", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-1959-8199", "@type": "schema:Person" diff --git a/data/nasca/nascabioschemas.jsonld b/data/nasca/nascabioschemas.jsonld index b4a92b5dd8e46..8f73896304a73 100644 --- a/data/nasca/nascabioschemas.jsonld +++ b/data/nasca/nascabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Automated program for side-chain resonance assignment and nuclear Overhauser effect (NOE) assignment from NOESY data. It does not require data from TOCSY experiments.NASCA casts the assignment problem into a Markov Random Field (MRF), and extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data.", "sc:name": "NASCA", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.cs.duke.edu/donaldlab/software/nasca/index.php" } \ No newline at end of file diff --git a/data/nassam/nassambioschemas.jsonld b/data/nassam/nassambioschemas.jsonld index b20f702367157..23f20972d4e73 100644 --- a/data/nassam/nassambioschemas.jsonld +++ b/data/nassam/nassambioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NASSAM", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://mfrlab.org/grafss/nassam/" } \ No newline at end of file diff --git a/data/nastiseq/nastiseqbioschemas.jsonld b/data/nastiseq/nastiseqbioschemas.jsonld index 5a5b1524cb121..0838a0edc2a80 100644 --- a/data/nastiseq/nastiseqbioschemas.jsonld +++ b/data/nastiseq/nastiseqbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "To identify cis-NATs using ssRNA-seq, a new computational method was developed based on model comparison that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries.", "sc:name": "NASTIseq", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/", "sc:version": "1.0" diff --git a/data/nastybugs/nastybugsbioschemas.jsonld b/data/nastybugs/nastybugsbioschemas.jsonld index 40ce4544a28d4..77f9c899ac103 100644 --- a/data/nastybugs/nastybugsbioschemas.jsonld +++ b/data/nastybugs/nastybugsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/nastybugs", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Greg Fedewa", - "Steve Tsang" + "Steve Tsang", + "Greg Fedewa" ], "sc:additionalType": "Command-line tool", "sc:description": "A Simple Method for Extracting Antimicrobial Resistance Information from metagenomic sequencing data.", diff --git a/data/natalieq/natalieqbioschemas.jsonld b/data/natalieq/natalieqbioschemas.jsonld index 8c52233f7eb60..63abe49683a9c 100644 --- a/data/natalieq/natalieqbioschemas.jsonld +++ b/data/natalieq/natalieqbioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.1186/1752-0509-8-40" }, - "pubmed:24690407", - "pmcid:PMC3998945" + "pmcid:PMC3998945", + "pubmed:24690407" ], "sc:description": "A web server for protein-protein interaction network querying.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "NatalieQ", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ibi.vu.nl/programs/natalieq/" } diff --git a/data/navicluster/naviclusterbioschemas.jsonld b/data/navicluster/naviclusterbioschemas.jsonld index 958d347feabf1..5574b7bc47e96 100644 --- a/data/navicluster/naviclusterbioschemas.jsonld +++ b/data/navicluster/naviclusterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Developed as an interactive, multi-scale navigation tool for large and complicated biological networks.", "sc:name": "NaviCluster", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://navicluster.cb.k.u-tokyo.ac.jp/" } \ No newline at end of file diff --git a/data/navigator/navigatorbioschemas.jsonld b/data/navigator/navigatorbioschemas.jsonld index 41d8541bae184..da49b1cbec81b 100644 --- a/data/navigator/navigatorbioschemas.jsonld +++ b/data/navigator/navigatorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto is a software package for visualizing and analyzing protein-protein interaction networks.NAViGaTOR is a powerful graphing application for 2D and 3D visualization of biological networks. Tools for manual and automated annontation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs.", "sc:name": "NAViGaTOR", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://ophid.utoronto.ca/navigator/" diff --git a/data/navikey/navikeybioschemas.jsonld b/data/navikey/navikeybioschemas.jsonld index f5ed746af1d04..d835269e213fc 100644 --- a/data/navikey/navikeybioschemas.jsonld +++ b/data/navikey/navikeybioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Universität Bayreuth, Department of Mycology", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:author": "Universität Bayreuth, Department of Mycology", "sc:contributor": "SNSB IT Center", @@ -21,8 +21,8 @@ "sc:license": "GPL-2.0", "sc:name": "NaviKey", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "SNSB IT Center", diff --git a/data/navise/navisebioschemas.jsonld b/data/navise/navisebioschemas.jsonld index 7dc719cc59e4b..16080812d6dc9 100644 --- a/data/navise/navisebioschemas.jsonld +++ b/data/navise/navisebioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-017-1698-5", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/navise", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ander Izeta", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5461685", { "@id": "https://doi.org/10.1186/S12859-017-1698-5" }, + "pmcid:PMC5461685", "pubmed:28587674" ], "sc:contributor": { @@ -36,18 +40,14 @@ "sc:name": "NaviSE", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/navise-superenhancer/" }, { "@id": "http://orcid.org/0000-0002-0013-3052", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/S12859-017-1698-5", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nbdc_rdf_portal/nbdc_rdf_portalbioschemas.jsonld b/data/nbdc_rdf_portal/nbdc_rdf_portalbioschemas.jsonld index ca11e5c128b96..0f4149e346d39 100644 --- a/data/nbdc_rdf_portal/nbdc_rdf_portalbioschemas.jsonld +++ b/data/nbdc_rdf_portal/nbdc_rdf_portalbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6301334", { "@id": "https://doi.org/10.1093/database/bay123" }, - "pubmed:30576482" + "pubmed:30576482", + "pmcid:PMC6301334" ], "sc:description": "Comprehensive repository for semantic data in life sciences.", "sc:featureList": [ @@ -36,9 +36,9 @@ "sc:license": "Unlicense", "sc:name": "NBDC RDF Portal", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://integbio.jp/rdf/" } diff --git a/data/nbrp_resources/nbrp_resourcesbioschemas.jsonld b/data/nbrp_resources/nbrp_resourcesbioschemas.jsonld index 7b1fa3aa6a66b..8ab007495dcf1 100644 --- a/data/nbrp_resources/nbrp_resourcesbioschemas.jsonld +++ b/data/nbrp_resources/nbrp_resourcesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "System for collecting, preserving and providing bioresources for use as experimental materials for life science research.", "sc:name": "NBRP resources", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.nbrp.jp/index.jsp" } \ No newline at end of file diff --git a/data/nbspred/nbspredbioschemas.jsonld b/data/nbspred/nbspredbioschemas.jsonld index c722f120f47fe..6000bc6af2f21 100644 --- a/data/nbspred/nbspredbioschemas.jsonld +++ b/data/nbspred/nbspredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Support vector machine-based high throughput pipeline for plant resistance protein NBSLRR (nucleotide binding site-leucine-rich repeats) prediction.", "sc:name": "NBSPred", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://soilecology.biol.lu.se/nbs/" } \ No newline at end of file diff --git a/data/ncats_bioplanet/ncats_bioplanetbioschemas.jsonld b/data/ncats_bioplanet/ncats_bioplanetbioschemas.jsonld index 21eb542a492e6..56456f7e432cb 100644 --- a/data/ncats_bioplanet/ncats_bioplanetbioschemas.jsonld +++ b/data/ncats_bioplanet/ncats_bioplanetbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "NCATS BioPlanet", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://tripod.nih.gov/bioplanet/" diff --git a/data/ncbi_assembly_archive/ncbi_assembly_archivebioschemas.jsonld b/data/ncbi_assembly_archive/ncbi_assembly_archivebioschemas.jsonld index 4ab56579cc673..c83c758897e3d 100644 --- a/data/ncbi_assembly_archive/ncbi_assembly_archivebioschemas.jsonld +++ b/data/ncbi_assembly_archive/ncbi_assembly_archivebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Links publically available assembly information with the NCBI Trace Archive's raw sequence data.", "sc:name": "NCBI Assembly Archive", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/projects/assembly/" diff --git a/data/ncbi_bookshelf/ncbi_bookshelfbioschemas.jsonld b/data/ncbi_bookshelf/ncbi_bookshelfbioschemas.jsonld index 5fcd426b127bd..65dfcb84193ac 100644 --- a/data/ncbi_bookshelf/ncbi_bookshelfbioschemas.jsonld +++ b/data/ncbi_bookshelf/ncbi_bookshelfbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Searchable collection of biomedical books linked to terms in PubMed abstracts; when viewing an abstract, click on Books link to see phrases in abstract hyperlinked to book sections.", "sc:name": "NCBI Bookshelf", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books" } \ No newline at end of file diff --git a/data/ncbi_dbprobe/ncbi_dbprobebioschemas.jsonld b/data/ncbi_dbprobe/ncbi_dbprobebioschemas.jsonld index c88fa0520e871..cdad5ac9cdf0d 100644 --- a/data/ncbi_dbprobe/ncbi_dbprobebioschemas.jsonld +++ b/data/ncbi_dbprobe/ncbi_dbprobebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.", "sc:name": "NCBI dbProbe", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/probe" } \ No newline at end of file diff --git a/data/ncbi_epigenomics/ncbi_epigenomicsbioschemas.jsonld b/data/ncbi_epigenomics/ncbi_epigenomicsbioschemas.jsonld index 4ac862570460b..c24c97d0b734f 100644 --- a/data/ncbi_epigenomics/ncbi_epigenomicsbioschemas.jsonld +++ b/data/ncbi_epigenomics/ncbi_epigenomicsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Resource for whole-genome epigenetic data sets. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. This resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes.", "sc:name": "NCBI Epigenomics", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/epigenomics" } \ No newline at end of file diff --git a/data/ncbi_gene/ncbi_genebioschemas.jsonld b/data/ncbi_gene/ncbi_genebioschemas.jsonld index c30077cd62331..64e57bb5c5778 100644 --- a/data/ncbi_gene/ncbi_genebioschemas.jsonld +++ b/data/ncbi_gene/ncbi_genebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Database of genes from NCBI RefSeq genomes.", "sc:name": "Database of genes from NCBI RefSeq genomes", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene" } \ No newline at end of file diff --git a/data/ncbi_genome_workbench/ncbi_genome_workbenchbioschemas.jsonld b/data/ncbi_genome_workbench/ncbi_genome_workbenchbioschemas.jsonld index be40a549154c2..e78befe42d6e6 100644 --- a/data/ncbi_genome_workbench/ncbi_genome_workbenchbioschemas.jsonld +++ b/data/ncbi_genome_workbench/ncbi_genome_workbenchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "NCBI Genome Workbench", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/tools/gbench/" } \ No newline at end of file diff --git a/data/ncbi_genotyping/ncbi_genotypingbioschemas.jsonld b/data/ncbi_genotyping/ncbi_genotypingbioschemas.jsonld index e4c8c0d94cc1f..44d8de3185c57 100644 --- a/data/ncbi_genotyping/ncbi_genotypingbioschemas.jsonld +++ b/data/ncbi_genotyping/ncbi_genotypingbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "Genotyping - NCBI", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi" diff --git a/data/ncbi_geo/ncbi_geobioschemas.jsonld b/data/ncbi_geo/ncbi_geobioschemas.jsonld index d21acbcbbbff9..c218e4c05ecfc 100644 --- a/data/ncbi_geo/ncbi_geobioschemas.jsonld +++ b/data/ncbi_geo/ncbi_geobioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "NCBI GEO", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/geo/" } \ No newline at end of file diff --git a/data/ncbi_mass_downloader/ncbi_mass_downloaderbioschemas.jsonld b/data/ncbi_mass_downloader/ncbi_mass_downloaderbioschemas.jsonld index 726b904246a50..84eb01cde4655 100644 --- a/data/ncbi_mass_downloader/ncbi_mass_downloaderbioschemas.jsonld +++ b/data/ncbi_mass_downloader/ncbi_mass_downloaderbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Francisco Pina Martins", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "This program will download sequences en masse from several NCBI databases (at the user's choice). After the downloading is finished, the program will check the resulting file for any missing sequences and continuously retry the download until all sequences are present in the local file. NCBI Data Usage Policies and Disclaimers may apply to downloaded data.", "sc:license": "GPL-3.0", "sc:name": "NCBI Mass Sequence Downloader", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/StuntsPT/NCBI_Mass_Downloader", "sc:version": "4.1" diff --git a/data/ncbi_resources/ncbi_resourcesbioschemas.jsonld b/data/ncbi_resources/ncbi_resourcesbioschemas.jsonld index c183949e151c3..10fbc224d5993 100644 --- a/data/ncbi_resources/ncbi_resourcesbioschemas.jsonld +++ b/data/ncbi_resources/ncbi_resourcesbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "The National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site.", "sc:name": "NCBI Resources", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov" } \ No newline at end of file diff --git a/data/ncigraph/bioconda_ncigraph.yaml b/data/ncigraph/bioconda_ncigraph.yaml index 54bcb8fa35535..79cd7a7985b2b 100644 --- a/data/ncigraph/bioconda_ncigraph.yaml +++ b/data/ncigraph/bioconda_ncigraph.yaml @@ -4,7 +4,6 @@ description: Provides various methods to load the pathways from the NCI Pathways home: https://bioconductor.org/packages/3.10/bioc/html/NCIgraph.html identifiers: - biotools:ncigraph -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-ncigraph diff --git a/data/ncigraph/ncigraphbioschemas.jsonld b/data/ncigraph/ncigraphbioschemas.jsonld index 1b72b2c5269a9..c1b24e7153942 100644 --- a/data/ncigraph/ncigraphbioschemas.jsonld +++ b/data/ncigraph/ncigraphbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "NCIgraph", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NCIgraph.html", "sc:version": "1.22.0" diff --git a/data/ncis/ncisbioschemas.jsonld b/data/ncis/ncisbioschemas.jsonld index 47aacdccd5066..9ea36d6617641 100644 --- a/data/ncis/ncisbioschemas.jsonld +++ b/data/ncis/ncisbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "NCIS (network-assisted co-clustering for the identification of cancer subtypes) combines molecular interaction network into co-clustering.", "sc:name": "NCIS", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioen-compbio.bioen.illinois.edu/NCIS/" } \ No newline at end of file diff --git a/data/ncoils/ncoilsbioschemas.jsonld b/data/ncoils/ncoilsbioschemas.jsonld index 0ba809371aebd..b21ed5364f47e 100644 --- a/data/ncoils/ncoilsbioschemas.jsonld +++ b/data/ncoils/ncoilsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ncoils", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "RostLab", "sc:url": "http://www.predictprotein.org", diff --git a/data/ncpred/ncpredbioschemas.jsonld b/data/ncpred/ncpredbioschemas.jsonld index ea0bfb8cb7714..7f3474406844f 100644 --- a/data/ncpred/ncpredbioschemas.jsonld +++ b/data/ncpred/ncpredbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "To identify non-coding RNA (ncRNA) signals within genomic regions, a classification tool was developed based on a hybrid random forest (RF) with a logistic regression model to efficiently discriminate short ncRNA sequences as well as long complex ncRNA sequences.", "sc:name": "NCpred", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "KMUTT", "sc:url": "http://ncrna-pred.com/HLRF.htm", diff --git a/data/ncrna/ncrnabioschemas.jsonld b/data/ncrna/ncrnabioschemas.jsonld index 6468973b4f6da..d35012acce34d 100644 --- a/data/ncrna/ncrnabioschemas.jsonld +++ b/data/ncrna/ncrnabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Non-translatable RNA transcripts that appear to work at the RNA level.", "sc:name": "Non-Coding RNA database", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://biobases.ibch.poznan.pl/ncRNA/" diff --git a/data/ncrnawsdl/ncrnawsdlbioschemas.jsonld b/data/ncrnawsdl/ncrnawsdlbioschemas.jsonld index e2121ec69b180..ee557a7855245 100644 --- a/data/ncrnawsdl/ncrnawsdlbioschemas.jsonld +++ b/data/ncrnawsdl/ncrnawsdlbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "NONCODE database integrates expression and functional long noncoding RNAs (lncRNA) data.", "sc:name": "ncRNAwsdl", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.noncode.org/index.php", "sc:version": "1" diff --git a/data/ndexr/ndexrbioschemas.jsonld b/data/ndexr/ndexrbioschemas.jsonld index d9834747dfda7..b6101901511c3 100644 --- a/data/ndexr/ndexrbioschemas.jsonld +++ b/data/ndexr/ndexrbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Dexter Pratt", + "Florian Auer", "Alex Ishkin", - "Frank Kramer", - "Florian Auer" + "Frank Kramer" ], "sc:additionalType": "Library", "sc:description": "This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation.", "sc:name": "ndexr", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ndexr.html" diff --git a/data/ndtree/ndtreebioschemas.jsonld b/data/ndtree/ndtreebioschemas.jsonld index 7cea5d46afba6..9f741c4d0f3c2 100644 --- a/data/ndtree/ndtreebioschemas.jsonld +++ b/data/ndtree/ndtreebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0087991", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ndtree", "@type": "sc:SoftwareApplication", @@ -16,27 +20,23 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:24505344", - "pubmed:24574290", - "pmcid:PMC3913712", { "@id": "https://doi.org/10.1371/journal.pone.0087991" - } + }, + "pmcid:PMC3913712", + "pubmed:24574290" ], "sc:description": "Phylogenic tree from reads using nucleotide difference method.", "sc:license": "Other", "sc:name": "NDtree", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "CBS", "sc:url": "http://cge.cbs.dtu.dk/services/NDtree/", "sc:version": "1.0" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0087991", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nearender/nearenderbioschemas.jsonld b/data/nearender/nearenderbioschemas.jsonld index ed6833c9bb9e6..46c53cb1f11ca 100644 --- a/data/nearender/nearenderbioschemas.jsonld +++ b/data/nearender/nearenderbioschemas.jsonld @@ -19,8 +19,8 @@ "biotools:primaryContact": "Ashwini Jeggari", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5374688", "pubmed:28361684", + "pmcid:PMC5374688", { "@id": "https://doi.org/10.1186/S12859-017-1534-Y" } @@ -31,9 +31,9 @@ }, "sc:name": "NEArender", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/NEArender/" } diff --git a/data/neartree/neartreebioschemas.jsonld b/data/neartree/neartreebioschemas.jsonld index 9293b7d525efe..8c5c832820ade 100644 --- a/data/neartree/neartreebioschemas.jsonld +++ b/data/neartree/neartreebioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-4451-1641", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1107/S1600576716004039", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/neartree", "@type": "sc:SoftwareApplication", @@ -17,11 +25,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27275134", "pmcid:PMC4886977", { "@id": "https://doi.org/10.1107/S1600576716004039" - } + }, + "pubmed:27275134" ], "sc:description": "NearTree is a software tool that constructs neartrees and provides a number of different query tools.", "sc:featureList": { @@ -32,14 +40,6 @@ "sc:operatingSystem": "Windows", "sc:url": "https://sourceforge.net/projects/neartree/", "sc:version": "5.1" - }, - { - "@id": "http://orcid.org/0000-0002-4451-1641", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1107/S1600576716004039", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/neat-enrich/neat-enrichbioschemas.jsonld b/data/neat-enrich/neat-enrichbioschemas.jsonld index 67c696094a836..b5f6353f8ec8b 100644 --- a/data/neat-enrich/neat-enrichbioschemas.jsonld +++ b/data/neat-enrich/neat-enrichbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-016-1203-6", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/neat-enrich", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:27597310", + "pmcid:PMC5011912", { "@id": "https://doi.org/10.1186/S12859-016-1203-6" - }, - "pmcid:PMC5011912" + } ], "sc:description": "Efficient network enrichment analysis test.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "GPL-3.0", "sc:name": "NEAT", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/neat/index.html" - }, - { - "@id": "https://doi.org/10.1186/S12859-016-1203-6", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/neat-ngs/neat-ngsbioschemas.jsonld b/data/neat-ngs/neat-ngsbioschemas.jsonld index cb3651209559b..5d6c29f59b19c 100644 --- a/data/neat-ngs/neat-ngsbioschemas.jsonld +++ b/data/neat-ngs/neat-ngsbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Admin", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:26830846", + "pmcid:PMC4736651", { "@id": "https://doi.org/10.1186/S12859-016-0902-3" - }, - "pubmed:26830846", - "pmcid:PMC4736651" + } ], "sc:description": "Framework for building fully automated NGS pipelines and analyses.", "sc:featureList": { diff --git a/data/neat/neatbioschemas.jsonld b/data/neat/neatbioschemas.jsonld index 5ef0bc293e539..7a2ded5a95f12 100644 --- a/data/neat/neatbioschemas.jsonld +++ b/data/neat/neatbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sylvain Brohée", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:18524799", "sc:description": "Suite of tools for the analysis of biological networks, clusters, classes and pathways. Tools are available as web services for integration into programmatic work flows.", "sc:license": "Apache-2.0", "sc:name": "NeAT", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://rsat.sb-roscoff.fr/index_neat.html" } \ No newline at end of file diff --git a/data/nebcutter/nebcutterbioschemas.jsonld b/data/nebcutter/nebcutterbioschemas.jsonld index bfcec378bf1d5..568fe42eb9838 100644 --- a/data/nebcutter/nebcutterbioschemas.jsonld +++ b/data/nebcutter/nebcutterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.", "sc:name": "NEBcutter", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://tools.neb.com/NEBcutter/index.php3" } \ No newline at end of file diff --git a/data/nebula/nebulabioschemas.jsonld b/data/nebula/nebulabioschemas.jsonld index 786f89dd846c7..5d5d1233d02e0 100644 --- a/data/nebula/nebulabioschemas.jsonld +++ b/data/nebula/nebulabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web service powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data.", "sc:name": "Nebula", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://nebula.curie.fr/" } \ No newline at end of file diff --git a/data/necklace/necklacebioschemas.jsonld b/data/necklace/necklacebioschemas.jsonld index a2750a20d21c1..f73da48ae5b5b 100644 --- a/data/necklace/necklacebioschemas.jsonld +++ b/data/necklace/necklacebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/necklace", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Nadia M Davidson", - "Alicia Oshlack" + "Alicia Oshlack", + "Nadia M Davidson" ], "sc:additionalType": "Command-line tool", "sc:description": "Combine reference and assembled transcriptomes for RNA-Seq analysis.", diff --git a/data/needle-api-ebi/needle-api-ebibioschemas.jsonld b/data/needle-api-ebi/needle-api-ebibioschemas.jsonld index 5d44da68d7f15..d0e2b9caf107d 100644 --- a/data/needle-api-ebi/needle-api-ebibioschemas.jsonld +++ b/data/needle-api-ebi/needle-api-ebibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Pairwise sequence alignment of DNA or protein sequences using Needleman-Wunsch global alignment.", "sc:name": "needle-api (EBI)", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/psa/emboss_needle_rest", diff --git a/data/needle/needlebioschemas.jsonld b/data/needle/needlebioschemas.jsonld index 1764c170b97c8..fc0a146dfee69 100644 --- a/data/needle/needlebioschemas.jsonld +++ b/data/needle/needlebioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "EMBOSS Contributors", "UK MRC", - "UK BBSRC" + "EMBOSS Contributors", + "UK BBSRC", + "Wellcome Trust" ], "sc:description": "Needleman-Wunsch global alignment of two sequences.", "sc:funder": [ - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "needle", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/needle.html", "sc:version": "r6" diff --git a/data/needleall/needleallbioschemas.jsonld b/data/needleall/needleallbioschemas.jsonld index f1a3c4044064e..9ba3802f5cf39 100644 --- a/data/needleall/needleallbioschemas.jsonld +++ b/data/needleall/needleallbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK MRC", "UK BBSRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "Wellcome Trust", + "UK MRC" ], "sc:description": "Many-to-many pairwise alignments of two sequence sets.", "sc:funder": [ - "Wellcome Trust", "UK MRC", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "needleall", @@ -31,8 +31,8 @@ "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/needleall.html", "sc:version": "r6" diff --git a/data/needles/needlesbioschemas.jsonld b/data/needles/needlesbioschemas.jsonld index 5e388558aad47..21d3b229fffe9 100644 --- a/data/needles/needlesbioschemas.jsonld +++ b/data/needles/needlesbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Large-scale genomic prediction with marker-by-environment interaction.", "sc:name": "Needles", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "Ghent Ubiversity", diff --git a/data/needlestack/needlestackbioschemas.jsonld b/data/needlestack/needlestackbioschemas.jsonld index 71128697a962b..b760dc8500d7a 100644 --- a/data/needlestack/needlestackbioschemas.jsonld +++ b/data/needlestack/needlestackbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Matthieu Foll", + "Aurelie Gabriel", "Nicolas Alcala", - "Tiffany Delhomme", - "Aurelie Gabriel" + "Tiffany Delhomme" ], "sc:additionalType": "Command-line tool", "sc:description": "Ultra-sensitive variant caller for multi-sample next generation sequencing data.", "sc:license": "GPL-3.0", "sc:name": "needlestack", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/IARCbioinfo/needlestack" diff --git a/data/neemp/neempbioschemas.jsonld b/data/neemp/neempbioschemas.jsonld index 5b09997639ea8..bb1f5d1d426e2 100644 --- a/data/neemp/neempbioschemas.jsonld +++ b/data/neemp/neempbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13321-016-0171-1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/neemp", "@type": "sc:SoftwareApplication", @@ -30,10 +26,10 @@ ], "edam:has_output": [ { - "@id": "edam:data_2526" + "@id": "edam:data_2048" }, { - "@id": "edam:data_2048" + "@id": "edam:data_2526" }, { "@id": "edam:data_1917" @@ -45,11 +41,11 @@ }, "sc:author": "Tomáš Raček", "sc:citation": [ - "pubmed:27803746", - "pmcid:PMC5067907", { "@id": "https://doi.org/10.1186/s13321-016-0171-1" - } + }, + "pmcid:PMC5067907", + "pubmed:27803746" ], "sc:description": "Main function is to perform EEM parameterization. Can be used to efficiently compute EEM charges, validate them against QM ones and to compute the parameter coverage.", "sc:featureList": { @@ -59,21 +55,25 @@ "sc:license": "GPL-3.0", "sc:name": "NEEMP", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ + "Central European Institute of Technology, Brno", "ELIXIR-CZ", "National Centre for Biomolecular Research, Masaryk University, Brno", - "mail.muni.cz", - "Central European Institute of Technology, Brno" + "mail.muni.cz" ], "sc:softwareHelp": { "@id": "http://webchem.ncbr.muni.cz/Wiki/NEEMP:UserManual" }, "sc:url": "http://ncbr.muni.cz/neemp", "sc:version": "1" + }, + { + "@id": "https://doi.org/10.1186/s13321-016-0171-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/negatome/negatomebioschemas.jsonld b/data/negatome/negatomebioschemas.jsonld index 1634c68169b26..e37897f2f7c27 100644 --- a/data/negatome/negatomebioschemas.jsonld +++ b/data/negatome/negatomebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions. The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and by analyzing protein complexes with known 3D structure. It can be used to evaluate protein and domain interactions from new experiments and improve the training of interaction prediction algorithms.", "sc:name": "Negatome", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://mips.helmholtz-muenchen.de/proj/ppi/negatome" diff --git a/data/nem/nembioschemas.jsonld b/data/nem/nembioschemas.jsonld index 2bf941ff9afdb..9a33b134dd513 100644 --- a/data/nem/nembioschemas.jsonld +++ b/data/nem/nembioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "nem", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/nem.html", "sc:version": "2.48.0" diff --git a/data/nembase4/nembase4bioschemas.jsonld b/data/nembase4/nembase4bioschemas.jsonld index 2b7b555a74f6c..f9a9338cafdf8 100644 --- a/data/nembase4/nembase4bioschemas.jsonld +++ b/data/nembase4/nembase4bioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NEMBASE4", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.nematodes.org/nembase4/" } \ No newline at end of file diff --git a/data/nemine/neminebioschemas.jsonld b/data/nemine/neminebioschemas.jsonld index 8e667419d17f1..652c4bdc4786a 100644 --- a/data/nemine/neminebioschemas.jsonld +++ b/data/nemine/neminebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Recognises gene and protein names in biomedical text.", "sc:name": "NEMine", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://text0.mib.man.ac.uk/~sasaki/bootstrep/nemine.html" } \ No newline at end of file diff --git a/data/neobio/neobiobioschemas.jsonld b/data/neobio/neobiobioschemas.jsonld index cee43f18bfe14..e8fd4444ed151 100644 --- a/data/neobio/neobiobioschemas.jsonld +++ b/data/neobio/neobiobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.", "sc:name": "NeoBio 1.0 pre-alpha", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://neobio.sourceforge.net/" } \ No newline at end of file diff --git a/data/neopeptide_analyser/neopeptide_analyserbioschemas.jsonld b/data/neopeptide_analyser/neopeptide_analyserbioschemas.jsonld index f2f2342918616..b1291a9aed1f3 100644 --- a/data/neopeptide_analyser/neopeptide_analyserbioschemas.jsonld +++ b/data/neopeptide_analyser/neopeptide_analyserbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/wellcomeopenres.11275.1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/neopeptide_analyser", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mandy Peffers", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:28503667", "pmcid:PMC5428739", { "@id": "https://doi.org/10.12688/wellcomeopenres.11275.1" - } + }, + "pubmed:28503667" ], "sc:description": "Neopeptide discovery in proteomics data.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "MIT", "sc:name": "Neopeptide Analyser", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/PGB-LIV/neo-pep-tool/releases/" + }, + { + "@id": "https://doi.org/10.12688/wellcomeopenres.11275.1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nep/nepbioschemas.jsonld b/data/nep/nepbioschemas.jsonld index e3257d9fd67b1..6d06438598c83 100644 --- a/data/nep/nepbioschemas.jsonld +++ b/data/nep/nepbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC4086065", + "pubmed:24782517", { "@id": "https://doi.org/10.1093/NAR/GKU318" - }, - "pubmed:24782517", - "pmcid:PMC4086065" + } ], "sc:description": "Epitope prediction based on antibody neutralization of viral strains with diverse sequences.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "NEP", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bioinformatics.niaid.nih.gov/nep/#home" } diff --git a/data/nephele/nephelebioschemas.jsonld b/data/nephele/nephelebioschemas.jsonld index 36d58d4cf245f..39782aed781a5 100644 --- a/data/nephele/nephelebioschemas.jsonld +++ b/data/nephele/nephelebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "NIAID, a cloud based tool for microbiome or metagenomics data analysis. Nephele allows you to process and analyze 16S raw data using pipelines based on QIIME and mothur. It also facilitates WGS functional analyses using bioBakery tools such as MetaPhlAn, HUMMAnN and metagenomic assembly using the a5-miseq/UDBA-UD.", "sc:name": "Nephele", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://nephele.niaid.nih.gov" diff --git a/data/neptune/neptunebioschemas.jsonld b/data/neptune/neptunebioschemas.jsonld index 4fdd734ddfc92..f0b688a2e5b0b 100644 --- a/data/neptune/neptunebioschemas.jsonld +++ b/data/neptune/neptunebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Locate genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches. The software identifies sequences that are sufficiently represented within inclusion targets and sufficiently absent from exclusion targets. The signature discovery process is accomplished using probabilistic models instead of heuristic strategies.", "sc:name": "Neptune", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://phac-nml.github.io/neptune/" } \ No newline at end of file diff --git a/data/nessm/nessmbioschemas.jsonld b/data/nessm/nessmbioschemas.jsonld index fe8f0746f7ac1..e41a7823a9920 100644 --- a/data/nessm/nessmbioschemas.jsonld +++ b/data/nessm/nessmbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0075448", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/nessm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:24124490", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0075448" }, - "pmcid:PMC3790878", - "pubmed:24124490" + "pmcid:PMC3790878" ], "sc:description": "A Next-Generation Sequencing Simulator for Metagenomics.", "sc:featureList": { @@ -32,6 +28,10 @@ "sc:name": "NeSSM", "sc:operatingSystem": "Linux", "sc:url": "http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0075448", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nest-gene/nest-genebioschemas.jsonld b/data/nest-gene/nest-genebioschemas.jsonld index 0ecc3a4c74a00..50b0720382b5f 100644 --- a/data/nest-gene/nest-genebioschemas.jsonld +++ b/data/nest-gene/nest-genebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Designed to predict the gene essentiality based on protein interaction network and gene expression or CRISPR screen results.", "sc:name": "NEST", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://nest.dfci.harvard.edu/" diff --git a/data/net-ge/net-gebioschemas.jsonld b/data/net-ge/net-gebioschemas.jsonld index 4cb66c5445952..6405bc532377b 100644 --- a/data/net-ge/net-gebioschemas.jsonld +++ b/data/net-ge/net-gebioschemas.jsonld @@ -9,15 +9,23 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2164-16-S8-S6", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-1838-8918", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/net-ge", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Pier Luigi Martelli", + "Samuele Bovo", { "@id": "http://orcid.org/0000-0002-1838-8918" - }, - "Pier Luigi Martelli", - "Samuele Bovo" + } ], "edam:has_input": { "@id": "edam:data_3021" @@ -27,10 +35,10 @@ "@id": "edam:data_2343" }, { - "@id": "edam:data_3028" + "@id": "edam:data_2600" }, { - "@id": "edam:data_2600" + "@id": "edam:data_3028" }, { "@id": "edam:data_1176" @@ -44,27 +52,27 @@ "@id": "edam:topic_1775" }, "sc:citation": [ - "pmcid:PMC4480278", - "pubmed:26110971", { "@id": "https://doi.org/10.1186/1471-2164-16-S8-S6" - } + }, + "pmcid:PMC4480278", + "pubmed:26110971" ], "sc:description": "Network-based enrichment analysis of gene sets.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_3083" }, { - "@id": "edam:operation_3083" + "@id": "edam:operation_3501" } ], "sc:isAccessibleForFree": true, "sc:name": "NET-GE", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:softwareHelp": { @@ -72,14 +80,6 @@ }, "sc:url": "http://net-ge.biocomp.unibo.it/", "sc:version": "1.0" - }, - { - "@id": "https://doi.org/10.1186/1471-2164-16-S8-S6", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-1838-8918", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/net-rstq/net-rstqbioschemas.jsonld b/data/net-rstq/net-rstqbioschemas.jsonld index f855765066228..ee6301e886c3f 100644 --- a/data/net-rstq/net-rstqbioschemas.jsonld +++ b/data/net-rstq/net-rstqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Software to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation.", "sc:name": "Net-RSTQ", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://compbio.cs.umn.edu/Net-RSTQ/" } \ No newline at end of file diff --git a/data/net_bio/net_biobioschemas.jsonld b/data/net_bio/net_biobioschemas.jsonld index 2a27c0cf0428f..bc5b555eb3486 100644 --- a/data/net_bio/net_biobioschemas.jsonld +++ b/data/net_bio/net_biobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "\".NET Bio is an open source library of common bioinformatics functions, intended to simplify the creation of life science applications.\nThe core library implements a range of file parsers and formatters for common file types, connectors to commonly-used web services such as NCBI BLAST, and standard algorithms for the comparison and assembly of DNA, RNA and protein sequences. Sample tools and code snippets are also included.\"", "sc:name": ".NET BIO", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bio.codeplex.com/" } \ No newline at end of file diff --git a/data/netaspgene/netaspgenebioschemas.jsonld b/data/netaspgene/netaspgenebioschemas.jsonld index 557234c405246..f35867fd25bdd 100644 --- a/data/netaspgene/netaspgenebioschemas.jsonld +++ b/data/netaspgene/netaspgenebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NetAspGene", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetAspGene/", diff --git a/data/netautoprobit/netautoprobitbioschemas.jsonld b/data/netautoprobit/netautoprobitbioschemas.jsonld index 1f6a157305b48..14bc4d3411d95 100644 --- a/data/netautoprobit/netautoprobitbioschemas.jsonld +++ b/data/netautoprobit/netautoprobitbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NetAutoProbit", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://math.bu.edu/people/kolaczyk/software.html" } \ No newline at end of file diff --git a/data/netbenchmark/netbenchmarkbioschemas.jsonld b/data/netbenchmark/netbenchmarkbioschemas.jsonld index 99a00ddd4c3d9..ee1e77e821888 100644 --- a/data/netbenchmark/netbenchmarkbioschemas.jsonld +++ b/data/netbenchmark/netbenchmarkbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-1574-5622", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/netbenchmark", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4587916", - "pubmed:26415849", { "@id": "https://doi.org/10.1186/s12859-015-0728-4" - } + }, + "pmcid:PMC4587916", + "pubmed:26415849" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-1574-5622" @@ -34,17 +38,13 @@ "sc:license": "CC-BY-NC-SA-4.0", "sc:name": "netbenchmark", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/netbenchmark.html", "sc:version": "1.6.0" }, - { - "@id": "http://orcid.org/0000-0003-1574-5622", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-015-0728-4", "@type": "sc:CreativeWork" diff --git a/data/netbiov/netbiovbioschemas.jsonld b/data/netbiov/netbiovbioschemas.jsonld index a531c8695717c..59c23e35d8077 100644 --- a/data/netbiov/netbiovbioschemas.jsonld +++ b/data/netbiov/netbiovbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Shailesh tripathi", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A package that provides an effective visualization of large biological networks.", "sc:license": "GPL-2.0", "sc:name": "netbiov", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/netbiov.html", "sc:version": "1.8.0" diff --git a/data/netbox/netboxbioschemas.jsonld b/data/netbox/netboxbioschemas.jsonld index a042c05226da2..ecde6b95c2557 100644 --- a/data/netbox/netboxbioschemas.jsonld +++ b/data/netbox/netboxbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "NetBox is a Java-based software tool for performing network analysis on human interaction networks. It is pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.", "sc:name": "NetBox", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cbio.mskcc.org/tools/netbox/index.html", "sc:version": "1.0" diff --git a/data/netcglyc/netcglycbioschemas.jsonld b/data/netcglyc/netcglycbioschemas.jsonld index f20ad1c9bb20b..dbf850eb9a010 100644 --- a/data/netcglyc/netcglycbioschemas.jsonld +++ b/data/netcglyc/netcglycbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/netcglyc", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:17494086", "sc:description": "Neural network predictions of C-mannosylation sites in mammalian proteins.", @@ -20,8 +20,8 @@ "sc:name": "NetCGlyc", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetCGlyc/", diff --git a/data/netchop/netchopbioschemas.jsonld b/data/netchop/netchopbioschemas.jsonld index c115d7c3d373c..f047c9d167fd8 100644 --- a/data/netchop/netchopbioschemas.jsonld +++ b/data/netchop/netchopbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7885-4311", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/netchop", "@type": "sc:SoftwareApplication", @@ -16,8 +20,8 @@ "@id": "http://orcid.org/0000-0001-7885-4311" }, "sc:additionalType": [ - "Web service", "Command-line tool", + "Web service", "Web application" ], "sc:citation": "pubmed:15744535", @@ -28,10 +32,6 @@ "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetChop/", "sc:version": "3.1" - }, - { - "@id": "http://orcid.org/0000-0001-7885-4311", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/netcomm/netcommbioschemas.jsonld b/data/netcomm/netcommbioschemas.jsonld index ddbc64b601cd7..5ad84179cc7a1 100644 --- a/data/netcomm/netcommbioschemas.jsonld +++ b/data/netcomm/netcommbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R package for use in both human protein-protein interaction network analyses as well as analyses of arbitrary networks.", "sc:name": "NetComm", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.shawlab.org/NetComm/" } \ No newline at end of file diff --git a/data/netcooperate/netcooperatebioschemas.jsonld b/data/netcooperate/netcooperatebioschemas.jsonld index 40a7d150d1b43..44a58ee7f89df 100644 --- a/data/netcooperate/netcooperatebioschemas.jsonld +++ b/data/netcooperate/netcooperatebioschemas.jsonld @@ -9,31 +9,27 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-015-0588-y", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/netcooperate", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Roie Levy", "Anat Kreimer", - "Shiri Freilich", "Elhanan Borenstein", - "Rogan Carr", - "Roie Levy" + "Shiri Freilich", + "Rogan Carr" ], "sc:additionalType": [ + "Web application", "Library", - "Command-line tool", - "Web application" + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC4434858", { "@id": "https://doi.org/10.1186/s12859-015-0588-y" }, - "pubmed:25980407", - "pmcid:PMC4434858" + "pubmed:25980407" ], "sc:description": "Determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms’ niches.", "sc:featureList": { @@ -42,11 +38,15 @@ "sc:license": "GPL-2.0", "sc:name": "NetCooperate", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://elbo.gs.washington.edu/software_netcooperate.html" + }, + { + "@id": "https://doi.org/10.1186/s12859-015-0588-y", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/netcorona/netcoronabioschemas.jsonld b/data/netcorona/netcoronabioschemas.jsonld index 0ae8c5ef23a3f..b2980b03e79a2 100644 --- a/data/netcorona/netcoronabioschemas.jsonld +++ b/data/netcorona/netcoronabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "NetCorona", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetCorona/", diff --git a/data/netcssp/netcsspbioschemas.jsonld b/data/netcssp/netcsspbioschemas.jsonld index 26f2753823d7f..113e4009bdff2 100644 --- a/data/netcssp/netcsspbioschemas.jsonld +++ b/data/netcssp/netcsspbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A web application based on contact-dependent secondary structure propensity calculations for predicting chameleon sub-sequences that may contribute to amyloid fibril formation. NetCSSP also contains precalculated non-native secondary structure propensities for 1.4 million fragments of 7 residue length from PDB structures.", "sc:name": "NetCSSP", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://cssp2.sookmyung.ac.kr" diff --git a/data/netctl/netctlbioschemas.jsonld b/data/netctl/netctlbioschemas.jsonld index 4069dd42ada45..10741cbe2b322 100644 --- a/data/netctl/netctlbioschemas.jsonld +++ b/data/netctl/netctlbioschemas.jsonld @@ -9,36 +9,36 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-8-424", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/netctl", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mette Voldby Larsen", "sc:additionalType": [ "Web service", - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": [ { "@id": "https://doi.org/10.1186/1471-2105-8-424" }, - "pubmed:17973982", - "pmcid:PMC2194739" + "pmcid:PMC2194739", + "pubmed:17973982" ], "sc:description": "Prediction of CTL epitopes in protein sequences.", "sc:license": "Other", "sc:name": "NetCTL", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetCTL/", "sc:version": "1.2" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-8-424", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/netctlpan/netctlpanbioschemas.jsonld b/data/netctlpan/netctlpanbioschemas.jsonld index 0f773ba73434a..e9867757a56b6 100644 --- a/data/netctlpan/netctlpanbioschemas.jsonld +++ b/data/netctlpan/netctlpanbioschemas.jsonld @@ -26,19 +26,19 @@ "@id": "edam:topic_3534" }, "sc:citation": [ - "pmcid:PMC2875469", { "@id": "https://doi.org/10.1007/s00251-010-0441-4" }, + "pmcid:PMC2875469", "pubmed:20379710" ], "sc:description": "Predict CTL epitopes in protein sequences.", "sc:featureList": [ { - "@id": "edam:operation_0416" + "@id": "edam:operation_2575" }, { - "@id": "edam:operation_2575" + "@id": "edam:operation_0416" } ], "sc:isAccessibleForFree": true, @@ -46,8 +46,8 @@ "sc:name": "NetCTLpan", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "CBS", "sc:softwareHelp": { diff --git a/data/netdecoder/netdecoderbioschemas.jsonld b/data/netdecoder/netdecoderbioschemas.jsonld index bc5295e9feb9a..ff2ddf92e82d9 100644 --- a/data/netdecoder/netdecoderbioschemas.jsonld +++ b/data/netdecoder/netdecoderbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/netdecoder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hu Li", - "Edroaldo Lummertz da Rocha" + "Edroaldo Lummertz da Rocha", + "Hu Li" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:26975659", "sc:description": "Novel network biology-based computational platform designed to integrate transcriptomes, interactomes and gene ontologies to identify phenotype-specific subnetworks.", "sc:name": "NetDecoder", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://netdecoder.hms.harvard.edu/" } \ No newline at end of file diff --git a/data/netdiseasesnp/netdiseasesnpbioschemas.jsonld b/data/netdiseasesnp/netdiseasesnpbioschemas.jsonld index b49b74efc4eac..0b1f70287e640 100644 --- a/data/netdiseasesnp/netdiseasesnpbioschemas.jsonld +++ b/data/netdiseasesnp/netdiseasesnpbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "http://orcid.org/0000-0001-6841-6676", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1371/journal.pone.0068370", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/netdiseasesnp", "@type": "sc:SoftwareApplication", @@ -34,10 +30,10 @@ "@id": "edam:topic_1775" }, "sc:citation": [ + "pmcid:PMC3723835", { "@id": "https://doi.org/10.1371/journal.pone.0068370" }, - "pmcid:PMC3723835", "pubmed:23935863" ], "sc:description": "The tool predicts whether a single non-synonymous SNP causes a disease or is invariant.", @@ -48,8 +44,8 @@ "sc:license": "Other", "sc:name": "NetDiseaseSNP", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "CBS", @@ -58,6 +54,10 @@ }, "sc:url": "http://www.cbs.dtu.dk/services/NetDiseaseSNP/", "sc:version": "1.0" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0068370", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/netgene2/netgene2bioschemas.jsonld b/data/netgene2/netgene2bioschemas.jsonld index 351db9b2557e2..3c497fbd2ec58 100644 --- a/data/netgene2/netgene2bioschemas.jsonld +++ b/data/netgene2/netgene2bioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/netgene2", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:8811101", "sc:description": "Neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.", "sc:license": "Other", "sc:name": "NetGene2", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetGene2/", diff --git a/data/netgo/netgobioschemas.jsonld b/data/netgo/netgobioschemas.jsonld index bf2b5d120cad9..147006667d333 100644 --- a/data/netgo/netgobioschemas.jsonld +++ b/data/netgo/netgobioschemas.jsonld @@ -25,30 +25,30 @@ "Web service" ], "sc:citation": [ - "pmcid:PMC6602452", "pubmed:31106361", { "@id": "https://doi.org/10.1093/NAR/GKZ388" - } + }, + "pmcid:PMC6602452" ], "sc:description": "Web server that is able to improve improve large-scale protein function prediction with massive network information.", "sc:featureList": [ - { - "@id": "edam:operation_3439" - }, { "@id": "edam:operation_1777" }, { "@id": "edam:operation_0267" + }, + { + "@id": "edam:operation_3439" } ], "sc:license": "Unlicense", "sc:name": "NetGO", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://issubmission.sjtu.edu.cn/netgo/" } diff --git a/data/nethet/nethetbioschemas.jsonld b/data/nethet/nethetbioschemas.jsonld index 1e31de32204c2..60d16fce366b5 100644 --- a/data/nethet/nethetbioschemas.jsonld +++ b/data/nethet/nethetbioschemas.jsonld @@ -22,9 +22,9 @@ "sc:license": "GPL-2.0", "sc:name": "nethet", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/nethet.html", "sc:version": "1.6.0" diff --git a/data/netlang/netlangbioschemas.jsonld b/data/netlang/netlangbioschemas.jsonld index 43923fd9811fb..6c49062139834 100644 --- a/data/netlang/netlangbioschemas.jsonld +++ b/data/netlang/netlangbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Lluís Barceló-Coblijn", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:28832598", - "pmcid:PMC5568436", { "@id": "https://doi.org/10.1371/journal.pone.0181341" - } + }, + "pmcid:PMC5568436", + "pubmed:28832598" ], "sc:description": "Linguistic analysis of corpora by means of complex networks.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "Netlang", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/lluisbc/Netlang-Software" }, diff --git a/data/netmatchstar/netmatchstarbioschemas.jsonld b/data/netmatchstar/netmatchstarbioschemas.jsonld index 8cfdaccc52fac..a2098699232ce 100644 --- a/data/netmatchstar/netmatchstarbioschemas.jsonld +++ b/data/netmatchstar/netmatchstarbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-9843-7638", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.6656.2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/netmatchstar", "@type": "sc:SoftwareApplication", @@ -34,10 +26,10 @@ "sc:description": "Find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models.", "sc:featureList": [ { - "@id": "edam:operation_3660" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_3660" } ], "sc:license": "CC-BY-NC-SA-3.0", @@ -49,6 +41,14 @@ ], "sc:url": "https://alpha.dmi.unict.it/netmatchstar/netmatchstar.html", "sc:version": "3.2" + }, + { + "@id": "http://orcid.org/0000-0001-9843-7638", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.6656.2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/netmhc/netmhcbioschemas.jsonld b/data/netmhc/netmhcbioschemas.jsonld index ef1ecf0ff4c8b..ba52b3e26323d 100644 --- a/data/netmhc/netmhcbioschemas.jsonld +++ b/data/netmhc/netmhcbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7885-4311", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1110/ps.0239403", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/netmhc", "@type": "sc:SoftwareApplication", @@ -20,11 +28,11 @@ "Web application" ], "sc:citation": [ - "pubmed:12717023", "pmcid:PMC2323871", { "@id": "https://doi.org/10.1110/ps.0239403" }, + "pubmed:12717023", "pubmed:18413329" ], "sc:description": "Prediction of binding of peptides to a number of different HLA alleles using artificial neural networks (ANNs).", @@ -37,14 +45,6 @@ "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetMHC/", "sc:version": "3.4" - }, - { - "@id": "http://orcid.org/0000-0001-7885-4311", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1110/ps.0239403", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/netmhccons/netmhcconsbioschemas.jsonld b/data/netmhccons/netmhcconsbioschemas.jsonld index 124a1aca807f1..46d9ab664863e 100644 --- a/data/netmhccons/netmhcconsbioschemas.jsonld +++ b/data/netmhccons/netmhcconsbioschemas.jsonld @@ -26,8 +26,8 @@ "sc:name": "NetMHCcons", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "CBS", "sc:url": "http://www.cbs.dtu.dk/services/NetMHCcons/", diff --git a/data/netmhcii/netmhciibioschemas.jsonld b/data/netmhcii/netmhciibioschemas.jsonld index 512f8d0af6502..7a8da40a7de64 100644 --- a/data/netmhcii/netmhciibioschemas.jsonld +++ b/data/netmhcii/netmhciibioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7885-4311", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-10-296", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/netmhcii", "@type": "sc:SoftwareApplication", @@ -38,10 +46,10 @@ "sc:description": "Predict binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks.", "sc:featureList": [ { - "@id": "edam:operation_0416" + "@id": "edam:operation_2575" }, { - "@id": "edam:operation_2575" + "@id": "edam:operation_0416" } ], "sc:isAccessibleForFree": true, @@ -57,14 +65,6 @@ }, "sc:url": "http://www.cbs.dtu.dk/services/NetMHCII/", "sc:version": "2.2" - }, - { - "@id": "http://orcid.org/0000-0001-7885-4311", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-10-296", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/netmhciipan/netmhciipanbioschemas.jsonld b/data/netmhciipan/netmhciipanbioschemas.jsonld index c99401199100e..da8437d2fe73c 100644 --- a/data/netmhciipan/netmhciipanbioschemas.jsonld +++ b/data/netmhciipan/netmhciipanbioschemas.jsonld @@ -39,18 +39,18 @@ "sc:description": "Predict binding of peptides to MHC class II molecules. The predictions are available for all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules.", "sc:featureList": [ { - "@id": "edam:operation_0416" + "@id": "edam:operation_2575" }, { - "@id": "edam:operation_2575" + "@id": "edam:operation_0416" } ], "sc:isAccessibleForFree": true, "sc:license": "Other", "sc:name": "NetMHCIIpan", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "CBS", "sc:softwareHelp": { diff --git a/data/netmhcpan/netmhcpanbioschemas.jsonld b/data/netmhcpan/netmhcpanbioschemas.jsonld index a6a844adad7a8..5cb0dacd8b7fa 100644 --- a/data/netmhcpan/netmhcpanbioschemas.jsonld +++ b/data/netmhcpan/netmhcpanbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkn840", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/netmhcpan", "@type": "sc:SoftwareApplication", @@ -24,8 +20,8 @@ "@id": "edam:data_1277" }, "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:applicationSubCategory": { "@id": "edam:topic_3534" @@ -34,8 +30,8 @@ { "@id": "https://doi.org/10.1093/nar/gkn840" }, - "pubmed:19002680", - "pmcid:PMC2686430" + "pmcid:PMC2686430", + "pubmed:19002680" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-0060-6486" @@ -43,10 +39,10 @@ "sc:description": "Predict binding of peptides to any known MHC molecule using artificial neural networks (ANNs).", "sc:featureList": [ { - "@id": "edam:operation_0416" + "@id": "edam:operation_2575" }, { - "@id": "edam:operation_2575" + "@id": "edam:operation_0416" } ], "sc:isAccessibleForFree": true, @@ -63,6 +59,10 @@ "sc:url": "http://www.cbs.dtu.dk/services/NetMHCpan/", "sc:version": "2.8" }, + { + "@id": "https://doi.org/10.1093/nar/gkn840", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0003-0060-6486", "@type": "schema:Person" diff --git a/data/netmhcstab/netmhcstabbioschemas.jsonld b/data/netmhcstab/netmhcstabbioschemas.jsonld index 62b1892879f38..60baa0927dfad 100644 --- a/data/netmhcstab/netmhcstabbioschemas.jsonld +++ b/data/netmhcstab/netmhcstabbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7885-4311", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/netmhcstab", "@type": "sc:SoftwareApplication", @@ -22,16 +26,12 @@ "sc:name": "NetMHCstab", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "CBS", "sc:url": "http://www.cbs.dtu.dk/services/NetMHCstab/", "sc:version": "1.0" - }, - { - "@id": "http://orcid.org/0000-0001-7885-4311", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/netnes/netnesbioschemas.jsonld b/data/netnes/netnesbioschemas.jsonld index 045bb49e8af8a..742d204752503 100644 --- a/data/netnes/netnesbioschemas.jsonld +++ b/data/netnes/netnesbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/netnes", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:description": "Prediction of the leucine-rich nuclear export signals (NES) in eukaryotic proteins.", "sc:license": "Other", "sc:name": "NetNES", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "CBS", diff --git a/data/netoglyc/netoglycbioschemas.jsonld b/data/netoglyc/netoglycbioschemas.jsonld index 220718de037cd..1084f3c600433 100644 --- a/data/netoglyc/netoglycbioschemas.jsonld +++ b/data/netoglyc/netoglycbioschemas.jsonld @@ -16,16 +16,16 @@ "@id": "http://orcid.org/0000-0002-8192-2829" }, "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": [ - "pubmed:9557871", - "pmcid:PMC3655468", "pubmed:23584533", { "@id": "https://doi.org/10.1038/emboj.2013.79" - } + }, + "pmcid:PMC3655468", + "pubmed:9557871" ], "sc:description": "Produce neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.", "sc:license": "Other", @@ -35,13 +35,13 @@ "sc:url": "http://www.cbs.dtu.dk/services/NetOGlyc/", "sc:version": "4.0" }, - { - "@id": "http://orcid.org/0000-0002-8192-2829", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1038/emboj.2013.79", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-8192-2829", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/netpathminer/netpathminerbioschemas.jsonld b/data/netpathminer/netpathminerbioschemas.jsonld index 66927d196cb99..e138fddb42edf 100644 --- a/data/netpathminer/netpathminerbioschemas.jsonld +++ b/data/netpathminer/netpathminerbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btu501", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/netpathminer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ahmed Mohamed", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ { "@id": "https://doi.org/10.1093/bioinformatics/btu501" }, - "pubmed:25075120", - "pmcid:PMC4609018" + "pmcid:PMC4609018", + "pubmed:25075120" ], "sc:description": "General framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations: metabolic, reactiomic and genic. It finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.", "sc:featureList": { @@ -37,10 +41,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NetPathMiner.html", "sc:version": "1.10.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btu501", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/netphorest/netphorestbioschemas.jsonld b/data/netphorest/netphorestbioschemas.jsonld index bd00913de0617..dfc03370dc9db 100644 --- a/data/netphorest/netphorestbioschemas.jsonld +++ b/data/netphorest/netphorestbioschemas.jsonld @@ -34,11 +34,11 @@ "@id": "edam:topic_0160" }, "sc:citation": [ + "pubmed:18765831", + "pmcid:PMC6215708", { "@id": "https://doi.org/10.1126/scisignal.1159433" - }, - "pmcid:PMC6215708", - "pubmed:18765831" + } ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-3161-8690" @@ -50,9 +50,9 @@ "sc:isAccessibleForFree": true, "sc:name": "NetPhorest", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "CBS", "sc:softwareHelp": { diff --git a/data/netphos/netphosbioschemas.jsonld b/data/netphos/netphosbioschemas.jsonld index 67fe9fcce9b72..7ef7c2713d0ff 100644 --- a/data/netphos/netphosbioschemas.jsonld +++ b/data/netphos/netphosbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Other", "sc:name": "NetPhos", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetPhos/", diff --git a/data/netphosbac/netphosbacbioschemas.jsonld b/data/netphosbac/netphosbacbioschemas.jsonld index 4643a1f923bfa..a35c66084f814 100644 --- a/data/netphosbac/netphosbacbioschemas.jsonld +++ b/data/netphosbac/netphosbacbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-3161-8690", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/netphosbac", "@type": "sc:SoftwareApplication", @@ -25,13 +21,17 @@ "sc:license": "Other", "sc:name": "NetPhosBac", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "CBS", "sc:url": "http://www.cbs.dtu.dk/services/NetPhosBac/", "sc:version": "1.0" + }, + { + "@id": "http://orcid.org/0000-0003-3161-8690", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/netphosk/netphoskbioschemas.jsonld b/data/netphosk/netphoskbioschemas.jsonld index c0ff515d47d55..629ffcc17d679 100644 --- a/data/netphosk/netphoskbioschemas.jsonld +++ b/data/netphosk/netphoskbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-6615-1141", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/netphosk", "@type": "sc:SoftwareApplication", @@ -25,13 +21,17 @@ "sc:license": "Other", "sc:name": "NetPhosK", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "CBS", "sc:url": "http://www.cbs.dtu.dk/services/NetPhosK/", "sc:version": "1.0" + }, + { + "@id": "http://orcid.org/0000-0001-6615-1141", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/netphosyeast/netphosyeastbioschemas.jsonld b/data/netphosyeast/netphosyeastbioschemas.jsonld index b29d97ba6111e..0624a35c6946a 100644 --- a/data/netphosyeast/netphosyeastbioschemas.jsonld +++ b/data/netphosyeast/netphosyeastbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7787-7853", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/netphosyeast", "@type": "sc:SoftwareApplication", @@ -21,17 +25,13 @@ "sc:license": "Other", "sc:name": "NetPhosYeast", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "CBS", "sc:url": "http://www.cbs.dtu.dk/services/NetPhosYeast/", "sc:version": "1.0" - }, - { - "@id": "http://orcid.org/0000-0001-7787-7853", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/netplantgene/netplantgenebioschemas.jsonld b/data/netplantgene/netplantgenebioschemas.jsonld index 1612a3e2d0408..7904e17a40532 100644 --- a/data/netplantgene/netplantgenebioschemas.jsonld +++ b/data/netplantgene/netplantgenebioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-0316-5866", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/netplantgene", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC146109", - "pubmed:8811101" + "pubmed:8811101", + "pmcid:PMC146109" ], "sc:contributor": { "@id": "https://orcid.org/0000-0003-0316-5866" @@ -24,17 +28,13 @@ "sc:license": "Other", "sc:name": "NetPlantGene", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "CBS", "sc:url": "http://www.cbs.dtu.dk/services/NetPGene/", "sc:version": "0.0" - }, - { - "@id": "https://orcid.org/0000-0003-0316-5866", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/netpredictor/netpredictorbioschemas.jsonld b/data/netpredictor/netpredictorbioschemas.jsonld index 0163b8aef0ea9..f7b3de879e740 100644 --- a/data/netpredictor/netpredictorbioschemas.jsonld +++ b/data/netpredictor/netpredictorbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "AGPL-3.0", "sc:name": "Netpredictor", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/abhik1368/Shiny_NetPredictor", "sc:version": "1.0.1" diff --git a/data/netprior/netpriorbioschemas.jsonld b/data/netprior/netpriorbioschemas.jsonld index e898fa4ef71ce..a27311e20b862 100644 --- a/data/netprior/netpriorbioschemas.jsonld +++ b/data/netprior/netpriorbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "netprioR", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/netprioR.html", diff --git a/data/netreg/netregbioschemas.jsonld b/data/netreg/netregbioschemas.jsonld index 23427e040466f..099871f3e760b 100644 --- a/data/netreg/netregbioschemas.jsonld +++ b/data/netreg/netregbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btx677", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/netreg", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC6030897", + "pubmed:29077797", { "@id": "https://doi.org/10.1093/bioinformatics/btx677" - }, - "pubmed:29077797" + } ], "sc:description": "Fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the loss function of the linear model.", "sc:featureList": { @@ -38,6 +34,10 @@ ], "sc:url": "https://bioconductor.org/packages/release/bioc/html/netReg.html", "sc:version": "3.7" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btx677", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/netresponse/netresponsebioschemas.jsonld b/data/netresponse/netresponsebioschemas.jsonld index fc05d52f86bf4..1fe6c39a3212e 100644 --- a/data/netresponse/netresponsebioschemas.jsonld +++ b/data/netresponse/netresponsebioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "netresponse", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/netresponse.html", "sc:version": "1.34.0" diff --git a/data/netsam/netsambioschemas.jsonld b/data/netsam/netsambioschemas.jsonld index dd65e981f2b64..c37c94c579616 100644 --- a/data/netsam/netsambioschemas.jsonld +++ b/data/netsam/netsambioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bing Zhang", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The Network Seriation and Modularization package takes an edge-list representation of a network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt or other network analysis.", "sc:license": "GPL-3.0", "sc:name": "NetSAM", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NetSAM.html", "sc:version": "1.14.0" diff --git a/data/netsim/netsimbioschemas.jsonld b/data/netsim/netsimbioschemas.jsonld index ad02fccf9391a..635d1317e2381 100644 --- a/data/netsim/netsimbioschemas.jsonld +++ b/data/netsim/netsimbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Barbara Di Camillo", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Gene-network simulator. Simulators are helpful to test and compare the accuracy of different reverse-engineering approaches in a variety of experimental conditions.", "sc:license": "GPL-2.0", "sc:name": "Netsim", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://www.medcomp.medicina.unipd.it/bioing/netsim/", diff --git a/data/netsmooth/netsmoothbioschemas.jsonld b/data/netsmooth/netsmoothbioschemas.jsonld index 4b09827e069a5..ee19be4c272d3 100644 --- a/data/netsmooth/netsmoothbioschemas.jsonld +++ b/data/netsmooth/netsmoothbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "netSmooth", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/netSmooth.html", diff --git a/data/netstart/netstartbioschemas.jsonld b/data/netstart/netstartbioschemas.jsonld index 0e8155d2351dc..10904ac501000 100644 --- a/data/netstart/netstartbioschemas.jsonld +++ b/data/netstart/netstartbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-9650-8965", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/netstart", "@type": "sc:SoftwareApplication", @@ -20,8 +16,8 @@ "@id": "https://orcid.org/0000-0001-9650-8965" }, "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:9322041", "sc:description": "Neural network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences.", @@ -29,12 +25,16 @@ "sc:name": "NetStart", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetStart/", "sc:version": "1.0" + }, + { + "@id": "https://orcid.org/0000-0001-9650-8965", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/netsurfp/netsurfpbioschemas.jsonld b/data/netsurfp/netsurfpbioschemas.jsonld index e9fc1f225693d..d3770ccc7851f 100644 --- a/data/netsurfp/netsurfpbioschemas.jsonld +++ b/data/netsurfp/netsurfpbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Other", "sc:name": "NetSurfP", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/NetSurfP/", diff --git a/data/netter/netterbioschemas.jsonld b/data/netter/netterbioschemas.jsonld index 4067cb7d37408..17afd9928b8b5 100644 --- a/data/netter/netterbioschemas.jsonld +++ b/data/netter/netterbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Re-ranking gene network inference predictions using structural network properties.", "sc:name": "Netter", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/netter/index.html", diff --git a/data/nettest/nettestbioschemas.jsonld b/data/nettest/nettestbioschemas.jsonld index cb2e8d6a34f1a..ebcd011a8bea2 100644 --- a/data/nettest/nettestbioschemas.jsonld +++ b/data/nettest/nettestbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web server for the characterization of directed or rooted reticulate networks, through their assignment to specific categories: “Tree”, “Tree-sibling”, “Tree-child”, “Galled-tree”, “Time-consistent”).", "sc:name": "NetTest", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://darwin.uvigo.es/software/nettest/" diff --git a/data/netutr/netutrbioschemas.jsonld b/data/netutr/netutrbioschemas.jsonld index b857cb8b12730..23ba16e2a6b65 100644 --- a/data/netutr/netutrbioschemas.jsonld +++ b/data/netutr/netutrbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Other", "sc:name": "NetUTR", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "CBS", diff --git a/data/netvenn/netvennbioschemas.jsonld b/data/netvenn/netvennbioschemas.jsonld index 7ec2f94f339e8..17425e374dc56 100644 --- a/data/netvenn/netvennbioschemas.jsonld +++ b/data/netvenn/netvennbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "NetVenn is a network-based web platform for the comparison and analysis of gene lists by combining Venn diagram and gene set enrichment.", "sc:name": "NetVenn", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://wheat.pw.usda.gov/NetVenn/" } \ No newline at end of file diff --git a/data/netview/netviewbioschemas.jsonld b/data/netview/netviewbioschemas.jsonld index d21aa1bf4ef71..d6c3d7c9d491b 100644 --- a/data/netview/netviewbioschemas.jsonld +++ b/data/netview/netviewbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Free web tool that allow end users to explore the human and mouse gene regulatory networks. Users can query the system by providing a gene identifier and the boundaries of the subnetwork being explored. The system provides the list of interactions, the enriched Gene Ontology Terms together with a graphical representation of the subnetwork.", "sc:name": "Netview", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://netview.tigem.it/netview_project/netview_tools.html" } \ No newline at end of file diff --git a/data/network2canvas/network2canvasbioschemas.jsonld b/data/network2canvas/network2canvasbioschemas.jsonld index 61b648f511aab..859e112f94788 100644 --- a/data/network2canvas/network2canvasbioschemas.jsonld +++ b/data/network2canvas/network2canvasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web application that provides an alternative way to view networks. N2C visualizes networks by placing nodes on a square toroidal canvas.", "sc:name": "Network2Canvas", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.maayanlab.net/N2C" diff --git a/data/network_archaeology/network_archaeologybioschemas.jsonld b/data/network_archaeology/network_archaeologybioschemas.jsonld index be7fb78bf5cb9..bef16873409ea 100644 --- a/data/network_archaeology/network_archaeologybioschemas.jsonld +++ b/data/network_archaeology/network_archaeologybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Framework to reconstruct a complete growth history of a present-day network given only a probabilistic model by which the network putatively evolved.", "sc:name": "Network Archaeology", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://cbcb.umd.edu/NetArch/" } \ No newline at end of file diff --git a/data/network_motif_clustering_toolbox/network_motif_clustering_toolboxbioschemas.jsonld b/data/network_motif_clustering_toolbox/network_motif_clustering_toolboxbioschemas.jsonld index 03291db4a2b9d..5b093e00687b6 100644 --- a/data/network_motif_clustering_toolbox/network_motif_clustering_toolboxbioschemas.jsonld +++ b/data/network_motif_clustering_toolbox/network_motif_clustering_toolboxbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Network Motif Clustering Toolbox", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/Network-Motif-Clustering-Toolbox", diff --git a/data/network_of_cancer_genes/network_of_cancer_genesbioschemas.jsonld b/data/network_of_cancer_genes/network_of_cancer_genesbioschemas.jsonld index 053fc078aa13c..881559d02310c 100644 --- a/data/network_of_cancer_genes/network_of_cancer_genesbioschemas.jsonld +++ b/data/network_of_cancer_genes/network_of_cancer_genesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Network of Cancer Genes collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, it provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network.", "sc:name": "Network of Cancer Genes", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://ncg.kcl.ac.uk/" } \ No newline at end of file diff --git a/data/networkanalys/networkanalysbioschemas.jsonld b/data/networkanalys/networkanalysbioschemas.jsonld index 4be1d2c9f346c..ca59314075481 100644 --- a/data/networkanalys/networkanalysbioschemas.jsonld +++ b/data/networkanalys/networkanalysbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Designed to perform protein-protein interacton (PPI) network analysis from gene expression data. It integrates differential expression analysis, network construction and network analysis.", "sc:name": "NetworkAnalys", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.networkanalyst.ca" } \ No newline at end of file diff --git a/data/networkanalyst/networkanalystbioschemas.jsonld b/data/networkanalyst/networkanalystbioschemas.jsonld index 92b79ef99b114..e579edde13b1d 100644 --- a/data/networkanalyst/networkanalystbioschemas.jsonld +++ b/data/networkanalyst/networkanalystbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Designed to support integrative analysis of gene expression data through statistical, visual and network-based approaches.", "sc:name": "NetworkAnalyst", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.networkanalyst.ca/NetworkAnalyst/" } \ No newline at end of file diff --git a/data/networkbma/networkbmabioschemas.jsonld b/data/networkbma/networkbmabioschemas.jsonld index e80cd5cbdf622..60b8b7f47dc36 100644 --- a/data/networkbma/networkbmabioschemas.jsonld +++ b/data/networkbma/networkbmabioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ka Yee Yeung", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An extension of Bayesian Model Averaging (BMA) for network construction using time series gene expression data. Includes assessment functions and sample test data.", "sc:license": "GPL-2.0", diff --git a/data/networkin/networkinbioschemas.jsonld b/data/networkin/networkinbioschemas.jsonld index 6b3e5dbe6e646..7b37d3a3cb6a1 100644 --- a/data/networkin/networkinbioschemas.jsonld +++ b/data/networkin/networkinbioschemas.jsonld @@ -9,19 +9,15 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/j.cell.2007.05.052", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/networkin", "@type": "sc:SoftwareApplication", "edam:has_input": [ { - "@id": "edam:data_2299" + "@id": "edam:data_2775" }, { - "@id": "edam:data_2775" + "@id": "edam:data_2299" } ], "edam:has_output": { @@ -32,11 +28,11 @@ "@id": "edam:topic_0160" }, "sc:citation": [ - "pmcid:PMC2692296", + "pubmed:17570479", { "@id": "https://doi.org/10.1016/j.cell.2007.05.052" }, - "pubmed:17570479" + "pmcid:PMC2692296" ], "sc:description": "Prediction of in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins.", "sc:featureList": { @@ -45,9 +41,9 @@ "sc:isAccessibleForFree": true, "sc:name": "NetworKIN", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "CBS", "sc:softwareHelp": { @@ -55,6 +51,10 @@ }, "sc:url": "http://www.networkin.info/", "sc:version": "2.0" + }, + { + "@id": "https://doi.org/10.1016/j.cell.2007.05.052", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/networkrandomizer/networkrandomizerbioschemas.jsonld b/data/networkrandomizer/networkrandomizerbioschemas.jsonld index b883c97a097df..63fbf86dbffa0 100644 --- a/data/networkrandomizer/networkrandomizerbioschemas.jsonld +++ b/data/networkrandomizer/networkrandomizerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Apache-2.0", "sc:name": "NetworkRandomizer", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://apps.cytoscape.org/apps/networkrandomizer", "sc:version": "1.1.3" diff --git a/data/neuroelectro/neuroelectrobioschemas.jsonld b/data/neuroelectro/neuroelectrobioschemas.jsonld index d61cb9eafc9ca..090c5ca67035e 100644 --- a/data/neuroelectro/neuroelectrobioschemas.jsonld +++ b/data/neuroelectro/neuroelectrobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "RESTful API which enables the extraction, visualization, and summarization of published data on neurons’ electrophysiological properties.", "sc:name": "NeuroElectro", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://neuroelectro.org/api/docs/", "sc:version": "1" diff --git a/data/neuromatic/neuromaticbioschemas.jsonld b/data/neuromatic/neuromaticbioschemas.jsonld index cc78459831a9f..6d5c42a4338c7 100644 --- a/data/neuromatic/neuromaticbioschemas.jsonld +++ b/data/neuromatic/neuromaticbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3389/fninf.2018.00014", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/neuromatic", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jason S. Rothman", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:29670519", { "@id": "https://doi.org/10.3389/fninf.2018.00014" }, + "pubmed:29670519", "pmcid:PMC5893720" ], "sc:description": "An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data.", @@ -38,10 +42,6 @@ ], "sc:url": "http://www.neuromatic.thinkrandom.com/", "sc:version": "3.0" - }, - { - "@id": "https://doi.org/10.3389/fninf.2018.00014", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/neuron/neuronbioschemas.jsonld b/data/neuron/neuronbioschemas.jsonld index fe88c357ee0e9..8291f1fcf3571 100644 --- a/data/neuron/neuronbioschemas.jsonld +++ b/data/neuron/neuronbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Neuron", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://phet.colorado.edu/en/simulation/neuron" } \ No newline at end of file diff --git a/data/neuronactivitytool/neuronactivitytoolbioschemas.jsonld b/data/neuronactivitytool/neuronactivitytoolbioschemas.jsonld index 48bc845548c90..328e09638144e 100644 --- a/data/neuronactivitytool/neuronactivitytoolbioschemas.jsonld +++ b/data/neuronactivitytool/neuronactivitytoolbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/neuronactivitytool", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Juan Prada", - "Robert Blum" + "Robert Blum", + "Juan Prada" ], "sc:additionalType": "Command-line tool", "sc:description": "tool to automatically extract, count, and localize calcium signals from the whole x,y-t image series. The tool is useful for an unbiased comparison of activity states of neurons, helps to assess local calcium transients, and even visualizes local homeostatic calcium activity.", "sc:name": "NeuronActivityTool", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/neuralactivitycubic/" diff --git a/data/neuroncyto_ii/neuroncyto_iibioschemas.jsonld b/data/neuroncyto_ii/neuroncyto_iibioschemas.jsonld index 707709f512133..54b353efd10e9 100644 --- a/data/neuroncyto_ii/neuroncyto_iibioschemas.jsonld +++ b/data/neuroncyto_ii/neuroncyto_iibioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1002/cyto.a.22872", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/neuroncyto_ii", "@type": "sc:SoftwareApplication", @@ -33,6 +29,10 @@ "sc:operatingSystem": "Windows", "sc:url": "https://sites.google.com/site/neuroncyto/", "sc:version": "1.0" + }, + { + "@id": "https://doi.org/10.1002/cyto.a.22872", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/neuropg/neuropgbioschemas.jsonld b/data/neuropg/neuropgbioschemas.jsonld index 848e3438bd315..ee2373a7b7352 100644 --- a/data/neuropg/neuropgbioschemas.jsonld +++ b/data/neuropg/neuropgbioschemas.jsonld @@ -18,8 +18,8 @@ { "@id": "https://doi.org/10.3389/fneng.2015.00001" }, - "pubmed:25784873", - "pmcid:PMC4345891" + "pmcid:PMC4345891", + "pubmed:25784873" ], "sc:description": "NeuroPG is an open source optical pattern generation software for neuroscience that combines digital micro-mirror device control, sample visualization, and data acquisition in one application.", "sc:featureList": { diff --git a/data/neuropid/neuropidbioschemas.jsonld b/data/neuropid/neuropidbioschemas.jsonld index e3936e163cab8..ea35ccbcda217 100644 --- a/data/neuropid/neuropidbioschemas.jsonld +++ b/data/neuropid/neuropidbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/neuropid", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Solange Karsenty (For web issues)", - "For scientific enquiries and technical enquiries" + "For scientific enquiries and technical enquiries", + "Solange Karsenty (For web issues)" ], "sc:additionalType": "Web application", "sc:description": "Prediction tool for neuropeptide precursors (NPPs) and neuromodulators.", "sc:name": "NeuroPID", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://neuropid.cs.huji.ac.il" } \ No newline at end of file diff --git a/data/neuropp/neuroppbioschemas.jsonld b/data/neuropp/neuroppbioschemas.jsonld index 2d55426e2032e..ca84276cb3298 100644 --- a/data/neuropp/neuroppbioschemas.jsonld +++ b/data/neuropp/neuroppbioschemas.jsonld @@ -22,8 +22,8 @@ "sc:name": "NeuroPP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://i.uestc.edu.cn/neuropeptide/neuropp/home.html" } \ No newline at end of file diff --git a/data/neuroserver/neuroserverbioschemas.jsonld b/data/neuroserver/neuroserverbioschemas.jsonld index b09931f78f811..4861f1e5c023d 100644 --- a/data/neuroserver/neuroserverbioschemas.jsonld +++ b/data/neuroserver/neuroserverbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "NeuroServer", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://openeeg.sourceforge.net/neuroserver_doku/" } \ No newline at end of file diff --git a/data/newcpgreport-ebi/newcpgreport-ebibioschemas.jsonld b/data/newcpgreport-ebi/newcpgreport-ebibioschemas.jsonld index b74d0c225d3be..cfa2b58643765 100644 --- a/data/newcpgreport-ebi/newcpgreport-ebibioschemas.jsonld +++ b/data/newcpgreport-ebi/newcpgreport-ebibioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "Web Production", - "EMBOSS" + "EMBOSS", + "Web Production" ], "sc:description": "Identification of potential CpG islands.", "sc:name": "newcpgreport (EBI)", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/seqstats/emboss_newcpgreport/", diff --git a/data/newcpgreport/newcpgreportbioschemas.jsonld b/data/newcpgreport/newcpgreportbioschemas.jsonld index 23bd92c67fc71..62eba9dc04081 100644 --- a/data/newcpgreport/newcpgreportbioschemas.jsonld +++ b/data/newcpgreport/newcpgreportbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK BBSRC", "Wellcome Trust", "EMBOSS Contributors", - "UK MRC", - "UK BBSRC" + "UK MRC" ], "sc:description": "Identify CpG islands in nucleotide sequence(s).", "sc:funder": [ - "UK BBSRC", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "newcpgreport", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/newcpgseek/newcpgseekbioschemas.jsonld b/data/newcpgseek/newcpgseekbioschemas.jsonld index 3a6d18d24c5d2..f8650867f8720 100644 --- a/data/newcpgseek/newcpgseekbioschemas.jsonld +++ b/data/newcpgseek/newcpgseekbioschemas.jsonld @@ -13,9 +13,9 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK MRC", - "EMBOSS Contributors", "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "EMBOSS Contributors" ], "sc:description": "Identify and report CpG-rich regions in nucleotide sequence(s).", "sc:funder": [ @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "newcpgseek", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/newseq/newseqbioschemas.jsonld b/data/newseq/newseqbioschemas.jsonld index 56278c0ecc56d..d08e5624b591b 100644 --- a/data/newseq/newseqbioschemas.jsonld +++ b/data/newseq/newseqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK MRC", "UK BBSRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK MRC", + "Wellcome Trust" ], "sc:description": "Create a sequence file from a typed-in sequence.", "sc:funder": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "newseq", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/newseq.html", "sc:version": "r6" diff --git a/data/nexgenex-tom/nexgenex-tombioschemas.jsonld b/data/nexgenex-tom/nexgenex-tombioschemas.jsonld index d33da89350827..0cf15360af457 100644 --- a/data/nexgenex-tom/nexgenex-tombioschemas.jsonld +++ b/data/nexgenex-tom/nexgenex-tombioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/NexGenEx-Tom", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hamed Bostan", - "Maria Luisa Chiusano" + "Maria Luisa Chiusano", + "Hamed Bostan" ], "sc:additionalType": [ "Web application", diff --git a/data/nextbio/nextbiobioschemas.jsonld b/data/nextbio/nextbiobioschemas.jsonld index 016dbb0594ae0..c49a3e66a856e 100644 --- a/data/nextbio/nextbiobioschemas.jsonld +++ b/data/nextbio/nextbiobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0013066", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/nextbio", "@type": "sc:SoftwareApplication", @@ -45,10 +41,14 @@ "sc:name": "NextBio gene-centric data", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.nextbio.com/" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0013066", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nextgene/nextgenebioschemas.jsonld b/data/nextgene/nextgenebioschemas.jsonld index c4ad31087f4b1..c3ed73a85077e 100644 --- a/data/nextgene/nextgenebioschemas.jsonld +++ b/data/nextgene/nextgenebioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/nextgene", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Product Sales and Marketing", + "Technical Service", "Contact Form", - "Technical Service" + "Product Sales and Marketing" ], "sc:additionalType": "Desktop application", "sc:description": "De novo and reference assembly of Roche/454, Illumina and SOLiD data. Uses a novel Condensation Assembly Tool approach where reads are joined via \"anchors\" into mini-contigs before assembly which reduces sequencing errors. Requires Win or MacOS.\n\nA desktop application for analyzing next generation sequencing data. It does not require scripting.", diff --git a/data/nextprot-cli/nextprot-clibioschemas.jsonld b/data/nextprot-cli/nextprot-clibioschemas.jsonld index 23facb3f28523..84aa631c67e65 100644 --- a/data/nextprot-cli/nextprot-clibioschemas.jsonld +++ b/data/nextprot-cli/nextprot-clibioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "GPL-2.0", "sc:name": "nextprot-cli", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "isb-sib.ch", diff --git a/data/nextprot/nextprotbioschemas.jsonld b/data/nextprot/nextprotbioschemas.jsonld index 6807f95fec9d1..ddf2b0064f5bb 100644 --- a/data/nextprot/nextprotbioschemas.jsonld +++ b/data/nextprot/nextprotbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-1813-6857", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/nextprot", "@type": "sc:SoftwareApplication", @@ -22,16 +26,12 @@ "sc:license": "CC-BY-4.0", "sc:name": "neXtProt", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "https://www.nextprot.org" - }, - { - "@id": "http://orcid.org/0000-0003-1813-6857", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/nextsv/nextsvbioschemas.jsonld b/data/nextsv/nextsvbioschemas.jsonld index 7af03884e863f..3d819033ccd46 100644 --- a/data/nextsv/nextsvbioschemas.jsonld +++ b/data/nextsv/nextsvbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "NextSV", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://github.com/Nextomics/NextSV" } \ No newline at end of file diff --git a/data/nffinder/nffinderbioschemas.jsonld b/data/nffinder/nffinderbioschemas.jsonld index 94ea0ffba46e4..f3518c5206ff9 100644 --- a/data/nffinder/nffinderbioschemas.jsonld +++ b/data/nffinder/nffinderbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "A. Pascual-Montano", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:25940629", { "@id": "https://doi.org/10.1093/NAR/GKV445" }, - "pmcid:PMC4489258" + "pmcid:PMC4489258", + "pubmed:25940629" ], "sc:description": "Combine experimental gene expression profiles and data from publicly available databases to identify conditions or experiments that induce similar or opposite gene expression patterns.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "NFFinder", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://nffinder.cnb.csic.es/" } diff --git a/data/nfp/nfpbioschemas.jsonld b/data/nfp/nfpbioschemas.jsonld index 12e88e3c9a89a..b81e8d44c80ae 100644 --- a/data/nfp/nfpbioschemas.jsonld +++ b/data/nfp/nfpbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1155/2017/7457131", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/nfp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yang Cao", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5322572", { "@id": "https://doi.org/10.1155/2017/7457131" }, + "pmcid:PMC5322572", "pubmed:28280740" ], "sc:description": "Characterizing and Comparing of Annotated Biological Networks.", @@ -28,16 +32,12 @@ "sc:license": "GPL-2.0", "sc:name": "NFP", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/NFP/index.html", "sc:version": "0.99.2" - }, - { - "@id": "https://doi.org/10.1155/2017/7457131", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ng-tas/ng-tasbioschemas.jsonld b/data/ng-tas/ng-tasbioschemas.jsonld index bdc483ccd2f67..a3cfc49b3c0e1 100644 --- a/data/ng-tas/ng-tasbioschemas.jsonld +++ b/data/ng-tas/ng-tasbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Carlos Caldas's la", "sc:additionalType": "Script", "sc:citation": [ - "pubmed:30609936", { "@id": "https://doi.org/10.1186/s13073-018-0611-9" }, - "pmcid:PMC6320579" + "pmcid:PMC6320579", + "pubmed:30609936" ], "sc:description": "Next Generation-Targeted Amplicon Sequencing (NG-TAS) - an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA.", "sc:featureList": [ @@ -31,10 +31,10 @@ "@id": "edam:operation_3202" }, { - "@id": "edam:operation_0308" + "@id": "edam:operation_3192" }, { - "@id": "edam:operation_3192" + "@id": "edam:operation_0308" } ], "sc:license": "GPL-3.0", diff --git a/data/ngl_viewer/ngl_viewerbioschemas.jsonld b/data/ngl_viewer/ngl_viewerbioschemas.jsonld index 39ce0f6abf9e4..5de8d82fc2d76 100644 --- a/data/ngl_viewer/ngl_viewerbioschemas.jsonld +++ b/data/ngl_viewer/ngl_viewerbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alexander Rose", "sc:additionalType": [ - "Library", "Command-line tool", - "Web application" + "Web application", + "Library" ], "sc:description": "Web application for molecular visualization. It is employed to display molecules like proteins and DNA/RNA with a variety of representations.", "sc:license": "MIT", "sc:name": "NGL VIewer", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "weirdbyte.de", "sc:url": "https://github.com/arose/ngl", diff --git a/data/ngless/nglessbioschemas.jsonld b/data/ngless/nglessbioschemas.jsonld index 48d13f003f88a..18db4bb8ad1d4 100644 --- a/data/ngless/nglessbioschemas.jsonld +++ b/data/ngless/nglessbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "NGLess", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://ngless.embl.de", "sc:version": "1.0.1" diff --git a/data/ngloc/nglocbioschemas.jsonld b/data/ngloc/nglocbioschemas.jsonld index 2e0dd0341fc24..76192a5cddabb 100644 --- a/data/ngloc/nglocbioschemas.jsonld +++ b/data/ngloc/nglocbioschemas.jsonld @@ -17,18 +17,18 @@ "@id": "https://bio.tools/ngloc", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Babu Guda", { "@id": "http://orcid.org/0000-0001-7304-3376" - } + }, + "Babu Guda" ], "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:22780965", + "pmcid:PMC3532370", { "@id": "https://doi.org/10.1186/1756-0500-5-351" - }, - "pmcid:PMC3532370" + } ], "sc:description": "An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The overall prediction accuracy varies from 85.3% to 91.4% across species.", "sc:featureList": { @@ -36,9 +36,9 @@ }, "sc:name": "ngLOC", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://genome.unmc.edu/ngLOC/index.html", "sc:version": "1.0" diff --git a/data/ngmlr/ngmlrbioschemas.jsonld b/data/ngmlr/ngmlrbioschemas.jsonld index 087df79917a3e..21e30ccef5f1e 100644 --- a/data/ngmlr/ngmlrbioschemas.jsonld +++ b/data/ngmlr/ngmlrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "NGMLR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/philres/ngmlr" } \ No newline at end of file diff --git a/data/ngs-qc_generator/ngs-qc_generatorbioschemas.jsonld b/data/ngs-qc_generator/ngs-qc_generatorbioschemas.jsonld index 035d174566956..ddb10580d0c85 100644 --- a/data/ngs-qc_generator/ngs-qc_generatorbioschemas.jsonld +++ b/data/ngs-qc_generator/ngs-qc_generatorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "NGS-QC Generator", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ngs-qc.org/" } \ No newline at end of file diff --git a/data/ngs-snp/ngs-snpbioschemas.jsonld b/data/ngs-snp/ngs-snpbioschemas.jsonld index ef949c570c3f9..505a2f1db8a37 100644 --- a/data/ngs-snp/ngs-snpbioschemas.jsonld +++ b/data/ngs-snp/ngs-snpbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btr372", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ngs-snp", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC3150039", - "pubmed:21697123", { "@id": "https://doi.org/10.1093/bioinformatics/btr372" - } + }, + "pubmed:21697123", + "pmcid:PMC3150039" ], "sc:description": "Collection of command-line scripts for providing annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl.", "sc:featureList": [ @@ -33,10 +37,6 @@ "sc:name": "NGS-SNP", "sc:operatingSystem": "Linux", "sc:url": "https://sites.ualberta.ca/~stothard/downloads/NGS-SNP/" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btr372", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ngs-trex/ngs-trexbioschemas.jsonld b/data/ngs-trex/ngs-trexbioschemas.jsonld index c7b8025390645..040571ffc9438 100644 --- a/data/ngs-trex/ngs-trexbioschemas.jsonld +++ b/data/ngs-trex/ngs-trexbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-14-S15-S10", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ngs-trex", "@type": "sc:SoftwareApplication", @@ -24,23 +28,19 @@ "sc:description": "Next Generation Sequencing Transcriptome profile explorer.", "sc:featureList": [ { - "@id": "edam:operation_3258" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3258" } ], "sc:name": "NGS-Trex", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.ngs-trex.disit.unipmn.it/Trex/cms/" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-14-S15-S10", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ngs_simulation/ngs_simulationbioschemas.jsonld b/data/ngs_simulation/ngs_simulationbioschemas.jsonld index 0a3863c79451e..c79890350309a 100644 --- a/data/ngs_simulation/ngs_simulationbioschemas.jsonld +++ b/data/ngs_simulation/ngs_simulationbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool simulates an Illumina run and provides plots of false positives and false negatives. It allows for a range of simulation parameters to be set.", "sc:name": "ngs_simulation", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", "sc:version": "1.0.0" diff --git a/data/ngscat/ngscatbioschemas.jsonld b/data/ngscat/ngscatbioschemas.jsonld index cfdea8923f5ca..9538bc7c41524 100644 --- a/data/ngscat/ngscatbioschemas.jsonld +++ b/data/ngscat/ngscatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "ngsCAT", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ngscat.clinbioinfosspa.es/ngscat" } \ No newline at end of file diff --git a/data/ngscheckmate/ngscheckmatebioschemas.jsonld b/data/ngscheckmate/ngscheckmatebioschemas.jsonld index e524621f1e14f..fc29238b416ba 100644 --- a/data/ngscheckmate/ngscheckmatebioschemas.jsonld +++ b/data/ngscheckmate/ngscheckmatebioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Peter J. Parkcorresponding author3,5", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:28369524", + "pmcid:PMC5499645", { "@id": "https://doi.org/10.1093/nar/gkx193" }, - "pmcid:PMC5499645" + "pubmed:28369524" ], "sc:description": "Checking sample matching for NGS data.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:license": "MIT", "sc:name": "NGSCheckMate", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/parklab/NGSCheckMate" diff --git a/data/ngscopy/ngscopybioschemas.jsonld b/data/ngscopy/ngscopybioschemas.jsonld index 015fdec0b2e40..59170e4ebd03e 100644 --- a/data/ngscopy/ngscopybioschemas.jsonld +++ b/data/ngscopy/ngscopybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "NGScopy", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NGScopy.html", "sc:version": "1.8.0" diff --git a/data/ngsea/ngseabioschemas.jsonld b/data/ngsea/ngseabioschemas.jsonld index f176d24e56b75..6a9958260f8b9 100644 --- a/data/ngsea/ngseabioschemas.jsonld +++ b/data/ngsea/ngseabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "NGSEA", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.inetbio.org/ngsea" diff --git a/data/ngsep/ngsepbioschemas.jsonld b/data/ngsep/ngsepbioschemas.jsonld index 2b0f15f42c234..db84adefa255c 100644 --- a/data/ngsep/ngsepbioschemas.jsonld +++ b/data/ngsep/ngsepbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jorge Duitama", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": "pubmed:31099384", "sc:description": "NGSEP (Next Generation Sequencing Experience Platform) - accurate variant calling across species and sequencing protocols.", "sc:license": "GPL-3.0", "sc:name": "NGSEP", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://ngsep.sf.net" } \ No newline at end of file diff --git a/data/ngsmethdb/ngsmethdbbioschemas.jsonld b/data/ngsmethdb/ngsmethdbbioschemas.jsonld index da239bf4f8344..19d309fd87584 100644 --- a/data/ngsmethdb/ngsmethdbbioschemas.jsonld +++ b/data/ngsmethdb/ngsmethdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Database that contains methylation data derived from next-generation sequencing (NGS). Two cytosine methylation contexts (CpG and CAG/CTG) are considered. Through a browser interface, the user can search for methylation states in a set of tissues, retrieve methylation values for a set of tissues in a given chromosomal region, or display the methylation of promoters among different tissues. The database is currently populated with human, mouse and Arabidopsis data.", "sc:name": "NGSmethDB", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioinfo2.ugr.es/NGSmethDB/gbrowse/" diff --git a/data/ngsoptwin/ngsoptwinbioschemas.jsonld b/data/ngsoptwin/ngsoptwinbioschemas.jsonld index 2859130258a50..c4cd52357a26e 100644 --- a/data/ngsoptwin/ngsoptwinbioschemas.jsonld +++ b/data/ngsoptwin/ngsoptwinbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NGSoptwin", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www1.maths.leeds.ac.uk/~arief/R/win/" } \ No newline at end of file diff --git a/data/ngsrelatev2/ngsrelatev2bioschemas.jsonld b/data/ngsrelatev2/ngsrelatev2bioschemas.jsonld index 8c249f8b7f73a..9bb5e2879791f 100644 --- a/data/ngsrelatev2/ngsrelatev2bioschemas.jsonld +++ b/data/ngsrelatev2/ngsrelatev2bioschemas.jsonld @@ -9,6 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-7576-5380", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ034", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0003-1941-5495", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/ngsRelateV2", "@type": "sc:SoftwareApplication", @@ -16,18 +28,18 @@ { "@id": "https://orcid.org/0000-0003-1941-5495" }, + "Ida Moltke", { "@id": "https://orcid.org/0000-0001-7576-5380" - }, - "Ida Moltke" + } ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6488770", { "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ034" }, - "pubmed:31042285", - "pmcid:PMC6488770" + "pubmed:31042285" ], "sc:description": "Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding.", "sc:featureList": [ @@ -44,22 +56,10 @@ "sc:license": "GPL-3.0", "sc:name": "ngsRelateV2", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/ANGSD/ngsRelate" - }, - { - "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ034", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0001-7576-5380", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0003-1941-5495", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/ngsutils/ngsutilsbioschemas.jsonld b/data/ngsutils/ngsutilsbioschemas.jsonld index b25099233165c..a3d73f35ab71e 100644 --- a/data/ngsutils/ngsutilsbioschemas.jsonld +++ b/data/ngsutils/ngsutilsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/ngsutils", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yunlong Liu (PI)", - "Marcus Breese (Primary developer)" + "Marcus Breese (Primary developer)", + "Yunlong Liu (PI)" ], "sc:additionalType": "Suite", "sc:citation": "pubmed:23314324", @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "NGSUtils", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ngsutils.org" } \ No newline at end of file diff --git a/data/ngsview/ngsviewbioschemas.jsonld b/data/ngsview/ngsviewbioschemas.jsonld index 85e46d08fb6ed..2991a8472b608 100644 --- a/data/ngsview/ngsviewbioschemas.jsonld +++ b/data/ngsview/ngsviewbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "High-throughput sequencing technologies introduce novel demands on tools available for data analysis. We have developed NGSView, a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. NGSView is available under an open source license and can be extended through a well documented API.", "sc:name": "NGSView", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ngsview.sourceforge.net/" } \ No newline at end of file diff --git a/data/nhlapred/nhlapredbioschemas.jsonld b/data/nhlapred/nhlapredbioschemas.jsonld index 3431f5b71c882..7d19e2cb4223b 100644 --- a/data/nhlapred/nhlapredbioschemas.jsonld +++ b/data/nhlapred/nhlapredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Allows to predict binding peptide for 67 MHC Class I alleles. This also allow to predict the proteasome cleavage site and binding peptide that have cleavage site at C terminus (potential T cell epitopes).", "sc:name": "nHLAPred", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.imtech.res.in/raghava/nhlapred/" } \ No newline at end of file diff --git a/data/nhphyml/nhphymlbioschemas.jsonld b/data/nhphyml/nhphymlbioschemas.jsonld index 89c675cbbcf0e..3176c127f2d3a 100644 --- a/data/nhphyml/nhphymlbioschemas.jsonld +++ b/data/nhphyml/nhphymlbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998).", "sc:name": "nhPhyML", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://doua.prabi.fr/software/nhphyml" } \ No newline at end of file diff --git a/data/niacs/niacsbioschemas.jsonld b/data/niacs/niacsbioschemas.jsonld index e38e1b09b029f..a042290ebb069 100644 --- a/data/niacs/niacsbioschemas.jsonld +++ b/data/niacs/niacsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NIACS", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software" } \ No newline at end of file diff --git a/data/nias-server/nias-serverbioschemas.jsonld b/data/nias-server/nias-serverbioschemas.jsonld index 10365699b2474..44731255fd2c1 100644 --- a/data/nias-server/nias-serverbioschemas.jsonld +++ b/data/nias-server/nias-serverbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Server to help the analysis of the conformational preferences of amino acid residues in proteins.", "sc:name": "NIAS-Server", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://sbcb.inf.ufrgs.br/npas/" } \ No newline at end of file diff --git a/data/nibr_2d-page/nibr_2d-pagebioschemas.jsonld b/data/nibr_2d-page/nibr_2d-pagebioschemas.jsonld index 845d2ebccdaee..56ab5cffe776c 100644 --- a/data/nibr_2d-page/nibr_2d-pagebioschemas.jsonld +++ b/data/nibr_2d-page/nibr_2d-pagebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:description": "World-wide gel-based proteomics database.", "sc:name": "NIBR 2D-PAGE", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.expasy.org/world-2dpage/" diff --git a/data/nieluter/nieluterbioschemas.jsonld b/data/nieluter/nieluterbioschemas.jsonld index 6009303111f55..6db74ac8e567b 100644 --- a/data/nieluter/nieluterbioschemas.jsonld +++ b/data/nieluter/nieluterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predictor that can be used to predict if your binding peptides are Naturally Presented Peptides (NPP) or parts of any protein are NPP.", "sc:name": "NIEluter", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://immunet.cn/nie/cgi-bin/nieluter.pl" } \ No newline at end of file diff --git a/data/niftyfit/niftyfitbioschemas.jsonld b/data/niftyfit/niftyfitbioschemas.jsonld index 69e1477894ab4..8716f824324bd 100644 --- a/data/niftyfit/niftyfitbioschemas.jsonld +++ b/data/niftyfit/niftyfitbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1007/s12021-016-9297-6", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-7667-3947", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/niftyfit", "@type": "sc:SoftwareApplication", @@ -26,10 +18,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:26972806", + "pmcid:PMC4896995", { "@id": "https://doi.org/10.1007/s12021-016-9297-6" - }, - "pmcid:PMC4896995" + } ], "sc:description": "A software package for multi-contrast Magnetic Resonance Imaging that provides a unified model-fitting framework.", "sc:featureList": { @@ -39,10 +31,18 @@ "sc:name": "NiftyFit", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/KCL-BMEIS/niftyreg" + }, + { + "@id": "https://doi.org/10.1007/s12021-016-9297-6", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-7667-3947", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/niftypet/niftypetbioschemas.jsonld b/data/niftypet/niftypetbioschemas.jsonld index b0652b840f362..a00d523b95b37 100644 --- a/data/niftypet/niftypetbioschemas.jsonld +++ b/data/niftypet/niftypetbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Pawel J. Markiewicz", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:29280050", - "pmcid:PMC5797201", { "@id": "https://doi.org/10.1007/s12021-017-9352-y" - } + }, + "pmcid:PMC5797201", + "pubmed:29280050" ], "sc:description": "Software platform, offering high-throughput PET image reconstruction as well as image processing and analysis.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "NiftyPET", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/pjmark/NiftyPET" } diff --git a/data/nimefi/nimefibioschemas.jsonld b/data/nimefi/nimefibioschemas.jsonld index 9009ad909fe06..b355fa13feefc 100644 --- a/data/nimefi/nimefibioschemas.jsonld +++ b/data/nimefi/nimefibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Gene regulatory network inference using multiple ensemble feature importance algorithms.", "sc:name": "NIMEFI", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/nimefi/nimefi/index.html", diff --git a/data/nipah/nipahbioschemas.jsonld b/data/nipah/nipahbioschemas.jsonld index 41f362cd3e563..7d3d3d57f78de 100644 --- a/data/nipah/nipahbioschemas.jsonld +++ b/data/nipah/nipahbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "Nipah", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://cospi.iiserpune.ac.in/Nipah" diff --git a/data/nipredict/nipredictbioschemas.jsonld b/data/nipredict/nipredictbioschemas.jsonld index 68e105c8095ad..f931efff5b8be 100644 --- a/data/nipredict/nipredictbioschemas.jsonld +++ b/data/nipredict/nipredictbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Method to predict nuclear import activity based on characterization of NLS-import receptor interaction using molecular interaction energy components (MIECs).", "sc:name": "NIpredict", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mleg.cse.sc.edu/NIpredict/" } \ No newline at end of file diff --git a/data/nipter/nipterbioschemas.jsonld b/data/nipter/nipterbioschemas.jsonld index 233f80c160fe7..dedc02a2cc9ec 100644 --- a/data/nipter/nipterbioschemas.jsonld +++ b/data/nipter/nipterbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-018-2557-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/NIPTeR", "@type": "sc:SoftwareApplication", @@ -32,11 +28,15 @@ "sc:license": "LGPL-3.0", "sc:name": "NIPTeR", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/molgenis/NIPTeR" + }, + { + "@id": "https://doi.org/10.1186/s12859-018-2557-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nir/nirbioschemas.jsonld b/data/nir/nirbioschemas.jsonld index 03f744fbe4901..bc4d6b585dd04 100644 --- a/data/nir/nirbioschemas.jsonld +++ b/data/nir/nirbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NIR", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://dibernardo.tigem.it/softwares/network-inference-by-reverse-engineering-nir" } \ No newline at end of file diff --git a/data/nitpicker/nitpickerbioschemas.jsonld b/data/nitpicker/nitpickerbioschemas.jsonld index 61abe9598a856..a60b1bd32eeb8 100644 --- a/data/nitpicker/nitpickerbioschemas.jsonld +++ b/data/nitpicker/nitpickerbioschemas.jsonld @@ -16,26 +16,26 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:30940082", - "pmcid:PMC6444531", { "@id": "https://doi.org/10.1186/s12859-019-2717-5" - } + }, + "pmcid:PMC6444531" ], "sc:description": "NITPicker (Next Iteration Time-point Picker) selects optimal time points (or spatial points along a single axis), that eliminates some of the biases caused by human decision-making, while maximising information about the shape of the underlying curves.", "sc:featureList": [ { - "@id": "edam:operation_3565" + "@id": "edam:operation_3800" }, { - "@id": "edam:operation_3800" + "@id": "edam:operation_3565" } ], "sc:license": "GPL-3.0", "sc:name": "NITPicker", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/package=NITPicker", "sc:version": "1.0.1" diff --git a/data/njplot/njplotbioschemas.jsonld b/data/njplot/njplotbioschemas.jsonld index 173dcd26946b0..1d5da26d5fc1b 100644 --- a/data/njplot/njplotbioschemas.jsonld +++ b/data/njplot/njplotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "NJplot is a tool for visualizing binary trees such as the phylogenetic trees output from the PHYLIP programs. Available for several platforms including Windows, MacOS, Linux and Solaris.", "sc:name": "NJplot", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://pbil.univ-lyon1.fr/software/njplot.html" } \ No newline at end of file diff --git a/data/nlr-parser/nlr-parserbioschemas.jsonld b/data/nlr-parser/nlr-parserbioschemas.jsonld index 668dfc59d07b9..93af9df3af157 100644 --- a/data/nlr-parser/nlr-parserbioschemas.jsonld +++ b/data/nlr-parser/nlr-parserbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool to rapidly annotate the NLR (nucleotide-binding leucine-rich repeat) complement from sequenced plant genomes.", "sc:name": "NLR-parser", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/steuernb/NLR-Parser" } \ No newline at end of file diff --git a/data/nlstradamus/nlstradamusbioschemas.jsonld b/data/nlstradamus/nlstradamusbioschemas.jsonld index 55aa0fbe903b0..2b54f5d2a871f 100644 --- a/data/nlstradamus/nlstradamusbioschemas.jsonld +++ b/data/nlstradamus/nlstradamusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Simple Hidden Markov Model for nuclear localization signal prediction.", "sc:name": "NLStradamus", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.moseslab.csb.utoronto.ca/NLStradamus/" } \ No newline at end of file diff --git a/data/nmd_classifier/nmd_classifierbioschemas.jsonld b/data/nmd_classifier/nmd_classifierbioschemas.jsonld index e7beb6bccb50c..3aa9d7e69a354 100644 --- a/data/nmd_classifier/nmd_classifierbioschemas.jsonld +++ b/data/nmd_classifier/nmd_classifierbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool for systematic classification of nonsense mediated decay (NMD) events.", "sc:name": "NMD classifier", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/transcriptome-analysis/" } \ No newline at end of file diff --git a/data/nmpdr/nmpdrbioschemas.jsonld b/data/nmpdr/nmpdrbioschemas.jsonld index b53867ce9c772..66ac3593640f6 100644 --- a/data/nmpdr/nmpdrbioschemas.jsonld +++ b/data/nmpdr/nmpdrbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.", "sc:name": "National microbial pathogen", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.nmpdr.org" } \ No newline at end of file diff --git a/data/nmrbox/nmrboxbioschemas.jsonld b/data/nmrbox/nmrboxbioschemas.jsonld index 11bf87bb40569..399de8d935085 100644 --- a/data/nmrbox/nmrboxbioschemas.jsonld +++ b/data/nmrbox/nmrboxbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "NMRbox", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.nmrbox.org/" } \ No newline at end of file diff --git a/data/nmrfam-sparky/nmrfam-sparkybioschemas.jsonld b/data/nmrfam-sparky/nmrfam-sparkybioschemas.jsonld index 9ca8e14818d77..325edf948c187 100644 --- a/data/nmrfam-sparky/nmrfam-sparkybioschemas.jsonld +++ b/data/nmrfam-sparky/nmrfam-sparkybioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU830", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/nmrfam-sparky", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC4393527", + "pubmed:25505092", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU830" - }, - "pubmed:25505092" + } ], "sc:description": "Enhanced software for biomolecular NMR spectroscopy.", "sc:featureList": { @@ -28,10 +32,6 @@ "sc:name": "NMRFAM-SPARKY", "sc:operatingSystem": "Linux", "sc:url": "http://pine.nmrfam.wisc.edu/download_packages.html" - }, - { - "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU830", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nmrnet/nmrnetbioschemas.jsonld b/data/nmrnet/nmrnetbioschemas.jsonld index bee2a54d5ffb1..33ff5ed0a9f6f 100644 --- a/data/nmrnet/nmrnetbioschemas.jsonld +++ b/data/nmrnet/nmrnetbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/nmrnet", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Piotr Klukowski", "Adam Gonczarek", - "Michał J Walczak" + "Michał J Walczak", + "Piotr Klukowski" ], "sc:additionalType": "Desktop application", "sc:description": "Deep learning approach to automated peak picking of protein NMR spectra (part of a Dumpling software).", diff --git a/data/nmrprocflow/nmrprocflowbioschemas.jsonld b/data/nmrprocflow/nmrprocflowbioschemas.jsonld index 12406c1c738a1..d51623fb615cb 100644 --- a/data/nmrprocflow/nmrprocflowbioschemas.jsonld +++ b/data/nmrprocflow/nmrprocflowbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/nmrprocflow", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:description": "An interactive 1D NMR spectra processing tool dedicated to metabolomics. This open source software provides a complete set of tools for processing and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization.", "sc:name": "NMRProcFlow", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://nmrprocflow.org/", "sc:version": "1.2" diff --git a/data/nmrstarlib/nmrstarlibbioschemas.jsonld b/data/nmrstarlib/nmrstarlibbioschemas.jsonld index 78e569f0f6f3f..3a31c1db0bf8c 100644 --- a/data/nmrstarlib/nmrstarlibbioschemas.jsonld +++ b/data/nmrstarlib/nmrstarlibbioschemas.jsonld @@ -9,14 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-017-1580-5", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/nmrstarlib", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Andrey Smelter", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:28302053", "pmcid:PMC5356280", + "pubmed:28302053", { "@id": "https://doi.org/10.1186/s12859-017-1580-5" } @@ -32,10 +36,6 @@ "Linux" ], "sc:url": "http://bioinformatics.cesb.uky.edu/Main/SoftwareDevelopment#nmrstarlib" - }, - { - "@id": "https://doi.org/10.1186/s12859-017-1580-5", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nmsim/nmsimbioschemas.jsonld b/data/nmsim/nmsimbioschemas.jsonld index 1a464e1dc7582..80c1b1cc252b4 100644 --- a/data/nmsim/nmsimbioschemas.jsonld +++ b/data/nmsim/nmsimbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NMSim", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.nmsim.de" } \ No newline at end of file diff --git a/data/nnalign/nnalignbioschemas.jsonld b/data/nnalign/nnalignbioschemas.jsonld index 4a4c48b60ca9c..ba51e876f2ee2 100644 --- a/data/nnalign/nnalignbioschemas.jsonld +++ b/data/nnalign/nnalignbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/nnalign", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Massimo Andreatta", - "Morten Nielsen" + "Morten Nielsen", + "Massimo Andreatta" ], "sc:additionalType": "Web application", "sc:description": "Discovering sequence motifs in quantitative peptide data. It allows generating artificial neural network models of receptor-ligand interactions. It takes as input a set of ligand sequences with target values; it returns a sequence alignment, a binding motif of the interaction, and a model that can be used to scan for occurrences of the motif in other sequences.", diff --git a/data/nndb/nndbbioschemas.jsonld b/data/nndb/nndbbioschemas.jsonld index 6c74093d2ab38..b88b2223a540a 100644 --- a/data/nndb/nndbbioschemas.jsonld +++ b/data/nndb/nndbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Nearest Neighbor Database (NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence-dependent parameters in plain text and html, literature references to experiments and usage tutorials. Also covered are parameters for predicting RNA folding free energy and enthalpy changes.", "sc:name": "NNDB", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://rna.urmc.rochester.edu/NNDB" } \ No newline at end of file diff --git a/data/nnnorm/nnnormbioschemas.jsonld b/data/nnnorm/nnnormbioschemas.jsonld index e6b3aeea04753..6179f68b39055 100644 --- a/data/nnnorm/nnnormbioschemas.jsonld +++ b/data/nnnorm/nnnormbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Adi Laurentiu Tarca", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.", "sc:license": "GPL-3.0", "sc:name": "nnNorm", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/nnNorm.html", "sc:version": "2.38.0" diff --git a/data/noa/noabioschemas.jsonld b/data/noa/noabioschemas.jsonld index c0fad63d5eadf..0002afe12ddae 100644 --- a/data/noa/noabioschemas.jsonld +++ b/data/noa/noabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The NOA (Network Ontology Analysis) plugin for Cytoscape implements the NOA algorithm for network-based enrichment analysis, which extends Gene Ontology annotations to network links, or edges.", "sc:name": "NOA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://nrnb.org/tools/noa/", "sc:version": "1.1" diff --git a/data/nobai/nobaibioschemas.jsonld b/data/nobai/nobaibioschemas.jsonld index f871c60406378..25e4930f3b4d8 100644 --- a/data/nobai/nobaibioschemas.jsonld +++ b/data/nobai/nobaibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Facilitates the search for the evolutionary history embedded in the structure of functional RNA molecules.", "sc:name": "NOBAI", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.manet.uiuc.edu/nobai/nobai.php" } \ No newline at end of file diff --git a/data/nod/nodbioschemas.jsonld b/data/nod/nodbioschemas.jsonld index 613591e09b421..0c7441db6210a 100644 --- a/data/nod/nodbioschemas.jsonld +++ b/data/nod/nodbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "NoD is a predictor of nucleolar localization sequences (NoLSs) in proteins. NoLSs are short basic motifs that localize proteins to the nucleolus, a sub-compartment of the nucleus. You can search the set of NoLSs predicted in 9531 human proteins out of the 43534 human proteins considered (from IPI version 3.40).", "sc:name": "NoD", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.compbio.dundee.ac.uk/www-nod/", diff --git a/data/nohtml/nohtmlbioschemas.jsonld b/data/nohtml/nohtmlbioschemas.jsonld index e0800460aa822..dbf077de797ff 100644 --- a/data/nohtml/nohtmlbioschemas.jsonld +++ b/data/nohtml/nohtmlbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "EMBOSS Contributors", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust", + "EMBOSS Contributors" ], "sc:description": "Remove mark-up (e.g. HTML tags) from an ASCII text file.", "sc:funder": [ "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "nohtml", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": [ diff --git a/data/noiseq/noiseqbioschemas.jsonld b/data/noiseq/noiseqbioschemas.jsonld index 923e167c5539b..804d4b34699bf 100644 --- a/data/noiseq/noiseqbioschemas.jsonld +++ b/data/noiseq/noiseqbioschemas.jsonld @@ -22,11 +22,11 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:26184878", + "pmcid:PMC4666377", { "@id": "https://doi.org/10.1093/nar/gkv711" - }, - "pmcid:PMC4666377", - "pubmed:26184878" + } ], "sc:description": "Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.", "sc:featureList": { diff --git a/data/noisy/noisybioschemas.jsonld b/data/noisy/noisybioschemas.jsonld index 85c3eea429c8f..8375945d6dcf3 100644 --- a/data/noisy/noisybioschemas.jsonld +++ b/data/noisy/noisybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Cleaning aligned sequences.", "sc:name": "noisy", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.bioinf.uni-leipzig.de/Software/noisy/", "sc:version": "1.5.12.1" diff --git a/data/nomad-ref/nomad-refbioschemas.jsonld b/data/nomad-ref/nomad-refbioschemas.jsonld index 1dfe171f3887f..10283febab2be 100644 --- a/data/nomad-ref/nomad-refbioschemas.jsonld +++ b/data/nomad-ref/nomad-refbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Normal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions.", "sc:name": "NOMAD-Ref", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://lorentz.immstr.pasteur.fr/nomad-ref.php" } \ No newline at end of file diff --git a/data/non-b_db/non-b_dbbioschemas.jsonld b/data/non-b_db/non-b_dbbioschemas.jsonld index 6f88e8bf77e13..284e4adcc8737 100644 --- a/data/non-b_db/non-b_dbbioschemas.jsonld +++ b/data/non-b_db/non-b_dbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "It is a non-canonical (non-B) structure database database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides alternative DNA structure predictions, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively.", "sc:name": "Non-B DB", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://nonb-abcc.ncifcrf.gov/apps/nBMST/default/" } \ No newline at end of file diff --git a/data/noncode/noncodebioschemas.jsonld b/data/noncode/noncodebioschemas.jsonld index 8ede4c6c1522f..e5340e0718a09 100644 --- a/data/noncode/noncodebioschemas.jsonld +++ b/data/noncode/noncodebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of all kinds of noncoding RNAs (except tRNAs and rRNAs). It also provides an efficient search option, allowing recovery of sequence, related publications and other information.", "sc:name": "NONCODE", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.noncode.org" } \ No newline at end of file diff --git a/data/noncoder/noncoderbioschemas.jsonld b/data/noncoder/noncoderbioschemas.jsonld index 0c063dd79993e..a8b924af63928 100644 --- a/data/noncoder/noncoderbioschemas.jsonld +++ b/data/noncoder/noncoderbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Thomas Braun", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:23012263", { "@id": "https://doi.org/10.1093/NAR/GKS877" }, - "pubmed:23012263", "pmcid:PMC3592461" ], "sc:description": "Exon array-based detection of long non-coding RNAs.", @@ -27,9 +27,9 @@ }, "sc:name": "Noncoder", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://noncoder.mpi-bn.mpg.de/" }, diff --git a/data/nondetects/nondetectsbioschemas.jsonld b/data/nondetects/nondetectsbioschemas.jsonld index 40afaca7e2de3..80660503a2275 100644 --- a/data/nondetects/nondetectsbioschemas.jsonld +++ b/data/nondetects/nondetectsbioschemas.jsonld @@ -29,37 +29,37 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0203" + "@id": "edam:topic_3519" }, { - "@id": "edam:topic_3519" + "@id": "edam:topic_0203" } ], "sc:citation": [ { "@id": "https://doi.org/10.1093/bioinformatics/btu239" }, - "pmcid:PMC4133581", - "pubmed:24764462" + "pubmed:24764462", + "pmcid:PMC4133581" ], "sc:description": "Methods to model and impute non-detects in the results of qPCR experiments.", "sc:featureList": [ { - "@id": "edam:operation_3557" + "@id": "edam:operation_3435" }, { "@id": "edam:operation_3566" }, { - "@id": "edam:operation_3435" + "@id": "edam:operation_3557" } ], "sc:license": "GPL-3.0", "sc:name": "nondetects", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/nondetects.html", "sc:version": "2.4.0" diff --git a/data/noreturn/noreturnbioschemas.jsonld b/data/noreturn/noreturnbioschemas.jsonld index ae336b821f68b..f62dddf0b7304 100644 --- a/data/noreturn/noreturnbioschemas.jsonld +++ b/data/noreturn/noreturnbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", + "UK BBSRC", "EMBOSS Contributors", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:description": "Remove carriage return from ASCII files.", "sc:funder": [ - "UK MRC", "Wellcome Trust", + "UK MRC", "UK BBSRC" ], "sc:license": "GPL-3.0", @@ -31,8 +31,8 @@ "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/noreturn.html", "sc:version": "r6" diff --git a/data/noreva/norevabioschemas.jsonld b/data/noreva/norevabioschemas.jsonld index 14a958ec7ec43..4991bfd632b0c 100644 --- a/data/noreva/norevabioschemas.jsonld +++ b/data/noreva/norevabioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Dr. Bo Li", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5570188", - "pubmed:28525573", { "@id": "https://doi.org/10.1093/nar/gkx449" - } + }, + "pmcid:PMC5570188", + "pubmed:28525573" ], "sc:description": "NORmalization and EVAluation of MS-based metabolomics data. Enables performance evaluation of various normalization methods from multiple perspectives. In particular, it integrates 5 well-established criteria, each with a distinct underlying theory, to ensure a more comprehensive evaluation than any single criterion. Moreover, it provides various available and popular normalization methods, with a unique feature of allowing quality control based correction sequentially followed by data normalization.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "NOREVA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://server.idrb.cqu.edu.cn/noreva/" diff --git a/data/normalize450k/normalize450kbioschemas.jsonld b/data/normalize450k/normalize450kbioschemas.jsonld index e4b61a080f519..aabaec40d9ebc 100644 --- a/data/normalize450k/normalize450kbioschemas.jsonld +++ b/data/normalize450k/normalize450kbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-1448-2509", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.3389/fgene.2015.00092", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/normalize450k", "@type": "sc:SoftwareApplication", @@ -28,8 +20,8 @@ "Library" ], "sc:citation": [ - "pmcid:PMC4354407", "pubmed:25806048", + "pmcid:PMC4354407", { "@id": "https://doi.org/10.3389/fgene.2015.00092" } @@ -37,21 +29,29 @@ "sc:description": "This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.", "sc:featureList": [ { - "@id": "edam:operation_3435" + "@id": "edam:operation_3659" }, { - "@id": "edam:operation_3659" + "@id": "edam:operation_3435" } ], "sc:license": "BSD-4-Clause", "sc:name": "normalize450K", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/normalize450K.html", "sc:version": "1.2.0" + }, + { + "@id": "http://orcid.org/0000-0003-1448-2509", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.3389/fgene.2015.00092", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/normalyzer/normalyzerbioschemas.jsonld b/data/normalyzer/normalyzerbioschemas.jsonld index 6ee36fa589e35..aadf67fc19f97 100644 --- a/data/normalyzer/normalyzerbioschemas.jsonld +++ b/data/normalyzer/normalyzerbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "A tool for overviewing the effects of different normalisation methods on omics data.", "sc:name": "Normalyzer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://quantitativeproteomics.org/normalyzer" } \ No newline at end of file diff --git a/data/normalyzerde/normalyzerdebioschemas.jsonld b/data/normalyzerde/normalyzerdebioschemas.jsonld index 721ba90ba9ee0..ae01762b1e35a 100644 --- a/data/normalyzerde/normalyzerdebioschemas.jsonld +++ b/data/normalyzerde/normalyzerdebioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "NormalyzerDE", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.quantitativeproteomics.org/normalyzerde" } \ No newline at end of file diff --git a/data/normexpression/normexpressionbioschemas.jsonld b/data/normexpression/normexpressionbioschemas.jsonld index d6a1860cd307b..dbd88e00c2107 100644 --- a/data/normexpression/normexpressionbioschemas.jsonld +++ b/data/normexpression/normexpressionbioschemas.jsonld @@ -16,26 +16,26 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC6503164", - "pubmed:31114611", { "@id": "https://doi.org/10.3389/fgene.2019.00400" - } + }, + "pubmed:31114611" ], "sc:description": "Framework for researchers to select the best method for the normalization of their gene expression data based on the evaluation of different methods in the principle of the consistency of metrics and the consistency of datasets.", "sc:featureList": [ { - "@id": "edam:operation_3192" + "@id": "edam:operation_0571" }, { - "@id": "edam:operation_0571" + "@id": "edam:operation_3192" } ], "sc:license": "Artistic-2.0", "sc:name": "NormExpression", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/NormExpression/index.html" }, diff --git a/data/normqpcr/normqpcrbioschemas.jsonld b/data/normqpcr/normqpcrbioschemas.jsonld index 0375eb6100d12..4fe062955fd27 100644 --- a/data/normqpcr/normqpcrbioschemas.jsonld +++ b/data/normqpcr/normqpcrbioschemas.jsonld @@ -14,15 +14,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "James Perkins", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ { "@id": "https://doi.org/10.1186/1471-2164-13-296" }, - "pmcid:PMC3443438", - "pubmed:22748112" + "pubmed:22748112", + "pmcid:PMC3443438" ], "sc:description": "Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data.", "sc:featureList": [ @@ -36,9 +36,9 @@ "sc:license": "GPL-3.0", "sc:name": "NormqPCR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NormqPCR.html", "sc:version": "1.20.0" diff --git a/data/normr/normrbioschemas.jsonld b/data/normr/normrbioschemas.jsonld index eadc5ca6c93c5..0e3d57d3ac74f 100644 --- a/data/normr/normrbioschemas.jsonld +++ b/data/normr/normrbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "normr", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/normr.html", "sc:version": "1.0.0" diff --git a/data/norsnet/norsnetbioschemas.jsonld b/data/norsnet/norsnetbioschemas.jsonld index 75649180fa4e2..a892024184b43 100644 --- a/data/norsnet/norsnetbioschemas.jsonld +++ b/data/norsnet/norsnetbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/norsnet", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": "Avner Schlessinger", "sc:citation": "pubmed:17658943", "sc:contributor": [ + "Jinfeng Liu", "Burkhard Rost", - "Grant 2R01-LM07329-01 from the National Library of Medicine", - "Jinfeng Liu" + "Grant 2R01-LM07329-01 from the National Library of Medicine" ], "sc:description": "Identification unstructured loops from sequence.", "sc:funder": "Grant 2R01-LM07329-01 from the National Library of Medicine", diff --git a/data/nospace/nospacebioschemas.jsonld b/data/nospace/nospacebioschemas.jsonld index ffb2f3035cf60..e13580d9e5067 100644 --- a/data/nospace/nospacebioschemas.jsonld +++ b/data/nospace/nospacebioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK MRC", "EMBOSS Contributors", - "UK BBSRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:description": "Remove whitespace from an ASCII text file.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "nospace", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/notab/notabbioschemas.jsonld b/data/notab/notabbioschemas.jsonld index 2079f0bec76a9..f5f723953bfa2 100644 --- a/data/notab/notabbioschemas.jsonld +++ b/data/notab/notabbioschemas.jsonld @@ -13,21 +13,21 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:description": "Replace tabs with spaces in an ASCII text file.", "sc:funder": [ + "Wellcome Trust", "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "notab", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ diff --git a/data/notseq/notseqbioschemas.jsonld b/data/notseq/notseqbioschemas.jsonld index a2c41993dbcb2..e03cfa323a1a1 100644 --- a/data/notseq/notseqbioschemas.jsonld +++ b/data/notseq/notseqbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "UK BBSRC", + "Wellcome Trust", "EMBOSS Contributors", - "Wellcome Trust" + "UK MRC" ], "sc:description": "Write to file a subset of an input stream of sequences.", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "notseq", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/notung/notungbioschemas.jsonld b/data/notung/notungbioschemas.jsonld index 67ba649232999..72aba97b92979 100644 --- a/data/notung/notungbioschemas.jsonld +++ b/data/notung/notungbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software tool that offers a unified framework for incorporating duplication/loss parsimony into phylogenetic tasks.", "sc:name": "Notung", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.cs.cmu.edu/~durand/Notung/" } \ No newline at end of file diff --git a/data/novoalign/novoalignbioschemas.jsonld b/data/novoalign/novoalignbioschemas.jsonld index 98c380d9d5f21..35a82edaa3c1b 100644 --- a/data/novoalign/novoalignbioschemas.jsonld +++ b/data/novoalign/novoalignbioschemas.jsonld @@ -9,30 +9,22 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/nmeth.4106", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-14-184", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/novoalign", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27941783", - "pmcid:PMC5792058", - "pubmed:23758764", + { + "@id": "https://doi.org/10.1038/nmeth.4106" + }, "pubmed:28286147", + "pubmed:23758764", "pmcid:PMC3694458", + "pmcid:PMC5792058", { "@id": "https://doi.org/10.1186/1471-2105-14-184" }, - { - "@id": "https://doi.org/10.1038/nmeth.4106" - } + "pubmed:27941783" ], "sc:description": "Tool designed for mapping short reads from Illumina, IonTorrent or 454 platforms onto a reference genome. This is a commercial product.", "sc:license": "Proprietary", @@ -42,6 +34,14 @@ "Mac" ], "sc:url": "http://www.novocraft.com/products/novoalign/" + }, + { + "@id": "https://doi.org/10.1038/nmeth.4106", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-184", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/novoaligncs/novoaligncsbioschemas.jsonld b/data/novoaligncs/novoaligncsbioschemas.jsonld index 19f89c56229e0..a30e601f4e686 100644 --- a/data/novoaligncs/novoaligncsbioschemas.jsonld +++ b/data/novoaligncs/novoaligncsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Proprietary", "sc:name": "NovoalignCS", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.novocraft.com/products/novoalign/" } \ No newline at end of file diff --git a/data/novor/novorbioschemas.jsonld b/data/novor/novorbioschemas.jsonld index 9c68514fa1d94..49ebfd057d349 100644 --- a/data/novor/novorbioschemas.jsonld +++ b/data/novor/novorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Fast, real-time peptide ''de novo'' sequencing engine.", "sc:name": "Novor", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.rapidnovor.com/" } \ No newline at end of file diff --git a/data/npact/npactbioschemas.jsonld b/data/npact/npactbioschemas.jsonld index c9922fc2360fa..9aeeae6bbf05c 100644 --- a/data/npact/npactbioschemas.jsonld +++ b/data/npact/npactbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Computational and graphical representation tool for gene identification and sequence annotation. Identifies sequence segments of any length with statistically-significant 3-base compositional periodicities and associated with ORF structures .", "sc:name": "NPACT", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://genome.ufl.edu/npact/" diff --git a/data/nparact/nparactbioschemas.jsonld b/data/nparact/nparactbioschemas.jsonld index b00fd0ea5f047..d04b2cae6d8c7 100644 --- a/data/nparact/nparactbioschemas.jsonld +++ b/data/nparact/nparactbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "http://orcid.org/0000-0003-2328-9612", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1016/j.mex.2016.05.006", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/nparact", "@type": "sc:SoftwareApplication", @@ -43,6 +39,10 @@ ], "sc:url": "https://cran.r-project.org/web/packages/nparACT/index.html", "sc:version": "0.8" + }, + { + "@id": "https://doi.org/10.1016/j.mex.2016.05.006", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/npcare/npcarebioschemas.jsonld b/data/npcare/npcarebioschemas.jsonld index b7d3b6a720662..8db7a3a0a921f 100644 --- a/data/npcare/npcarebioschemas.jsonld +++ b/data/npcare/npcarebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The Database of Natural Products for CAncer gene REgulation in Cancer Types.", "sc:name": "NPCARE", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://silver.sejong.ac.kr/npcare" } \ No newline at end of file diff --git a/data/npd_ws/npd_wsbioschemas.jsonld b/data/npd_ws/npd_wsbioschemas.jsonld index 7bc88d467b7a3..d9b11776debe8 100644 --- a/data/npd_ws/npd_wsbioschemas.jsonld +++ b/data/npd_ws/npd_wsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This service provides various ways to retrieve information from The Nuclear Protein Database.", "sc:name": "NPD WS", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://npd.hgu.mrc.ac.uk/user/services", "sc:version": "1" diff --git a/data/npdock/npdockbioschemas.jsonld b/data/npdock/npdockbioschemas.jsonld index 5adc9ebcb56fd..653c9a1bc0305 100644 --- a/data/npdock/npdockbioschemas.jsonld +++ b/data/npdock/npdockbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NPDock", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://genesilico.pl/NPDock" } \ No newline at end of file diff --git a/data/npgsea/npgseabioschemas.jsonld b/data/npgsea/npgseabioschemas.jsonld index d693281ab4078..f6c768f75bc2f 100644 --- a/data/npgsea/npgseabioschemas.jsonld +++ b/data/npgsea/npgseabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-015-0571-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/npgsea", "@type": "sc:SoftwareApplication", @@ -37,10 +41,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/npGSEA.html", "sc:version": "1.10.0" - }, - { - "@id": "https://doi.org/10.1186/s12859-015-0571-7", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nplb/nplbbioschemas.jsonld b/data/nplb/nplbbioschemas.jsonld index 8694d088ef1f6..381b774004a19 100644 --- a/data/nplb/nplbbioschemas.jsonld +++ b/data/nplb/nplbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Efficient, organism-independent method for characterizing such diverse architectures directly from experimentally identified genome-wide TSSs, without relying on known promoter elements.", "sc:name": "NPLB", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://nplb.ncl.res.in/" } \ No newline at end of file diff --git a/data/nppred/nppredbioschemas.jsonld b/data/nppred/nppredbioschemas.jsonld index 7f5c0168cdaf2..0433c54a48d23 100644 --- a/data/nppred/nppredbioschemas.jsonld +++ b/data/nppred/nppredbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-10-22", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/nppred", "@type": "sc:SoftwareApplication", @@ -21,11 +17,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC2632991", { "@id": "https://doi.org/10.1186/1471-2105-10-22" }, - "pubmed:19152693" + "pubmed:19152693", + "pmcid:PMC2632991" ], "sc:description": "NpPred is a method developed for predicting nuclear proteins. This method has been developed on a non-redundant dataset consists of 2710 nuclear and 7662 non-nuclear proteins.", "sc:featureList": { @@ -33,12 +29,16 @@ }, "sc:name": "NpPred", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/nppred/" }, + { + "@id": "https://doi.org/10.1186/1471-2105-10-22", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0002-8902-2876", "@type": "schema:Person" diff --git a/data/nps-protein/nps-proteinbioschemas.jsonld b/data/nps-protein/nps-proteinbioschemas.jsonld index a62ce7b20508d..2d0f04407ef84 100644 --- a/data/nps-protein/nps-proteinbioschemas.jsonld +++ b/data/nps-protein/nps-proteinbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/nps-protein", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Gilbert DELEAGE", - "Raphael TERREUX" + "Raphael TERREUX", + "Gilbert DELEAGE" ], "sc:additionalType": "Web service", "sc:citation": "pubmed:10694887", @@ -20,8 +20,8 @@ "sc:name": "NPS", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_server.html" } \ No newline at end of file diff --git a/data/nps/npsbioschemas.jsonld b/data/nps/npsbioschemas.jsonld index 1b5f3b001b53f..b67b9f8378d44 100644 --- a/data/nps/npsbioschemas.jsonld +++ b/data/nps/npsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.", "sc:name": "NPS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://liulab.dfci.harvard.edu/NPS/" diff --git a/data/npseq/npseqbioschemas.jsonld b/data/npseq/npseqbioschemas.jsonld index c6a6769028ed1..d12112cbaa7a4 100644 --- a/data/npseq/npseqbioschemas.jsonld +++ b/data/npseq/npseqbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "npSeq", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www3.nd.edu/~jli9/research.html#npseq" } \ No newline at end of file diff --git a/data/nq-flipper/nq-flipperbioschemas.jsonld b/data/nq-flipper/nq-flipperbioschemas.jsonld index f53cbaed903aa..b8eacd6720804 100644 --- a/data/nq-flipper/nq-flipperbioschemas.jsonld +++ b/data/nq-flipper/nq-flipperbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.", "sc:name": "NQ-Flipper", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php" } \ No newline at end of file diff --git a/data/nrg-cing/nrg-cingbioschemas.jsonld b/data/nrg-cing/nrg-cingbioschemas.jsonld index 211a28d4272e1..34723b956bce2 100644 --- a/data/nrg-cing/nrg-cingbioschemas.jsonld +++ b/data/nrg-cing/nrg-cingbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/nrg-cing", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Jurgen F. Doreleijers", "Geerten W. Vuister", - "Gert Vriend", - "Jurgen F. Doreleijers" + "Gert Vriend" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:22139937", diff --git a/data/nrpred/nrpredbioschemas.jsonld b/data/nrpred/nrpredbioschemas.jsonld index 6241db4dc89b1..3b64243fc6f3c 100644 --- a/data/nrpred/nrpredbioschemas.jsonld +++ b/data/nrpred/nrpredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SVM based tool for the classification of nuclear receptors on the basis of amino acid composition or dipeptide composition. The overall prediction accuracy of amino acid composition and dipeptide composition based methods is 82.6% and 97.2%", "sc:name": "NRpred", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/nrpred/" diff --git a/data/nrprof/nrprofbioschemas.jsonld b/data/nrprof/nrprofbioschemas.jsonld index 31810b03b7ffd..0c358fe044ff4 100644 --- a/data/nrprof/nrprofbioschemas.jsonld +++ b/data/nrprof/nrprofbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "NRProF", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://jjwanglab.org:8080/hkubioinfo/NRProF/NRProF.jsp" } \ No newline at end of file diff --git a/data/nrps-pks/nrps-pksbioschemas.jsonld b/data/nrps-pks/nrps-pksbioschemas.jsonld index 01f97dba121e7..5b69224c0adbe 100644 --- a/data/nrps-pks/nrps-pksbioschemas.jsonld +++ b/data/nrps-pks/nrps-pksbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "NRPS-PKS", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://nrps.igs.umaryland.edu/" } \ No newline at end of file diff --git a/data/nrpspredictor2/nrpspredictor2bioschemas.jsonld b/data/nrpspredictor2/nrpspredictor2bioschemas.jsonld index 312ad5f90cb4f..9238bec532810 100644 --- a/data/nrpspredictor2/nrpspredictor2bioschemas.jsonld +++ b/data/nrpspredictor2/nrpspredictor2bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "NRPSpredictor2 is a web server for predicting bacterial non-ribosomal peptide synthetases (NRPS) adenylation domain specificity.", "sc:name": "NRPSpredictor2", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://nrps.informatik.uni-tuebingen.de/" } \ No newline at end of file diff --git a/data/nrwrh/nrwrhbioschemas.jsonld b/data/nrwrh/nrwrhbioschemas.jsonld index 385bd46be15a3..79e524aae6b35 100644 --- a/data/nrwrh/nrwrhbioschemas.jsonld +++ b/data/nrwrh/nrwrhbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Predict the potential target proteins of the given drug. It is proposed based on the assumption that similar drugs often target similar target proteins and the framework of Random Walk with Restart (RWR).", "sc:name": "NRWRH", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://doc.aporc.org/wiki/NRWRH" } \ No newline at end of file diff --git a/data/nsdna/nsdnabioschemas.jsonld b/data/nsdna/nsdnabioschemas.jsonld index 0eef2a034ff07..dcf9fb065e729 100644 --- a/data/nsdna/nsdnabioschemas.jsonld +++ b/data/nsdna/nsdnabioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKW1038", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/nsdna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:27899613", "pmcid:PMC5210534", { "@id": "https://doi.org/10.1093/NAR/GKW1038" - }, - "pubmed:27899613" + } ], "sc:description": "A manually curated database of experimentally supported ncRNAs associated with nervous system diseases.", "sc:featureList": { @@ -32,10 +28,14 @@ "sc:name": "NSDNA", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bio-bigdata.net/nsdna/home.jsp" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKW1038", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nsimscan/nsimscanbioschemas.jsonld b/data/nsimscan/nsimscanbioschemas.jsonld index 6dc521c7d6748..c6388e83c3917 100644 --- a/data/nsimscan/nsimscanbioschemas.jsonld +++ b/data/nsimscan/nsimscanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "NSimScan", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/abadona/qsimscan" } \ No newline at end of file diff --git a/data/nsite/nsitebioschemas.jsonld b/data/nsite/nsitebioschemas.jsonld index b10221349a430..f98bb42f15bff 100644 --- a/data/nsite/nsitebioschemas.jsonld +++ b/data/nsite/nsitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Programs that perform searches for statistically significant (non-random) motifs of known human, animal and plant one-box and composite REs in a single genomic sequence, in a pair of aligned homologous sequences and in a set of functionally related sequences, respectively.", "sc:name": "NSITE", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.softberry.com/freedownloadhelp/nsite/description.html" } \ No newline at end of file diff --git a/data/nsmap/nsmapbioschemas.jsonld b/data/nsmap/nsmapbioschemas.jsonld index 7c2b8253620d8..60080438d5f86 100644 --- a/data/nsmap/nsmapbioschemas.jsonld +++ b/data/nsmap/nsmapbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Designed to identify and quantify isoforms from RNA-seq by incorporating a sparsity term into expression level estimation to enable isoform structure prediction and expression estimation simultaneously.", "sc:name": "NSMAP", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sites.google.com/site/nsmapforrnaseq/home", "sc:version": "0.1.0" diff --git a/data/nsrrr/nsrrrbioschemas.jsonld b/data/nsrrr/nsrrrbioschemas.jsonld index 0d392f2bc59b8..ecdca1dc3af71 100644 --- a/data/nsrrr/nsrrrbioschemas.jsonld +++ b/data/nsrrr/nsrrrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Multivariate regression model capable of using prior biological knowledge expressed as gene interaction networks to guide the search for associations between gene expression and DNA methylation signatures.", "sc:name": "NsRRR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www2.imperial.ac.uk/~gmontana/nsrrr.htm" } \ No newline at end of file diff --git a/data/nssnpanalyzer/nssnpanalyzerbioschemas.jsonld b/data/nssnpanalyzer/nssnpanalyzerbioschemas.jsonld index 4efe5c6489630..63555e57ae743 100644 --- a/data/nssnpanalyzer/nssnpanalyzerbioschemas.jsonld +++ b/data/nssnpanalyzer/nssnpanalyzerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated.", "sc:name": "nsSNPAnalyzer", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://snpanalyzer.uthsc.edu/" diff --git a/data/ntcard/ntcardbioschemas.jsonld b/data/ntcard/ntcardbioschemas.jsonld index cf10c2e2d37b6..9c72dbaecaffa 100644 --- a/data/ntcard/ntcardbioschemas.jsonld +++ b/data/ntcard/ntcardbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "ntCard", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/bcgsc/ntCard" } \ No newline at end of file diff --git a/data/ntedit/nteditbioschemas.jsonld b/data/ntedit/nteditbioschemas.jsonld index 146067e16c3ec..4f284eae0aba7 100644 --- a/data/ntedit/nteditbioschemas.jsonld +++ b/data/ntedit/nteditbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "ntEdit", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/bcgsc/ntedit" } \ No newline at end of file diff --git a/data/nthseq/nthseqbioschemas.jsonld b/data/nthseq/nthseqbioschemas.jsonld index b4304cf8ef337..e1c3a1d7d0a4e 100644 --- a/data/nthseq/nthseqbioschemas.jsonld +++ b/data/nthseq/nthseqbioschemas.jsonld @@ -13,15 +13,15 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", + "UK MRC", "UK BBSRC", - "EMBOSS Contributors", - "UK MRC" + "EMBOSS Contributors" ], "sc:description": "Write to file a single sequence from an input stream of sequences.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "nthseq", diff --git a/data/nthseqset/nthseqsetbioschemas.jsonld b/data/nthseqset/nthseqsetbioschemas.jsonld index 6af818e83945f..b185618636a93 100644 --- a/data/nthseqset/nthseqsetbioschemas.jsonld +++ b/data/nthseqset/nthseqsetbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", + "UK BBSRC", "Wellcome Trust", "EMBOSS Contributors", - "UK BBSRC" + "UK MRC" ], "sc:description": "Read and write (return) one set of sequences from many.", "sc:funder": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "nthseqset", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/ntue/ntuebioschemas.jsonld b/data/ntue/ntuebioschemas.jsonld index 111ca64b3a666..9df1021693ab6 100644 --- a/data/ntue/ntuebioschemas.jsonld +++ b/data/ntue/ntuebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "NtUE", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioclues.org/NtUE/index.php" } \ No newline at end of file diff --git a/data/ntw/ntwbioschemas.jsonld b/data/ntw/ntwbioschemas.jsonld index 2d41140db1b65..516208d4d9f01 100644 --- a/data/ntw/ntwbioschemas.jsonld +++ b/data/ntw/ntwbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "NTW", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NTW.html", "sc:version": "1.24.0" diff --git a/data/nucgen/nucgenbioschemas.jsonld b/data/nucgen/nucgenbioschemas.jsonld index 181a80ff03e8a..05db66c748019 100644 --- a/data/nucgen/nucgenbioschemas.jsonld +++ b/data/nucgen/nucgenbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Reads wedge (or local doublet) and basepair parameters calculates local helical parameters from local doublet parameters, then applies the base-pair and helical parameters to succesive  basepairs after transforming the already generated ones to bring the topmost one in the (x-y) plane.", "sc:name": "NUCGEN", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://nucleix.mbu.iisc.ernet.in/nucgen/index.htm" } \ No newline at end of file diff --git a/data/nucleardb/nucleardbbioschemas.jsonld b/data/nucleardb/nucleardbbioschemas.jsonld index ad3db81115fe8..87488cf4e841c 100644 --- a/data/nucleardb/nucleardbbioschemas.jsonld +++ b/data/nucleardb/nucleardbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A molecular-class information system that collects, combines, validates and stores large amounts of data on Nuclear Hormone Receptors (NHRs). Contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models.", "sc:name": "NucleaRDB", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.receptors.org/nucleardb/" } \ No newline at end of file diff --git a/data/nucleofinder/nucleofinderbioschemas.jsonld b/data/nucleofinder/nucleofinderbioschemas.jsonld index 32d22bcd7d0d9..74d928192d45f 100644 --- a/data/nucleofinder/nucleofinderbioschemas.jsonld +++ b/data/nucleofinder/nucleofinderbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Addresses both the positional heterogeneity across cells and experimental biases by seeking nucleosomes consistently positioned in a cell population and showing a significant enrichment relative to a control sample.", "sc:name": "NucleoFinder", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://sites.google.com/site/beckerjeremie/home/nucleofinder", "sc:version": "1.0" diff --git a/data/nucleos/nucleosbioschemas.jsonld b/data/nucleos/nucleosbioschemas.jsonld index bd6e0da2c5503..07beaa2005a36 100644 --- a/data/nucleos/nucleosbioschemas.jsonld +++ b/data/nucleos/nucleosbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Nucleos", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ELIXIR-ITA-TORVERGATA", "sc:url": "http://nucleos.bio.uniroma2.it/nucleos", diff --git a/data/nucleosim/nucleosimbioschemas.jsonld b/data/nucleosim/nucleosimbioschemas.jsonld index 18cb97ceed02b..bcebfd86a0557 100644 --- a/data/nucleosim/nucleosimbioschemas.jsonld +++ b/data/nucleosim/nucleosimbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "nucleoSim", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/nucleoSim.html", "sc:version": "1.2.0" diff --git a/data/nucler/nuclerbioschemas.jsonld b/data/nucler/nuclerbioschemas.jsonld index 86fb972facdd1..fe93e99ac72d3 100644 --- a/data/nucler/nuclerbioschemas.jsonld +++ b/data/nucler/nuclerbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ricard Illa", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:21653521", "sc:description": "Nucleosome positioning for Tiling Arrays and NGS experiments.", "sc:license": "GPL-3.0", "sc:name": "nucleR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/nucleR.html", "sc:version": "2.6.0" diff --git a/data/nucleusj/nucleusjbioschemas.jsonld b/data/nucleusj/nucleusjbioschemas.jsonld index 489d27c13102d..b65409dfd03dd 100644 --- a/data/nucleusj/nucleusjbioschemas.jsonld +++ b/data/nucleusj/nucleusjbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D.", "sc:name": "NucleusJ", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start" } \ No newline at end of file diff --git a/data/nucloc/nuclocbioschemas.jsonld b/data/nucloc/nuclocbioschemas.jsonld index e2b089f1359fa..621c9e1745e10 100644 --- a/data/nucloc/nuclocbioschemas.jsonld +++ b/data/nucloc/nuclocbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Set of computational tools designed to analyze gene positioning in yeast nuclei by automated processing of fluorescence microscopy images.", "sc:name": "nucloc", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.nucloc.org/index.html" } \ No newline at end of file diff --git a/data/nucpred/nucpredbioschemas.jsonld b/data/nucpred/nucpredbioschemas.jsonld index aa6368fec53fb..4cdf9f255e566 100644 --- a/data/nucpred/nucpredbioschemas.jsonld +++ b/data/nucpred/nucpredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "NucPred", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "bils.se", diff --git a/data/nucwave/nucwavebioschemas.jsonld b/data/nucwave/nucwavebioschemas.jsonld index 9bed0d4d6401d..3d1af93cabab4 100644 --- a/data/nucwave/nucwavebioschemas.jsonld +++ b/data/nucwave/nucwavebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Bioinformatic tool that generates nucleosome occupation maps.", "sc:name": "NUCwave", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://nucleosome.usal.es/nucwave/" } \ No newline at end of file diff --git a/data/nudge/nudgebioschemas.jsonld b/data/nudge/nudgebioschemas.jsonld index 29dd2c56cfdc8..828e8e31b6568 100644 --- a/data/nudge/nudgebioschemas.jsonld +++ b/data/nudge/nudgebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "N. Dean", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample).", "sc:license": "GPL-2.0", "sc:name": "nudge", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/nudge.html", "sc:version": "1.40.0" diff --git a/data/nullarbor/nullarborbioschemas.jsonld b/data/nullarbor/nullarborbioschemas.jsonld index 0bade7edaf7d3..9d9712d585681 100644 --- a/data/nullarbor/nullarborbioschemas.jsonld +++ b/data/nullarbor/nullarborbioschemas.jsonld @@ -17,11 +17,11 @@ "sc:additionalType": "Command-line tool", "sc:author": "Torsten Seemann", "sc:contributor": [ - "DM Bulach", - "MB Schultz", "BP Howden", + "MB Schultz", "A Goncalves da Silva", - "JC Kwong" + "JC Kwong", + "DM Bulach" ], "sc:description": "Pipeline to generate complete public health microbiology reports from isolates sequenced with Illumina paired-end sequencing.", "sc:license": "GPL-2.0", diff --git a/data/nuparm-plus/nuparm-plusbioschemas.jsonld b/data/nuparm-plus/nuparm-plusbioschemas.jsonld index 597b060c4dde3..8e5bc4b707c05 100644 --- a/data/nuparm-plus/nuparm-plusbioschemas.jsonld +++ b/data/nuparm-plus/nuparm-plusbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Program for analysis of sequence dependent variations in nucleic apdb_id (DNA & RNA) double helices.", "sc:name": "NUPARM-Plus", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://nucleix.mbu.iisc.ernet.in/nuparm/" } \ No newline at end of file diff --git a/data/nupop/nupopbioschemas.jsonld b/data/nupop/nupopbioschemas.jsonld index d056978a570d6..c757bb8733367 100644 --- a/data/nupop/nupopbioschemas.jsonld +++ b/data/nupop/nupopbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ji-Ping Wang", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "R package for Nucleosome Positioning Prediction. This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available.", "sc:license": "GPL-2.0", "sc:name": "NuPoP", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/NuPoP.html", "sc:version": "1.24.0" diff --git a/data/nust/nustbioschemas.jsonld b/data/nust/nustbioschemas.jsonld index 12448d791de75..2eff401b27e0a 100644 --- a/data/nust/nustbioschemas.jsonld +++ b/data/nust/nustbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "NuST is a set of tools and data sets that can be used to analyze the aggregation of a set of genes along the genome coordinate, at different scales of observation.", "sc:name": "NuST", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.lcqb.upmc.fr/nust/" } \ No newline at end of file diff --git a/data/nvt/nvtbioschemas.jsonld b/data/nvt/nvtbioschemas.jsonld index 95e3ce7e93729..becbea1d3d73e 100644 --- a/data/nvt/nvtbioschemas.jsonld +++ b/data/nvt/nvtbioschemas.jsonld @@ -15,8 +15,8 @@ "CUBE-AT" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An R package for the assessment of RNA-Seq normalization methods.", "sc:name": "NVT", diff --git a/data/nwdisplay/nwdisplaybioschemas.jsonld b/data/nwdisplay/nwdisplaybioschemas.jsonld index e916d4cd615fe..89ee57d2a91cb 100644 --- a/data/nwdisplay/nwdisplaybioschemas.jsonld +++ b/data/nwdisplay/nwdisplaybioschemas.jsonld @@ -9,31 +9,31 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1748-7188-3-7", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/nwdisplay", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Galaxy Support Team", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC2464588", "pubmed:18577231", { "@id": "https://doi.org/10.1186/1748-7188-3-7" - }, - "pmcid:PMC2464588" + } ], "sc:description": "Display a phylogenetic tree as SVG.", "sc:name": "nwdisplay", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://cegg.unige.ch/newick_utils", "sc:version": "1.6" + }, + { + "@id": "https://doi.org/10.1186/1748-7188-3-7", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/nxsensor/nxsensorbioschemas.jsonld b/data/nxsensor/nxsensorbioschemas.jsonld index 1ad2d65715e48..f8b895585f8a2 100644 --- a/data/nxsensor/nxsensorbioschemas.jsonld +++ b/data/nxsensor/nxsensorbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "NXSensor", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.sfu.ca/~ibajic/NXSensor/" } \ No newline at end of file diff --git a/data/o-miner/o-minerbioschemas.jsonld b/data/o-miner/o-minerbioschemas.jsonld index ea9fac3b5205c..ed5637b23e060 100644 --- a/data/o-miner/o-minerbioschemas.jsonld +++ b/data/o-miner/o-minerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Webserver that automates the analysis and annotation of complex -omics data. Specifically deals with genomics and transcriptomics data.", "sc:name": "O-miner", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.o-miner.org" } \ No newline at end of file diff --git a/data/oases/oasesbioschemas.jsonld b/data/oases/oasesbioschemas.jsonld index adfd750e6e800..f4597fde712db 100644 --- a/data/oases/oasesbioschemas.jsonld +++ b/data/oases/oasesbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/oases", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Marcel Schulz", - "Daniel Zerbino" + "Daniel Zerbino", + "Marcel Schulz" ], "sc:additionalType": "Workflow", "sc:citation": "pubmed:22368243", @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "Oases", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/dzerbino/oases" } \ No newline at end of file diff --git a/data/oasis/oasisbioschemas.jsonld b/data/oasis/oasisbioschemas.jsonld index 5f0db2790fcc6..bc6bb06565f1a 100644 --- a/data/oasis/oasisbioschemas.jsonld +++ b/data/oasis/oasisbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "It is a web application that allows for the fast and flexible online analysis of small-RNA-seq data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data, and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis generates downloadable interactive web reports for easy visualization, exploration, and analysis of data on a local system.", "sc:name": "Oasis", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://oasis.dzne.de" } \ No newline at end of file diff --git a/data/oat/oatbioschemas.jsonld b/data/oat/oatbioschemas.jsonld index e280a3cc86274..6ef2515a49ff7 100644 --- a/data/oat/oatbioschemas.jsonld +++ b/data/oat/oatbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "OAT", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ezbiocloud.net/sw/oat" } \ No newline at end of file diff --git a/data/obcol/obcolbioschemas.jsonld b/data/obcol/obcolbioschemas.jsonld index 175d481f2cf5f..dcf94f0d5997f 100644 --- a/data/obcol/obcolbioschemas.jsonld +++ b/data/obcol/obcolbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software we designed to perform organelle-based colocalisation analysis from multi-fluorophore microscopy 2D, 3D and 4D cell imaging.", "sc:name": "OBCOL", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://obcol.imb.uq.edu.au/" } \ No newline at end of file diff --git a/data/obitools/obitoolsbioschemas.jsonld b/data/obitools/obitoolsbioschemas.jsonld index 0d5c1cdff03d3..2db27e2ecca8b 100644 --- a/data/obitools/obitoolsbioschemas.jsonld +++ b/data/obitools/obitoolsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "OBITools", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://git.metabarcoding.org/obitools/obitools/wikis/home" } \ No newline at end of file diff --git a/data/occugene/occugenebioschemas.jsonld b/data/occugene/occugenebioschemas.jsonld index 0c0b0f4227443..d827189376677 100644 --- a/data/occugene/occugenebioschemas.jsonld +++ b/data/occugene/occugenebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "occugene", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/occugene.html", "sc:version": "1.34.0" diff --git a/data/occupeak/occupeakbioschemas.jsonld b/data/occupeak/occupeakbioschemas.jsonld index 0ecbd7b268391..2a929d9d63913 100644 --- a/data/occupeak/occupeakbioschemas.jsonld +++ b/data/occupeak/occupeakbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC4061025", - "pubmed:24936875", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0099844" - } + }, + "pubmed:24936875", + "pmcid:PMC4061025" ], "sc:description": "ChIP-Seq Peak Calling Based on Internal Background Modelling.", "sc:featureList": { @@ -27,8 +27,8 @@ }, "sc:name": "OccuPeak", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.hartfaalcentrum.nl/index.php?main=files&fileName=ManualOccuPeak_V2.pdf&description=Occupeak%20manual&sub=ManualOccuPeak_V2" }, diff --git a/data/ocg/ocgbioschemas.jsonld b/data/ocg/ocgbioschemas.jsonld index 45fa6a966ba6c..6c94a7b07c206 100644 --- a/data/ocg/ocgbioschemas.jsonld +++ b/data/ocg/ocgbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Creates an overlapping class system from an unweighted simple graph G = (V,E).OCG is essentially a hierarchical ascending algorithm. By default, it will fuse the initial classes until further fusions do not increase the modularity but other options are available.", "sc:name": "OCG", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://tagc.univ-mrs.fr/tagc/index.php/software/17" } \ No newline at end of file diff --git a/data/ochem/ochembioschemas.jsonld b/data/ochem/ochembioschemas.jsonld index e52467ea46475..381ba6fe973a0 100644 --- a/data/ochem/ochembioschemas.jsonld +++ b/data/ochem/ochembioschemas.jsonld @@ -35,9 +35,9 @@ }, "sc:name": "Online Chemical Modeling Environment", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.ochem.eu", "sc:version": "v.2.4.98" diff --git a/data/ocma/ocmabioschemas.jsonld b/data/ocma/ocmabioschemas.jsonld index 5f96ef6a17297..0af1acb2fa93e 100644 --- a/data/ocma/ocmabioschemas.jsonld +++ b/data/ocma/ocmabioschemas.jsonld @@ -17,16 +17,16 @@ "@id": "https://bio.tools/OCMA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Zhi Xiong", - "Quan Long" + "Quan Long", + "Zhi Xiong" ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6325911", + "pubmed:30482799", { "@id": "https://doi.org/10.1534/g3.118.200908" - }, - "pubmed:30482799", - "pmcid:PMC6325911" + } ], "sc:description": "Out-of-Core Matrices Analyzer (OCMA) uses state-of-the-art computational techniques that can nimbly perform eigen and Singular Value Decomposition (SVD) analyses.", "sc:featureList": { diff --git a/data/ocplus/ocplusbioschemas.jsonld b/data/ocplus/ocplusbioschemas.jsonld index ec3e8bbe418cb..eaf3d78259279 100644 --- a/data/ocplus/ocplusbioschemas.jsonld +++ b/data/ocplus/ocplusbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "OCplus", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OCplus.html", diff --git a/data/ocsana/ocsanabioschemas.jsonld b/data/ocsana/ocsanabioschemas.jsonld index a08a46ba7ca93..3d5ba5020011a 100644 --- a/data/ocsana/ocsanabioschemas.jsonld +++ b/data/ocsana/ocsanabioschemas.jsonld @@ -20,9 +20,9 @@ "sc:description": "OCSANA is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes", "sc:name": "OCSANA", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinfo-out.curie.fr/projects/ocsana/OCSANA.html" }, diff --git a/data/ocsestdb/ocsestdbbioschemas.jsonld b/data/ocsestdb/ocsestdbbioschemas.jsonld index 28e87388c19b5..60a48b137a28f 100644 --- a/data/ocsestdb/ocsestdbbioschemas.jsonld +++ b/data/ocsestdb/ocsestdbbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12870-014-0399-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ocsestdb", "@type": "sc:SoftwareApplication", "sc:additionalType": "Workflow", "sc:citation": [ + "pubmed:25604238", "pmcid:PMC4312456", { "@id": "https://doi.org/10.1186/s12870-014-0399-8" - }, - "pubmed:25604238" + } ], "sc:description": "Developed to provide users a comprehansive seed expression sequence tags database of oil crops for comparative analysis. In ocsEASTdb, it provided ESTs and unigenes detail information of four oil crop species, A.hypogaea, B.napus (high or low oil), G.max, S.indicum.", "sc:featureList": [ @@ -40,10 +36,14 @@ "sc:name": "ocsESTdb", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ocri-genomics.org/ocsESTdb/" + }, + { + "@id": "https://doi.org/10.1186/s12870-014-0399-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/octanol/octanolbioschemas.jsonld b/data/octanol/octanolbioschemas.jsonld index 6c81aa9dd1d8a..b46dd3ac834fc 100644 --- a/data/octanol/octanolbioschemas.jsonld +++ b/data/octanol/octanolbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "EMBOSS Contributors", "UK BBSRC", "Wellcome Trust", - "UK MRC", - "EMBOSS Contributors" + "UK MRC" ], "sc:description": "Draw a White-Wimley protein hydropathy plot.", "sc:funder": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "octanol", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/octopus-toolkit/octopus-toolkitbioschemas.jsonld b/data/octopus-toolkit/octopus-toolkitbioschemas.jsonld index 7da4a7f1b73eb..138b14ea860a6 100644 --- a/data/octopus-toolkit/octopus-toolkitbioschemas.jsonld +++ b/data/octopus-toolkit/octopus-toolkitbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gky083", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/octopus-toolkit", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5961211", - "pubmed:29420797", { "@id": "https://doi.org/10.1093/nar/gky083" - } + }, + "pubmed:29420797", + "pmcid:PMC5961211" ], "sc:description": "Retrieve and process large sets of next-generation sequencing (NGS) data with a single step. Automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, bwtool, Samtools FastQC, Trimmomatic, HISAT2, STAR, and HOMER applications.", "sc:featureList": [ @@ -29,24 +33,20 @@ "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2403" + "@id": "edam:operation_0239" }, { - "@id": "edam:operation_0239" + "@id": "edam:operation_2403" } ], "sc:license": "GPL-3.0", "sc:name": "OCTOPUS-toolkit", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://octopus-toolkit2.readthedocs.io/en/latest/", "sc:version": "2.1.1" - }, - { - "@id": "https://doi.org/10.1093/nar/gky083", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/octopus/octopusbioschemas.jsonld b/data/octopus/octopusbioschemas.jsonld index 748dc8bb74544..8c9d74e5a5181 100644 --- a/data/octopus/octopusbioschemas.jsonld +++ b/data/octopus/octopusbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "OCTOPUS", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "bils.se", "sc:url": "http://octopus.cbr.su.se/", diff --git a/data/odae/odaebioschemas.jsonld b/data/odae/odaebioschemas.jsonld index 5f6dfbd8a1dbd..7180f7dfc169f 100644 --- a/data/odae/odaebioschemas.jsonld +++ b/data/odae/odaebioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2729-1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ODAE", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Oliver He", "sc:additionalType": "Ontology", "sc:citation": [ + "pubmed:31074377", "pmcid:PMC6509876", { "@id": "https://doi.org/10.1186/s12859-019-2729-1" - }, - "pubmed:31074377" + } ], "sc:description": "Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions.", "sc:featureList": [ @@ -40,11 +36,15 @@ "sc:license": "Unlicense", "sc:name": "ODAE", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/ODAE-ontology/ODAE" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2729-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/odam/odambioschemas.jsonld b/data/odam/odambioschemas.jsonld index d61d74bc9c8b4..e1cfddf406621 100644 --- a/data/odam/odambioschemas.jsonld +++ b/data/odam/odambioschemas.jsonld @@ -16,8 +16,8 @@ "@id": "https://orcid.org/0000-0002-6687-7169" }, "sc:additionalType": [ - "Web application", "Desktop application", + "Web application", "Web API" ], "sc:author": { @@ -27,9 +27,9 @@ "sc:license": "GPL-3.0", "sc:name": "ODAM", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://pmb-bordeaux.fr/dataexplorer/", "sc:version": "1.1" diff --git a/data/odb/odbbioschemas.jsonld b/data/odb/odbbioschemas.jsonld index 29f169151a886..ba5cdbeaef87c 100644 --- a/data/odb/odbbioschemas.jsonld +++ b/data/odb/odbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Contains all known and conserved operons in completely sequenced genomes.", "sc:name": "ODB", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://operondb.jp/" diff --git a/data/oddcomp/oddcompbioschemas.jsonld b/data/oddcomp/oddcompbioschemas.jsonld index 410a548211612..3420b4dd5ec88 100644 --- a/data/oddcomp/oddcompbioschemas.jsonld +++ b/data/oddcomp/oddcompbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "Wellcome Trust", + "EMBOSS Contributors", "UK BBSRC", - "EMBOSS Contributors" + "UK MRC", + "Wellcome Trust" ], "sc:description": "Identify proteins with specified sequence word composition.", "sc:funder": [ - "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "oddcomp", diff --git a/data/odseq/odseqbioschemas.jsonld b/data/odseq/odseqbioschemas.jsonld index 50edd89133457..9c75f891db587 100644 --- a/data/odseq/odseqbioschemas.jsonld +++ b/data/odseq/odseqbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "José Jiménez", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Performs outlier detection of sequences in a multiple sequence alignment using bootstrap of predefined distance metrics. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This package implements the OD-seq algorithm for aligned sequences and a variant using string kernels for unaligned sequences.", "sc:license": "MIT", "sc:name": "odseq", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/odseq.html", "sc:version": "1.2.0" diff --git a/data/oefinder/oefinderbioschemas.jsonld b/data/oefinder/oefinderbioschemas.jsonld index 15137d4ff4159..b4e95e8624d43 100644 --- a/data/oefinder/oefinderbioschemas.jsonld +++ b/data/oefinder/oefinderbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/oefinder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Stewart R", - "Leng N" + "Leng N", + "Stewart R" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:26743507", diff --git a/data/off-spotter/off-spotterbioschemas.jsonld b/data/off-spotter/off-spotterbioschemas.jsonld index c877e4a48845b..2e9ec69dc3b7c 100644 --- a/data/off-spotter/off-spotterbioschemas.jsonld +++ b/data/off-spotter/off-spotterbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Off-Spotter", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cm.jefferson.edu/Off-Spotter/" } \ No newline at end of file diff --git a/data/off-target_pipeline/off-target_pipelinebioschemas.jsonld b/data/off-target_pipeline/off-target_pipelinebioschemas.jsonld index e96f9c7d00078..f0338fa4c230f 100644 --- a/data/off-target_pipeline/off-target_pipelinebioschemas.jsonld +++ b/data/off-target_pipeline/off-target_pipelinebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Platform intended to carry out a recently introduced chemical systems biology approach for secondary target identification, but may also be useful to other applications in bioinformatics and drug discovery. Researchers can predict and compare protein functional sites, conduct structure-based docking, compute binding energy and compare electrostatic potential distribution within cavities.", "sc:name": "OFF-TARGET PIPELINE", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sites.google.com/site/offtargetpipeline/home" } \ No newline at end of file diff --git a/data/og/ogbioschemas.jsonld b/data/og/ogbioschemas.jsonld index 63aed25d006d3..9592103eb1ce7 100644 --- a/data/og/ogbioschemas.jsonld +++ b/data/og/ogbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-019-2828-Z", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/OG", "@type": "sc:SoftwareApplication", @@ -29,10 +33,10 @@ "@id": "edam:operation_0555" }, { - "@id": "edam:operation_0544" + "@id": "edam:operation_3478" }, { - "@id": "edam:operation_3478" + "@id": "edam:operation_0544" } ], "sc:license": "GPL-3.0", @@ -43,10 +47,6 @@ ], "sc:url": "https://github.com/meringlab/og_consistency_pipeline" }, - { - "@id": "https://doi.org/10.1186/S12859-019-2828-Z", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0001-7734-9102", "@type": "schema:Person" diff --git a/data/ogdraw/ogdrawbioschemas.jsonld b/data/ogdraw/ogdrawbioschemas.jsonld index 2fbf323d6eebc..dd1931fa13c27 100644 --- a/data/ogdraw/ogdrawbioschemas.jsonld +++ b/data/ogdraw/ogdrawbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool that enables the user to quickly generate high-quality graphical maps of circular DNA sequences. Though especially designed and optimized for the display of small organelle genomes like the chloroplast or mitochondrial genome, it is applicable to all circular DNA sequences. The input data can be provided as GenBank files or GenBank accession numbers.", "sc:name": "OGdraw", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://ogdraw.mpimp-golm.mpg.de/" } \ No newline at end of file diff --git a/data/ogee/ogeebioschemas.jsonld b/data/ogee/ogeebioschemas.jsonld index 2118f0770a558..3d170d67cab78 100644 --- a/data/ogee/ogeebioschemas.jsonld +++ b/data/ogee/ogeebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "OGEE", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://ogeedb.embl.de/" } \ No newline at end of file diff --git a/data/ognm/ognmbioschemas.jsonld b/data/ognm/ognmbioschemas.jsonld index fa9b0389a5668..29e943a467bd6 100644 --- a/data/ognm/ognmbioschemas.jsonld +++ b/data/ognm/ognmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.", "sc:name": "oGNM", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm" } \ No newline at end of file diff --git a/data/ogsa/ogsabioschemas.jsonld b/data/ogsa/ogsabioschemas.jsonld index f7fb4dc311d77..5afa6d493745f 100644 --- a/data/ogsa/ogsabioschemas.jsonld +++ b/data/ogsa/ogsabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "OGSA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OGSA.html", "sc:version": "1.4.0" diff --git a/data/ogtree_2/ogtree_2bioschemas.jsonld b/data/ogtree_2/ogtree_2bioschemas.jsonld index 258dea57d0e10..6f3bf94413cb3 100644 --- a/data/ogtree_2/ogtree_2bioschemas.jsonld +++ b/data/ogtree_2/ogtree_2bioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "OGtree 2", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://genome.cs.nthu.edu.tw/OGtree2.0/" } \ No newline at end of file diff --git a/data/ohana/ohanabioschemas.jsonld b/data/ohana/ohanabioschemas.jsonld index ca788e31f5ab2..144d8072d5567 100644 --- a/data/ohana/ohanabioschemas.jsonld +++ b/data/ohana/ohanabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Fast admixture analysis and population tree estimation for SNP and NGS data.", "sc:name": "Ohana", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/jade-cheng/ohana" } \ No newline at end of file diff --git a/data/oi_gene/oi_genebioschemas.jsonld b/data/oi_gene/oi_genebioschemas.jsonld index 02a98f469aa84..bc0390d0c0979 100644 --- a/data/oi_gene/oi_genebioschemas.jsonld +++ b/data/oi_gene/oi_genebioschemas.jsonld @@ -28,11 +28,11 @@ "@id": "edam:topic_0634" }, "sc:citation": [ - "pmcid:PMC3322236", "pubmed:22482805", { "@id": "https://doi.org/10.1016/j.ajhg.2012.02.026" - } + }, + "pmcid:PMC3322236" ], "sc:description": "All published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP and LEPRE1 genes.", "sc:featureList": { @@ -40,9 +40,9 @@ }, "sc:name": "Osteogenesis imperfecta collagen mutation", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://oi.gene.le.ac.uk" } diff --git a/data/oli2go/oli2gobioschemas.jsonld b/data/oli2go/oli2gobioschemas.jsonld index c5333d7c27bbe..7301c161bec91 100644 --- a/data/oli2go/oli2gobioschemas.jsonld +++ b/data/oli2go/oli2gobioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Automated multiplex oligonucleotide design. Performs primer and different hybridization probe designs as well as specificity and cross dimer checks in a single run.", "sc:name": "Oli2go", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://oli2go.ait.ac.at/" diff --git a/data/oligo-analysis/oligo-analysisbioschemas.jsonld b/data/oligo-analysis/oligo-analysisbioschemas.jsonld index 2033c4b564596..5cc6cfcb6b104 100644 --- a/data/oligo-analysis/oligo-analysisbioschemas.jsonld +++ b/data/oligo-analysis/oligo-analysisbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-8799-8584", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/oligo-analysis", "@type": "sc:SoftwareApplication", @@ -29,12 +25,16 @@ "sc:license": "AFL-3.0", "sc:name": "RSAT oligo-analysis", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "RSAT", "sc:url": "http://teaching.rsat.eu/oligo-analysis_form.cgi", "sc:version": "1" + }, + { + "@id": "https://orcid.org/0000-0002-8799-8584", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/oligo/oligobioschemas.jsonld b/data/oligo/oligobioschemas.jsonld index 5e6dedd6c4d92..992a1e3a040e5 100644 --- a/data/oligo/oligobioschemas.jsonld +++ b/data/oligo/oligobioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btq431", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/oligo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Benilton Carvalho", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:20688976", - "pmcid:PMC2944196", { "@id": "https://doi.org/10.1093/bioinformatics/btq431" - } + }, + "pmcid:PMC2944196", + "pubmed:20688976" ], "sc:description": "A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).", "sc:featureList": { @@ -37,10 +41,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/oligo.html", "sc:version": "1.38.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btq431", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/oligocalc/oligocalcbioschemas.jsonld b/data/oligocalc/oligocalcbioschemas.jsonld index 237743003ecb7..553e1a81142fe 100644 --- a/data/oligocalc/oligocalcbioschemas.jsonld +++ b/data/oligocalc/oligocalcbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5’ and 3’ chemical modifications and predict potential hairpin loop formation.", "sc:name": "OligoCalc", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.basic.northwestern.edu/biotools/OligoCalc.html" } \ No newline at end of file diff --git a/data/oligoclasses/bioconda_oligoclasses.yaml b/data/oligoclasses/bioconda_oligoclasses.yaml index a797f95fb83d3..d56a35ccb5987 100644 --- a/data/oligoclasses/bioconda_oligoclasses.yaml +++ b/data/oligoclasses/bioconda_oligoclasses.yaml @@ -4,7 +4,6 @@ description: This package contains class definitions, validity checks, and initi home: https://bioconductor.org/packages/3.10/bioc/html/oligoClasses.html identifiers: - biotools:oligoclasses -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-oligoclasses diff --git a/data/oligoheatmap/oligoheatmapbioschemas.jsonld b/data/oligoheatmap/oligoheatmapbioschemas.jsonld index c4c4107c68603..0d17b5975f10d 100644 --- a/data/oligoheatmap/oligoheatmapbioschemas.jsonld +++ b/data/oligoheatmap/oligoheatmapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "OligoHeatMap", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.bioinfomed.fr/__Tools/ohm/" } \ No newline at end of file diff --git a/data/oligowiz/oligowizbioschemas.jsonld b/data/oligowiz/oligowizbioschemas.jsonld index 2df96f6457083..51207f9a496b0 100644 --- a/data/oligowiz/oligowizbioschemas.jsonld +++ b/data/oligowiz/oligowizbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Henrik Bjorn Nielsen", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Intelligent design of oligonucleotides for DNA microarrays.", "sc:license": "Other", diff --git a/data/olin/olinbioschemas.jsonld b/data/olin/olinbioschemas.jsonld index 5f8fc9f2158a1..d80902aade078 100644 --- a/data/olin/olinbioschemas.jsonld +++ b/data/olin/olinbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-6245-8071", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/olin", "@type": "sc:SoftwareApplication", @@ -20,20 +16,24 @@ "@id": "http://orcid.org/0000-0002-6245-8071" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:15585527", "sc:description": "Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data.", "sc:license": "GPL-2.0", "sc:name": "OLIN", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OLIN.html", "sc:version": "1.52.0" + }, + { + "@id": "http://orcid.org/0000-0002-6245-8071", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/olingui/olinguibioschemas.jsonld b/data/olingui/olinguibioschemas.jsonld index 22fdde6353eb6..4f2968a6fcfff 100644 --- a/data/olingui/olinguibioschemas.jsonld +++ b/data/olingui/olinguibioschemas.jsonld @@ -25,8 +25,8 @@ "sc:name": "OLINgui", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OLINgui.html", "sc:version": "1.48.0" diff --git a/data/ols-dialog/ols-dialogbioschemas.jsonld b/data/ols-dialog/ols-dialogbioschemas.jsonld index 803b91a8da32f..f28c8a7136f11 100644 --- a/data/ols-dialog/ols-dialogbioschemas.jsonld +++ b/data/ols-dialog/ols-dialogbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Java front end to the ontology lookup service (OLS).", "sc:name": "Ols-dialog", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://compomics.github.io/projects/ols-dialog.html", diff --git a/data/ols_dialog/ols_dialogbioschemas.jsonld b/data/ols_dialog/ols_dialogbioschemas.jsonld index 468556af439a2..263d5f497afaf 100644 --- a/data/ols_dialog/ols_dialogbioschemas.jsonld +++ b/data/ols_dialog/ols_dialogbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Java front end to the Ontology Lookup Service allowing easy access to an extensive list of biomedical ontologies.", "sc:name": "OLS Dialog", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://code.google.com/p/ols-dialog/" } \ No newline at end of file diff --git a/data/olympus/olympusbioschemas.jsonld b/data/olympus/olympusbioschemas.jsonld index 2de68741b73b9..0ecb991f62003 100644 --- a/data/olympus/olympusbioschemas.jsonld +++ b/data/olympus/olympusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Automated hybrid clustering method in the field of time series gene expression analysis.", "sc:name": "OLYMPUS", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://biosignal.med.upatras.gr/wordpress/?page_id=173" } \ No newline at end of file diff --git a/data/oma/omabioschemas.jsonld b/data/oma/omabioschemas.jsonld index 2331c9de142a0..84d82dacc4dec 100644 --- a/data/oma/omabioschemas.jsonld +++ b/data/oma/omabioschemas.jsonld @@ -9,28 +9,32 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gku1158", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/oma", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christophe Dessimoz", "edam:has_input": [ - { - "@id": "edam:data_2974" - }, { "@id": "edam:data_3671" }, { - "@id": "edam:data_3021" + "@id": "edam:data_2974" }, { "@id": "edam:data_0842" + }, + { + "@id": "edam:data_3021" } ], "sc:additionalType": [ + "Desktop application", "Database portal", - "Web application", - "Desktop application" + "Web application" ], "sc:citation": [ "pmcid:PMC4383958", @@ -51,10 +55,6 @@ ], "sc:provider": "SIB", "sc:url": "http://omabrowser.org/oma/home/" - }, - { - "@id": "https://doi.org/10.1093/nar/gku1158", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/omadb/omadbbioschemas.jsonld b/data/omadb/omadbbioschemas.jsonld index 95e1d44dce8cc..f6a1043ccc1c2 100644 --- a/data/omadb/omadbbioschemas.jsonld +++ b/data/omadb/omadbbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "OmaDB", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OmaDB.html", "sc:version": "1.0.1" diff --git a/data/omblast/omblastbioschemas.jsonld b/data/omblast/omblastbioschemas.jsonld index 8c47d27afed22..2fd47ff76a49f 100644 --- a/data/omblast/omblastbioschemas.jsonld +++ b/data/omblast/omblastbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/OMBlast", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kevin Y. Yip", - "Ting-Fung Chan" + "Ting-Fung Chan", + "Kevin Y. Yip" ], "sc:additionalType": "Command-line tool", "sc:description": "Alignment tool for optical mapping using a seed-and-extend approach.", "sc:license": "GPL-3.0", "sc:name": "OMBlast", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/TF-Chan-Lab/OMBlast" } \ No newline at end of file diff --git a/data/omero/omerobioschemas.jsonld b/data/omero/omerobioschemas.jsonld index 4b13ebb9af4a0..37ae73d137015 100644 --- a/data/omero/omerobioschemas.jsonld +++ b/data/omero/omerobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Client-server Java software for visualisation, management and analysis of biological microscope images.", "sc:name": "OMERO", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.openmicroscopy.org/omero/" } \ No newline at end of file diff --git a/data/ometa/ometabioschemas.jsonld b/data/ometa/ometabioschemas.jsonld index a22402296d376..20d095cd30062 100644 --- a/data/ometa/ometabioschemas.jsonld +++ b/data/ometa/ometabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "OMeta", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/JCVenterInstitute/OMeta-Public" } \ No newline at end of file diff --git a/data/omia/omiabioschemas.jsonld b/data/omia/omiabioschemas.jsonld index b6f5ced9850f4..9b8a7307922a6 100644 --- a/data/omia/omiabioschemas.jsonld +++ b/data/omia/omiabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-9178-3965", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/omia", "@type": "sc:SoftwareApplication", @@ -21,11 +17,11 @@ }, "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:16381939", "pmcid:PMC1347514", { "@id": "https://doi.org/10.1093/nar/gkj152" - }, - "pubmed:16381939" + } ], "sc:description": "A catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 233 animal species (other than human and mouse and rats, which have their own resources).", "sc:featureList": { @@ -34,15 +30,19 @@ "sc:license": "Not licensed", "sc:name": "OMIA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://omia.angis.org.au/home/" }, { "@id": "https://doi.org/10.1093/nar/gkj152", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-9178-3965", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/omicabel/omicabelbioschemas.jsonld b/data/omicabel/omicabelbioschemas.jsonld index 1a5b0936fe9ab..3d2da3642daaa 100644 --- a/data/omicabel/omicabelbioschemas.jsonld +++ b/data/omicabel/omicabelbioschemas.jsonld @@ -23,10 +23,10 @@ "sc:description": "It allows rapid mixed-model based genome-wide association analysis; it efficiently handles large datasets, and both single trait and multiple trait (\"omics\") analysis.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_3557" }, { - "@id": "edam:operation_3557" + "@id": "edam:operation_3196" } ], "sc:license": "GPL-3.0", diff --git a/data/omicade4/omicade4bioschemas.jsonld b/data/omicade4/omicade4bioschemas.jsonld index a75183e6e217f..6e8f15dba218a 100644 --- a/data/omicade4/omicade4bioschemas.jsonld +++ b/data/omicade4/omicade4bioschemas.jsonld @@ -25,35 +25,35 @@ } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0203" + "@id": "edam:topic_3303" }, { - "@id": "edam:topic_3391" + "@id": "edam:topic_0203" }, { - "@id": "edam:topic_2229" + "@id": "edam:topic_0091" }, { - "@id": "edam:topic_0091" + "@id": "edam:topic_2229" }, { - "@id": "edam:topic_3303" + "@id": "edam:topic_3391" }, { "@id": "edam:topic_3518" } ], "sc:citation": [ + "pubmed:24884486", + "pmcid:PMC4053266", { "@id": "https://doi.org/10.1186/1471-2105-15-162" - }, - "pmcid:PMC4053266", - "pubmed:24884486" + } ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-1395-9734" @@ -75,13 +75,13 @@ "sc:url": "http://bioconductor.org/packages/release/bioc/html/omicade4.html", "sc:version": "1.14.0" }, - { - "@id": "https://doi.org/10.1186/1471-2105-15-162", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-1395-9734", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-15-162", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/omicbrowse/omicbrowsebioschemas.jsonld b/data/omicbrowse/omicbrowsebioschemas.jsonld index 00496055d5a2c..123ac51bf32d7 100644 --- a/data/omicbrowse/omicbrowsebioschemas.jsonld +++ b/data/omicbrowse/omicbrowsebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. Multiple users may access a common dataset.", "sc:name": "OmicBrowse", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://sourceforge.net/projects/omicbrowse/" } \ No newline at end of file diff --git a/data/omiccircos/omiccircosbioschemas.jsonld b/data/omiccircos/omiccircosbioschemas.jsonld index c485a713ac592..737e0a1360e96 100644 --- a/data/omiccircos/omiccircosbioschemas.jsonld +++ b/data/omiccircos/omiccircosbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "OmicCircos", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OmicCircos.html", "sc:version": "1.12.0" diff --git a/data/omicplotr/omicplotrbioschemas.jsonld b/data/omicplotr/omicplotrbioschemas.jsonld index 520f6a1d51ac9..d4806387339c6 100644 --- a/data/omicplotr/omicplotrbioschemas.jsonld +++ b/data/omicplotr/omicplotrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "omicplotR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/omicplotR.html", "sc:version": "1.0.1" diff --git a/data/omicrexposome/omicrexposomebioschemas.jsonld b/data/omicrexposome/omicrexposomebioschemas.jsonld index ea74d1242dbe2..b12008d0ad46d 100644 --- a/data/omicrexposome/omicrexposomebioschemas.jsonld +++ b/data/omicrexposome/omicrexposomebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "omicRexposome", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/omicRexposome.html", diff --git a/data/omics_pipe/omics_pipebioschemas.jsonld b/data/omics_pipe/omics_pipebioschemas.jsonld index a328cb561ca18..fa15500101522 100644 --- a/data/omics_pipe/omics_pipebioschemas.jsonld +++ b/data/omics_pipe/omics_pipebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Open-source, modular computational platform that automates best practice multi-omics data analysis pipelines published in Nature Protocols and other commonly used pipelines, such as GATK.", "sc:name": "Omics Pipe", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://sulab.org/tools/omics-pipe/" } \ No newline at end of file diff --git a/data/omicsdi/omicsdibioschemas.jsonld b/data/omicsdi/omicsdibioschemas.jsonld index c0d1ee1752820..d9d5fe32cafdd 100644 --- a/data/omicsdi/omicsdibioschemas.jsonld +++ b/data/omicsdi/omicsdibioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/omicsdi", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web API", - "Database portal" + "Database portal", + "Web API" ], "sc:description": "Provides dataset discovery across a heterogeneous, distributed group of Transcriptomics, Genomics, Proteomics and Metabolomics data resources.", "sc:license": "Apache-2.0", diff --git a/data/omicsmarker/omicsmarkerbioschemas.jsonld b/data/omicsmarker/omicsmarkerbioschemas.jsonld index 539f01ca0495b..d2ffea94d816d 100644 --- a/data/omicsmarker/omicsmarkerbioschemas.jsonld +++ b/data/omicsmarker/omicsmarkerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "OmicsMarkeR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OmicsMarkeR.html", "sc:version": "1.6.0" diff --git a/data/omicsnet/omicsnetbioschemas.jsonld b/data/omicsnet/omicsnetbioschemas.jsonld index 9b35d818dafa9..5f1366af61844 100644 --- a/data/omicsnet/omicsnetbioschemas.jsonld +++ b/data/omicsnet/omicsnetbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Network visual analytics system for creating and exploring relationships among genes, proteins, miRNAs, metabolites or transcription factors in three-dimensional (3D) space.", "sc:name": "OmicsNet", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.omicsnet.ca/OmicsNet/" diff --git a/data/omicsprint/omicsprintbioschemas.jsonld b/data/omicsprint/omicsprintbioschemas.jsonld index 882af1d62e721..b60101d2bcf31 100644 --- a/data/omicsprint/omicsprintbioschemas.jsonld +++ b/data/omicsprint/omicsprintbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "omicsPrint", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/omicsPrint.html", "sc:version": "1.0.0" diff --git a/data/omim/omimbioschemas.jsonld b/data/omim/omimbioschemas.jsonld index 254394b919279..035b50a2bfdf8 100644 --- a/data/omim/omimbioschemas.jsonld +++ b/data/omim/omimbioschemas.jsonld @@ -14,41 +14,41 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ada Hamosh", "sc:additionalType": [ + "Database portal", "Web application", - "Web API", - "Database portal" + "Web API" ], "sc:citation": [ + "pmcid:PMC539987", + "pubmed:15608251", { "@id": "https://doi.org/10.1093/nar/gki033" - }, - "pmcid:PMC539987", - "pubmed:15608251" + } ], "sc:description": "Online Mendelian inheritance in Man (OMIM) - catalog of human genes and genetic disorders with descriptive text, references, and links to many NCBI resources including GenBank and PubMed.", "sc:featureList": [ { - "@id": "edam:operation_0224" - }, - { - "@id": "edam:operation_3436" + "@id": "edam:operation_3763" }, { "@id": "edam:operation_0282" }, { - "@id": "edam:operation_3763" + "@id": "edam:operation_0224" }, { "@id": "edam:operation_3197" + }, + { + "@id": "edam:operation_3436" } ], "sc:license": "Unlicense", "sc:name": "OMIM", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM" }, diff --git a/data/omim_explorer/omim_explorerbioschemas.jsonld b/data/omim_explorer/omim_explorerbioschemas.jsonld index a897ea5490c54..a37abe6ead941 100644 --- a/data/omim_explorer/omim_explorerbioschemas.jsonld +++ b/data/omim_explorer/omim_explorerbioschemas.jsonld @@ -31,24 +31,24 @@ "@id": "edam:operation_3778" }, { - "@id": "edam:operation_3096" + "@id": "edam:operation_3083" }, { - "@id": "edam:operation_3083" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_3226" + "@id": "edam:operation_3096" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_3226" } ], "sc:license": "Other", "sc:name": "OMIM explorer", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.omimexplorer.com/" } diff --git a/data/omiras/omirasbioschemas.jsonld b/data/omiras/omirasbioschemas.jsonld index 9dd6b18abb50c..c6c953f5a976d 100644 --- a/data/omiras/omirasbioschemas.jsonld +++ b/data/omiras/omirasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.", "sc:name": "omiRas", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://tools.genxpro.net/omiras/" } \ No newline at end of file diff --git a/data/omnibiomarker/omnibiomarkerbioschemas.jsonld b/data/omnibiomarker/omnibiomarkerbioschemas.jsonld index 77461b6d62c07..57da3e83dde2d 100644 --- a/data/omnibiomarker/omnibiomarkerbioschemas.jsonld +++ b/data/omnibiomarker/omnibiomarkerbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/omnibiomarker", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "May D. Wang", - "John H. Phan" + "John H. Phan", + "May D. Wang" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:22893372", "sc:description": "Web-based bioinformatics application that addresses the microarray “curse of dimensionality” problem as well as the software standards problem.", "sc:name": "omniBiomarker", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://omnibiomarker.bme.gatech.edu/" } \ No newline at end of file diff --git a/data/omnipath/omnipathbioschemas.jsonld b/data/omnipath/omnipathbioschemas.jsonld index 00c5a22dd27e2..d96e79fca8a0a 100644 --- a/data/omnipath/omnipathbioschemas.jsonld +++ b/data/omnipath/omnipathbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A comprehensive integrated resource of signaling pathways in activity flow representation, enzyme-substrate interactions in protein post-translational modifications, protein complexes, protein annotations and protein roles in inter-cellular signaling.", "sc:name": "OmniPath", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://omnipathdb.org/" } \ No newline at end of file diff --git a/data/omokage_search/omokage_searchbioschemas.jsonld b/data/omokage_search/omokage_searchbioschemas.jsonld index fb826d8127468..c9d2239386b35 100644 --- a/data/omokage_search/omokage_searchbioschemas.jsonld +++ b/data/omokage_search/omokage_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A shape similarity search service for 3D structures of macromolecules. By comparing global shapes, and ignoring details, similar-shaped structures are searched.", "sc:name": "Omokage search", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://pdbj.org/emnavi/omo-search.php" } \ No newline at end of file diff --git a/data/ompdb/ompdbbioschemas.jsonld b/data/ompdb/ompdbbioschemas.jsonld index e8002ed7cbee7..e26a9c55d12fc 100644 --- a/data/ompdb/ompdbbioschemas.jsonld +++ b/data/ompdb/ompdbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "OMPdb", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.ompdb.org/", "sc:version": "1.3" diff --git a/data/omssa_parser/omssa_parserbioschemas.jsonld b/data/omssa_parser/omssa_parserbioschemas.jsonld index fd36c4b33334f..f4dbcb6b5f1d5 100644 --- a/data/omssa_parser/omssa_parserbioschemas.jsonld +++ b/data/omssa_parser/omssa_parserbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/omssa_parser", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "Java based parser for OMSSA (Open Mass Spectrometry Search Algorithm) omx files.", "sc:name": "OMSSA Parser", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://compomics.github.io/projects/omssa-parser.html", diff --git a/data/omssagui/omssaguibioschemas.jsonld b/data/omssagui/omssaguibioschemas.jsonld index 5982897300f27..1d818a454be10 100644 --- a/data/omssagui/omssaguibioschemas.jsonld +++ b/data/omssagui/omssaguibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Apache-2.0", "sc:name": "OMSSAGUI", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://bitbucket.org/lp-csic-uab/omssagui" } \ No newline at end of file diff --git a/data/omtools/omtoolsbioschemas.jsonld b/data/omtools/omtoolsbioschemas.jsonld index 32a8c4154dea5..3cb57278aa84f 100644 --- a/data/omtools/omtoolsbioschemas.jsonld +++ b/data/omtools/omtoolsbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/omtools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ting-Fung Chan", - "Kevin Y. Yip" + "Kevin Y. Yip", + "Ting-Fung Chan" ], "sc:additionalType": "Command-line tool", "sc:description": "Visualizing and processing optical mapping data.", "sc:name": "OMTools", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/TF-Chan-Lab/OMTools" } \ No newline at end of file diff --git a/data/omwsa/omwsabioschemas.jsonld b/data/omwsa/omwsabioschemas.jsonld index 6d647203a3cdb..a91c8eee97288 100644 --- a/data/omwsa/omwsabioschemas.jsonld +++ b/data/omwsa/omwsabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "OMWSA (optimized moving window spectral analysis) is a new method and a visualization tool for detecting DNA repeats in a 2D plane of location and frequency by using optimized moving window spectral analysis.", "sc:name": "OMWSA", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.hy8.com/bioinformatics.htm" } \ No newline at end of file diff --git a/data/oncocnv/oncocnvbioschemas.jsonld b/data/oncocnv/oncocnvbioschemas.jsonld index 52465bff46924..d86a7dc3f1dc1 100644 --- a/data/oncocnv/oncocnvbioschemas.jsonld +++ b/data/oncocnv/oncocnvbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Package to detect copy number changes in Deep Sequencing data developed by OncoDNA.", "sc:name": "ONCOCNV", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://oncocnv.curie.fr/" } \ No newline at end of file diff --git a/data/oncodrivefm/oncodrivefmbioschemas.jsonld b/data/oncodrivefm/oncodrivefmbioschemas.jsonld index 3423e7da97143..0feffbccf1bcc 100644 --- a/data/oncodrivefm/oncodrivefmbioschemas.jsonld +++ b/data/oncodrivefm/oncodrivefmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Detects candidate cancer driver genes and pathways from catalogs of somatic mutations in a cohort of tumors by computing the bias towards the accumulation of functional mutations (FM bias).", "sc:name": "OncodriveFM", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bg.upf.edu/group/projects/oncodrive-fm.php" } \ No newline at end of file diff --git a/data/oncomix/oncomixbioschemas.jsonld b/data/oncomix/oncomixbioschemas.jsonld index 47aebf69fa6ef..4f2a99188707e 100644 --- a/data/oncomix/oncomixbioschemas.jsonld +++ b/data/oncomix/oncomixbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "oncomix", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/oncomix.html", diff --git a/data/oncoscore/oncoscorebioschemas.jsonld b/data/oncoscore/oncoscorebioschemas.jsonld index 7f54cced724ae..e17a5c39f9695 100644 --- a/data/oncoscore/oncoscorebioschemas.jsonld +++ b/data/oncoscore/oncoscorebioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Daniele Ramazzotti", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.", "sc:license": "GPL-3.0", diff --git a/data/oncosimulr/oncosimulrbioschemas.jsonld b/data/oncosimulr/oncosimulrbioschemas.jsonld index d3f4cd1bba388..36669a4fdad5e 100644 --- a/data/oncosimulr/oncosimulrbioschemas.jsonld +++ b/data/oncosimulr/oncosimulrbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-015-0466-7", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/oncosimulr", "@type": "sc:SoftwareApplication", @@ -31,23 +27,23 @@ } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ - { - "@id": "edam:topic_3056" - }, { "@id": "edam:topic_2640" }, { "@id": "edam:topic_3524" + }, + { + "@id": "edam:topic_3056" } ], "sc:citation": [ - "pubmed:25879190", "pmcid:PMC4339747", + "pubmed:25879190", { "@id": "https://doi.org/10.1186/s12859-015-0466-7" } @@ -59,9 +55,9 @@ "sc:license": "GPL-3.0", "sc:name": "OncoSimulR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OncoSimulR.html", "sc:version": "2.4.0" @@ -69,6 +65,10 @@ { "@id": "http://orcid.org/0000-0002-6637-9039", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/s12859-015-0466-7", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/oncotator/oncotatorbioschemas.jsonld b/data/oncotator/oncotatorbioschemas.jsonld index 3e9b6a5b31cb0..5777ff17fe30f 100644 --- a/data/oncotator/oncotatorbioschemas.jsonld +++ b/data/oncotator/oncotatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web application to annotate point mutations and indels with functional data relevant to cancer researchers. Annotations include gene names, functional consequence (e.g. Missense), PolyPhen-2 predictions, and cancer-specific annotations from resources such as COSMIC, Tumorscape, and published MutSig results.", "sc:name": "Oncotator", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.broadinstitute.org/oncotator/" } \ No newline at end of file diff --git a/data/ond-crf/ond-crfbioschemas.jsonld b/data/ond-crf/ond-crfbioschemas.jsonld index 3b6d2e7af2915..70cb377939c16 100644 --- a/data/ond-crf/ond-crfbioschemas.jsonld +++ b/data/ond-crf/ond-crfbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Predicting order and disorder in proteins using conditional random fields.", "sc:name": "OnD-CRF", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "bils.se", "sc:url": "http://babel.ucmp.umu.se/ond-crf/", diff --git a/data/one_to_three/one_to_threebioschemas.jsonld b/data/one_to_three/one_to_threebioschemas.jsonld index 358b2e2df702f..6f7067e94c68b 100644 --- a/data/one_to_three/one_to_threebioschemas.jsonld +++ b/data/one_to_three/one_to_threebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "One to Three converts single letter translations to three letter translations.", "sc:name": "One to Three", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinformatics.org/sms2/one_to_three.html" } \ No newline at end of file diff --git a/data/onesense/onesensebioschemas.jsonld b/data/onesense/onesensebioschemas.jsonld index d32081bc317ee..5054603b4b87d 100644 --- a/data/onesense/onesensebioschemas.jsonld +++ b/data/onesense/onesensebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "oneSENSE", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/oneSENSE.html", "sc:version": "1.2.0" diff --git a/data/online_sbml_validator/online_sbml_validatorbioschemas.jsonld b/data/online_sbml_validator/online_sbml_validatorbioschemas.jsonld index 3aa541e7ebed4..c83c6cb8070c8 100644 --- a/data/online_sbml_validator/online_sbml_validatorbioschemas.jsonld +++ b/data/online_sbml_validator/online_sbml_validatorbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Check the syntax and internal consistency of files in SBML (The Systems Biology Markup Language) format.", "sc:name": "Online SBML Validator", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://sbml.org/Facilities/Documentation/Validator_Web_API", diff --git a/data/onlinefdr/onlinefdrbioschemas.jsonld b/data/onlinefdr/onlinefdrbioschemas.jsonld index bfea93fb748ba..15b99c86d3865 100644 --- a/data/onlinefdr/onlinefdrbioschemas.jsonld +++ b/data/onlinefdr/onlinefdrbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "onlineFDR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://bioconductor.org/packages/devel/bioc/html/onlineFDR.html", "sc:version": "1.3.0" diff --git a/data/onto-tools/onto-toolsbioschemas.jsonld b/data/onto-tools/onto-toolsbioschemas.jsonld index 11ed469c66ee8..581d0702066b5 100644 --- a/data/onto-tools/onto-toolsbioschemas.jsonld +++ b/data/onto-tools/onto-toolsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Onto-Tools", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://vortex.cs.wayne.edu/Projects.html" } \ No newline at end of file diff --git a/data/ontobrowser/ontobrowserbioschemas.jsonld b/data/ontobrowser/ontobrowserbioschemas.jsonld index 4081e393fd1e1..7e92bb36dbcfa 100644 --- a/data/ontobrowser/ontobrowserbioschemas.jsonld +++ b/data/ontobrowser/ontobrowserbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Philippe MARC", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:author": "Carlo Ravagli", "sc:contributor": [ - "Innovative Medicines Initiative Joint Undertaking under grant agreement n° 115002", + "Philippe Marc", "Francois Pognan", - "Philippe Marc" + "Innovative Medicines Initiative Joint Undertaking under grant agreement n° 115002" ], "sc:description": "The tool was developed to manage ontologies (and controlled terminologies e.g. CDISC SEND). The primary goal of the tool is to provide an online collaborative solution for expert curators to map code list terms (sourced from multiple systems/databases) to preferred ontology terms. Other key features include visualisation of ontologies in hierarchical/graph format, advanced search capabilities, peer review/approval workflow and web service access to data.", "sc:funder": "Innovative Medicines Initiative Joint Undertaking under grant agreement n° 115002", "sc:license": "Apache-2.0", "sc:name": "OntoBrowser", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "free.fr", diff --git a/data/ontocat/ontocatbioschemas.jsonld b/data/ontocat/ontocatbioschemas.jsonld index 85ff9ce0b35fa..4fe1ba05ae546 100644 --- a/data/ontocat/ontocatbioschemas.jsonld +++ b/data/ontocat/ontocatbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Natalja Kurbatova", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides a simple interface to ontologies described in widely used standard formats, stored locally in the filesystem or accessible online.", "sc:license": "Apache-2.0", "sc:name": "ontoCAT", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ontoCAT.html", "sc:version": "1.26.0" diff --git a/data/ontocount/ontocountbioschemas.jsonld b/data/ontocount/ontocountbioschemas.jsonld index 19a5f802718a4..6e05d5cbc9d1e 100644 --- a/data/ontocount/ontocountbioschemas.jsonld +++ b/data/ontocount/ontocountbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK BBSRC", + "Wellcome Trust", "EMBOSS Contributors", "UK MRC" ], @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "ontocount", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/ontoget/ontogetbioschemas.jsonld b/data/ontoget/ontogetbioschemas.jsonld index 4aa4679f21d01..4860a54855065 100644 --- a/data/ontoget/ontogetbioschemas.jsonld +++ b/data/ontoget/ontogetbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "UK MRC", + "Wellcome Trust", "EMBOSS Contributors", - "Wellcome Trust" + "UK BBSRC", + "UK MRC" ], "sc:description": "Get ontology term(s).", "sc:funder": [ - "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "ontoget", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/ontogetcommon/ontogetcommonbioschemas.jsonld b/data/ontogetcommon/ontogetcommonbioschemas.jsonld index 777e6d45fbfab..bf98553f750da 100644 --- a/data/ontogetcommon/ontogetcommonbioschemas.jsonld +++ b/data/ontogetcommon/ontogetcommonbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "UK MRC", + "Wellcome Trust", "EMBOSS Contributors", - "Wellcome Trust" + "UK BBSRC", + "UK MRC" ], "sc:description": "Get common ancestor for terms.", "sc:funder": [ @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "ontogetcommon", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/ontogetcommon.html", "sc:version": "r6" diff --git a/data/ontogetdown/ontogetdownbioschemas.jsonld b/data/ontogetdown/ontogetdownbioschemas.jsonld index 22d24e7a9f763..141ab144a482d 100644 --- a/data/ontogetdown/ontogetdownbioschemas.jsonld +++ b/data/ontogetdown/ontogetdownbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "Wellcome Trust", + "EMBOSS Contributors", "UK BBSRC", - "EMBOSS Contributors" + "UK MRC" ], "sc:description": "Get ontology term(s) by parent id.", "sc:funder": [ - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "ontogetdown", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/ontogetobsolete/ontogetobsoletebioschemas.jsonld b/data/ontogetobsolete/ontogetobsoletebioschemas.jsonld index be4b2826161a5..836d7465e2bc6 100644 --- a/data/ontogetobsolete/ontogetobsoletebioschemas.jsonld +++ b/data/ontogetobsolete/ontogetobsoletebioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "EMBOSS Contributors", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Get ontology ontology terms.", "sc:funder": [ - "UK MRC", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "ontogetobsolete", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/ontogetroot/ontogetrootbioschemas.jsonld b/data/ontogetroot/ontogetrootbioschemas.jsonld index 68f421c51c85f..03f5bb1277e64 100644 --- a/data/ontogetroot/ontogetrootbioschemas.jsonld +++ b/data/ontogetroot/ontogetrootbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", + "EMBOSS Contributors", "UK BBSRC", - "UK MRC", - "EMBOSS Contributors" + "Wellcome Trust", + "UK MRC" ], "sc:description": "Get ontology root terms by child identifier.", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "ontogetroot", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/ontogetsibs/ontogetsibsbioschemas.jsonld b/data/ontogetsibs/ontogetsibsbioschemas.jsonld index 1977da2f5a1d2..57760911a1f01 100644 --- a/data/ontogetsibs/ontogetsibsbioschemas.jsonld +++ b/data/ontogetsibs/ontogetsibsbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK BBSRC", "EMBOSS Contributors", + "UK BBSRC", + "Wellcome Trust", "UK MRC" ], "sc:description": "Get ontology term(s) by id with common parent.", "sc:funder": [ - "UK BBSRC", "UK MRC", + "UK BBSRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "ontogetsibs", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ diff --git a/data/ontogetup/ontogetupbioschemas.jsonld b/data/ontogetup/ontogetupbioschemas.jsonld index 8020b1288268a..382685959e5fe 100644 --- a/data/ontogetup/ontogetupbioschemas.jsonld +++ b/data/ontogetup/ontogetupbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", "EMBOSS Contributors", - "Wellcome Trust" + "UK BBSRC", + "Wellcome Trust", + "UK MRC" ], "sc:description": "Get ontology term(s) by id of child.", "sc:funder": [ - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "ontogetup", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/ontogetup.html", "sc:version": "r6" diff --git a/data/ontoisobsolete/ontoisobsoletebioschemas.jsonld b/data/ontoisobsolete/ontoisobsoletebioschemas.jsonld index 4d87cc0f8de07..74b619f0cdbee 100644 --- a/data/ontoisobsolete/ontoisobsoletebioschemas.jsonld +++ b/data/ontoisobsolete/ontoisobsoletebioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK MRC", "UK BBSRC", + "Wellcome Trust", "EMBOSS Contributors" ], "sc:description": "Report whether an ontology term id is obsolete.", "sc:funder": [ "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "ontoisobsolete", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/ontoisobsolete.html", "sc:version": "r6" diff --git a/data/ontologizer/ontologizerbioschemas.jsonld b/data/ontologizer/ontologizerbioschemas.jsonld index d098d03297821..98eb414e45372 100644 --- a/data/ontologizer/ontologizerbioschemas.jsonld +++ b/data/ontologizer/ontologizerbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/ontologizer", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", "Command-line tool", + "Web application", "Desktop application" ], "sc:description": "A Tool for Statistical Analysis and Visualization of High-Throughput Biological Data Using Gene Ontology.", "sc:name": "Ontologizer", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://ontologizer.de/" } \ No newline at end of file diff --git a/data/ontoproc/ontoprocbioschemas.jsonld b/data/ontoproc/ontoprocbioschemas.jsonld index daae99d13b50a..9506941c2102d 100644 --- a/data/ontoproc/ontoprocbioschemas.jsonld +++ b/data/ontoproc/ontoprocbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "ontoProc", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ontoProc.html", diff --git a/data/ontoquest_ws/ontoquest_wsbioschemas.jsonld b/data/ontoquest_ws/ontoquest_wsbioschemas.jsonld index 75b756fb78a32..fb847793fa241 100644 --- a/data/ontoquest_ws/ontoquest_wsbioschemas.jsonld +++ b/data/ontoquest_ws/ontoquest_wsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Download a NIF ontology file.", "sc:name": "OntoQuest WS", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain", "sc:version": "1" diff --git a/data/ontoquestmain/ontoquestmainbioschemas.jsonld b/data/ontoquestmain/ontoquestmainbioschemas.jsonld index f2288a6ae35a7..7d4a86801320e 100644 --- a/data/ontoquestmain/ontoquestmainbioschemas.jsonld +++ b/data/ontoquestmain/ontoquestmainbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Search terms starting for the query used for auto-complete service.", "sc:name": "OntoQuestMain", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain#OntoQuestMain-%28updatedon03%2F10%2F2010%29", "sc:version": "1" diff --git a/data/ontotext/ontotextbioschemas.jsonld b/data/ontotext/ontotextbioschemas.jsonld index 849b4d02f4ff3..183024ab4b625 100644 --- a/data/ontotext/ontotextbioschemas.jsonld +++ b/data/ontotext/ontotextbioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", + "UK MRC", "EMBOSS Contributors", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:description": "Get ontology term(s) original full text.", "sc:funder": [ - "Wellcome Trust", "UK MRC", + "Wellcome Trust", "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "ontotext", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/ontotext.html", "sc:version": "r6" diff --git a/data/oommppaa/oommppaabioschemas.jsonld b/data/oommppaa/oommppaabioschemas.jsonld index a5de8b4ad0d2f..5c28136c8e8f8 100644 --- a/data/oommppaa/oommppaabioschemas.jsonld +++ b/data/oommppaa/oommppaabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Novel computational tool designed to inform compound design by combining structural and activity data. It uses 3D matched molecular pairs to contextualise both activity and inactivity data in its relevant protein environment.", "sc:name": "OOMMPPAA", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://oommppaa.sgc.ox.ac.uk/OOMMPPAA/" } \ No newline at end of file diff --git a/data/oompa/oompabioschemas.jsonld b/data/oompa/oompabioschemas.jsonld index 590026a438945..b184891ad0900 100644 --- a/data/oompa/oompabioschemas.jsonld +++ b/data/oompa/oompabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Object-oriented microarray and proteomics analysis library implemented in R using S4 classes and compatible with BioConductor.", "sc:name": "OOMPA", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioinformatics.mdanderson.org/main/OOMPA:Overview" diff --git a/data/opal/opalbioschemas.jsonld b/data/opal/opalbioschemas.jsonld index c3dcf5f9ab634..826cd8b897038 100644 --- a/data/opal/opalbioschemas.jsonld +++ b/data/opal/opalbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/opal", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alok Sharma", - "Ashwini Patil" + "Ashwini Patil", + "Alok Sharma" ], "sc:additionalType": "Web application", "sc:description": "Prediction of MoRF regions in intrinsically disordered protein sequences.", "sc:name": "OPAL", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.alok-ai-lab.com/tools/opal/" } \ No newline at end of file diff --git a/data/opal_ws/opal_wsbioschemas.jsonld b/data/opal_ws/opal_wsbioschemas.jsonld index d6444ea9f5b03..7d00364679743 100644 --- a/data/opal_ws/opal_wsbioschemas.jsonld +++ b/data/opal_ws/opal_wsbioschemas.jsonld @@ -11,10 +11,10 @@ "@id": "https://bio.tools/opal_ws", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Luca Clementi", "Wilfred Li", + "Sriram Krishnan", "Nadya Williams", - "Sriram Krishnan" + "Luca Clementi" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:20529877", diff --git a/data/open-community_profiling_assessment_tool/open-community_profiling_assessment_toolbioschemas.jsonld b/data/open-community_profiling_assessment_tool/open-community_profiling_assessment_toolbioschemas.jsonld index 282c90b95b6f4..2c496db7047bd 100644 --- a/data/open-community_profiling_assessment_tool/open-community_profiling_assessment_toolbioschemas.jsonld +++ b/data/open-community_profiling_assessment_tool/open-community_profiling_assessment_toolbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Open-community Profiling Assessment tooL (OPAL)", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/CAMI-challenge/OPAL" } \ No newline at end of file diff --git a/data/open_babel/open_babelbioschemas.jsonld b/data/open_babel/open_babelbioschemas.jsonld index b323739057533..3cccbac0f5b85 100644 --- a/data/open_babel/open_babelbioschemas.jsonld +++ b/data/open_babel/open_babelbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": [ "Web application", - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Chemical toolbox designed to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.", "sc:name": "Open Babel", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://openbabel.org/wiki/Main_Page" } \ No newline at end of file diff --git a/data/open_phacts/open_phactsbioschemas.jsonld b/data/open_phacts/open_phactsbioschemas.jsonld index ad106e7ebdd09..2e1a9c6241b8e 100644 --- a/data/open_phacts/open_phactsbioschemas.jsonld +++ b/data/open_phacts/open_phactsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Other", "sc:name": "Open PHACTS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://www.openphacts.org/" } \ No newline at end of file diff --git a/data/open_phacts_api/open_phacts_apibioschemas.jsonld b/data/open_phacts_api/open_phacts_apibioschemas.jsonld index 44d865c31135f..b429ffaccc85b 100644 --- a/data/open_phacts_api/open_phacts_apibioschemas.jsonld +++ b/data/open_phacts_api/open_phacts_apibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "CC-BY-3.0", "sc:name": "Open PHACTS API", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "Open PHACTS Foundation", "sc:url": "https://dev.openphacts.org/docs/2.1", diff --git a/data/open_phacts_explorer/open_phacts_explorerbioschemas.jsonld b/data/open_phacts_explorer/open_phacts_explorerbioschemas.jsonld index 72161e3d60ef3..732ed985ebd90 100644 --- a/data/open_phacts_explorer/open_phacts_explorerbioschemas.jsonld +++ b/data/open_phacts_explorer/open_phacts_explorerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "Open PHACTS Explorer", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ diff --git a/data/open_source_registry_system_for_rare_diseases_osse/open_source_registry_system_for_rare_diseases_ossebioschemas.jsonld b/data/open_source_registry_system_for_rare_diseases_osse/open_source_registry_system_for_rare_diseases_ossebioschemas.jsonld index f1ad4865efa9d..29ae3d359b80a 100644 --- a/data/open_source_registry_system_for_rare_diseases_osse/open_source_registry_system_for_rare_diseases_ossebioschemas.jsonld +++ b/data/open_source_registry_system_for_rare_diseases_osse/open_source_registry_system_for_rare_diseases_ossebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "OSSE", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://www.osse-register.de/en/", diff --git a/data/open_targets/open_targetsbioschemas.jsonld b/data/open_targets/open_targetsbioschemas.jsonld index 2fbcc1e0acba7..b9096945a5946 100644 --- a/data/open_targets/open_targetsbioschemas.jsonld +++ b/data/open_targets/open_targetsbioschemas.jsonld @@ -12,19 +12,19 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": [ "Database portal", - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": [ - "pubmed:27899665", - "pmcid:PMC5210543" + "pmcid:PMC5210543", + "pubmed:27899665" ], "sc:description": "data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases.\nidentification and prioritization of biological targets for follow-up.\nintegrated genome-wide data from a broad range of data sources: evidence from genetics, genomics, transcriptomics, drugs, animal models and scientific literature to score and rank target-disease associations for drug target identification.\neither a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease.", "sc:license": "Unlicense", "sc:name": "Open Targets", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.opentargets.org/" diff --git a/data/open_targets_platform/open_targets_platformbioschemas.jsonld b/data/open_targets_platform/open_targets_platformbioschemas.jsonld index e8560a6e9595e..0fc69a94d3cee 100644 --- a/data/open_targets_platform/open_targets_platformbioschemas.jsonld +++ b/data/open_targets_platform/open_targets_platformbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Apache-2.0", "sc:name": "Open Targets Platform", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://www.targetvalidation.org/" } \ No newline at end of file diff --git a/data/open_tg-gates/open_tg-gatesbioschemas.jsonld b/data/open_tg-gates/open_tg-gatesbioschemas.jsonld index dc70a31e0bddf..f1a5608ffb83c 100644 --- a/data/open_tg-gates/open_tg-gatesbioschemas.jsonld +++ b/data/open_tg-gates/open_tg-gatesbioschemas.jsonld @@ -12,14 +12,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hiroshi Yamada", "sc:additionalType": [ - "Web API", - "Database portal" + "Database portal", + "Web API" ], "sc:description": "It is a public toxicogenomics database based on the Japanese Toxicogenomics Projects (TGP and TGP2), developed so that a wider community of researchers could utilize the fruits of this research. This API provides access to the RNA microarray (Affymetrix) samples from Open TG-GATEs. Rat data, as well as human data is provided, for repeat and single doses.\",", "sc:name": "Open TG-GATEs API", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://toxico.nibiohn.go.jp/english/" diff --git a/data/openalea/openaleabioschemas.jsonld b/data/openalea/openaleabioschemas.jsonld index cf92a39f2cb55..a87f6f0bdb5f3 100644 --- a/data/openalea/openaleabioschemas.jsonld +++ b/data/openalea/openaleabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Open source project primarily aimed at the plant research community.It is a distributed collaborative effort to develop Python libraries and tools which address the needs of current and future work in Plant Architecture modeling. Includes modules to represent, analyse, and model the functioning and growth of plant architecture.", "sc:name": "OpenAlea", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://openalea.gforge.inria.fr/" } \ No newline at end of file diff --git a/data/openastexviewer/openastexviewerbioschemas.jsonld b/data/openastexviewer/openastexviewerbioschemas.jsonld index 6294f00e68b0e..cb0b5d53b9ba9 100644 --- a/data/openastexviewer/openastexviewerbioschemas.jsonld +++ b/data/openastexviewer/openastexviewerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Java molecular graphics program that assists in structure based drug design. It can be used as an Applet in a web page or as a desktop application.", "sc:name": "OpenAstexViewer 3.0", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://openastexviewer.net/web/" diff --git a/data/openchrom/openchrombioschemas.jsonld b/data/openchrom/openchrombioschemas.jsonld index 1042490d1c005..20fceebc71268 100644 --- a/data/openchrom/openchrombioschemas.jsonld +++ b/data/openchrom/openchrombioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Open source tool for mass spectrometry and chromatography.", "sc:name": "OpenChrom", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://www.openchrom.net/" } \ No newline at end of file diff --git a/data/opencyto/opencytobioschemas.jsonld b/data/opencyto/opencytobioschemas.jsonld index 16d50879be5bf..21b0c7d45f003 100644 --- a/data/opencyto/opencytobioschemas.jsonld +++ b/data/opencyto/opencytobioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pcbi.1003806", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/opencyto", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mike Jiang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:25167361", - "pmcid:PMC4148203", { "@id": "https://doi.org/10.1371/journal.pcbi.1003806" - } + }, + "pmcid:PMC4148203", + "pubmed:25167361" ], "sc:description": "This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.", "sc:featureList": { @@ -31,16 +35,12 @@ "sc:license": "Artistic-2.0", "sc:name": "openCyto", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/openCyto.html", "sc:version": "1.12.1" - }, - { - "@id": "https://doi.org/10.1371/journal.pcbi.1003806", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/openflu/openflubioschemas.jsonld b/data/openflu/openflubioschemas.jsonld index f44bc8097afc0..e82e0df60e510 100644 --- a/data/openflu/openflubioschemas.jsonld +++ b/data/openflu/openflubioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The OpenFlu database (OpenFluDB) is part of a collaborative effort to share observations on the evolution of Influenza virus in both animals and humans. It contains genomic and protein sequences as well as epidemiological data from more than 25'000 isolates.", "sc:name": "OpenFlu", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://openflu.vital-it.ch/" } \ No newline at end of file diff --git a/data/opengrowth/opengrowthbioschemas.jsonld b/data/opengrowth/opengrowthbioschemas.jsonld index 8b04ce066079b..6fcaff17d3a5f 100644 --- a/data/opengrowth/opengrowthbioschemas.jsonld +++ b/data/opengrowth/opengrowthbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Research program which grows new ligands in proteins by connecting small organic fragments.", "sc:name": "OpenGrowth", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://faculty.chemistry.harvard.edu/shakhnovich/software/opengrowth" } \ No newline at end of file diff --git a/data/openhicamm/openhicammbioschemas.jsonld b/data/openhicamm/openhicammbioschemas.jsonld index fbe224952b925..4495e7baae3ee 100644 --- a/data/openhicamm/openhicammbioschemas.jsonld +++ b/data/openhicamm/openhicammbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/j.isci.2018.03.017", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/openhicamm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Erwin Frise", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5993205", { "@id": "https://doi.org/10.1016/j.isci.2018.03.017" }, - "pubmed:29888763" + "pubmed:29888763", + "pmcid:PMC5993205" ], "sc:description": "Open High-content acquisition workflow plugin for Micro-Manager.", "sc:featureList": { @@ -35,6 +31,10 @@ "Mac" ], "sc:url": "https://github.com/bdgp/OpenHiCAMM" + }, + { + "@id": "https://doi.org/10.1016/j.isci.2018.03.017", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/openmm/openmmbioschemas.jsonld b/data/openmm/openmmbioschemas.jsonld index 6b4cd499531c1..209967234d246 100644 --- a/data/openmm/openmmbioschemas.jsonld +++ b/data/openmm/openmmbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Peter Eastman", "sc:additionalType": [ - "Web application", - "Library" + "Library", + "Web application" ], "sc:description": "A toolkit for molecular simulation.", "sc:license": "MIT", "sc:name": "OpenMM", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://openmm.org/", "sc:version": "7.0" diff --git a/data/openms/openmsbioschemas.jsonld b/data/openms/openmsbioschemas.jsonld index 5cfff43159671..7528386fb0702 100644 --- a/data/openms/openmsbioschemas.jsonld +++ b/data/openms/openmsbioschemas.jsonld @@ -18,14 +18,14 @@ "sc:license": "BSD-3-Clause", "sc:name": "OpenMS", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": [ "Eberhard-Karls-Universität Tübingen", - "Freie Universität Berlin", - "ETH Zürich" + "ETH Zürich", + "Freie Universität Berlin" ], "sc:url": "http://www.openms.de", "sc:version": "2.0.0" diff --git a/data/openphacts-vis-compoundinfo/openphacts-vis-compoundinfobioschemas.jsonld b/data/openphacts-vis-compoundinfo/openphacts-vis-compoundinfobioschemas.jsonld index 9cfaf150a39ba..58ce87ccb39fc 100644 --- a/data/openphacts-vis-compoundinfo/openphacts-vis-compoundinfobioschemas.jsonld +++ b/data/openphacts-vis-compoundinfo/openphacts-vis-compoundinfobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Displays the information available in the Open PHACTS Linked Data cache about a compound.", "sc:name": "openphacts-vis-compoundinfo", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "BioJS", "sc:url": "https://github.com/openphacts/openphacts-vis-compoundinfo", diff --git a/data/openprimer/openprimerbioschemas.jsonld b/data/openprimer/openprimerbioschemas.jsonld index a787cedc67fb6..193a14182dd3e 100644 --- a/data/openprimer/openprimerbioschemas.jsonld +++ b/data/openprimer/openprimerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "openPrimeR", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/openPrimeR.html", "sc:version": "1.2.0" diff --git a/data/openprimerui/openprimeruibioschemas.jsonld b/data/openprimerui/openprimeruibioschemas.jsonld index e1752239ebc3d..8d2c99b3b041d 100644 --- a/data/openprimerui/openprimeruibioschemas.jsonld +++ b/data/openprimerui/openprimeruibioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "openPrimeRui", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/openPrimeRui.html", "sc:version": "1.2.0" diff --git a/data/opensegspim/opensegspimbioschemas.jsonld b/data/opensegspim/opensegspimbioschemas.jsonld index b2eae736616fc..a090a283cbf68 100644 --- a/data/opensegspim/opensegspimbioschemas.jsonld +++ b/data/opensegspim/opensegspimbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Sohail Ahmed", - "Laurent Gole", - "Weimiao Yu" + "Weimiao Yu", + "Laurent Gole" ], "sc:additionalType": "Desktop application", "sc:description": "3D automatic quantitative analysis tool for Single Plane Illumination Microscopy data.", diff --git a/data/openspim/openspimbioschemas.jsonld b/data/openspim/openspimbioschemas.jsonld index ab15ee342113a..4ce198e4b8296 100644 --- a/data/openspim/openspimbioschemas.jsonld +++ b/data/openspim/openspimbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Open Access platform for applying and enhancing Selective Plane Illumination Microscopy (SPIM).", "sc:name": "OpenSPIM", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://openspim.org/" } \ No newline at end of file diff --git a/data/openswath/openswathbioschemas.jsonld b/data/openswath/openswathbioschemas.jsonld index 41048390a8045..62b76ea24e89d 100644 --- a/data/openswath/openswathbioschemas.jsonld +++ b/data/openswath/openswathbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "OpenSWATH", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.openswath.org", "sc:version": "OpenMS 2.4.0" diff --git a/data/opentrials/opentrialsbioschemas.jsonld b/data/opentrials/opentrialsbioschemas.jsonld index 41b652bdff4db..13ea0ec4a782e 100644 --- a/data/opentrials/opentrialsbioschemas.jsonld +++ b/data/opentrials/opentrialsbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "OpenTrials is a collaboration between Open Knowledge International and Dr Ben Goldacre from the University of Oxford DataLab. It aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally.", "sc:name": "OpenTrials API", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://opentrials.net/" } \ No newline at end of file diff --git a/data/opossom/opossombioschemas.jsonld b/data/opossom/opossombioschemas.jsonld index e2d2c1d27e4f5..14b1c004974b0 100644 --- a/data/opossom/opossombioschemas.jsonld +++ b/data/opossom/opossombioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Henry Loeffler-Wirth", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:26063839", "sc:description": "This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.", "sc:license": "GPL-2.0", "sc:name": "oposSOM", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/oposSOM.html", diff --git a/data/oppar/opparbioschemas.jsonld b/data/oppar/opparbioschemas.jsonld index 9cfbf0cf97f29..f99e9aadd9d58 100644 --- a/data/oppar/opparbioschemas.jsonld +++ b/data/oppar/opparbioschemas.jsonld @@ -35,8 +35,8 @@ "sc:license": "GPL-2.0", "sc:name": "oppar", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/oppar.html", diff --git a/data/optcluster/optclusterbioschemas.jsonld b/data/optcluster/optclusterbioschemas.jsonld index a1e248e209c4a..fd16a51ce2d27 100644 --- a/data/optcluster/optclusterbioschemas.jsonld +++ b/data/optcluster/optclusterbioschemas.jsonld @@ -9,25 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.6026/97320630013101", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/optcluster", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Susmita Datta", "Somnath Datta", - "Michael Sekula" + "Michael Sekula", + "Susmita Datta" ], "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5450252", { "@id": "https://doi.org/10.6026/97320630013101" }, - "pubmed:28584451" + "pubmed:28584451", + "pmcid:PMC5450252" ], "sc:description": "Cluster analysis using statistical and biological validation measures for both continuous and count data.", "sc:featureList": { @@ -36,11 +32,15 @@ "sc:license": "GPL-2.0", "sc:name": "optCluster", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/optCluster/index.html" + }, + { + "@id": "https://doi.org/10.6026/97320630013101", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/optflux/optfluxbioschemas.jsonld b/data/optflux/optfluxbioschemas.jsonld index 6b0ecae1ab9df..995a3d20bb710 100644 --- a/data/optflux/optfluxbioschemas.jsonld +++ b/data/optflux/optfluxbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Open-source and modular software to support in silico metabolic engineering tasks aimed at being the reference computational application in the field.", "sc:name": "OptFlux", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.optflux.org/" } \ No newline at end of file diff --git a/data/optimir/optimirbioschemas.jsonld b/data/optimir/optimirbioschemas.jsonld index 713c97c5f6057..149d2629fa7f0 100644 --- a/data/optimir/optimirbioschemas.jsonld +++ b/data/optimir/optimirbioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC6521604", + "pubmed:30819774", { "@id": "https://doi.org/10.1261/rna.069708.118" - }, - "pubmed:30819774" + } ], "sc:description": "Algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis.", "sc:featureList": [ @@ -36,8 +36,8 @@ "sc:license": "GPL-3.0", "sc:name": "OPTIMIR", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/FlorianThibord/OptimiR" }, diff --git a/data/optimizer/optimizerbioschemas.jsonld b/data/optimizer/optimizerbioschemas.jsonld index a0496f5a0e7bb..7862845e2500d 100644 --- a/data/optimizer/optimizerbioschemas.jsonld +++ b/data/optimizer/optimizerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.", "sc:name": "OPTIMIZER", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://genomes.urv.es/OPTIMIZER/" } \ No newline at end of file diff --git a/data/optimus_primer/optimus_primerbioschemas.jsonld b/data/optimus_primer/optimus_primerbioschemas.jsonld index 2a307df5f0c38..dab41be1c13cf 100644 --- a/data/optimus_primer/optimus_primerbioschemas.jsonld +++ b/data/optimus_primer/optimus_primerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Optimus Primer", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://op.pgx.ca" } \ No newline at end of file diff --git a/data/optisel/optiselbioschemas.jsonld b/data/optisel/optiselbioschemas.jsonld index 39d5e9734f6d5..130a88b718e5d 100644 --- a/data/optisel/optiselbioschemas.jsonld +++ b/data/optisel/optiselbioschemas.jsonld @@ -19,27 +19,27 @@ "biotools:primaryContact": "Robin Wellmann", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:30642239", { "@id": "https://doi.org/10.1186/s12859-018-2450-5" }, - "pubmed:30642239", "pmcid:PMC6332575" ], "sc:description": "Framework for the optimization of breeding programs via optimum contribution selection and mate allocation.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_0487" }, { - "@id": "edam:operation_0487" + "@id": "edam:operation_3196" } ], "sc:license": "GPL-2.0", "sc:name": "optiSel", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/package=optiSel", "sc:version": "2.0.2" diff --git a/data/optitope/optitopebioschemas.jsonld b/data/optitope/optitopebioschemas.jsonld index 506dcf07c47de..651d6cf620b73 100644 --- a/data/optitope/optitopebioschemas.jsonld +++ b/data/optitope/optitopebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "OptiTope", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.epitoolkit.de/" } \ No newline at end of file diff --git a/data/opweight/opweightbioschemas.jsonld b/data/opweight/opweightbioschemas.jsonld index f1e11894ef2fa..5eaf64c898408 100644 --- a/data/opweight/opweightbioschemas.jsonld +++ b/data/opweight/opweightbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "OPWeight", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OPWeight.html", "sc:version": "1.2.0" diff --git a/data/orange-bioinformatics/orange-bioinformaticsbioschemas.jsonld b/data/orange-bioinformatics/orange-bioinformaticsbioschemas.jsonld index 120ef12be18f8..1245492a62b46 100644 --- a/data/orange-bioinformatics/orange-bioinformaticsbioschemas.jsonld +++ b/data/orange-bioinformatics/orange-bioinformaticsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-5864-7056", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/orange-bioinformatics", "@type": "sc:SoftwareApplication", @@ -30,6 +26,10 @@ ], "sc:url": "http://pythonhosted.org/Orange-Bioinformatics/", "sc:version": "2.5.40" + }, + { + "@id": "http://orcid.org/0000-0002-5864-7056", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/orange/orangebioschemas.jsonld b/data/orange/orangebioschemas.jsonld index cb41c300c94ee..53286ddfdabc8 100644 --- a/data/orange/orangebioschemas.jsonld +++ b/data/orange/orangebioschemas.jsonld @@ -13,24 +13,24 @@ "@id": "https://bio.tools/orange", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Blaž Zupan", - "Janez Demsar" + "Janez Demsar", + "Blaž Zupan" ], "sc:additionalType": [ "Command-line tool", "Desktop application" ], "sc:author": [ + "Andrej Čopar", + "Tomaž Curk", "Martin Stražar", - "Jernej Kernc", - "Vesna Tanko", + "Janez Demšar", "Aleš Erjavec", - "Andrej Čopar", - "Marko Toplak", "Lan Žagar", - "Janez Demšar", "Anže Starič", - "Tomaž Curk" + "Vesna Tanko", + "Marko Toplak", + "Jernej Kernc" ], "sc:citation": "pubmed:17586552", "sc:contributor": { @@ -45,8 +45,8 @@ "Windows" ], "sc:provider": [ - "ELIXIR-SI-hackathon", - "Faculty of Computer and Information Science, University of Ljubljana, Slovenia" + "Faculty of Computer and Information Science, University of Ljubljana, Slovenia", + "ELIXIR-SI-hackathon" ], "sc:url": "https://orange.biolab.si/", "sc:version": "2.7" diff --git a/data/orange_network/orange_networkbioschemas.jsonld b/data/orange_network/orange_networkbioschemas.jsonld index fce5a6d55f371..9295136c10fdf 100644 --- a/data/orange_network/orange_networkbioschemas.jsonld +++ b/data/orange_network/orange_networkbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Blaž Zupan", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:author": "Jernej Kernc", "sc:description": "A network analysis extension for a data mining software Orange. Network add-on includes components for network generation, network analysis, clustering and access to SNAP network database. All features can be combined with powerful visualizations, bioinformatics tools and data mining techniques from the core Orange data mining framework.", "sc:license": "GPL-3.0", "sc:name": "Orange Network", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "Laboratory for Bioinformatics, University of Ljubljana", diff --git a/data/orcae/orcaebioschemas.jsonld b/data/orcae/orcaebioschemas.jsonld index b5deb16507efe..48ae113a56265 100644 --- a/data/orcae/orcaebioschemas.jsonld +++ b/data/orcae/orcaebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ORCAE", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "PSB", "sc:url": "http://bioinformatics.psb.ugent.be/orcae/", diff --git a/data/orcid/orcidbioschemas.jsonld b/data/orcid/orcidbioschemas.jsonld index d6bcf2e07f06d..c2df032f7b4a5 100644 --- a/data/orcid/orcidbioschemas.jsonld +++ b/data/orcid/orcidbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "ORCID provides a persistent digital identifier that distinguishes you from every other researcher and, through integration in key research workflows such as manuscript and grant submission, supports automated linkages between you and your professional activities ensuring that your work is recognized.", "sc:name": "Orcid API", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://orcid.org/" } \ No newline at end of file diff --git a/data/orderedlist/orderedlistbioschemas.jsonld b/data/orderedlist/orderedlistbioschemas.jsonld index 40460f891165d..baa60715bc5aa 100644 --- a/data/orderedlist/orderedlistbioschemas.jsonld +++ b/data/orderedlist/orderedlistbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "OrderedList", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OrderedList.html", "sc:version": "1.46.0" diff --git a/data/ordino/ordinobioschemas.jsonld b/data/ordino/ordinobioschemas.jsonld index 4d5bbc0346236..49147d9ef97fc 100644 --- a/data/ordino/ordinobioschemas.jsonld +++ b/data/ordino/ordinobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MPL-2.0", "sc:name": "Ordino", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://ordino.caleydoapp.org/" } \ No newline at end of file diff --git a/data/ordo/ordobioschemas.jsonld b/data/ordo/ordobioschemas.jsonld index 89b4972b1d06d..2989c0dc58137 100644 --- a/data/ordo/ordobioschemas.jsonld +++ b/data/ordo/ordobioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact Form", "sc:additionalType": [ - "Web application", "Database portal", + "Web application", "Ontology" ], "sc:description": "The Orphanet Rare Disease Ontology (ORDO) - structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features. It integrates a classification of rare diseases, relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).", "sc:license": "Apache-2.0", "sc:name": "ORDO", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "Inserm US14", "sc:url": "http://www.ebi.ac.uk/ols/ontologies/ordo", diff --git a/data/oreganno/oregannobioschemas.jsonld b/data/oreganno/oregannobioschemas.jsonld index 500a86ab10db0..0e4d20a2f3153 100644 --- a/data/oreganno/oregannobioschemas.jsonld +++ b/data/oreganno/oregannobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations.", "sc:name": "ORegAnno", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.oreganno.org/" } \ No newline at end of file diff --git a/data/orfer/orferbioschemas.jsonld b/data/orfer/orferbioschemas.jsonld index 66bf33dca5498..cdc7296cb0123 100644 --- a/data/orfer/orferbioschemas.jsonld +++ b/data/orfer/orferbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "ORFer (Open Reading Frame Retrieval) reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.The open reading frame corresponding to the protein sequences is extracted from the XML and displayed. ORFer has a database interface that allows for storing the retrieved sequences in a local SQL database.", "sc:name": "ORFer", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.proteinstrukturfabrik.de/orfer/", "sc:version": "1.3.2.2" diff --git a/data/orfpredictor/orfpredictorbioschemas.jsonld b/data/orfpredictor/orfpredictorbioschemas.jsonld index 9459975f5d5b8..8aedb2306bf2a 100644 --- a/data/orfpredictor/orfpredictorbioschemas.jsonld +++ b/data/orfpredictor/orfpredictorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "OrfPredictor is designed for prediction of Open Reading Frames (ORFs) and coding regions of a batch of EST or cDNA sequences.", "sc:name": "OrfPredictor", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioinformatics.ysu.edu/tools/OrfPredictor.html" } \ No newline at end of file diff --git a/data/organismdbi/bioconda_organismdbi.yaml b/data/organismdbi/bioconda_organismdbi.yaml index 8e14f90c8534e..0e10ac3a90f4e 100644 --- a/data/organismdbi/bioconda_organismdbi.yaml +++ b/data/organismdbi/bioconda_organismdbi.yaml @@ -5,7 +5,6 @@ description: The package enables a simple unified interface to several annotatio home: https://bioconductor.org/packages/3.10/bioc/html/OrganismDbi.html identifiers: - biotools:organismdbi -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-organismdbi summary: Software to enable the smooth interfacing of different database packages diff --git a/data/organismdbi/organismdbibioschemas.jsonld b/data/organismdbi/organismdbibioschemas.jsonld index 09a38b25c22cf..8c6a8d4f39e8b 100644 --- a/data/organismdbi/organismdbibioschemas.jsonld +++ b/data/organismdbi/organismdbibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "OrganismDbi", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OrganismDbi.html", "sc:version": "1.16.0" diff --git a/data/organisms/organismsbioschemas.jsonld b/data/organisms/organismsbioschemas.jsonld index ddd50518741ef..e4e1b9951a637 100644 --- a/data/organisms/organismsbioschemas.jsonld +++ b/data/organisms/organismsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0065390", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/organisms", "@type": "sc:SoftwareApplication", @@ -24,11 +28,11 @@ "@id": "edam:topic_0218" }, "sc:citation": [ + "pmcid:PMC3688812", + "pubmed:23823062", { "@id": "https://doi.org/10.1371/journal.pone.0065390" - }, - "pubmed:23823062", - "pmcid:PMC3688812" + } ], "sc:description": "ORGANISMS is a weekly updated web resource that facilitates taxonomy-aware search and retrieval of articles. To this end, the the resource performs named entity recognition of terms from the NCBI Taxonomy on PubMed abstracts. The resource further provides download files of organism-disease and organism-tissue associations extracted through automatic text mining.", "sc:featureList": { @@ -39,14 +43,10 @@ "sc:name": "ORGANISMS", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://organisms.jensenlab.org/" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0065390", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/oridb/oridbbioschemas.jsonld b/data/oridb/oridbbioschemas.jsonld index 61bbd6fc8c193..1d14dc265cfdd 100644 --- a/data/oridb/oridbbioschemas.jsonld +++ b/data/oridb/oridbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "DNA origin of replication database: contains genome-wide mapping studies. Databases available for yeast Saccharomyces cervisiae and S. pombe.", "sc:name": "OriDB", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.oridb.org/index.php" diff --git a/data/orio/oriobioschemas.jsonld b/data/orio/oriobioschemas.jsonld index c029d9c5e18d1..1f2aff7295cf8 100644 --- a/data/orio/oriobioschemas.jsonld +++ b/data/orio/oriobioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Contact Form", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28402545", { "@id": "https://doi.org/10.1093/NAR/GKX270" }, + "pubmed:28402545", "pmcid:PMC5449597" ], "sc:description": "Online Resource for Integrative Omics- a web-based platform for rapid integration of next generation sequencing data..", @@ -36,9 +36,9 @@ ], "sc:name": "ORIO", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://orio.niehs.nih.gov/" } diff --git a/data/oriogen/oriogenbioschemas.jsonld b/data/oriogen/oriogenbioschemas.jsonld index 8500be8766f18..ca4439dc8d800 100644 --- a/data/oriogen/oriogenbioschemas.jsonld +++ b/data/oriogen/oriogenbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "ORIOGEN (Order Restricted Inference for Ordered Gene Expression) analyzes gene expression data obtained from time-course/dose-response studies.", "sc:name": "ORIOGEN", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.niehs.nih.gov/research/resources/software/biostatistics/oriogen/index.cfm", diff --git a/data/orion/orionbioschemas.jsonld b/data/orion/orionbioschemas.jsonld index fecb797f755a2..6b056c7dcb221 100644 --- a/data/orion/orionbioschemas.jsonld +++ b/data/orion/orionbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "New fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure.", "sc:name": "ORION", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.dsimb.inserm.fr/orion/" } \ No newline at end of file diff --git a/data/orione/orionebioschemas.jsonld b/data/orione/orionebioschemas.jsonld index 9e87e0c8f12b3..2b322391a87de 100644 --- a/data/orione/orionebioschemas.jsonld +++ b/data/orione/orionebioschemas.jsonld @@ -15,13 +15,13 @@ "sc:description": "Specialized domain server for integrative analysis of NGS microbial data, that covers the whole life cycle of microbiology research data, bringing together all the tools to perform steps such as quality check, alignment, assembly, scaffolding and annotation.", "sc:name": "Orione", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ - "ELIXIR-ITA-CRS4", - "CRS4" + "CRS4", + "ELIXIR-ITA-CRS4" ], "sc:url": "http://orione.crs4.it", "sc:version": "1" diff --git a/data/oritfinder/oritfinderbioschemas.jsonld b/data/oritfinder/oritfinderbioschemas.jsonld index dbf1456b17100..a630a5182ca00 100644 --- a/data/oritfinder/oritfinderbioschemas.jsonld +++ b/data/oritfinder/oritfinderbioschemas.jsonld @@ -23,9 +23,9 @@ "sc:description": "Rapid identification of the origin of transfer site (oriT) of a conjugative plasmid or chromosome-borne integrative and conjugative element. With a combination of similarity searches for the oriTDB-archived oriT nucleotide sequences and the co-localization of the flanking relaxase homologous genes, the oriTfinder can predict the oriT region with high accuracy in the DNA sequence of a bacterial plasmid or chromosome in minutes.", "sc:name": "oriTfinder", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo-mml.sjtu.edu.cn/oriTfinder", "sc:version": "1.1" diff --git a/data/orphadata/orphadatabioschemas.jsonld b/data/orphadata/orphadatabioschemas.jsonld index 35043985078a5..838a2817dd668 100644 --- a/data/orphadata/orphadatabioschemas.jsonld +++ b/data/orphadata/orphadatabioschemas.jsonld @@ -24,13 +24,13 @@ "sc:license": "CC-BY-4.0", "sc:name": "Orphadata", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ - "Orphanet Inserm", - "Inserm US14" + "Inserm US14", + "Orphanet Inserm" ], "sc:url": "http://www.orphadata.org/" } \ No newline at end of file diff --git a/data/orphanet/orphanetbioschemas.jsonld b/data/orphanet/orphanetbioschemas.jsonld index 3b5a1314a73c3..c7b3646c55924 100644 --- a/data/orphanet/orphanetbioschemas.jsonld +++ b/data/orphanet/orphanetbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/orphanet", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:description": "Information on rare diseases and orphan drugs.", "sc:name": "Orphanet", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "Inserm US14", "sc:url": "http://www.orpha.net/consor/cgi-bin/index.php" diff --git a/data/orthodb/orthodbbioschemas.jsonld b/data/orthodb/orthodbbioschemas.jsonld index a48ed730d9729..9ddcb6dc5d1b4 100644 --- a/data/orthodb/orthodbbioschemas.jsonld +++ b/data/orthodb/orthodbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "OrthoDB", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://www.orthodb.org/" diff --git a/data/orthodisease/orthodiseasebioschemas.jsonld b/data/orthodisease/orthodiseasebioschemas.jsonld index b829089988ddc..4ed15c45945b9 100644 --- a/data/orthodisease/orthodiseasebioschemas.jsonld +++ b/data/orthodisease/orthodiseasebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A database of disease gene orthologs.", "sc:name": "Orthodisease", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://orthodisease.sbc.su.se/" diff --git a/data/orthograph/orthographbioschemas.jsonld b/data/orthograph/orthographbioschemas.jsonld index 4f3667f3b84e6..9b2b6b4f58f15 100644 --- a/data/orthograph/orthographbioschemas.jsonld +++ b/data/orthograph/orthographbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1529-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/orthograph", "@type": "sc:SoftwareApplication", @@ -25,8 +21,8 @@ "Workflow" ], "sc:citation": [ - "pmcid:PMC5312442", "pubmed:28209129", + "pmcid:PMC5312442", { "@id": "https://doi.org/10.1186/s12859-017-1529-8" } @@ -38,6 +34,10 @@ "sc:license": "GPL-3.0", "sc:name": "Orthograph", "sc:url": "https://mptrsen.github.io/Orthograph/" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1529-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ortholugedb/ortholugedbbioschemas.jsonld b/data/ortholugedb/ortholugedbbioschemas.jsonld index 9c4585b568e85..30e8767d54abc 100644 --- a/data/ortholugedb/ortholugedbbioschemas.jsonld +++ b/data/ortholugedb/ortholugedbbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gks1241", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ortholugedb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Brinkman lab at Simon Fraser University", "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:23203876", "pmcid:PMC3531125", { "@id": "https://doi.org/10.1093/nar/gks1241" - }, - "pubmed:23203876" + } ], "sc:description": "Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. Also contains reciprocal best hit-based ortholog predictions, in-paralog predictions (recently duplicated genes) and proposed ortholog groups.", "sc:featureList": { @@ -31,6 +27,10 @@ }, "sc:name": "OrtholugeDB", "sc:url": "http://www.pathogenomics.sfu.ca/ortholugedb/" + }, + { + "@id": "https://doi.org/10.1093/nar/gks1241", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/orthoscope/orthoscopebioschemas.jsonld b/data/orthoscope/orthoscopebioschemas.jsonld index 4bdf929479dff..81f185ded1142 100644 --- a/data/orthoscope/orthoscopebioschemas.jsonld +++ b/data/orthoscope/orthoscopebioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/molbev/msy226", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ORTHOSCOPE", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jun Inoue", "sc:additionalType": [ - "Web service", - "Desktop application" + "Desktop application", + "Web service" ], "sc:citation": [ { @@ -31,10 +27,10 @@ "sc:description": "Automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa.", "sc:featureList": [ { - "@id": "edam:operation_0544" + "@id": "edam:operation_3478" }, { - "@id": "edam:operation_3478" + "@id": "edam:operation_0544" }, { "@id": "edam:operation_0552" @@ -43,11 +39,15 @@ "sc:license": "Unlicense", "sc:name": "ORTHOSCOPE", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.orthoscope.jp" + }, + { + "@id": "https://doi.org/10.1093/molbev/msy226", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/orthovenn/orthovennbioschemas.jsonld b/data/orthovenn/orthovennbioschemas.jsonld index 27a4e7d4a0b3b..cc77286ae29a8 100644 --- a/data/orthovenn/orthovennbioschemas.jsonld +++ b/data/orthovenn/orthovennbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkv487", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/orthovenn", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:25964301", + "pmcid:PMC4489293", { "@id": "https://doi.org/10.1093/nar/gkv487" }, - "pmcid:PMC4489293" + "pubmed:25964301" ], "sc:description": "Web platform for comparison and annotation of orthologous gene clusters among multiple species.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "OrthoVenn", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.bioinfogenome.net/OrthoVenn/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkv487", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/orthovenn2/orthovenn2bioschemas.jsonld b/data/orthovenn2/orthovenn2bioschemas.jsonld index 7b29d97844667..0f571c8fd03bf 100644 --- a/data/orthovenn2/orthovenn2bioschemas.jsonld +++ b/data/orthovenn2/orthovenn2bioschemas.jsonld @@ -15,23 +15,23 @@ "biotools:primaryContact": "Yi Wang", "sc:additionalType": [ "Web application", - "Web service", - "Web API" + "Web API", + "Web service" ], "sc:citation": [ - "pubmed:31053848", + "pmcid:PMC6602458", { "@id": "https://doi.org/10.1093/NAR/GKZ333" }, - "pmcid:PMC6602458" + "pubmed:31053848" ], "sc:description": "Web server for whole-genome comparison and annotation of orthologous clusters across multiple species.", "sc:license": "Unlicense", "sc:name": "OrthoVenn2", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://orthovenn2.bioinfotoolkits.net" }, diff --git a/data/orthsearchservice/orthsearchservicebioschemas.jsonld b/data/orthsearchservice/orthsearchservicebioschemas.jsonld index 921bd996bd10c..92a82a716c3be 100644 --- a/data/orthsearchservice/orthsearchservicebioschemas.jsonld +++ b/data/orthsearchservice/orthsearchservicebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Orthologue Search Service", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://dove.embl-heidelberg.de/Blast2e/" } \ No newline at end of file diff --git a/data/oryzabase/oryzabasebioschemas.jsonld b/data/oryzabase/oryzabasebioschemas.jsonld index dc8335149e4e3..30f9e75ea2e2c 100644 --- a/data/oryzabase/oryzabasebioschemas.jsonld +++ b/data/oryzabase/oryzabasebioschemas.jsonld @@ -27,18 +27,18 @@ "sc:description": "Integrated rice genetic map and mutant database at the National Institute of Genetics in Japan.", "sc:featureList": [ { - "@id": "edam:operation_0224" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_0224" } ], "sc:license": "Not licensed", "sc:name": "Oryzabase", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://shigen.nig.ac.jp/rice/oryzabase/" } diff --git a/data/osanalyzer/osanalyzerbioschemas.jsonld b/data/osanalyzer/osanalyzerbioschemas.jsonld index 7e6d09d6190de..277cecb7c12ef 100644 --- a/data/osanalyzer/osanalyzerbioschemas.jsonld +++ b/data/osanalyzer/osanalyzerbioschemas.jsonld @@ -9,25 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3390/microarrays5040024", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-1522-4504", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/osanalyzer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Giuseppe Agapito", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:27669316", "pmcid:PMC5197943", { "@id": "https://doi.org/10.3390/microarrays5040024" - } + }, + "pubmed:27669316" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-1522-4504" @@ -44,6 +36,14 @@ "Mac" ], "sc:url": "https://sites.google.com/site/overallsurvivalanalyzer/" + }, + { + "@id": "http://orcid.org/0000-0002-1522-4504", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.3390/microarrays5040024", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/osat/osatbioschemas.jsonld b/data/osat/osatbioschemas.jsonld index 49b2dec3fa864..d5337e5a31e2b 100644 --- a/data/osat/osatbioschemas.jsonld +++ b/data/osat/osatbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Li Yan", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A sizable genomics study often involves the use of multiple batches. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. This tool is developed to facilitate the allocation of samples to different batches. It produces setup that optimizes the even distribution of samples in groups of biological interest into batches, reducing the confounding or correlation between batches and variables.", "sc:license": "Artistic-2.0", "sc:name": "OSAT", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OSAT.html", "sc:version": "1.22.0" diff --git a/data/osca/oscabioschemas.jsonld b/data/osca/oscabioschemas.jsonld index a5e75af2de0b2..1c47d76d96ebd 100644 --- a/data/osca/oscabioschemas.jsonld +++ b/data/osca/oscabioschemas.jsonld @@ -13,16 +13,16 @@ "@id": "https://bio.tools/OSCA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jian Yang", - "Futao Zhang" + "Futao Zhang", + "Jian Yang" ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:31138268", "pmcid:PMC6537380", { "@id": "https://doi.org/10.1186/s13059-019-1718-z" - } + }, + "pubmed:31138268" ], "sc:description": "OSCA (OmicS-data-based Complex trait Analysis) is a software tool for the analysis of complex traits using multi-omics data.", "sc:featureList": [ @@ -30,18 +30,18 @@ "@id": "edam:operation_3232" }, { - "@id": "edam:operation_3659" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3659" } ], "sc:license": "MIT", "sc:name": "OSCA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://cnsgenomics.com/software/osca/#Overview" }, diff --git a/data/oscope/oscopebioschemas.jsonld b/data/oscope/oscopebioschemas.jsonld index 5467044b3aaa7..ef025bc36d60f 100644 --- a/data/oscope/oscopebioschemas.jsonld +++ b/data/oscope/oscopebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ning Leng", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Statistical pipeline developed to identify and recover the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. It includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.", "sc:license": "Artistic-2.0", "sc:name": "Oscope", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Oscope.html", "sc:version": "1.4.0" diff --git a/data/osdb_api/osdb_apibioschemas.jsonld b/data/osdb_api/osdb_apibioschemas.jsonld index 3627298ce1f30..71029fe9fa6d0 100644 --- a/data/osdb_api/osdb_apibioschemas.jsonld +++ b/data/osdb_api/osdb_apibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Access to organic compound spectral data", "sc:name": "OSDB API", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://osdb.info" diff --git a/data/osml/osmlbioschemas.jsonld b/data/osml/osmlbioschemas.jsonld index 626a159f13a9a..ce397ef76a810 100644 --- a/data/osml/osmlbioschemas.jsonld +++ b/data/osml/osmlbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "OSML", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.csbio.sjtu.edu.cn:8080/OSML/" } \ No newline at end of file diff --git a/data/osprey_vis/osprey_visbioschemas.jsonld b/data/osprey_vis/osprey_visbioschemas.jsonld index 206f5ab5bc7fc..74c215c27e25a 100644 --- a/data/osprey_vis/osprey_visbioschemas.jsonld +++ b/data/osprey_vis/osprey_visbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "The Osprey Network Visualization System", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://biodata.mshri.on.ca/osprey" } \ No newline at end of file diff --git a/data/osse/ossebioschemas.jsonld b/data/osse/ossebioschemas.jsonld index 73c1c1d35e7b7..337559e3cf524 100644 --- a/data/osse/ossebioschemas.jsonld +++ b/data/osse/ossebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Other", "sc:name": "OSSE", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://osse.bii.a-star.edu.sg/index.php" diff --git a/data/osteoporosatlas/osteoporosatlasbioschemas.jsonld b/data/osteoporosatlas/osteoporosatlasbioschemas.jsonld index e938b3ccc2082..7a76492770152 100644 --- a/data/osteoporosatlas/osteoporosatlasbioschemas.jsonld +++ b/data/osteoporosatlas/osteoporosatlasbioschemas.jsonld @@ -25,11 +25,11 @@ "Database portal" ], "sc:citation": [ + "pubmed:31086734", "pmcid:PMC6487800", { "@id": "https://doi.org/10.7717/PEERJ.6778" - }, - "pubmed:31086734" + } ], "sc:description": "Human osteoporosis-related gene database.", "sc:featureList": [ @@ -43,9 +43,9 @@ "sc:license": "Unlicense", "sc:name": "OsteoporosAtlas", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://biokb.ncpsb.org/osteoporosis/" } diff --git a/data/ostrfpd/ostrfpdbioschemas.jsonld b/data/ostrfpd/ostrfpdbioschemas.jsonld index 6a918b41732b2..58f327ee8f7ef 100644 --- a/data/ostrfpd/ostrfpdbioschemas.jsonld +++ b/data/ostrfpd/ostrfpdbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mallika Imwong", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": [ { "@id": "https://doi.org/10.1177/1176934319843130" }, - "pmcid:PMC6482647", - "pubmed:31040636" + "pubmed:31040636", + "pmcid:PMC6482647" ], "sc:description": "Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer.", "sc:featureList": [ @@ -34,18 +34,18 @@ "@id": "edam:operation_0237" }, { - "@id": "edam:operation_0308" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_0308" } ], "sc:license": "GPL-3.0", "sc:name": "OSTRFPD", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/vivekmathema/OSTRFPD" } diff --git a/data/oswitch/oswitchbioschemas.jsonld b/data/oswitch/oswitchbioschemas.jsonld index fb7d12d078882..9526d9f3f7cb1 100644 --- a/data/oswitch/oswitchbioschemas.jsonld +++ b/data/oswitch/oswitchbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Provides quick and simple Docker based virtual environments on Macs and compute clusters alike for reproducible bioinformatics.", "sc:name": "oswitch", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/wurmlab/oswitch", "sc:version": "0.2.6" diff --git a/data/otp/otpbioschemas.jsonld b/data/otp/otpbioschemas.jsonld index 5716dafe99389..cad6e27d509d4 100644 --- a/data/otp/otpbioschemas.jsonld +++ b/data/otp/otpbioschemas.jsonld @@ -11,21 +11,21 @@ "@id": "https://bio.tools/otp", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:author": "OTP Development Team", "sc:description": "Automation platform for managing next generation sequencing (NGS) data. The application provides support in all steps of this process including data transfer from temporary to final storage, execution of data quality monitoring programs and alignment of reads to the reference genome using BWA based pipeline.", "sc:name": "One Touch Pipeline (OTP)", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EilsLabs", "hdhub", - "German Cancer Research Center (DKFZ)" + "German Cancer Research Center (DKFZ)", + "EilsLabs" ], "sc:url": "https://otp.dkfz.de/" } \ No newline at end of file diff --git a/data/otubase/otubasebioschemas.jsonld b/data/otubase/otubasebioschemas.jsonld index 4f14b80c421b9..064d50b5b31c5 100644 --- a/data/otubase/otubasebioschemas.jsonld +++ b/data/otubase/otubasebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "OTUbase", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OTUbase.html", diff --git a/data/oufti/ouftibioschemas.jsonld b/data/oufti/ouftibioschemas.jsonld index 6d7c47a5d7c27..ec83747cea6cd 100644 --- a/data/oufti/ouftibioschemas.jsonld +++ b/data/oufti/ouftibioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1111/mmi.13264", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/oufti", "@type": "sc:SoftwareApplication", @@ -32,10 +36,6 @@ "Mac" ], "sc:url": "http://www.oufti.org/" - }, - { - "@id": "https://doi.org/10.1111/mmi.13264", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/out2summary/out2summarybioschemas.jsonld b/data/out2summary/out2summarybioschemas.jsonld index 3d9db4c87b994..c23fe69f964d4 100644 --- a/data/out2summary/out2summarybioschemas.jsonld +++ b/data/out2summary/out2summarybioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Collects Sequest and TurboSequest *.out files to HTML for use with INTERACT.", "sc:name": "Out2Summary", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://tools.proteomecenter.org/out2summary.php" } \ No newline at end of file diff --git a/data/outlierd/outlierdbioschemas.jsonld b/data/outlierd/outlierdbioschemas.jsonld index e91a0fbc3b7e8..78c92565aade7 100644 --- a/data/outlierd/outlierdbioschemas.jsonld +++ b/data/outlierd/outlierdbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sukwoo Kim", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data.", "sc:license": "GPL-2.0", "sc:name": "OutlierD", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/OutlierD.html", "sc:version": "1.38.0" diff --git a/data/outlyzer/outlyzerbioschemas.jsonld b/data/outlyzer/outlyzerbioschemas.jsonld index 254c43e146c62..ada6f06634e28 100644 --- a/data/outlyzer/outlyzerbioschemas.jsonld +++ b/data/outlyzer/outlyzerbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.18632/oncotarget.13103", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/outlyzer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laurent Castéra", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27825131", { "@id": "https://doi.org/10.18632/oncotarget.13103" }, + "pubmed:27825131", "pmcid:PMC5346729" ], "sc:description": "OutLyzer is a new variant-caller designed for the specific and sensitive detection of mutations for research and diagnostic purposes.", @@ -30,10 +34,6 @@ "sc:operatingSystem": "Linux", "sc:url": "https://github.com/EtieM/outLyzer", "sc:version": "2.0" - }, - { - "@id": "https://doi.org/10.18632/oncotarget.13103", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ova/ovabioschemas.jsonld b/data/ova/ovabioschemas.jsonld index 7e89977765f3d..d048c5e01d2dd 100644 --- a/data/ova/ovabioschemas.jsonld +++ b/data/ova/ovabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Online variant filtering and prioritisation application. Ontology Variant Analysis Tool can filter your VCF files on a wide array of criteria. Remaining genes are prioritisated based on their functional and phenotypic profile similarity to a user supplied phenotype.", "sc:name": "OVA", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://dna2.leeds.ac.uk:8080/OVA/index.jsp" } \ No newline at end of file diff --git a/data/ovnip/ovnipbioschemas.jsonld b/data/ovnip/ovnipbioschemas.jsonld index 472c33c575788..e20247ec16114 100644 --- a/data/ovnip/ovnipbioschemas.jsonld +++ b/data/ovnip/ovnipbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "OVNIp", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://wwwappli.nantes.inra.fr:8180/OVNIp/" } \ No newline at end of file diff --git a/data/oxypred/oxypredbioschemas.jsonld b/data/oxypred/oxypredbioschemas.jsonld index 3ebe8172cfab9..0cdb9d1c89e70 100644 --- a/data/oxypred/oxypredbioschemas.jsonld +++ b/data/oxypred/oxypredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Predict the Oxygen Binding Proteins, Which is carrying Erythrocruorin, Hemoglobin, Myoglobin, Hemerithrin, Leghemoglobin and Hemocyanin.", "sc:name": "Oxypred", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.imtech.res.in/raghava/oxypred/" } \ No newline at end of file diff --git a/data/p-binder/p-binderbioschemas.jsonld b/data/p-binder/p-binderbioschemas.jsonld index ae45880d0d7ef..eff8fa9335e6b 100644 --- a/data/p-binder/p-binderbioschemas.jsonld +++ b/data/p-binder/p-binderbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for predicting the binding sites on pair of given proteins.", "sc:name": "P-Binder", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://sites.google.com/site/guofeics/p-binder" } \ No newline at end of file diff --git a/data/p-match/p-matchbioschemas.jsonld b/data/p-match/p-matchbioschemas.jsonld index 43fd057a24d18..1bc99fb283433 100644 --- a/data/p-match/p-matchbioschemas.jsonld +++ b/data/p-match/p-matchbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "P-Match", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi" } \ No newline at end of file diff --git a/data/p-sams/p-samsbioschemas.jsonld b/data/p-sams/p-samsbioschemas.jsonld index b89c99246b062..c450d40e7e7c8 100644 --- a/data/p-sams/p-samsbioschemas.jsonld +++ b/data/p-sams/p-samsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants.", "sc:name": "P-SAMS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://p-sams.carringtonlab.org/" diff --git a/data/p-scan/p-scanbioschemas.jsonld b/data/p-scan/p-scanbioschemas.jsonld index 3337ffa0d33ce..19d89e0783706 100644 --- a/data/p-scan/p-scanbioschemas.jsonld +++ b/data/p-scan/p-scanbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/p-scan", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "L. Young", "P. J. Munson", - "V. V. Prabhu", - "L. Young" + "V. V. Prabhu" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:10820484", "sc:description": "Software of Peak quantification using Statistical Comparative ANalysis.", "sc:name": "P-SCAN", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://abs.cit.nih.gov/pscan/" } \ No newline at end of file diff --git a/data/p-trap/p-trapbioschemas.jsonld b/data/p-trap/p-trapbioschemas.jsonld index 0e3cf659cdba8..10fb4b8ab38e4 100644 --- a/data/p-trap/p-trapbioschemas.jsonld +++ b/data/p-trap/p-trapbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It is a free and new open source software that automatically recognizes, from numeric images, the structure of a panicle and the seeds on the panicle. The software processes and quantifies several traits related to the structures of the panicles, detects and counts the grains, and measures their shape parameters. It offers both efficient results and friendly environment for users to perform their experiments. Manual processing is not repeatable because dry panicles are vulnerable to damage.", "sc:name": "P-TRAP", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinfo.mpl.ird.fr/index.php?option=com_content&view=article&id=102&Itemid=2" } \ No newline at end of file diff --git a/data/p2rp/p2rpbioschemas.jsonld b/data/p2rp/p2rpbioschemas.jsonld index c3871c223152d..883cc3b4e92b9 100644 --- a/data/p2rp/p2rpbioschemas.jsonld +++ b/data/p2rp/p2rpbioschemas.jsonld @@ -19,8 +19,8 @@ "biotools:primaryContact": "P2RP Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC3637814", "pubmed:23601859", + "pmcid:PMC3637814", { "@id": "https://doi.org/10.1186/1471-2164-14-269" } @@ -31,9 +31,9 @@ }, "sc:name": "Predicted Prokaryotic Regulatory Proteins (P2RP)", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.p2rp.org/index.php?PHPSESSID=a025bb831c57e0ec4c48933ac0685725" } diff --git a/data/p4p/p4pbioschemas.jsonld b/data/p4p/p4pbioschemas.jsonld index 05c0b0d58ccae..dbbcdf45801a4 100644 --- a/data/p4p/p4pbioschemas.jsonld +++ b/data/p4p/p4pbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkx389", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/p4p", "@type": "sc:SoftwareApplication", @@ -35,6 +31,10 @@ ], "sc:name": "P4P", "sc:url": "http://sing-group.org/p4p" + }, + { + "@id": "https://doi.org/10.1093/nar/gkx389", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/p53/p53bioschemas.jsonld b/data/p53/p53bioschemas.jsonld index b02a2111d0071..f06f50f251d4f 100644 --- a/data/p53/p53bioschemas.jsonld +++ b/data/p53/p53bioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "Unlicense", "sc:name": "p53", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "bils.se", "sc:url": "http://persson-group.scilifelab.se/p53/" diff --git a/data/p53mutagene/p53mutagenebioschemas.jsonld b/data/p53mutagene/p53mutagenebioschemas.jsonld index 2a3df14e15bdd..5530547ffdba5 100644 --- a/data/p53mutagene/p53mutagenebioschemas.jsonld +++ b/data/p53mutagene/p53mutagenebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "First online tool for statistical validation of hypotheses regarding the effect of p53 mutational status on gene regulation in cancer.", "sc:name": "p53MutaGene", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.chemoprofiling.org/cgi-bin/GEO/tp53/web_run_tp53.V1.pl" diff --git a/data/pa-sub/pa-subbioschemas.jsonld b/data/pa-sub/pa-subbioschemas.jsonld index 574994714b319..b6f248057e012 100644 --- a/data/pa-sub/pa-subbioschemas.jsonld +++ b/data/pa-sub/pa-subbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This tool can be used to predict the subcellular localization of proteins using established machine learning techniques.", "sc:name": "PA-SUB", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.cs.ualberta.ca/~bioinfo/PA/Sub/" } \ No newline at end of file diff --git a/data/paa/paabioschemas.jsonld b/data/paa/paabioschemas.jsonld index b69a79c882301..ae5e75cbb29e3 100644 --- a/data/paa/paabioschemas.jsonld +++ b/data/paa/paabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-0737-1114", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/paa", "@type": "sc:SoftwareApplication", @@ -30,10 +26,10 @@ ], "edam:has_output": [ { - "@id": "edam:data_2872" + "@id": "edam:data_2884" }, { - "@id": "edam:data_2884" + "@id": "edam:data_2872" } ], "sc:additionalType": [ @@ -42,10 +38,10 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3360" + "@id": "edam:topic_0121" }, { - "@id": "edam:topic_0121" + "@id": "edam:topic_3360" }, { "@id": "edam:topic_3518" @@ -55,11 +51,11 @@ "@id": "http://orcid.org/0000-0003-0737-1114" }, "sc:citation": [ + "pubmed:26803161", + "pmcid:PMC4866526", { "@id": "https://doi.org/10.1093/bioinformatics/btw037" - }, - "pubmed:26803161", - "pmcid:PMC4866526" + } ], "sc:contributor": "Martin Eisenacher", "sc:description": "It imports single color (protein) microarray data that has been saved in gpr file format. After preprocessing univariate feature preselection is performed. Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Thereto, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. It provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.", @@ -70,15 +66,15 @@ "sc:license": "BSD-3-Clause", "sc:name": "PAA - Protein Array Analyzer", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ - "BioInfra.Prot", - "This work is supported by de.NBI, a project of the BMBF [FKZ 031 A 534A].", "This work was supported by P.U.R.E., a project of Nordrhein-Westfalen, a federal state of Germany.", - "Ruhr-Universitaet Bochum, Medizinisches Proteom-Center (MPC)" + "Ruhr-Universitaet Bochum, Medizinisches Proteom-Center (MPC)", + "This work is supported by de.NBI, a project of the BMBF [FKZ 031 A 534A].", + "BioInfra.Prot" ], "sc:softwareHelp": { "@id": "https://www.bioconductor.org/packages/release/bioc/manuals/PAA/man/PAA.pdf" @@ -89,6 +85,10 @@ { "@id": "https://doi.org/10.1093/bioinformatics/btw037", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-0737-1114", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pacbio_sequencing_simulator/pacbio_sequencing_simulatorbioschemas.jsonld b/data/pacbio_sequencing_simulator/pacbio_sequencing_simulatorbioschemas.jsonld index 837a5f8629013..04e20cac5ed3c 100644 --- a/data/pacbio_sequencing_simulator/pacbio_sequencing_simulatorbioschemas.jsonld +++ b/data/pacbio_sequencing_simulator/pacbio_sequencing_simulatorbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2901-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/PacBio_Sequencing_Simulator", "@type": "sc:SoftwareApplication", @@ -24,20 +28,16 @@ "sc:description": "Sequencing simulator for PacBio sequencing with a high fidelity.", "sc:featureList": [ { - "@id": "edam:operation_3798" + "@id": "edam:operation_0524" }, { - "@id": "edam:operation_0524" + "@id": "edam:operation_3798" } ], "sc:license": "GPL-3.0", "sc:name": "PaSS", "sc:operatingSystem": "Linux", "sc:url": "http://cgm.sjtu.edu.cn/PaSS/" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2901-7", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/packmem/packmembioschemas.jsonld b/data/packmem/packmembioschemas.jsonld index ae86b25538e97..b96d25cbeb64d 100644 --- a/data/packmem/packmembioschemas.jsonld +++ b/data/packmem/packmembioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "PackMem", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://packmem.ipmc.cnrs.fr/index.html" } \ No newline at end of file diff --git a/data/packmol-memgen/packmol-memgenbioschemas.jsonld b/data/packmol-memgen/packmol-memgenbioschemas.jsonld index 7c940355a0ad5..897d336a7cb6e 100644 --- a/data/packmol-memgen/packmol-memgenbioschemas.jsonld +++ b/data/packmol-memgen/packmol-memgenbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "PACKMOL-Memgen", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://ambermd.org/AmberTools.php" } \ No newline at end of file diff --git a/data/pacman/pacmanbioschemas.jsonld b/data/pacman/pacmanbioschemas.jsonld index bfad54e170b24..e132554e3389b 100644 --- a/data/pacman/pacmanbioschemas.jsonld +++ b/data/pacman/pacmanbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Generates publication quality images of methylated motifs counts, locations and non-methylated locations, on one or both strands of the DNA. The user can apply several filters on the gff data to avoid bad quality modifications or low coverage, for example. The optional filters are the IPDratio, the coverage and the identification quality value (idqv). This web page requires upload of a bacterial full or draft genome, together with the motifs.gff file of a PacBio sequencing analysis.", "sc:name": "PACMAN", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://www.unifr.ch/bugfri/pacman", diff --git a/data/pacomplex/pacomplexbioschemas.jsonld b/data/pacomplex/pacomplexbioschemas.jsonld index c1cf0928f247b..0c3ed75574d1c 100644 --- a/data/pacomplex/pacomplexbioschemas.jsonld +++ b/data/pacomplex/pacomplexbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "PAComplex is a web server for inferring peptide antigen families and binding models from T-cell receptor-peptide MHC complexes.", "sc:name": "PAComplex", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://PAcomplex.life.nctu.edu.tw" } \ No newline at end of file diff --git a/data/padog/padogbioschemas.jsonld b/data/padog/padogbioschemas.jsonld index 5e38a0254ad1c..fa1de2d87a5f9 100644 --- a/data/padog/padogbioschemas.jsonld +++ b/data/padog/padogbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Adi Laurentiu Tarca", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package implements a general purpose gene set analysis method that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.", "sc:license": "GPL-2.0", "sc:name": "PADOG", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PADOG.html", "sc:version": "1.16.0" diff --git a/data/padre/padrebioschemas.jsonld b/data/padre/padrebioschemas.jsonld index 1da0352a2502a..ab387b0b89d7c 100644 --- a/data/padre/padrebioschemas.jsonld +++ b/data/padre/padrebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Padre", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.uea.ac.uk/computing/padre" } \ No newline at end of file diff --git a/data/padua/paduabioschemas.jsonld b/data/padua/paduabioschemas.jsonld index b938729f4f795..4cb8e6a198eae 100644 --- a/data/padua/paduabioschemas.jsonld +++ b/data/padua/paduabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "BSD-2-Clause", "sc:name": "PaDuA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/mfitzp/padua" } \ No newline at end of file diff --git a/data/pagal/pagalbioschemas.jsonld b/data/pagal/pagalbioschemas.jsonld index ac2378d843399..65fcafa3e56d7 100644 --- a/data/pagal/pagalbioschemas.jsonld +++ b/data/pagal/pagalbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.4952.3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pagal", "@type": "sc:SoftwareApplication", @@ -17,27 +21,23 @@ { "@id": "https://doi.org/10.12688/F1000RESEARCH.4952.3" }, - "pubmed:25352981", - "pmcid:PMC4207245" + "pmcid:PMC4207245", + "pubmed:25352981" ], "sc:description": "Properties and corresponding graphics of alpha helical structures in proteins.", "sc:featureList": [ - { - "@id": "edam:operation_0321" - }, { "@id": "edam:operation_0407" }, { "@id": "edam:operation_0394" + }, + { + "@id": "edam:operation_0321" } ], "sc:name": "Pagal", "sc:url": "https://github.com/sanchak/pagal" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.4952.3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pageman/pagemanbioschemas.jsonld b/data/pageman/pagemanbioschemas.jsonld index 2788f18a0b9db..c87c1a91f1845 100644 --- a/data/pageman/pagemanbioschemas.jsonld +++ b/data/pageman/pagemanbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "PageMan is a tool to get a quick overview of multiparallel experiments. PageMan also helps comparing experiments from different organisms.", "sc:name": "PageMan", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mapman.gabipd.org/web/guest/pageman", "sc:version": "0.12" diff --git a/data/pager/pagerbioschemas.jsonld b/data/pager/pagerbioschemas.jsonld index 94e267891c2dc..0c1823a0ea493 100644 --- a/data/pager/pagerbioschemas.jsonld +++ b/data/pager/pagerbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-017-1889-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pager", "@type": "sc:SoftwareApplication", @@ -27,15 +31,11 @@ }, "sc:name": "PAGER", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://discovery.informatics.uab.edu/PAGER/" - }, - { - "@id": "https://doi.org/10.1186/s12859-017-1889-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/paice/paicebioschemas.jsonld b/data/paice/paicebioschemas.jsonld index ae095d7237b0a..8bb84ed7cb684 100644 --- a/data/paice/paicebioschemas.jsonld +++ b/data/paice/paicebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PAICE", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sourceforge.net/projects/paice/", "sc:version": "2.92" diff --git a/data/pair/pairbioschemas.jsonld b/data/pair/pairbioschemas.jsonld index c7b3606bcfd59..b5a3534457131 100644 --- a/data/pair/pairbioschemas.jsonld +++ b/data/pair/pairbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Experimentally reported molecular interactions and predicted interactions in A. thaliana. It predicts interactions by a fine-tuned support vector machine model that integrates indirect evidences for interaction, such as gene co-expressions, domain interactions, shared GO annotations, co-localizations, phylogenetic profile similarities and homologous interactions in other organisms. It features a user-friendly query interface, providing rich annotation on the relationships between two proteins.", "sc:name": "PAIR", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.cls.zju.edu.cn/pair/" } \ No newline at end of file diff --git a/data/paircompviz/bioconda_paircompviz.yaml b/data/paircompviz/bioconda_paircompviz.yaml index f7f1532878c51..c27d1cb9d352d 100644 --- a/data/paircompviz/bioconda_paircompviz.yaml +++ b/data/paircompviz/bioconda_paircompviz.yaml @@ -8,7 +8,6 @@ description: This package provides visualization of the results from the multipl home: https://bioconductor.org/packages/3.10/bioc/html/paircompviz.html identifiers: - biotools:paircompviz -- doi:10.1038/nmeth.3252 license: GPL (>=3.0) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-paircompviz diff --git a/data/paircompviz/paircompvizbioschemas.jsonld b/data/paircompviz/paircompvizbioschemas.jsonld index d187339c79802..907c065fe30a8 100644 --- a/data/paircompviz/paircompvizbioschemas.jsonld +++ b/data/paircompviz/paircompvizbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michal Burda", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.", "sc:license": "GPL-3.0", "sc:name": "paircompviz", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/paircompviz.html", "sc:version": "1.12.0" diff --git a/data/pairheatmap/pairheatmapbioschemas.jsonld b/data/pairheatmap/pairheatmapbioschemas.jsonld index c0cfc4d06ea19..537ceafa5d520 100644 --- a/data/pairheatmap/pairheatmapbioschemas.jsonld +++ b/data/pairheatmap/pairheatmapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool to compare two heatmaps and discover patterns within and across groups.", "sc:name": "pairheatmap", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://cran.r-project.org/web/packages/pairheatmap/index.html" } \ No newline at end of file diff --git a/data/pal2nal/pal2nalbioschemas.jsonld b/data/pal2nal/pal2nalbioschemas.jsonld index 78d9cdc9eef08..6bcbf4dcf55ef 100644 --- a/data/pal2nal/pal2nalbioschemas.jsonld +++ b/data/pal2nal/pal2nalbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.", "sc:name": "PAL2NAL", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.bork.embl.de/pal2nal/" diff --git a/data/palalign/palalignbioschemas.jsonld b/data/palalign/palalignbioschemas.jsonld index 3c4e4a2663a8c..0065b52d66e37 100644 --- a/data/palalign/palalignbioschemas.jsonld +++ b/data/palalign/palalignbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software of alignment of metabolic pathways without abstraction.", "sc:name": "palAlign", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinformatics.cise.ufl.edu/palAlign.html" } \ No newline at end of file diff --git a/data/paleomix/paleomixbioschemas.jsonld b/data/paleomix/paleomixbioschemas.jsonld index fb5ffe79b531e..dca2a0d593cd0 100644 --- a/data/paleomix/paleomixbioschemas.jsonld +++ b/data/paleomix/paleomixbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/paleomix", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ludovic Orlando", - "Mikkel Schubert" + "Mikkel Schubert", + "Ludovic Orlando" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:24722405", "sc:description": "User-friendly package designed for Unix-like systems and largely automates the analyses related to whole genome re-sequencing. It is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP calling, and metagenomic profiling.", "sc:name": "PALEOMIX", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://geogenetics.ku.dk/publications/paleomix" } \ No newline at end of file diff --git a/data/pales/palesbioschemas.jsonld b/data/pales/palesbioschemas.jsonld index 063fcf474fa56..f29e4be9a27b1 100644 --- a/data/pales/palesbioschemas.jsonld +++ b/data/pales/palesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software for analysis of residual dipolar couplings. Its main component is the Prediction of ALignmEnt from Structure simulation that predicts the magnitude and orientation of a sterically induced alignment tensor from a solute’s (protein/nucleic acid/oligosaccharide) three-dimensional shape.", "sc:name": "PALES", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www3.mpibpc.mpg.de/groups/zweckstetter/_links/software_pales.htm" } \ No newline at end of file diff --git a/data/palindrome/palindromebioschemas.jsonld b/data/palindrome/palindromebioschemas.jsonld index 9eb4641b8431c..d4fbab2698fa4 100644 --- a/data/palindrome/palindromebioschemas.jsonld +++ b/data/palindrome/palindromebioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "UK MRC", + "EMBOSS Contributors", "Wellcome Trust", - "EMBOSS Contributors" + "UK BBSRC", + "UK MRC" ], "sc:description": "Find inverted repeats in nucleotide sequence(s).", "sc:funder": [ - "UK MRC", "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "palindrome", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/palindrome.html", "sc:version": "r6" diff --git a/data/palmapper/palmapperbioschemas.jsonld b/data/palmapper/palmapperbioschemas.jsonld index a4c869997d495..3c8a720d65f54 100644 --- a/data/palmapper/palmapperbioschemas.jsonld +++ b/data/palmapper/palmapperbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "PALMapper", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.fml.tuebingen.mpg.de/raetsch/suppl/palmapper" } \ No newline at end of file diff --git a/data/palmsiever/palmsieverbioschemas.jsonld b/data/palmsiever/palmsieverbioschemas.jsonld index 48208d2e8b757..e0489c1e014ae 100644 --- a/data/palmsiever/palmsieverbioschemas.jsonld +++ b/data/palmsiever/palmsieverbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Platform designed for the visualization and analysis of single-molecule localization microscopy data. It includes interactive browsing, filtering and analysis, plus the ability to extend its functionality through plugins.", "sc:name": "PALMsiever", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/PALMsiever/palm-siever/wiki" } \ No newline at end of file diff --git a/data/pals/palsbioschemas.jsonld b/data/pals/palsbioschemas.jsonld index 025f3b56a53cc..e0354b2a42d19 100644 --- a/data/pals/palsbioschemas.jsonld +++ b/data/pals/palsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The tool highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.", "sc:name": "PaLS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://pals.bioinfo.cnio.es" } \ No newline at end of file diff --git a/data/paml/pamlbioschemas.jsonld b/data/paml/pamlbioschemas.jsonld index 3ee38175e4ca9..a3482fb07347c 100644 --- a/data/paml/pamlbioschemas.jsonld +++ b/data/paml/pamlbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:description": "Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.", "sc:name": "PAML", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://abacus.gene.ucl.ac.uk/software/paml.html" diff --git a/data/pan-tetris/pan-tetrisbioschemas.jsonld b/data/pan-tetris/pan-tetrisbioschemas.jsonld index 922785da8366a..1b8b2b051a9aa 100644 --- a/data/pan-tetris/pan-tetrisbioschemas.jsonld +++ b/data/pan-tetris/pan-tetrisbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Pan-Tetris is our interactive software tool that enables the visual inspection of gene occurrences in a pan-genome table. It allows the user to modify the composition of such pan gene groups with an aggregation technique that is inspired by the famous Tetris game.", "sc:name": "Pan-Tetris", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://it.inf.uni-tuebingen.de/?page_id=920", diff --git a/data/pan4draft/pan4draftbioschemas.jsonld b/data/pan4draft/pan4draftbioschemas.jsonld index bf48a550ca2fe..e889c1fbb0b38 100644 --- a/data/pan4draft/pan4draftbioschemas.jsonld +++ b/data/pan4draft/pan4draftbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "Pan4Draft", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.computationalbiology.ufpa.br/pan4drafts" diff --git a/data/panacea/panaceabioschemas.jsonld b/data/panacea/panaceabioschemas.jsonld index 311b4c42f0e94..3b67f4f3500ea 100644 --- a/data/panacea/panaceabioschemas.jsonld +++ b/data/panacea/panaceabioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://orcid.org/0000-0002-1916-1029", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/s12859-018-2250-y", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/panacea", "@type": "sc:SoftwareApplication", @@ -21,8 +25,8 @@ }, "sc:additionalType": "Suite", "sc:citation": [ - "pubmed:29945570", "pmcid:PMC6020400", + "pubmed:29945570", { "@id": "https://doi.org/10.1186/s12859-018-2250-y" } @@ -34,15 +38,11 @@ "sc:license": "GPL-2.0", "sc:name": "PanACEA", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/JCVenterInstitute/PanACEA" - }, - { - "@id": "https://doi.org/10.1186/s12859-018-2250-y", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/panada/panadabioschemas.jsonld b/data/panada/panadabioschemas.jsonld index e71ec838adc17..8fcea008ea497 100644 --- a/data/panada/panadabioschemas.jsonld +++ b/data/panada/panadabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Protein similarity network generation method for Cytoscape.", "sc:name": "PANADA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/download/", diff --git a/data/panalyzer/panalyzerbioschemas.jsonld b/data/panalyzer/panalyzerbioschemas.jsonld index 5bf46cd9457d9..051b67dd1ba5a 100644 --- a/data/panalyzer/panalyzerbioschemas.jsonld +++ b/data/panalyzer/panalyzerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A tool for rearranging peptide sequences from shotgun proteomics into inferred proteins.", "sc:name": "PAnalyzer", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://code.google.com/archive/p/ehu-bio/wikis/PAnalyzer.wiki" } \ No newline at end of file diff --git a/data/panda-view/panda-viewbioschemas.jsonld b/data/panda-view/panda-viewbioschemas.jsonld index b9232fabc58ce..f428a1a909989 100644 --- a/data/panda-view/panda-viewbioschemas.jsonld +++ b/data/panda-view/panda-viewbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/PANDA-view", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Cheng Chang", - "Yunping Zhu" + "Yunping Zhu", + "Cheng Chang" ], "sc:additionalType": "Desktop application", "sc:description": "Tool for statistical analysis and visualization of quantitative proteomics data", diff --git a/data/panda/pandabioschemas.jsonld b/data/panda/pandabioschemas.jsonld index 9118b995e798d..54ad1a5738d9f 100644 --- a/data/panda/pandabioschemas.jsonld +++ b/data/panda/pandabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast.", "sc:name": "PANDA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://sites.google.com/a/channing.harvard.edu/kimberlyglass/tools/panda" } \ No newline at end of file diff --git a/data/panda_associations/panda_associationsbioschemas.jsonld b/data/panda_associations/panda_associationsbioschemas.jsonld index cfc9adaeb7180..03ce20d6ca403 100644 --- a/data/panda_associations/panda_associationsbioschemas.jsonld +++ b/data/panda_associations/panda_associationsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PAnDA is an algorithm for the prediction of direct and indirect TF binding events.", "sc:name": "PAnDA (Protein And DNA Associations)", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://s.tartaglialab.com/new_submission/panda" } \ No newline at end of file diff --git a/data/panda_xplorer/panda_xplorerbioschemas.jsonld b/data/panda_xplorer/panda_xplorerbioschemas.jsonld index ded4f028711e3..8bdbb2f93caf3 100644 --- a/data/panda_xplorer/panda_xplorerbioschemas.jsonld +++ b/data/panda_xplorer/panda_xplorerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A data visualization tool capable of annotating genes with any data type and graphically displaying the result within the context of pathways.", "sc:name": "PANDA XPLORER", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioinformaticstools.mayo.edu/research/panda/" } \ No newline at end of file diff --git a/data/pandar/pandarbioschemas.jsonld b/data/pandar/pandarbioschemas.jsonld index 807a4b99569f1..81cca73c3b4a1 100644 --- a/data/pandar/pandarbioschemas.jsonld +++ b/data/pandar/pandarbioschemas.jsonld @@ -17,8 +17,8 @@ "@id": "https://bio.tools/pandar", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dan Schlauch", - "Joseph N. Paulson" + "Joseph N. Paulson", + "Dan Schlauch" ], "sc:additionalType": [ "Command-line tool", @@ -38,9 +38,9 @@ "sc:license": "GPL-2.0", "sc:name": "pandaR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pandaR.html", "sc:version": "1.6.0" diff --git a/data/pandora/pandorabioschemas.jsonld b/data/pandora/pandorabioschemas.jsonld index bad46c1de9917..3dd611dc042a8 100644 --- a/data/pandora/pandorabioschemas.jsonld +++ b/data/pandora/pandorabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The PANDORA web server integrates annotations for the biological analysis of sets of genes, proteins or peptides.", "sc:name": "PANDORA", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.pandora.cs.huji.ac.il" } \ No newline at end of file diff --git a/data/pandrugs/pandrugsbioschemas.jsonld b/data/pandrugs/pandrugsbioschemas.jsonld index 3b379727c4469..628a56ab8125a 100644 --- a/data/pandrugs/pandrugsbioschemas.jsonld +++ b/data/pandrugs/pandrugsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-2773-2343", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/pandrugs", "@type": "sc:SoftwareApplication", @@ -30,12 +26,16 @@ "sc:license": "GPL-3.0", "sc:name": "PanDrugs", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://www.pandrugs.org/", "sc:version": "2018.06.18" + }, + { + "@id": "https://orcid.org/0000-0003-2773-2343", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/panelapp/panelappbioschemas.jsonld b/data/panelapp/panelappbioschemas.jsonld index f3e8ec19434e8..43b1ffef3bf17 100644 --- a/data/panelapp/panelappbioschemas.jsonld +++ b/data/panelapp/panelappbioschemas.jsonld @@ -11,10 +11,10 @@ "@id": "https://bio.tools/panelapp", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web service", - "Database portal", + "Web API", "Web application", - "Web API" + "Database portal", + "Web service" ], "sc:description": "Genomics England PanelApp is a publically-available knowledgebase that allows virtual gene panels related to human disorders to be created, stored and queried. It includes a crowdsourcing tool that allows genes to be added or reviewed by experts throughout the worldwide scientific community, providing an opportunity for the standardisation of gene panels, and a consensus on which genes have sufficient evidence for disease association.", "sc:name": "PanelApp", diff --git a/data/panfp/panfpbioschemas.jsonld b/data/panfp/panfpbioschemas.jsonld index bdcc64aedafda..c74ee94ca1b4b 100644 --- a/data/panfp/panfpbioschemas.jsonld +++ b/data/panfp/panfpbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "This software is a tool to predict functional composition of microbial communities based on communities survey data which builds a pangenome for each OTU and assigns the pangenome’s functional profile to the OTU.", "sc:name": "PanFP", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/srjun/PanFP" } \ No newline at end of file diff --git a/data/pangaea/pangaeabioschemas.jsonld b/data/pangaea/pangaeabioschemas.jsonld index cd1f9d1f0f6d9..286d14e197132 100644 --- a/data/pangaea/pangaeabioschemas.jsonld +++ b/data/pangaea/pangaeabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PANGAEA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.pangaea.de/" } \ No newline at end of file diff --git a/data/pangea/pangeabioschemas.jsonld b/data/pangea/pangeabioschemas.jsonld index e2f587338dacf..659fa187eea6d 100644 --- a/data/pangea/pangeabioschemas.jsonld +++ b/data/pangea/pangeabioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "PanGEA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.kofler.or.at/bioinformatics/PanGEA" } \ No newline at end of file diff --git a/data/pannbuilder/pannbuilderbioschemas.jsonld b/data/pannbuilder/pannbuilderbioschemas.jsonld index 1cd76a341fa09..5d921041948ab 100644 --- a/data/pannbuilder/pannbuilderbioschemas.jsonld +++ b/data/pannbuilder/pannbuilderbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Li Hong", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Processing annotation data from public data repositories and building protein-centric annotation data packages.", "sc:license": "GPL-2.0", "sc:name": "PAnnBuilder", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PAnnBuilder.html", "sc:version": "1.38.0" diff --git a/data/pannotator/pannotatorbioschemas.jsonld b/data/pannotator/pannotatorbioschemas.jsonld index 460acd6b5b17e..ce56d7a04c9e4 100644 --- a/data/pannotator/pannotatorbioschemas.jsonld +++ b/data/pannotator/pannotatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Automated pipeline for the annotation of closely related genomes well suited for pangenome studies.", "sc:name": "PANNOTATOR", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bnet.egr.vcu.edu/pannotator/pannotator.php" } \ No newline at end of file diff --git a/data/panorama/panoramabioschemas.jsonld b/data/panorama/panoramabioschemas.jsonld index 2f674fe370024..68a0b17f5409b 100644 --- a/data/panorama/panoramabioschemas.jsonld +++ b/data/panorama/panoramabioschemas.jsonld @@ -19,26 +19,26 @@ "biotools:primaryContact": "Brendan MacLean", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:25102069", + "pmcid:PMC4156235", { "@id": "https://doi.org/10.1021/PR5006636" - }, - "pmcid:PMC4156235", - "pubmed:25102069" + } ], "sc:description": "A web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments.", "sc:featureList": [ { - "@id": "edam:operation_3801" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_3801" } ], "sc:name": "Panorama", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://panoramaweb.org/project/home/begin.view?" } diff --git a/data/panoromix/panoromixbioschemas.jsonld b/data/panoromix/panoromixbioschemas.jsonld index d196f1482c6a4..817dd34d06fa8 100644 --- a/data/panoromix/panoromixbioschemas.jsonld +++ b/data/panoromix/panoromixbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PanoromiX", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://bioinfo-abcc.ncifcrf.gov/panoromics/" } \ No newline at end of file diff --git a/data/panow/panowbioschemas.jsonld b/data/panow/panowbioschemas.jsonld index 621c9d7d8b571..6c5870c9f9644 100644 --- a/data/panow/panowbioschemas.jsonld +++ b/data/panow/panowbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "PANOW (Poisson Approximation for the Number of Occurrences of Words)is a software dedicated to the search of rare words in biological sequences (over- or under-represented words in DNA or protein sequences).", "sc:name": "PANOW", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.math-evry.cnrs.fr/logiciels/panow", "sc:version": "1.0" diff --git a/data/panp/panpbioschemas.jsonld b/data/panp/panpbioschemas.jsonld index 5581b188fd66c..9fadc186f4832 100644 --- a/data/panp/panpbioschemas.jsonld +++ b/data/panp/panpbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Peter Warren", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. It is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.", "sc:license": "GPL-2.0", "sc:name": "panp", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/panp.html", "sc:version": "1.44.0" diff --git a/data/panr/panrbioschemas.jsonld b/data/panr/panrbioschemas.jsonld index 75d52d095bef9..510198e3baf43 100644 --- a/data/panr/panrbioschemas.jsonld +++ b/data/panr/panrbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xin Wang", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.", "sc:license": "Artistic-2.0", "sc:name": "PANR", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PANR.html", "sc:version": "1.20.0" diff --git a/data/panther/pantherbioschemas.jsonld b/data/panther/pantherbioschemas.jsonld index 6356465c0fce9..f38fa43174be0 100644 --- a/data/panther/pantherbioschemas.jsonld +++ b/data/panther/pantherbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PANTHER Tools", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.pantherdb.org/tools/" } \ No newline at end of file diff --git a/data/pantherscore/pantherscorebioschemas.jsonld b/data/pantherscore/pantherscorebioschemas.jsonld index a231748e6e862..4d3a3d7f813ad 100644 --- a/data/pantherscore/pantherscorebioschemas.jsonld +++ b/data/pantherscore/pantherscorebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Score protein sequences against the entire PANTHER HMM library and analyze your sequences.", "sc:name": "pantherScore", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.pantherdb.org/downloads/", "sc:version": "1.03" diff --git a/data/panvizgenerator/panvizgeneratorbioschemas.jsonld b/data/panvizgenerator/panvizgeneratorbioschemas.jsonld index 163571b626871..623620aea83d6 100644 --- a/data/panvizgenerator/panvizgeneratorbioschemas.jsonld +++ b/data/panvizgenerator/panvizgeneratorbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "PanVizGenerator", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PanVizGenerator.html", "sc:version": "1.2.0" diff --git a/data/papa/papabioschemas.jsonld b/data/papa/papabioschemas.jsonld index 71873fd0c9a64..0da66c2610464 100644 --- a/data/papa/papabioschemas.jsonld +++ b/data/papa/papabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "PAPA is a flexible tool for pleiotropic pathway analysis utilizing GWAS summary results.", "sc:name": "PAPA", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://sourceforge.net/projects/papav1/" } \ No newline at end of file diff --git a/data/paparazzi/paparazzibioschemas.jsonld b/data/paparazzi/paparazzibioschemas.jsonld index f3d8e2bf1e314..959138fc63080 100644 --- a/data/paparazzi/paparazzibioschemas.jsonld +++ b/data/paparazzi/paparazzibioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PAPARA(ZZ)I", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ElsevierSoftwareX/SOFTX-D-16-00015", "sc:version": "v2.6" diff --git a/data/paperbot/paperbotbioschemas.jsonld b/data/paperbot/paperbotbioschemas.jsonld index 0eff5d88e4a38..fe4e5ce30f03e 100644 --- a/data/paperbot/paperbotbioschemas.jsonld +++ b/data/paperbot/paperbotbioschemas.jsonld @@ -14,19 +14,19 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:30678631", + "pmcid:PMC6345070", { "@id": "https://doi.org/10.1186/s12859-019-2613-z" }, - "pmcid:PMC6345070" + "pubmed:30678631" ], "sc:description": "Open-source web-based search and metadata organization of scientific literature.", "sc:featureList": [ { - "@id": "edam:operation_0305" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_0305" }, { "@id": "edam:operation_2422" @@ -34,8 +34,8 @@ ], "sc:name": "PaperBot", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://paperbot.ai/" diff --git a/data/papi/papibioschemas.jsonld b/data/papi/papibioschemas.jsonld index 62a6d94785801..e014e8b498611 100644 --- a/data/papi/papibioschemas.jsonld +++ b/data/papi/papibioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Raphael Aggio", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The Pathway Activity Profiling is an R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. It generates hypothesis that improves the final biological interpretation.", "sc:license": "GPL-2.0", "sc:name": "PAPi", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PAPi.html", "sc:version": "1.14.0" diff --git a/data/paragraph/paragraphbioschemas.jsonld b/data/paragraph/paragraphbioschemas.jsonld index 7735cbc8e98c7..ab5c164e71408 100644 --- a/data/paragraph/paragraphbioschemas.jsonld +++ b/data/paragraph/paragraphbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Paragraph", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/Illumina/paragraph" } \ No newline at end of file diff --git a/data/parallelgwas/parallelgwasbioschemas.jsonld b/data/parallelgwas/parallelgwasbioschemas.jsonld index 9885d99c5e8d5..bada63a343b03 100644 --- a/data/parallelgwas/parallelgwasbioschemas.jsonld +++ b/data/parallelgwas/parallelgwasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Developing parallel computing tools for genome-wide association studies.", "sc:name": "parallelGWAS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://en.osdn.jp/projects/parallelgwas/" } \ No newline at end of file diff --git a/data/parallelnewhybrid/parallelnewhybridbioschemas.jsonld b/data/parallelnewhybrid/parallelnewhybridbioschemas.jsonld index a991f5431ddc8..421784efd5a5f 100644 --- a/data/parallelnewhybrid/parallelnewhybridbioschemas.jsonld +++ b/data/parallelnewhybrid/parallelnewhybridbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An R package for the parallelization of hybrid detection using newhybrid.", "sc:name": "parallelnewhybrid", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/bwringe/parallelnewhybrid" } \ No newline at end of file diff --git a/data/paralyzer/paralyzerbioschemas.jsonld b/data/paralyzer/paralyzerbioschemas.jsonld index 32b0b3cc10cbe..58b0fbd2f3506 100644 --- a/data/paralyzer/paralyzerbioschemas.jsonld +++ b/data/paralyzer/paralyzerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool to analyze cross-linking and immunoprecipitation data (CLIP)", "sc:name": "PARalyzer", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/" } \ No newline at end of file diff --git a/data/parameciumdb/parameciumdbbioschemas.jsonld b/data/parameciumdb/parameciumdbbioschemas.jsonld index 3d67f9a49f53d..f662d4d143c92 100644 --- a/data/parameciumdb/parameciumdbbioschemas.jsonld +++ b/data/parameciumdb/parameciumdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "ParameciumDB", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://paramecium.i2bc.paris-saclay.fr" } \ No newline at end of file diff --git a/data/paratome/paratomebioschemas.jsonld b/data/paratome/paratomebioschemas.jsonld index 82264717c61b3..945e4d1713fe5 100644 --- a/data/paratome/paratomebioschemas.jsonld +++ b/data/paratome/paratomebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web tool for the identification of Antigen Binding Regions (ABRs) in antibodies. It accepts as an input the sequences or 3D structures (in PDB format) of antibodies.", "sc:name": "Paratome", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.ofranlab.org/paratome/" } \ No newline at end of file diff --git a/data/parbibit/parbibitbioschemas.jsonld b/data/parbibit/parbibitbioschemas.jsonld index b80225c3ffee8..4ff939b09fccb 100644 --- a/data/parbibit/parbibitbioschemas.jsonld +++ b/data/parbibit/parbibitbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Parallel tool to accelerate the search of biclusters on binary datasets, especially useful for gene expression data. This tool receives as input the expression values of n genes and m samples in a file with ARFF extension and returns a file with the biclustering information.", "sc:name": "ParBiBit", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://sourceforge.net/projects/parbibit/" } \ No newline at end of file diff --git a/data/parfr/parfrbioschemas.jsonld b/data/parfr/parfrbioschemas.jsonld index 8d2566a4acff3..77e1f44932684 100644 --- a/data/parfr/parfrbioschemas.jsonld +++ b/data/parfr/parfrbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PaRFR", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www2.imperial.ac.uk/~gmontana/parfr.htm" } \ No newline at end of file diff --git a/data/pargenes/pargenesbioschemas.jsonld b/data/pargenes/pargenesbioschemas.jsonld index af2ba1f80e4f3..6c55b6f516c5d 100644 --- a/data/pargenes/pargenesbioschemas.jsonld +++ b/data/pargenes/pargenesbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "ParGenes", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/BenoitMorel/ParGenes" } \ No newline at end of file diff --git a/data/parglms/parglmsbioschemas.jsonld b/data/parglms/parglmsbioschemas.jsonld index e1ffd14d07733..77f7f30a41366 100644 --- a/data/parglms/parglmsbioschemas.jsonld +++ b/data/parglms/parglmsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "parglms", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/parglms.html", "sc:version": "1.12.0" diff --git a/data/parmigene/parmigenebioschemas.jsonld b/data/parmigene/parmigenebioschemas.jsonld index 621f641ce5226..d7cb407347f0a 100644 --- a/data/parmigene/parmigenebioschemas.jsonld +++ b/data/parmigene/parmigenebioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "AGPL-3.0", "sc:name": "parmigene", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://cran.r-project.org/web/packages/parmigene/index.html", diff --git a/data/parody/bioconda_parody.yaml b/data/parody/bioconda_parody.yaml index c892df3814730..14f9415375736 100644 --- a/data/parody/bioconda_parody.yaml +++ b/data/parody/bioconda_parody.yaml @@ -4,7 +4,6 @@ description: routines for univariate and multivariate outlier detection with a f home: https://bioconductor.org/packages/3.10/bioc/html/parody.html identifiers: - biotools:parody -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-parody summary: Parametric And Resistant Outlier DYtection diff --git a/data/parody/parodybioschemas.jsonld b/data/parody/parodybioschemas.jsonld index 29c29b5d8b3fd..6a0715f1c58e4 100644 --- a/data/parody/parodybioschemas.jsonld +++ b/data/parody/parodybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "parody", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/parody.html", "sc:version": "1.32.0" diff --git a/data/pars/parsbioschemas.jsonld b/data/pars/parsbioschemas.jsonld index 4a4d268ad72ab..341cb51f4d77d 100644 --- a/data/pars/parsbioschemas.jsonld +++ b/data/pars/parsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Server for the prediction of allosteric and regulatory sites on protein structures. It queries protein dynamics and structural conservation to identify pockets that may exert a regulatory effect upon binding of a small-molecule ligand.", "sc:name": "PARS", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioinf.uab.cat/cgi-bin/pars-cgi/pars.pl" diff --git a/data/parseq/parseqbioschemas.jsonld b/data/parseq/parseqbioschemas.jsonld index 12c6dd8028fe1..db8ee53139900 100644 --- a/data/parseq/parseqbioschemas.jsonld +++ b/data/parseq/parseqbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/parseq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hugues Richard", "Pierre Nicolas", + "Hugues Richard", "Bogdan Mirauta" ], "sc:additionalType": "Command-line tool", diff --git a/data/parsnip/parsnipbioschemas.jsonld b/data/parsnip/parsnipbioschemas.jsonld index 5a9b2471fa744..637c7037becf7 100644 --- a/data/parsnip/parsnipbioschemas.jsonld +++ b/data/parsnip/parsnipbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Sequence-based protein solubility prediction using gradient boosting machine.", "sc:name": "PaRSnIP", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/RedaRawi/PaRSnIP" diff --git a/data/partek_genomics_suite/partek_genomics_suitebioschemas.jsonld b/data/partek_genomics_suite/partek_genomics_suitebioschemas.jsonld index e4a79bc1b5251..3104e3a852ce2 100644 --- a/data/partek_genomics_suite/partek_genomics_suitebioschemas.jsonld +++ b/data/partek_genomics_suite/partek_genomics_suitebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Easy to use software providing A to Z analysis for all Next Generation Sequencing and Microarray data.", "sc:name": "Partek Genomics Suite", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.partek.com" diff --git a/data/particlestats/particlestatsbioschemas.jsonld b/data/particlestats/particlestatsbioschemas.jsonld index c4a9859ab43de..d84a2c0e4897a 100644 --- a/data/particlestats/particlestatsbioschemas.jsonld +++ b/data/particlestats/particlestatsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web server for particle motility analysis such as cytoskeleton. Input is X,Y coordinates of objects in time and output is novel analyses, graphical plots and statistics for motile objects.", "sc:name": "ParticleStats", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.ParticleStats.com" diff --git a/data/parties/partiesbioschemas.jsonld b/data/parties/partiesbioschemas.jsonld index 27dffb8721da6..90fa30151cd32 100644 --- a/data/parties/partiesbioschemas.jsonld +++ b/data/parties/partiesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms.", "sc:name": "ParTIES", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/oarnaiz/ParTIES" } \ No newline at end of file diff --git a/data/partifold/partifoldbioschemas.jsonld b/data/partifold/partifoldbioschemas.jsonld index 02932be95f23b..5bfe13c57111e 100644 --- a/data/partifold/partifoldbioschemas.jsonld +++ b/data/partifold/partifoldbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software to investigate the folding landscape of TMBs (Transmembrane Beta-barrel Proteins).", "sc:name": "partiFold", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://partifold.csail.mit.edu/" diff --git a/data/partigenedb/partigenedbbioschemas.jsonld b/data/partigenedb/partigenedbbioschemas.jsonld index 34ecaff22011d..7d9fcb4feae7d 100644 --- a/data/partigenedb/partigenedbbioschemas.jsonld +++ b/data/partigenedb/partigenedbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of about 300 partial genomes from eukaryotic organisms that have been assembled from EST data.", "sc:name": "PartiGeneDB", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.partigenedb.org/" } \ No newline at end of file diff --git a/data/partsgenie/partsgeniebioschemas.jsonld b/data/partsgenie/partsgeniebioschemas.jsonld index f71ee60f5b3f9..613c17878f3a2 100644 --- a/data/partsgenie/partsgeniebioschemas.jsonld +++ b/data/partsgenie/partsgeniebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Integrated tool for optimizing and sharing synthetic biology parts.", "sc:name": "PartsGenie", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://parts.synbiochem.co.uk/#" } \ No newline at end of file diff --git a/data/pascca/pasccabioschemas.jsonld b/data/pascca/pasccabioschemas.jsonld index 115cb5ccd4ea2..6e54f7a1f8075 100644 --- a/data/pascca/pasccabioschemas.jsonld +++ b/data/pascca/pasccabioschemas.jsonld @@ -22,22 +22,22 @@ ], "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6343338", "pubmed:30669970", { "@id": "https://doi.org/10.1186/s12864-019-5433-7" - }, - "pmcid:PMC6343338" + } ], "sc:description": "R package for analyses of alternative polyadenylation (APA) related gene expression, including the characterization of poly(A) sites, quantification of association between genes with/without repeated measurements, clustering of APA-related genes to infer significant APA specific gene modules, and the evaluation of clustering performance with a variety of indexes.", "sc:featureList": [ - { - "@id": "edam:operation_2495" - }, { "@id": "edam:operation_0313" }, { "@id": "edam:operation_3766" + }, + { + "@id": "edam:operation_2495" } ], "sc:license": "Apache-2.0", diff --git a/data/pasd-qc/pasd-qcbioschemas.jsonld b/data/pasd-qc/pasd-qcbioschemas.jsonld index a07fd233fc48b..b162376602cab 100644 --- a/data/pasd-qc/pasd-qcbioschemas.jsonld +++ b/data/pasd-qc/pasd-qcbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkx1195", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pasd-qc", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ ], "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5829578", + "pubmed:29186545", { "@id": "https://doi.org/10.1093/nar/gkx1195" - }, - "pubmed:29186545", - "pmcid:PMC5829578" + } ], "sc:description": "Quality control for single cell whole-genome sequencing data using power spectral density estimation.", "sc:featureList": { @@ -30,15 +34,11 @@ }, "sc:name": "PaSD-qc", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/parklab/PaSDqc" - }, - { - "@id": "https://doi.org/10.1093/nar/gkx1195", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pasgal/pasgalbioschemas.jsonld b/data/pasgal/pasgalbioschemas.jsonld index c7e62c0ef16a8..c07ed0f798642 100644 --- a/data/pasgal/pasgalbioschemas.jsonld +++ b/data/pasgal/pasgalbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/PaSGAL", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Srinivas Aluru", - "Haowen Zhang" + "Haowen Zhang", + "Srinivas Aluru" ], "sc:additionalType": "Command-line tool", "sc:description": "PaSGAL (Parallel Sequence to Graph Aligner) is designed to accelerate local sequence alignment of sequences to directed acyclic sequence graphs (DAGs), e.g., variation graphs, splicing graphs.", @@ -20,8 +20,8 @@ "sc:name": "PaSGAL", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://alurulab.cc.gatech.edu/PaSGAL" } \ No newline at end of file diff --git a/data/pasmet/pasmetbioschemas.jsonld b/data/pasmet/pasmetbioschemas.jsonld index 151195023200b..27f1b39ce96a7 100644 --- a/data/pasmet/pasmetbioschemas.jsonld +++ b/data/pasmet/pasmetbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-based platform for predicting, modelling and analysing metabolic systems. It is a non-commercial and user-friendly tool for assisting non-experts in mathematical modelling, computing or programming to work on computational biology.", "sc:name": "PASMet", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://pasmet.riken.jp/" } \ No newline at end of file diff --git a/data/pasnet/pasnetbioschemas.jsonld b/data/pasnet/pasnetbioschemas.jsonld index 728e989e23743..e8a5cc2a7cb90 100644 --- a/data/pasnet/pasnetbioschemas.jsonld +++ b/data/pasnet/pasnetbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "PASNet", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/DataX-JieHao/PASNet" } \ No newline at end of file diff --git a/data/past/pastbioschemas.jsonld b/data/past/pastbioschemas.jsonld index e4f6572359cd8..d0a5fd73b228b 100644 --- a/data/past/pastbioschemas.jsonld +++ b/data/past/pastbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PAST", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://past.in.tum.de/" } \ No newline at end of file diff --git a/data/pasta/pastabioschemas.jsonld b/data/pasta/pastabioschemas.jsonld index a90b80e0d9f6a..ad7d1d9351f7b 100644 --- a/data/pasta/pastabioschemas.jsonld +++ b/data/pasta/pastabioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0003-4525-7793", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/nar/gku399", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/pasta", @@ -28,18 +28,18 @@ "sc:additionalType": "Web application", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0128" + "@id": "edam:topic_0080" }, { - "@id": "edam:topic_0080" + "@id": "edam:topic_0128" } ], "sc:citation": [ + "pmcid:PMC4086119", "pubmed:24848016", { "@id": "https://doi.org/10.1093/nar/gku399" - }, - "pmcid:PMC4086119" + } ], "sc:description": "A web server predictor for amyloid aggregation propensity from protein sequences.", "sc:featureList": { @@ -47,20 +47,20 @@ }, "sc:name": "PASTA", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": [ - "ELIXIR-ITA-PADOVA", - "University of Padua, Department of Biomedical Sciences, BioComputing UP lab" + "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", + "ELIXIR-ITA-PADOVA" ], "sc:url": "http://protein.bio.unipd.it/pasta2/index.html", "sc:version": "2.0" }, { - "@id": "https://doi.org/10.1093/nar/gku399", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0003-4525-7793", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pasteseq/pasteseqbioschemas.jsonld b/data/pasteseq/pasteseqbioschemas.jsonld index 823ddfabbfff1..273cd1e99ba5b 100644 --- a/data/pasteseq/pasteseqbioschemas.jsonld +++ b/data/pasteseq/pasteseqbioschemas.jsonld @@ -14,21 +14,21 @@ "sc:contributor": [ "Wellcome Trust", "EMBOSS Contributors", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:description": "Insert one sequence into another.", "sc:funder": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "pasteseq", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/patch-surfer/patch-surferbioschemas.jsonld b/data/patch-surfer/patch-surferbioschemas.jsonld index dd0cd8746e183..a81cf396d197e 100644 --- a/data/patch-surfer/patch-surferbioschemas.jsonld +++ b/data/patch-surfer/patch-surferbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Method used to predict the binding ligand for a protein. The method used the 3 Dimensional Zernike Descriptor (3DZD) and Approximate Patch Position (APP) to describe the features of different patches of the protein pocket.", "sc:name": "Patch-Surfer", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://kiharalab.org/patchsurfer2.0/" diff --git a/data/patchd/patchdbioschemas.jsonld b/data/patchd/patchdbioschemas.jsonld index 3e525e46e93a8..051f56905f516 100644 --- a/data/patchd/patchdbioschemas.jsonld +++ b/data/patchd/patchdbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PatchD", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://wwwlabs.uhnresearch.ca/tillier/PatchDWEB/PatchDWEP.php" } \ No newline at end of file diff --git a/data/patchdock/patchdockbioschemas.jsonld b/data/patchdock/patchdockbioschemas.jsonld index 3a0edea65a865..7768dfc5bd010 100644 --- a/data/patchdock/patchdockbioschemas.jsonld +++ b/data/patchdock/patchdockbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "PatchDock Administrator", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:15980490", "sc:description": "PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria.", "sc:name": "PatchDock", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/PatchDock/" } \ No newline at end of file diff --git a/data/patchfinder/patchfinderbioschemas.jsonld b/data/patchfinder/patchfinderbioschemas.jsonld index bda4cd57c0597..9f02f3cbd4690 100644 --- a/data/patchfinder/patchfinderbioschemas.jsonld +++ b/data/patchfinder/patchfinderbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A server for the detection of highly conserved protein surfaces.", "sc:name": "PatchFinder", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://patchfinder.tau.ac.il/", diff --git a/data/patchsearch/patchsearchbioschemas.jsonld b/data/patchsearch/patchsearchbioschemas.jsonld index 7b2e323b9ae0b..5a2f86fd1448d 100644 --- a/data/patchsearch/patchsearchbioschemas.jsonld +++ b/data/patchsearch/patchsearchbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/PatchSearch", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Julien Rey", "Gautier Moroy", + "Julien Rey", "Frédéric Guyon" ], "sc:additionalType": "Web application", diff --git a/data/patchwork/patchworkbioschemas.jsonld b/data/patchwork/patchworkbioschemas.jsonld index 0a496bc6b0f6f..bc5be02f4673a 100644 --- a/data/patchwork/patchworkbioschemas.jsonld +++ b/data/patchwork/patchworkbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Bioinformatic tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, low tumor cell content or are aneuploid. The first takes BAM files as input whereas CG takes input from CompleteGenomics files.", "sc:name": "Patchwork", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://patchwork.r-forge.r-project.org/", diff --git a/data/patentdata/patentdatabioschemas.jsonld b/data/patentdata/patentdatabioschemas.jsonld index 3ed3926b00fdd..92613e4c2980f 100644 --- a/data/patentdata/patentdatabioschemas.jsonld +++ b/data/patentdata/patentdatabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents.", "sc:name": "EBI patent sequence database", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ebi.ac.uk/patentdata/nr/" } \ No newline at end of file diff --git a/data/path2models/path2modelsbioschemas.jsonld b/data/path2models/path2modelsbioschemas.jsonld index 8e992f67cb45a..87dee5cec83ad 100644 --- a/data/path2models/path2modelsbioschemas.jsonld +++ b/data/path2models/path2modelsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "Path2Models", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.ebi.ac.uk/biomodels-main/path2models" diff --git a/data/path2ppi/path2ppibioschemas.jsonld b/data/path2ppi/path2ppibioschemas.jsonld index 2fc74ffff3d1e..c3d625abd8cb2 100644 --- a/data/path2ppi/path2ppibioschemas.jsonld +++ b/data/path2ppi/path2ppibioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Oliver Philipp", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:26733452", "sc:description": "Package to predict pathway specific protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available.", diff --git a/data/pathbase/pathbasebioschemas.jsonld b/data/pathbase/pathbasebioschemas.jsonld index 5995e39c444e6..d35d25706adf4 100644 --- a/data/pathbase/pathbasebioschemas.jsonld +++ b/data/pathbase/pathbasebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PathBase", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.pathbase.net/", "sc:version": "1" diff --git a/data/pathbinder/pathbinderbioschemas.jsonld b/data/pathbinder/pathbinderbioschemas.jsonld index 22d0298e01e44..744b13ea6c4a0 100644 --- a/data/pathbinder/pathbinderbioschemas.jsonld +++ b/data/pathbinder/pathbinderbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Unique, plant-based tool to explore literature, and to annotate metabolic and regulatory interactions and biomolecules.", "sc:name": "PathBinder", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.metnetdb.org/MetNet_PathBinder.htm" } \ No newline at end of file diff --git a/data/pathblast/pathblastbioschemas.jsonld b/data/pathblast/pathblastbioschemas.jsonld index defd512292fee..2a7e44d64cb1a 100644 --- a/data/pathblast/pathblastbioschemas.jsonld +++ b/data/pathblast/pathblastbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for cross-species comparison of protein interaction networks. It takes a short protein interaction path as input and searches against an available protein-protein interation network specified by the user.", "sc:name": "PathBLAST", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.pathblast.org/" diff --git a/data/pathcnn/pathcnnbioschemas.jsonld b/data/pathcnn/pathcnnbioschemas.jsonld index baa9a537b83cb..093c2bcf5afb8 100644 --- a/data/pathcnn/pathcnnbioschemas.jsonld +++ b/data/pathcnn/pathcnnbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "PathCNN", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/sedab/PathCNN" } \ No newline at end of file diff --git a/data/pathcrosstalk/pathcrosstalkbioschemas.jsonld b/data/pathcrosstalk/pathcrosstalkbioschemas.jsonld index dd0f50f1978a3..4a4f85c5cba98 100644 --- a/data/pathcrosstalk/pathcrosstalkbioschemas.jsonld +++ b/data/pathcrosstalk/pathcrosstalkbioschemas.jsonld @@ -17,8 +17,8 @@ "@id": "https://bio.tools/PATHcrosstalk", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Zhangsheng Yu", - "Botao Fa" + "Botao Fa", + "Zhangsheng Yu" ], "sc:additionalType": "Library", "sc:citation": [ @@ -35,8 +35,8 @@ "sc:license": "LGPL-3.0", "sc:name": "PATHcrosstalk", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/fabotao/PATHcrosstalk" diff --git a/data/pathdeseq/pathdeseqbioschemas.jsonld b/data/pathdeseq/pathdeseqbioschemas.jsonld index b8f4d98f572d0..6d3b4079f8e25 100644 --- a/data/pathdeseq/pathdeseqbioschemas.jsonld +++ b/data/pathdeseq/pathdeseqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Powerful differential expression analysis incorporating network topology for next-generation sequencing data.", "sc:name": "pathDESeq", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/MalathiSIDona/pathDESeq" } \ No newline at end of file diff --git a/data/pathema/pathemabioschemas.jsonld b/data/pathema/pathemabioschemas.jsonld index 256a3385c36ce..cd0174660a71e 100644 --- a/data/pathema/pathemabioschemas.jsonld +++ b/data/pathema/pathemabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "It is a site for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses.", "sc:name": "Pathema", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://pathema.jcvi.org" } \ No newline at end of file diff --git a/data/pathfindr/pathfindrbioschemas.jsonld b/data/pathfindr/pathfindrbioschemas.jsonld index 2bff144eb5504..f7c47053ecc8a 100644 --- a/data/pathfindr/pathfindrbioschemas.jsonld +++ b/data/pathfindr/pathfindrbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-5980-8002", + "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0003-2090-3621", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/pathfindR", "@type": "sc:SoftwareApplication", @@ -16,8 +24,8 @@ "@id": "https://orcid.org/0000-0003-2090-3621" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:author": [ { @@ -31,20 +39,12 @@ "sc:license": "MIT", "sc:name": "pathfindR", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/egeulgen/pathfindR", "sc:version": "1.0.0, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.4.0, 1.4.1, 1.4.2" - }, - { - "@id": "https://orcid.org/0000-0003-2090-3621", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0001-5980-8002", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pathfxweb/pathfxwebbioschemas.jsonld b/data/pathfxweb/pathfxwebbioschemas.jsonld index 3f0bf9c088e5e..6ef7132e10e2a 100644 --- a/data/pathfxweb/pathfxwebbioschemas.jsonld +++ b/data/pathfxweb/pathfxwebbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "PathFXweb", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.pathfxweb.net/" diff --git a/data/pathicular/pathicularbioschemas.jsonld b/data/pathicular/pathicularbioschemas.jsonld index 26e7c2df36820..16f42539a3b9a 100644 --- a/data/pathicular/pathicularbioschemas.jsonld +++ b/data/pathicular/pathicularbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Cytoscape plug-in that identifies path motifs in integrated networks and arranges them in a modular structure.", "sc:name": "Pathicular", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/Pathicular", diff --git a/data/pathiways/pathiwaysbioschemas.jsonld b/data/pathiways/pathiwaysbioschemas.jsonld index d2118922f11e3..8ced2927bd19d 100644 --- a/data/pathiways/pathiwaysbioschemas.jsonld +++ b/data/pathiways/pathiwaysbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PATHiWAYS", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://pathiways.babelomics.org/" } \ No newline at end of file diff --git a/data/pathjam/pathjambioschemas.jsonld b/data/pathjam/pathjambioschemas.jsonld index dedd942a7713c..151fd04fdaccf 100644 --- a/data/pathjam/pathjambioschemas.jsonld +++ b/data/pathjam/pathjambioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Web server which integrates pathway-related annotations from several public sources (Reactome, KEGG, Biocarta, etc) making easier the understanding of gene lists of interest.", "sc:name": "PathJam", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.pathjam.org/server/api/", "sc:version": "1" diff --git a/data/pathme/pathmebioschemas.jsonld b/data/pathme/pathmebioschemas.jsonld index 5ab6db78ce5a2..5a7491f24ee68 100644 --- a/data/pathme/pathmebioschemas.jsonld +++ b/data/pathme/pathmebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2863-9", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/PathMe", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Web application" ], "sc:citation": [ - "pmcid:PMC6521546", "pubmed:31092193", { "@id": "https://doi.org/10.1186/s12859-019-2863-9" - } + }, + "pmcid:PMC6521546" ], "sc:description": "Python package that transforms pathway knowledge from three major pathway databases into a unified abstraction using Biological Expression Language as the pivotal, integrative schema.", "sc:featureList": [ @@ -43,11 +39,15 @@ "sc:license": "Apache-2.0", "sc:name": "PathMe", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://pathme.scai.fraunhofer.de/" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2863-9", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pathnet/pathnetbioschemas.jsonld b/data/pathnet/pathnetbioschemas.jsonld index 77c44868b8313..afa657d0c2ee2 100644 --- a/data/pathnet/pathnetbioschemas.jsonld +++ b/data/pathnet/pathnetbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1751-0473-7-10", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pathnet", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jason B. Smith", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pmcid:PMC3563509", - "pubmed:23006764", { "@id": "https://doi.org/10.1186/1751-0473-7-10" - } + }, + "pmcid:PMC3563509", + "pubmed:23006764" ], "sc:description": "This tool uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression.", "sc:featureList": { @@ -32,15 +36,11 @@ "sc:name": "PathNet", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PathNet.html", "sc:version": "1.14.0" - }, - { - "@id": "https://doi.org/10.1186/1751-0473-7-10", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pathospotter-k/pathospotter-kbioschemas.jsonld b/data/pathospotter-k/pathospotter-kbioschemas.jsonld index 070c56657d7f1..c89da1b3c8dc6 100644 --- a/data/pathospotter-k/pathospotter-kbioschemas.jsonld +++ b/data/pathospotter-k/pathospotter-kbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computational tool for the automatic identification of glomerular lesions in histological images of kidneys.", "sc:name": "PathoSpotter-K", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/geogob/PathoSpotter-K" } \ No newline at end of file diff --git a/data/pathostat/bioconda_pathostat.yaml b/data/pathostat/bioconda_pathostat.yaml index 948c736128a78..82592d0011cab 100644 --- a/data/pathostat/bioconda_pathostat.yaml +++ b/data/pathostat/bioconda_pathostat.yaml @@ -7,7 +7,6 @@ description: The purpose of this package is to perform Statistical Microbiome An home: https://bioconductor.org/packages/3.10/bioc/html/PathoStat.html identifiers: - biotools:pathostat -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-pathostat diff --git a/data/pathostat/pathostatbioschemas.jsonld b/data/pathostat/pathostatbioschemas.jsonld index 10401b64b009c..68adc0cab1e91 100644 --- a/data/pathostat/pathostatbioschemas.jsonld +++ b/data/pathostat/pathostatbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "PathoStat", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PathoStat.html", "sc:version": "1.0.0" diff --git a/data/pathpred/pathpredbioschemas.jsonld b/data/pathpred/pathpredbioschemas.jsonld index 7b89cd83b6c19..6215a040b4adc 100644 --- a/data/pathpred/pathpredbioschemas.jsonld +++ b/data/pathpred/pathpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Enzyme catalyzed metabolic pathway prediction server. Beginning with a query compound and chemical logic of enzymatic reactions (chemical structure transformation patterns of small molecules), biodegradation pathways of environmental compounds and biosynthesis pathways of secondary metabolites are predicted.", "sc:name": "PathPred", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.genome.jp/tools/pathpred/" } \ No newline at end of file diff --git a/data/pathprint/pathprintbioschemas.jsonld b/data/pathprint/pathprintbioschemas.jsonld index 567ca5b5f4547..fd3cad32fb7dd 100644 --- a/data/pathprint/pathprintbioschemas.jsonld +++ b/data/pathprint/pathprintbioschemas.jsonld @@ -16,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC3971351", - "pubmed:23890051", { "@id": "https://doi.org/10.1186/gm472" - } + }, + "pubmed:23890051" ], "sc:description": "Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a 'pathway fingerprint', a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "GPL-1.0", "sc:name": "pathprint", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pathprint.html", "sc:version": "1.10.4" diff --git a/data/pathrender/bioconda_pathrender.yaml b/data/pathrender/bioconda_pathrender.yaml index 409d495392978..4d9b1d5a8cfc2 100644 --- a/data/pathrender/bioconda_pathrender.yaml +++ b/data/pathrender/bioconda_pathrender.yaml @@ -3,7 +3,6 @@ description: build graphs from pathway databases, render them by Rgraphviz. home: https://bioconductor.org/packages/3.10/bioc/html/pathRender.html identifiers: - biotools:pathrender -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-pathrender diff --git a/data/pathrender/pathrenderbioschemas.jsonld b/data/pathrender/pathrenderbioschemas.jsonld index a1d1a53391a22..0b005cbabcf41 100644 --- a/data/pathrender/pathrenderbioschemas.jsonld +++ b/data/pathrender/pathrenderbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "pathRender", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pathRender.html", "sc:version": "1.42.0" diff --git a/data/pathrings/pathringsbioschemas.jsonld b/data/pathrings/pathringsbioschemas.jsonld index cc45a8dd2c6b4..5bf7073d3b778 100644 --- a/data/pathrings/pathringsbioschemas.jsonld +++ b/data/pathrings/pathringsbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Admin", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:25982732", - "pmcid:PMC4436019", { "@id": "https://doi.org/10.1186/S12859-015-0585-1" - } + }, + "pubmed:25982732", + "pmcid:PMC4436019" ], "sc:description": "A web-based tool for exploration of ortholog and expression data in biological pathways.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:name": "PathRings", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://raven.anr.udel.edu/~sunliang/PathRings/" }, diff --git a/data/pathrnet/pathrnetbioschemas.jsonld b/data/pathrnet/pathrnetbioschemas.jsonld index 415c7389e8c98..8b2c24ec19b0c 100644 --- a/data/pathrnet/pathrnetbioschemas.jsonld +++ b/data/pathrnet/pathrnetbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/pathrnet", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Yidong Chen", "Jia Meng", "yufei.huang@utsa.edu", - "Shou-Jiang Gao", - "Yidong Chen" + "Shou-Jiang Gao" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:21143778", "sc:description": "A novel network model and a reconstruction approach PATTERN are proposed for reconstructing the context specific time varying regulatory networks by integrating microarray gene expression profiles and existing knowledge of pathways and transcription factors.", "sc:name": "PathRNet", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://compgenomics.utsa.edu/tvnet.html" } \ No newline at end of file diff --git a/data/pathscore/pathscorebioschemas.jsonld b/data/pathscore/pathscorebioschemas.jsonld index 71f4457a4524e..da2395de1ac4c 100644 --- a/data/pathscore/pathscorebioschemas.jsonld +++ b/data/pathscore/pathscorebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients.", "sc:name": "PathScore", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://pathscore.publichealth.yale.edu/" } \ No newline at end of file diff --git a/data/pathvar/pathvarbioschemas.jsonld b/data/pathvar/pathvarbioschemas.jsonld index 1b3d822db1795..a17ecf563e8ec 100644 --- a/data/pathvar/pathvarbioschemas.jsonld +++ b/data/pathvar/pathvarbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Samuel Zimmerman", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.", "sc:license": "GPL-2.0", "sc:name": "pathVar", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pathVar.html", "sc:version": "1.4.0" diff --git a/data/pathview/pathviewbioschemas.jsonld b/data/pathview/pathviewbioschemas.jsonld index a9db5621cfe5e..c1f133703a4d4 100644 --- a/data/pathview/pathviewbioschemas.jsonld +++ b/data/pathview/pathviewbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btt285", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pathview", "@type": "sc:SoftwareApplication", @@ -18,8 +22,8 @@ "Library" ], "sc:citation": [ - "pubmed:23740750", "pmcid:PMC3702256", + "pubmed:23740750", { "@id": "https://doi.org/10.1093/bioinformatics/btt285" } @@ -27,25 +31,21 @@ "sc:description": "Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.", "sc:featureList": [ { - "@id": "edam:operation_3083" + "@id": "edam:operation_2497" }, { - "@id": "edam:operation_2497" + "@id": "edam:operation_3083" } ], "sc:license": "GPL-3.0", "sc:name": "pathview", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pathview.html", "sc:version": "1.14.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btt285", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pathview_web/pathview_webbioschemas.jsonld b/data/pathview_web/pathview_webbioschemas.jsonld index e85b1ecd0a511..6252eed73ad64 100644 --- a/data/pathview_web/pathview_webbioschemas.jsonld +++ b/data/pathview_web/pathview_webbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkx372", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pathview_web", "@type": "sc:SoftwareApplication", @@ -27,10 +31,6 @@ }, "sc:name": "Pathview Web", "sc:url": "https://pathview.uncc.edu/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkx372", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pathvisio/pathvisiobioschemas.jsonld b/data/pathvisio/pathvisiobioschemas.jsonld index 87d02998a2c3e..aa6f642dc37a7 100644 --- a/data/pathvisio/pathvisiobioschemas.jsonld +++ b/data/pathvisio/pathvisiobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pcbi.1004085", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/pathvisio", "@type": "sc:SoftwareApplication", @@ -31,24 +27,28 @@ "sc:description": "Free open-source biological pathway analysis software that allows you to draw, edit and analyze biological pathways.", "sc:featureList": [ { - "@id": "edam:operation_2497" + "@id": "edam:operation_3096" }, { "@id": "edam:operation_3083" }, { - "@id": "edam:operation_3096" + "@id": "edam:operation_2497" } ], "sc:license": "Apache-2.0", "sc:name": "PathVisio", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.pathvisio.org/", "sc:version": "3.3.0" + }, + { + "@id": "https://doi.org/10.1371/journal.pcbi.1004085", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pathway_commons/pathway_commonsbioschemas.jsonld b/data/pathway_commons/pathway_commonsbioschemas.jsonld index e62c76f980953..f51428064046d 100644 --- a/data/pathway_commons/pathway_commonsbioschemas.jsonld +++ b/data/pathway_commons/pathway_commonsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Collection of publicly available pathways from multiple organisms.", "sc:name": "Pathway Commons", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.pathwaycommons.org/pc/webservice.do?cmd=help", "sc:version": "1" diff --git a/data/pathway_hunter_tool/pathway_hunter_toolbioschemas.jsonld b/data/pathway_hunter_tool/pathway_hunter_toolbioschemas.jsonld index c5bcec605e374..6feaaa343eb36 100644 --- a/data/pathway_hunter_tool/pathway_hunter_toolbioschemas.jsonld +++ b/data/pathway_hunter_tool/pathway_hunter_toolbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Pathway Hunter Tool (PHT) uses shortest path analysis to reconstruct and visualize biochemical pathways. The user can find the shortest path between two metabolites, or find all reachable products or educts for a given metabolite.", "sc:name": "Pathway Hunter Tool", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://pht.tu-bs.de/" } \ No newline at end of file diff --git a/data/pathway_inspector/pathway_inspectorbioschemas.jsonld b/data/pathway_inspector/pathway_inspectorbioschemas.jsonld index 672ad486583c6..94a0bc24b7497 100644 --- a/data/pathway_inspector/pathway_inspectorbioschemas.jsonld +++ b/data/pathway_inspector/pathway_inspectorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web application helping researchers to find patterns of expression in complex RNAseq experiments.", "sc:name": "Pathway Inspector", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "FEM Research and Innovation Center", diff --git a/data/pathway_miner/pathway_minerbioschemas.jsonld b/data/pathway_miner/pathway_minerbioschemas.jsonld index b4960c5dd3e74..933c39472579e 100644 --- a/data/pathway_miner/pathway_minerbioschemas.jsonld +++ b/data/pathway_miner/pathway_minerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for searching lists of genes for associations in known pathway data from KEGG, BioCarta, and GenMAPP. Also provides statistical analyses.", "sc:name": "Pathway Miner", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.biorag.org/pathway.html" } \ No newline at end of file diff --git a/data/pathway_projector/pathway_projectorbioschemas.jsonld b/data/pathway_projector/pathway_projectorbioschemas.jsonld index f39218cd92115..1f2a92585dd36 100644 --- a/data/pathway_projector/pathway_projectorbioschemas.jsonld +++ b/data/pathway_projector/pathway_projectorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Pathway Projector", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.g-language.org/PathwayProjector/" } \ No newline at end of file diff --git a/data/pathway_tools/pathway_toolsbioschemas.jsonld b/data/pathway_tools/pathway_toolsbioschemas.jsonld index a2f880f9692af..5ff88a8890091 100644 --- a/data/pathway_tools/pathway_toolsbioschemas.jsonld +++ b/data/pathway_tools/pathway_toolsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Supports creation, editing, querying, visualization, and analysis of PGDBs. The software also allows users to publish a PGDB on the Web for access by the scientific community. A PGDB is a bioinformatics DB that integrates genomic data with detailed functional annotations of the genome, such as descriptions of metabolic and signalling pathways, and of the regulatory network.", "sc:name": "Pathway Tools", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioinformatics.ai.sri.com/ptools/" diff --git a/data/pathwaycommons_sparql_endpoint/pathwaycommons_sparql_endpointbioschemas.jsonld b/data/pathwaycommons_sparql_endpoint/pathwaycommons_sparql_endpointbioschemas.jsonld index 537c292e6dc75..d3b6b5fbcae83 100644 --- a/data/pathwaycommons_sparql_endpoint/pathwaycommons_sparql_endpointbioschemas.jsonld +++ b/data/pathwaycommons_sparql_endpoint/pathwaycommons_sparql_endpointbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-0185-8861", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/PathwayCommons_SPARQL_endpoint", "@type": "sc:SoftwareApplication", @@ -25,6 +21,10 @@ "sc:name": "PathwayCommons SPARQL endpoint", "sc:url": "http://rdf.pathwaycommons.org/sparql/", "sc:version": "11" + }, + { + "@id": "https://orcid.org/0000-0003-0185-8861", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pathwaycommons_web_service_api/pathwaycommons_web_service_apibioschemas.jsonld b/data/pathwaycommons_web_service_api/pathwaycommons_web_service_apibioschemas.jsonld index 924cfdd046e7f..8d81010d6645c 100644 --- a/data/pathwaycommons_web_service_api/pathwaycommons_web_service_apibioschemas.jsonld +++ b/data/pathwaycommons_web_service_api/pathwaycommons_web_service_apibioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-0185-8861", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/PathwayCommons_web_service_API", "@type": "sc:SoftwareApplication", @@ -20,14 +16,18 @@ "@id": "https://orcid.org/0000-0003-0185-8861" }, "sc:additionalType": [ - "Web service", - "Web API" + "Web API", + "Web service" ], "sc:citation": "pubmed:21071392", "sc:description": "Pathway Commons integrates a number of pathway and molecular interaction databases supporting BioPAX and PSI-MI formats into one large BioPAX model, which can be queried using our web API (documented below). This API can be used by computational biologists to download custom subsets of pathway data for analysis, or can be used to incorporate powerful biological pathway and network information retrieval and query functionality into websites and software.", "sc:name": "PathwayCommons web service API", "sc:url": "https://www.pathwaycommons.org/pc2/home", "sc:version": "11" + }, + { + "@id": "https://orcid.org/0000-0003-0185-8861", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pathwaymatrix/pathwaymatrixbioschemas.jsonld b/data/pathwaymatrix/pathwaymatrixbioschemas.jsonld index daafc946a9d2e..4b818beb110ac 100644 --- a/data/pathwaymatrix/pathwaymatrixbioschemas.jsonld +++ b/data/pathwaymatrix/pathwaymatrixbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Presents novel methods to visualize and interact with representations of signaling pathways. It provides visual anayltics tools that allow systems biologists and cancer researchers to find patterns in the relationships and reactions between proteins and protein complexes.", "sc:name": "PathwayMatrix", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/CreativeCodingLab/PathwayMatrix" diff --git a/data/pathwaysplice/pathwaysplicebioschemas.jsonld b/data/pathwaysplice/pathwaysplicebioschemas.jsonld index 66d08abbd3599..fd62648db27e2 100644 --- a/data/pathwaysplice/pathwaysplicebioschemas.jsonld +++ b/data/pathwaysplice/pathwaysplicebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "LGPL-2.0", "sc:name": "PathwaySplice", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://bioconductor.org/packages/release/bioc/html/PathwaySplice.html", "sc:version": "1.4.0" diff --git a/data/patient_archive/patient_archivebioschemas.jsonld b/data/patient_archive/patient_archivebioschemas.jsonld index 982b4a1776c7a..67060062e1e43 100644 --- a/data/patient_archive/patient_archivebioschemas.jsonld +++ b/data/patient_archive/patient_archivebioschemas.jsonld @@ -21,34 +21,34 @@ "Web application" ], "sc:citation": [ - "pubmed:26119816", { "@id": "https://doi.org/10.1093/database/bav005" }, - "pmcid:PMC4572507", - "pmcid:PMC4343077", - "pubmed:25725061", { "@id": "https://doi.org/10.1016/j.ajhg.2015.05.020" - } + }, + "pubmed:26119816", + "pubmed:25725061", + "pmcid:PMC4572507", + "pmcid:PMC4343077" ], "sc:description": "A platform developed by Kinghorn Center of Clinical Genomics (KCCG) for managing, sharing and discussing patient cases (clinical and genomic information).", "sc:featureList": [ - { - "@id": "edam:operation_3280" - }, { "@id": "edam:operation_3096" }, { "@id": "edam:operation_3431" + }, + { + "@id": "edam:operation_3280" } ], "sc:name": "KCCG Patient Archive", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://patientarchive.org/#/home", "sc:version": "2.2.4" diff --git a/data/patman/patmanbioschemas.jsonld b/data/patman/patmanbioschemas.jsonld index ce525e657d5e0..0ad1da107471f 100644 --- a/data/patman/patmanbioschemas.jsonld +++ b/data/patman/patmanbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/patman", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kay Pruefer", - "Udo Stenzel" + "Udo Stenzel", + "Kay Pruefer" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:18467344", diff --git a/data/patmatch/patmatchbioschemas.jsonld b/data/patmatch/patmatchbioschemas.jsonld index fdf8f342460c8..92c3a411bedcc 100644 --- a/data/patmatch/patmatchbioschemas.jsonld +++ b/data/patmatch/patmatchbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PatMatch", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl" } \ No newline at end of file diff --git a/data/patmatdb/patmatdbbioschemas.jsonld b/data/patmatdb/patmatdbbioschemas.jsonld index 39ddb44db631b..d952cdbcc35f3 100644 --- a/data/patmatdb/patmatdbbioschemas.jsonld +++ b/data/patmatdb/patmatdbbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Search protein sequences with a sequence motif.", "sc:funder": [ + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "patmatdb", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/patmatdb.html", "sc:version": "r6" diff --git a/data/patmatmotifs/patmatmotifsbioschemas.jsonld b/data/patmatmotifs/patmatmotifsbioschemas.jsonld index b342c5fc72c61..bdebfea60de58 100644 --- a/data/patmatmotifs/patmatmotifsbioschemas.jsonld +++ b/data/patmatmotifs/patmatmotifsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", + "UK MRC", "EMBOSS Contributors", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:description": "Scan a protein sequence with motifs from the PROSITE database.", "sc:funder": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "patmatmotifs", diff --git a/data/patristic/patristicbioschemas.jsonld b/data/patristic/patristicbioschemas.jsonld index 727c7d978ef13..59ff485b79f5a 100644 --- a/data/patristic/patristicbioschemas.jsonld +++ b/data/patristic/patristicbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Patristic", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.bioinformatics.org/patristic/" } \ No newline at end of file diff --git a/data/patrocles/patroclesbioschemas.jsonld b/data/patrocles/patroclesbioschemas.jsonld index 589fa3eff5d82..f78521d3c76a3 100644 --- a/data/patrocles/patroclesbioschemas.jsonld +++ b/data/patrocles/patroclesbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation.", "sc:name": "Patrocles", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.patrocles.org" } \ No newline at end of file diff --git a/data/patsearch/patsearchbioschemas.jsonld b/data/patsearch/patsearchbioschemas.jsonld index 44bb673554350..68e8b6abc25a9 100644 --- a/data/patsearch/patsearchbioschemas.jsonld +++ b/data/patsearch/patsearchbioschemas.jsonld @@ -15,13 +15,13 @@ "sc:description": "A pattern matcher that is able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices.", "sc:name": "PatSearch", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ - "C.N.R. - Institute of Biomedical Technology", - "ELIXIR-ITA-CNR" + "ELIXIR-ITA-CNR", + "C.N.R. - Institute of Biomedical Technology" ], "sc:url": "http://itbtools.ba.itb.cnr.it/patsearch" } \ No newline at end of file diff --git a/data/patsi/patsibioschemas.jsonld b/data/patsi/patsibioschemas.jsonld index 3935ae5325e3d..97b0b083f7082 100644 --- a/data/patsi/patsibioschemas.jsonld +++ b/data/patsi/patsibioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/pATsi", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "A database of paralogs and single copy genes in Arabidopsis thaliana. Database of single copy and duplicated genes in the Arabidopsis genome. It is a collection that integrates comparative results at genomic level to identify any form of gene duplication in the genome. It makes accessible single genes with specific classifications.", "sc:license": "Unlicense", "sc:name": "pATsi", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://cab.unina.it/athparalog/main2.html", "sc:version": "1" diff --git a/data/patternexplorer/patternexplorerbioschemas.jsonld b/data/patternexplorer/patternexplorerbioschemas.jsonld index 6adab92eba6bb..ada592a195325 100644 --- a/data/patternexplorer/patternexplorerbioschemas.jsonld +++ b/data/patternexplorer/patternexplorerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A web application to define, extract, and analyze structural patterns or biomolecular complexes in real-time.", "sc:name": "PatternExplorer", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "Masaryk University, Brno, Czech Republic", diff --git a/data/patternlab/patternlabbioschemas.jsonld b/data/patternlab/patternlabbioschemas.jsonld index 0a1041e83db8e..8998194fb5936 100644 --- a/data/patternlab/patternlabbioschemas.jsonld +++ b/data/patternlab/patternlabbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Suite of pattern recognition software for interpretation of quantiative proteomics data.", "sc:name": "PatternLab", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://pcarvalho.com/patternlab/" } \ No newline at end of file diff --git a/data/patternquery/patternquerybioschemas.jsonld b/data/patternquery/patternquerybioschemas.jsonld index 3fa902c5497e3..7a7af806f2d77 100644 --- a/data/patternquery/patternquerybioschemas.jsonld +++ b/data/patternquery/patternquerybioschemas.jsonld @@ -16,16 +16,16 @@ ], "sc:author": "David Sehnal", "sc:contributor": [ - "Lukáš Pravda", "Radka Svobodová Vařeková", + "Lukáš Pravda", "Crina-Maria Ionescu" ], "sc:description": "A web application to define, extract, and analyze structural patterns or biomolecular complexes in real-time.", "sc:name": "PatternQuery", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "Masaryk University, Brno, Czech Republic", "sc:url": "http://ncbr.muni.cz/PatternQuery", diff --git a/data/paxdb/paxdbbioschemas.jsonld b/data/paxdb/paxdbbioschemas.jsonld index 46216c2c10ebc..f128e5fc0cbf3 100644 --- a/data/paxdb/paxdbbioschemas.jsonld +++ b/data/paxdb/paxdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "PaxDb contains estimated abundance values for a large number of proteins in several different species. Furthermore, it contains information about inter-species variation of protein abundances.", "sc:name": "PaxDb", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://pax-db.org/" } \ No newline at end of file diff --git a/data/paxtools/paxtoolsbioschemas.jsonld b/data/paxtools/paxtoolsbioschemas.jsonld index 882abbb10b217..2cf95a3270a52 100644 --- a/data/paxtools/paxtoolsbioschemas.jsonld +++ b/data/paxtools/paxtoolsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Paxtools", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.biopax.org/paxtools.php" } \ No newline at end of file diff --git a/data/paxtoolsr/paxtoolsrbioschemas.jsonld b/data/paxtoolsr/paxtoolsrbioschemas.jsonld index b576cdc29e054..68053e6d93f7b 100644 --- a/data/paxtoolsr/paxtoolsrbioschemas.jsonld +++ b/data/paxtoolsr/paxtoolsrbioschemas.jsonld @@ -20,28 +20,28 @@ "@id": "edam:data_2600" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0602" + "@id": "edam:topic_2229" }, { - "@id": "edam:topic_2229" + "@id": "edam:topic_0602" } ], "sc:citation": [ - "pmcid:PMC4824129", { "@id": "https://doi.org/10.1093/bioinformatics/btv733" }, + "pmcid:PMC4824129", "pubmed:26685306" ], "sc:description": "The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC). Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC.", "sc:featureList": [ { - "@id": "edam:operation_3660" + "@id": "edam:operation_0335" }, { "@id": "edam:operation_2421" @@ -50,7 +50,7 @@ "@id": "edam:operation_1781" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_3660" }, { "@id": "edam:operation_3083" @@ -59,9 +59,9 @@ "sc:license": "GPL-3.0", "sc:name": "paxtoolsr", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/paxtoolsr.html", "sc:version": "1.8.0" diff --git a/data/pazar/pazarbioschemas.jsonld b/data/pazar/pazarbioschemas.jsonld index 3bcfde9b72151..e33c0d530a4ab 100644 --- a/data/pazar/pazarbioschemas.jsonld +++ b/data/pazar/pazarbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PAZAR", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.pazar.info/" } \ No newline at end of file diff --git a/data/pbase/pbasebioschemas.jsonld b/data/pbase/pbasebioschemas.jsonld index ecaabb8f2b685..d03a9dbb8788c 100644 --- a/data/pbase/pbasebioschemas.jsonld +++ b/data/pbase/pbasebioschemas.jsonld @@ -15,16 +15,16 @@ "Laurent Gatto" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A set of classes and functions to investigate and understand protein sequence data in the context of a proteomics experiment.", "sc:license": "GPL-3.0", "sc:name": "Pbase", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Pbase.html", "sc:version": "0.14.0" diff --git a/data/pbeq-solver/pbeq-solverbioschemas.jsonld b/data/pbeq-solver/pbeq-solverbioschemas.jsonld index a5340985d822b..43a50b8363777 100644 --- a/data/pbeq-solver/pbeq-solverbioschemas.jsonld +++ b/data/pbeq-solver/pbeq-solverbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PBEQ-Solver is a wb based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann equations and interactively display the eletrostatic potential.", "sc:name": "PBEQ-Solver", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.charmm-gui.org/?doc=input/pbeqsolver" } \ No newline at end of file diff --git a/data/pbil/pbilbioschemas.jsonld b/data/pbil/pbilbioschemas.jsonld index c56695fe3049e..cd164f74c91fb 100644 --- a/data/pbil/pbilbioschemas.jsonld +++ b/data/pbil/pbilbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/pbil", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Gilbert DELEAGE", - "Raphael TERREUX" + "Raphael TERREUX", + "Gilbert DELEAGE" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:12824334", diff --git a/data/pblat/pblatbioschemas.jsonld b/data/pblat/pblatbioschemas.jsonld index 95afe52fe2cb8..dbe57638e6db0 100644 --- a/data/pblat/pblatbioschemas.jsonld +++ b/data/pblat/pblatbioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2597-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/pblat", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "M. Wang", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:30646844", { "@id": "https://doi.org/10.1186/s12859-019-2597-8" }, - "pubmed:30646844", "pmcid:PMC6334396" ], "sc:description": "Multithread blat algorithm speeding up aligning sequences to genomes.", "sc:featureList": [ { - "@id": "edam:operation_3198" + "@id": "edam:operation_0302" }, { - "@id": "edam:operation_0302" + "@id": "edam:operation_3198" } ], "sc:license": "Unlicense", "sc:name": "pblat", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/icebert/pblat" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2597-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pbm/pbmbioschemas.jsonld b/data/pbm/pbmbioschemas.jsonld index d72268d329bb9..cf902ce399b74 100644 --- a/data/pbm/pbmbioschemas.jsonld +++ b/data/pbm/pbmbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "PBM Analysis Suite provides the in-house tools and the procedural methods used in the analysis of universal protein binding microarrays (PBMs) synthesized by Agilent Techonologies", "sc:name": "PBM", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://thebrain.bwh.harvard.edu/PBMAnalysisSuite/index.html" diff --git a/data/pboost/pboostbioschemas.jsonld b/data/pboost/pboostbioschemas.jsonld index 37ca325e4133b..09341a8e0e8a3 100644 --- a/data/pboost/pboostbioschemas.jsonld +++ b/data/pboost/pboostbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "GPU based tool for parallel permutation tests in genome-wide association studies.", "sc:name": "PBOOST", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioinformatics.ust.hk/" } \ No newline at end of file diff --git a/data/pbrowse/pbrowsebioschemas.jsonld b/data/pbrowse/pbrowsebioschemas.jsonld index 336b245219236..26e18cd45c1cc 100644 --- a/data/pbrowse/pbrowsebioschemas.jsonld +++ b/data/pbrowse/pbrowsebioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKW1358", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/pbrowse", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5605237", - "pubmed:28100700", { "@id": "https://doi.org/10.1093/NAR/GKW1358" - } + }, + "pubmed:28100700", + "pmcid:PMC5605237" ], "sc:description": "A web-based platform for real-time collaborative exploration of genomic data.", "sc:featureList": [ @@ -37,11 +33,15 @@ "sc:license": "BSD-2-Clause", "sc:name": "PBrowse", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://pbrowse.victorchang.edu.au/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKW1358", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pca-pam50/pca-pam50bioschemas.jsonld b/data/pca-pam50/pca-pam50bioschemas.jsonld index f3c6f7c0f6b79..37072f6f0798f 100644 --- a/data/pca-pam50/pca-pam50bioschemas.jsonld +++ b/data/pca-pam50/pca-pam50bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "PCA-PAM50", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "ftp://ftp.wriwindber.org/" } \ No newline at end of file diff --git a/data/pcadapt/pcadaptbioschemas.jsonld b/data/pcadapt/pcadaptbioschemas.jsonld index 515ba957c9b64..bfc39323e4805 100644 --- a/data/pcadapt/pcadaptbioschemas.jsonld +++ b/data/pcadapt/pcadaptbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Software to detect footprints of local adaptation in population genetics data set.", "sc:name": "PCAdapt", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://membres-timc.imag.fr/Nicolas.Duforet-Frebourg/PCAdapt.html" } \ No newline at end of file diff --git a/data/pcaexplorer/pcaexplorerbioschemas.jsonld b/data/pcaexplorer/pcaexplorerbioschemas.jsonld index 934836c96a8c6..cfe5ec5aa80bb 100644 --- a/data/pcaexplorer/pcaexplorerbioschemas.jsonld +++ b/data/pcaexplorer/pcaexplorerbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "MIT", "sc:name": "pcaExplorer", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pcaExplorer.html", diff --git a/data/pcagopromoter/pcagopromoterbioschemas.jsonld b/data/pcagopromoter/pcagopromoterbioschemas.jsonld index b54a420f0e9a2..f620d5182bda8 100644 --- a/data/pcagopromoter/pcagopromoterbioschemas.jsonld +++ b/data/pcagopromoter/pcagopromoterbioschemas.jsonld @@ -18,8 +18,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Morten Hansen", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pubmed:22384239", @@ -35,9 +35,9 @@ "sc:license": "GPL-2.0", "sc:name": "pcaGoPromoter", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pcaGoPromoter.html", "sc:version": "1.18.0" diff --git a/data/pcaj/pcajbioschemas.jsonld b/data/pcaj/pcajbioschemas.jsonld index db436102ec0eb..91a5d6000eeb1 100644 --- a/data/pcaj/pcajbioschemas.jsonld +++ b/data/pcaj/pcajbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "PCAj (Principal component analysis for Japanese)predicts population structure of Japanese samples using genome-wide SNP genotypes.  It creates a 2D scatterplot of predicted principal components based on the probabilistic PCA.", "sc:name": "PCAj", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://kumasakanatsuhiko.jp/projects/pcaj/" diff --git a/data/pcamethods/pcamethodsbioschemas.jsonld b/data/pcamethods/pcamethodsbioschemas.jsonld index 980dbafb170d2..7f9fc402b7622 100644 --- a/data/pcamethods/pcamethodsbioschemas.jsonld +++ b/data/pcamethods/pcamethodsbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "pcaMethods", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pcaMethods.html", "sc:version": "1.66.0" diff --git a/data/pcan/pcanbioschemas.jsonld b/data/pcan/pcanbioschemas.jsonld index b0298f2927ff3..3c6f97c44edbf 100644 --- a/data/pcan/pcanbioschemas.jsonld +++ b/data/pcan/pcanbioschemas.jsonld @@ -9,58 +9,58 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-6257-9730", - "@type": "schema:Person" - }, - { - "@id": "http://orcid.org/0000-0002-3571-0374", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1401-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/pcan", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "http://orcid.org/0000-0002-3571-0374" + "@id": "http://orcid.org/0000-0001-6257-9730" }, { - "@id": "http://orcid.org/0000-0001-6257-9730" + "@id": "http://orcid.org/0000-0002-3571-0374" } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC5142268", + "pubmed:27923364", { "@id": "https://doi.org/10.1186/s12859-016-1401-2" - }, - "pubmed:27923364" + } ], "sc:description": "Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).", "sc:featureList": [ { - "@id": "edam:operation_0277" + "@id": "edam:operation_2451" }, { - "@id": "edam:operation_2451" + "@id": "edam:operation_0277" } ], "sc:license": "CC-BY-NC-ND-4.0", "sc:name": "PCAN", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PCAN.html", "sc:version": "1.2.1" + }, + { + "@id": "http://orcid.org/0000-0001-6257-9730", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/s12859-016-1401-2", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-3571-0374", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pcareduce/pcareducebioschemas.jsonld b/data/pcareduce/pcareducebioschemas.jsonld index e5195b64882a1..bd4c4fa6471dc 100644 --- a/data/pcareduce/pcareducebioschemas.jsonld +++ b/data/pcareduce/pcareducebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Novel agglomerative clustering method to generate a cell state hierarchy where each cluster branch is associated with a principal component of variation that can be used to differentiate two cell states.", "sc:name": "pcaReduce", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/JustinaZ/pcaReduce" } \ No newline at end of file diff --git a/data/pcasuite/pcasuitebioschemas.jsonld b/data/pcasuite/pcasuitebioschemas.jsonld index 7879615a6cdaf..afca517b89a88 100644 --- a/data/pcasuite/pcasuitebioschemas.jsonld +++ b/data/pcasuite/pcasuitebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:description": "Allows the user to compress Molecular Dynamics (MD) trajectories using Principal Component Analysis (PCA) algorithms. This technique offers a good compression ratio at the expense of losing some precision in the trajectory.", "sc:name": "PCASuite", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://mmb.pcb.ub.edu/software/pcasuite/" diff --git a/data/pcddb/pcddbbioschemas.jsonld b/data/pcddb/pcddbbioschemas.jsonld index c3654e3edd8aa..239d01d2febb0 100644 --- a/data/pcddb/pcddbbioschemas.jsonld +++ b/data/pcddb/pcddbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PCDDB", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://pcddb.cryst.bbk.ac.uk" } \ No newline at end of file diff --git a/data/pcetk/pcetkbioschemas.jsonld b/data/pcetk/pcetkbioschemas.jsonld index 19e4328e35cd9..63a8bbfc6e483 100644 --- a/data/pcetk/pcetkbioschemas.jsonld +++ b/data/pcetk/pcetkbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Pcetk", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/mfx9/pcetk" } \ No newline at end of file diff --git a/data/pcgr/pcgrbioschemas.jsonld b/data/pcgr/pcgrbioschemas.jsonld index a975d4a4cdb21..37b60dfbc66ea 100644 --- a/data/pcgr/pcgrbioschemas.jsonld +++ b/data/pcgr/pcgrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "PCGR", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/sigven/pcgr" } \ No newline at end of file diff --git a/data/pchat/pchatbioschemas.jsonld b/data/pchat/pchatbioschemas.jsonld index 7ef227c63b17d..0b08c8603ec2f 100644 --- a/data/pchat/pchatbioschemas.jsonld +++ b/data/pchat/pchatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Principal Component of Heritability Association Test", "sc:name": "PCHAT", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://wpicr.wpic.pitt.edu/WPICCompGen/PCHAT/PCHAT.htm" } \ No newline at end of file diff --git a/data/pci-ss/pci-ssbioschemas.jsonld b/data/pci-ss/pci-ssbioschemas.jsonld index c1dd70dc555e0..4431a4b5bd900 100644 --- a/data/pci-ss/pci-ssbioschemas.jsonld +++ b/data/pci-ss/pci-ssbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "PCI-SS is a method of predicting protein secondary structure using a PCI-based classifier and also a consensus method to combine PCI with PSIPRED.", "sc:name": "PCI-SS", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioinf.sce.carleton.ca/PCISS/start.php" diff --git a/data/pci/pcibioschemas.jsonld b/data/pci/pcibioschemas.jsonld index 2a7a3aef8ed51..92b13e24dd3f5 100644 --- a/data/pci/pcibioschemas.jsonld +++ b/data/pci/pcibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Calculates the barcode gap probability of correct identification (PCI) of species.", "sc:name": "PCI", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/software/program.html?uid=17" diff --git a/data/pcircrna_finder/pcircrna_finderbioschemas.jsonld b/data/pcircrna_finder/pcircrna_finderbioschemas.jsonld index c262f2306bf66..f9b1db81d4aa7 100644 --- a/data/pcircrna_finder/pcircrna_finderbioschemas.jsonld +++ b/data/pcircrna_finder/pcircrna_finderbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/pcircrna_finder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Li Chen", - "Longjiang Fan" + "Longjiang Fan", + "Li Chen" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:27493192", "sc:description": "Software for circRNA prediction in plants.", "sc:name": "PcircRNA_finder", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ibi.zju.edu.cn/bioinplant/tools/manual.htm" } \ No newline at end of file diff --git a/data/pcit/pcitbioschemas.jsonld b/data/pcit/pcitbioschemas.jsonld index a82520a81b9db..5a0b80ae5b3b5 100644 --- a/data/pcit/pcitbioschemas.jsonld +++ b/data/pcit/pcitbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "PCIT", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://cran.r-project.org/package=PCIT", diff --git a/data/pcleavage/pcleavagebioschemas.jsonld b/data/pcleavage/pcleavagebioschemas.jsonld index a3408993ee821..c2164bb026a54 100644 --- a/data/pcleavage/pcleavagebioschemas.jsonld +++ b/data/pcleavage/pcleavagebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool that uses a support vector machine to predict immunoproteasome and constitutive proteasome cleavage sites in antigenic sequences.", "sc:name": "Pcleavage", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/pcleavage/" diff --git a/data/pclogit/pclogitbioschemas.jsonld b/data/pclogit/pclogitbioschemas.jsonld index 3bae7fe73cd3f..46006a7859eca 100644 --- a/data/pclogit/pclogitbioschemas.jsonld +++ b/data/pclogit/pclogitbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "R package for penalized conditional/unconditional logistic regression using a network-based peanlty for matched/unmatched case-control data with grouped or graph-constrained variables. The algorithm is efficient for fitting the regularization path and for providing selection probabilities of each predictor for the anaylsis of high-dimensional matched/unmatched case-control data. It uses cyclical coordinate descent in a pathwise fashion.", "sc:name": "pclogit", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.columbia.edu/~sw2206/softwares.htm", "sc:version": "0.1" diff --git a/data/pclust/pclustbioschemas.jsonld b/data/pclust/pclustbioschemas.jsonld index aad0e539d7738..3474dffdc6297 100644 --- a/data/pclust/pclustbioschemas.jsonld +++ b/data/pclust/pclustbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTT451", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/pclust", "@type": "sc:SoftwareApplication", @@ -31,11 +27,15 @@ }, "sc:name": "Pclust", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://prodata.swmed.edu/pclust/server.cgi" + }, + { + "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTT451", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pcoils/pcoilsbioschemas.jsonld b/data/pcoils/pcoilsbioschemas.jsonld index 2fb49061a4038..c35a044a483a3 100644 --- a/data/pcoils/pcoilsbioschemas.jsonld +++ b/data/pcoils/pcoilsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "PCOILS is a new COILS version that uses profiles as inputs", "sc:name": "PCOILS", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://toolkit.tuebingen.mpg.de/#/tools/pcoils" } \ No newline at end of file diff --git a/data/pcons/pconsbioschemas.jsonld b/data/pcons/pconsbioschemas.jsonld index c45faa0617616..2bdca3d627ebe 100644 --- a/data/pcons/pconsbioschemas.jsonld +++ b/data/pcons/pconsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Pcons.net", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://pcons.net/" } \ No newline at end of file diff --git a/data/pcot2/bioconda_pcot2.yaml b/data/pcot2/bioconda_pcot2.yaml index 8db4e0ee44c74..03b0e4bc78208 100644 --- a/data/pcot2/bioconda_pcot2.yaml +++ b/data/pcot2/bioconda_pcot2.yaml @@ -6,7 +6,6 @@ description: PCOT2 is a permutation-based method for investigating changes in th home: https://bioconductor.org/packages/3.10/bioc/html/pcot2.html identifiers: - biotools:pcot2 -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-pcot2 diff --git a/data/pcp/pcpbioschemas.jsonld b/data/pcp/pcpbioschemas.jsonld index 6af8926b1405b..0b8b6c5c72968 100644 --- a/data/pcp/pcpbioschemas.jsonld +++ b/data/pcp/pcpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Protein Complex Prediction from Protein Interaction Networks.", "sc:name": "PCP", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sites.google.com/site/proteincomplexprediction/", "sc:version": "v1" diff --git a/data/pcpheno/bioconda_pcpheno.yaml b/data/pcpheno/bioconda_pcpheno.yaml index 40d1ff37f9924..b0900f887616e 100644 --- a/data/pcpheno/bioconda_pcpheno.yaml +++ b/data/pcpheno/bioconda_pcpheno.yaml @@ -4,7 +4,6 @@ description: Tools to integrate, annotate, and link phenotypes to cellular organ home: https://bioconductor.org/packages/3.10/bioc/html/PCpheno.html identifiers: - biotools:pcpheno -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-pcpheno summary: Phenotypes and cellular organizational units diff --git a/data/pcpheno/pcphenobioschemas.jsonld b/data/pcpheno/pcphenobioschemas.jsonld index c4dba0aaa8aa1..fae3ad97485ea 100644 --- a/data/pcpheno/pcphenobioschemas.jsonld +++ b/data/pcpheno/pcphenobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nolwenn Le Meur", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.", "sc:license": "Artistic-2.0", "sc:name": "PCpheno", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PCpheno.html", "sc:version": "1.36.0" diff --git a/data/pcrclipreads/pcrclipreadsbioschemas.jsonld b/data/pcrclipreads/pcrclipreadsbioschemas.jsonld index 7cf433f7c0dcc..7b3d5cc7b6c07 100644 --- a/data/pcrclipreads/pcrclipreadsbioschemas.jsonld +++ b/data/pcrclipreads/pcrclipreadsbioschemas.jsonld @@ -21,8 +21,8 @@ "Linux" ], "sc:provider": [ - "Institut du Thorax, Nantes, France", - "univ-nantes.fr" + "univ-nantes.fr", + "Institut du Thorax, Nantes, France" ], "sc:url": "https://github.com/lindenb/jvarkit/wiki/PcrClipReads", "sc:version": "1.0" diff --git a/data/pcrpi-db/pcrpi-dbbioschemas.jsonld b/data/pcrpi-db/pcrpi-dbbioschemas.jsonld index 2a7f9c68e4e83..db73cc26b54c1 100644 --- a/data/pcrpi-db/pcrpi-dbbioschemas.jsonld +++ b/data/pcrpi-db/pcrpi-dbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PCRPi-DB", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.bioinsilico.org/PCRPIDB" } \ No newline at end of file diff --git a/data/pcrsetup/pcrsetupbioschemas.jsonld b/data/pcrsetup/pcrsetupbioschemas.jsonld index 4055ee8290379..7d6cadaa1c3e5 100644 --- a/data/pcrsetup/pcrsetupbioschemas.jsonld +++ b/data/pcrsetup/pcrsetupbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "PCRsetup is a tool for planning PCR and qPCR reactions, mixing solutions. The higher quality of primers is help to save PCR efficiency at changing PCR conditions. PCR reaction can set up in room temperature and performed without hot-start enzymes.", "sc:name": "PCRsetup", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://primerdigital.com/tools/ReactionMixture.html" } \ No newline at end of file diff --git a/data/pcrtiler/pcrtilerbioschemas.jsonld b/data/pcrtiler/pcrtilerbioschemas.jsonld index 5b8c33c5db085..b407a6f1c2c91 100644 --- a/data/pcrtiler/pcrtilerbioschemas.jsonld +++ b/data/pcrtiler/pcrtilerbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/pcrtiler", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "alain.gervais@USherbrooke.ca", - "Contact Form" + "Contact Form", + "alain.gervais@USherbrooke.ca" ], "sc:additionalType": [ - "Web application", - "Desktop application" + "Desktop application", + "Web application" ], "sc:citation": "pubmed:20519202", "sc:description": "Allows for the automated design of tiled primer pairs for any number of genomic loci. Based on Primer3 and BLAST analysis for cross-hybridization.", "sc:name": "PCRTiler", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://pcrtiler.genap.ca/PCRTiler/" } \ No newline at end of file diff --git a/data/pcs/pcsbioschemas.jsonld b/data/pcs/pcsbioschemas.jsonld index c27dda814ce70..3546c33b69996 100644 --- a/data/pcs/pcsbioschemas.jsonld +++ b/data/pcs/pcsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Stand-alone pakage to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3′-UTRs.", "sc:name": "PCS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfo.au.tsinghua.edu.cn/software/pcs/" } \ No newline at end of file diff --git a/data/pcscs/pcscsbioschemas.jsonld b/data/pcscs/pcscsbioschemas.jsonld index 4a5c01711737c..73166c7ff52f8 100644 --- a/data/pcscs/pcscsbioschemas.jsonld +++ b/data/pcscs/pcscsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Theoretical power calculator for D2 and D2*. The sofware facilitates the use of D2 or D2* for sequence or genome comparison and for evaluation of statistical power for detecting the relationship between the sequences.", "sc:name": "PCSCS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://meta.cmb.usc.edu/d2/" diff --git a/data/pcxn/pcxnbioschemas.jsonld b/data/pcxn/pcxnbioschemas.jsonld index 40d5c21b89982..c4707de0d6826 100644 --- a/data/pcxn/pcxnbioschemas.jsonld +++ b/data/pcxn/pcxnbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Powerful new framework for interrogation of global pathway relationships.", "sc:name": "PCxN", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://pcxn.org:8080/" diff --git a/data/pdart/pdartbioschemas.jsonld b/data/pdart/pdartbioschemas.jsonld index 6b5a478d3c882..39552d180d67c 100644 --- a/data/pdart/pdartbioschemas.jsonld +++ b/data/pdart/pdartbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PDART", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://cmb.bnu.edu.cn/pdart/" } \ No newline at end of file diff --git a/data/pdb-blast/pdb-blastbioschemas.jsonld b/data/pdb-blast/pdb-blastbioschemas.jsonld index 8aa8e6a71a31c..b752a6c56d8a5 100644 --- a/data/pdb-blast/pdb-blastbioschemas.jsonld +++ b/data/pdb-blast/pdb-blastbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Two step protocol which uses BLAST to identify putative protein structures similar to a query sequence.", "sc:name": "PDB-BLAST", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/pdbblast/", diff --git a/data/pdb-explorer/pdb-explorerbioschemas.jsonld b/data/pdb-explorer/pdb-explorerbioschemas.jsonld index fb104c5bc6875..d964db2c7aa35 100644 --- a/data/pdb-explorer/pdb-explorerbioschemas.jsonld +++ b/data/pdb-explorer/pdb-explorerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web application for the interactive visualization of chemical space of RCSB Protein Data Bank (PDB) characterized by protein shape fingerprint (3DP) and shape similarity search for molecules in PDB.", "sc:name": "PDB-Explorer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.cheminfo.org/pdbexplorer/" } \ No newline at end of file diff --git a/data/pdb-tools/pdb-toolsbioschemas.jsonld b/data/pdb-tools/pdb-toolsbioschemas.jsonld index 3ed9a1f1fddb6..43d92f2b20ae8 100644 --- a/data/pdb-tools/pdb-toolsbioschemas.jsonld +++ b/data/pdb-tools/pdb-toolsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Set of command line python scripts that manipulate wwPDB protein and nucleic acid structure files. There are many programs, both open source and proprietary, that perform similar tasks; however, most of these tools are buried within programs of larger functionality.", "sc:name": "pdb-tools", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://code.google.com/p/pdb-tools/", "sc:version": "0.2.1" diff --git a/data/pdb/pdbbioschemas.jsonld b/data/pdb/pdbbioschemas.jsonld index c44f59243bdc7..51d39ddbf0b74 100644 --- a/data/pdb/pdbbioschemas.jsonld +++ b/data/pdb/pdbbioschemas.jsonld @@ -11,14 +11,14 @@ "@id": "https://bio.tools/pdb", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web API" + "Web API", + "Database portal" ], "sc:description": "Global repository for all bona fide protein structure data. Single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. It also has RESTful interface to search and retrieve data from the Protein Data Bank (PDB).", "sc:name": "The Protein Data Bank (PDB)", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "Instruct", diff --git a/data/pdb2pqr/pdb2pqrbioschemas.jsonld b/data/pdb2pqr/pdb2pqrbioschemas.jsonld index 68d925183a48c..6854dee36da9a 100644 --- a/data/pdb2pqr/pdb2pqrbioschemas.jsonld +++ b/data/pdb2pqr/pdb2pqrbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PDB2PQR", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://pdb2pqr.sourceforge.net/" } \ No newline at end of file diff --git a/data/pdb_extract/pdb_extractbioschemas.jsonld b/data/pdb_extract/pdb_extractbioschemas.jsonld index 2cd602372d2d2..10fdd22d4ed2b 100644 --- a/data/pdb_extract/pdb_extractbioschemas.jsonld +++ b/data/pdb_extract/pdb_extractbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Tools and examples for extracting mmCIF data from structure determination applications.", "sc:name": "pdb_extract", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html", "sc:version": "3.11" diff --git a/data/pdb_hydro/pdb_hydrobioschemas.jsonld b/data/pdb_hydro/pdb_hydrobioschemas.jsonld index 342d6227083a5..b70630c7ea9aa 100644 --- a/data/pdb_hydro/pdb_hydrobioschemas.jsonld +++ b/data/pdb_hydro/pdb_hydrobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.", "sc:name": "PDB_Hydro", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://lorentz.immstr.pasteur.fr/solvate_mutate.php" } \ No newline at end of file diff --git a/data/pdb_redo/pdb_redobioschemas.jsonld b/data/pdb_redo/pdb_redobioschemas.jsonld index ac0e5d929192c..cd42aff8045b6 100644 --- a/data/pdb_redo/pdb_redobioschemas.jsonld +++ b/data/pdb_redo/pdb_redobioschemas.jsonld @@ -20,8 +20,8 @@ "sc:description": "The PDB_REDO databank contains alternative (in many cases higher quality) versions of Protein Data Bank (PDB) structure models that were optimised by model refinement and rebuilding. \nThe structure models are supplemented by validation data that describe model quality and model changes with respect to the PDB version.\nAs the models are consistently treated, they are more suited for large-scale analysis of protein structure than their PDB counterparts.", "sc:name": "PDB_REDO databank", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.cmbi.ru.nl/pdb_redo" diff --git a/data/pdbe/pdbebioschemas.jsonld b/data/pdbe/pdbebioschemas.jsonld index aa61dae271bab..40dae33b9059d 100644 --- a/data/pdbe/pdbebioschemas.jsonld +++ b/data/pdbe/pdbebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Protein Data Bank in Europe is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. The database infrastructure is based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules.", "sc:name": "PDBe", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.ebi.ac.uk/pdbe/" } \ No newline at end of file diff --git a/data/pdbefold/pdbefoldbioschemas.jsonld b/data/pdbefold/pdbefoldbioschemas.jsonld index ea8740239f616..fbd1b10e9dac8 100644 --- a/data/pdbefold/pdbefoldbioschemas.jsonld +++ b/data/pdbefold/pdbefoldbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Identification and comparison of similar proteins based on secondary structure.", "sc:name": "PDBeFold", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://pdbe.org/fold", diff --git a/data/pdbemotif/pdbemotifbioschemas.jsonld b/data/pdbemotif/pdbemotifbioschemas.jsonld index 8d7dc974eb582..8a94ab0c9a0ec 100644 --- a/data/pdbemotif/pdbemotifbioschemas.jsonld +++ b/data/pdbemotif/pdbemotifbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The output provides info about ligand interactions, PROSITE patterns and small 3D structure motifs. The interface provides an ability to form a search criteria for similar sites/motifs.", "sc:name": "PDBeMotif", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/pdbe-site/pdbemotif/start?tab=upload", diff --git a/data/pdbepisa/pdbepisabioschemas.jsonld b/data/pdbepisa/pdbepisabioschemas.jsonld index a122a1dfadb0d..33f29326ceb8d 100644 --- a/data/pdbepisa/pdbepisabioschemas.jsonld +++ b/data/pdbepisa/pdbepisabioschemas.jsonld @@ -13,14 +13,14 @@ "biotools:primaryContact": "Michael Wainwright", "sc:additionalType": "Web application", "sc:author": [ - "PDBe development team", - "Michael Wainwright" + "Michael Wainwright", + "PDBe development team" ], "sc:description": "Exploration of macromolecular interfaces and prediction of probable quaternary structures.", "sc:name": "PDBePISA", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "EMBL-EBI", diff --git a/data/pdbest/pdbestbioschemas.jsonld b/data/pdbest/pdbestbioschemas.jsonld index b662f9dc7c377..12aa455102fcf 100644 --- a/data/pdbest/pdbestbioschemas.jsonld +++ b/data/pdbest/pdbestbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Gonçalves WR", - "de Melo-Minardi RC", - "Pires DE" + "Pires DE", + "de Melo-Minardi RC" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:25910698", "sc:description": "Freely available platform for manipulating, filtering and normalizing biomolecules in Protein Data Bank (PDB) and mmCIF structure files.", "sc:name": "PDBest", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.pdbest.dcc.ufmg.br/" } \ No newline at end of file diff --git a/data/pdbexplore/pdbexplorebioschemas.jsonld b/data/pdbexplore/pdbexplorebioschemas.jsonld index 892722fa80efd..8417c473376b7 100644 --- a/data/pdbexplore/pdbexplorebioschemas.jsonld +++ b/data/pdbexplore/pdbexplorebioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Jose Dana", "sc:additionalType": "Web application", "sc:author": [ - "PDBe development team", - "Jose Dana" + "Jose Dana", + "PDBe development team" ], "sc:description": "Search and alignment of protein sequences in PDB.", "sc:name": "PDBeXplore: sequence similarity search", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://pdbe.org/FASTA", diff --git a/data/pdbfinder/pdbfinderbioschemas.jsonld b/data/pdbfinder/pdbfinderbioschemas.jsonld index a92693e98f7a1..3cd6f3bbe1508 100644 --- a/data/pdbfinder/pdbfinderbioschemas.jsonld +++ b/data/pdbfinder/pdbfinderbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This database holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries. It is not useful to search in atomic coordinates: it is meant to ad searches in the administrative records of PDB files.", "sc:name": "PDBFINDER reformatted PDB files", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://swift.cmbi.ru.nl/gv/pdbfinder/" } \ No newline at end of file diff --git a/data/pdbinout/pdbinoutbioschemas.jsonld b/data/pdbinout/pdbinoutbioschemas.jsonld index d848512e403fd..deac6c644a174 100644 --- a/data/pdbinout/pdbinoutbioschemas.jsonld +++ b/data/pdbinout/pdbinoutbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Open-source, Python-based tool for processing and conversion of various versions of PDB file format for biostructural applications.", "sc:name": "PDBinout", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://pdbinout.ibch.poznan.pl/" } \ No newline at end of file diff --git a/data/pdbsitescan/pdbsitescanbioschemas.jsonld b/data/pdbsitescan/pdbsitescanbioschemas.jsonld index bad0e2c25afc8..5a33c9a3b9c9b 100644 --- a/data/pdbsitescan/pdbsitescanbioschemas.jsonld +++ b/data/pdbsitescan/pdbsitescanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.", "sc:name": "PDBSiteScan", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html" } \ No newline at end of file diff --git a/data/pdbsum/pdbsumbioschemas.jsonld b/data/pdbsum/pdbsumbioschemas.jsonld index 729ddeb7cfc75..77177d6e91b42 100644 --- a/data/pdbsum/pdbsumbioschemas.jsonld +++ b/data/pdbsum/pdbsumbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkt940", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-5528-0087", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/pdbsum", "@type": "sc:SoftwareApplication", @@ -34,11 +26,11 @@ "@id": "edam:topic_2814" }, "sc:citation": [ + "pubmed:24153109", + "pmcid:PMC3965036", { "@id": "https://doi.org/10.1093/nar/gkt940" - }, - "pubmed:24153109", - "pmcid:PMC3965036" + } ], "sc:description": "At-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.", "sc:featureList": { @@ -46,11 +38,19 @@ }, "sc:name": "PDBsum overview of macromolecular structures", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://www.ebi.ac.uk/pdbsum/" + }, + { + "@id": "http://orcid.org/0000-0001-5528-0087", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/nar/gkt940", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pdbsum_generate/pdbsum_generatebioschemas.jsonld b/data/pdbsum_generate/pdbsum_generatebioschemas.jsonld index a1521ec533cc4..cb3d094cff9be 100644 --- a/data/pdbsum_generate/pdbsum_generatebioschemas.jsonld +++ b/data/pdbsum_generate/pdbsum_generatebioschemas.jsonld @@ -13,16 +13,16 @@ "biotools:primaryContact": "Roman Laskowski", "sc:additionalType": "Web application", "sc:author": [ - "Thornton Group", - "Roman Laskowski" + "Roman Laskowski", + "Thornton Group" ], "sc:contributor": "Victor Chiskoff", "sc:description": "Generate a full set of PDBsum structural analyses.", "sc:name": "PDBsum Generate", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html", diff --git a/data/pdbusqlextractor/pdbusqlextractorbioschemas.jsonld b/data/pdbusqlextractor/pdbusqlextractorbioschemas.jsonld index 810512a06cb99..c7964fa74e9ee 100644 --- a/data/pdbusqlextractor/pdbusqlextractorbioschemas.jsonld +++ b/data/pdbusqlextractor/pdbusqlextractorbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3390/molecules24010179", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/PDBUSQLExtractor", "@type": "sc:SoftwareApplication", @@ -24,10 +28,10 @@ "sc:description": "Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment.", "sc:featureList": [ { - "@id": "edam:operation_1812" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_1812" }, { "@id": "edam:operation_0279" @@ -37,14 +41,10 @@ "sc:name": "PDBUSQLExtractor", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://zti.polsl.pl/w3/dmrozek/science/pdbusqlext.htm" - }, - { - "@id": "https://doi.org/10.3390/molecules24010179", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pdegem/pdegembioschemas.jsonld b/data/pdegem/pdegembioschemas.jsonld index eea17b1d4ff7c..f741a72606e42 100644 --- a/data/pdegem/pdegembioschemas.jsonld +++ b/data/pdegem/pdegembioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "PDEGEM (Positional Dependent Energy Guided Expression Model ) is a robust nonlinear regression model to estimate the abundance of transcripts", "sc:name": "PDEGEM", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.math.pku.edu.cn/teachers/dengmh/PDEGEM/", "sc:version": "20140325" diff --git a/data/pdeparams/pdeparamsbioschemas.jsonld b/data/pdeparams/pdeparamsbioschemas.jsonld index 55a43930b7def..d90f9b71902e8 100644 --- a/data/pdeparams/pdeparamsbioschemas.jsonld +++ b/data/pdeparams/pdeparamsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "PDEparams", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://github.com/systemsmedicine/PDE_params" } \ No newline at end of file diff --git a/data/pdestrian/pdestrianbioschemas.jsonld b/data/pdestrian/pdestrianbioschemas.jsonld index 9a6af8f532448..8ee39d91b6289 100644 --- a/data/pdestrian/pdestrianbioschemas.jsonld +++ b/data/pdestrian/pdestrianbioschemas.jsonld @@ -15,34 +15,34 @@ "Dr. Chris de Graaf" ], "sc:additionalType": [ + "Web API", "Command-line tool", "Database portal", - "Web API", "Web application" ], "sc:author": [ - "Chris de Graaf", - "Georgi K. Kanev", "Albert J. Kooistra", + "Chris de Graaf", + "Division of Medicinal Chemistry (Vrije Universiteit Amsterdam)", "Chimed Jansen", - "Division of Medicinal Chemistry (Vrije Universiteit Amsterdam)" + "Georgi K. Kanev" ], "sc:contributor": [ "TI Pharma grant T4-302", - "European Commission seventh Framework Programme FP7-HEALTH-2013-INNOVATION-1, PDE4NPD (no. 602666)", "Iwan J.P. de Esch", - "Rob Leurs" + "Rob Leurs", + "European Commission seventh Framework Programme FP7-HEALTH-2013-INNOVATION-1, PDE4NPD (no. 602666)" ], "sc:description": "The database revolves around the protein structure of catalytic PDE domains and the way PDE inhibitors can interact with them. It contains a systematic analysis of all phosphodiesterase (PDE) catalytic domain crystal structures present in the Protein Data Bank (PDB) with a focus on PDE-ligand interactions.", "sc:funder": [ - "TI Pharma grant T4-302", - "European Commission seventh Framework Programme FP7-HEALTH-2013-INNOVATION-1, PDE4NPD (no. 602666)" + "European Commission seventh Framework Programme FP7-HEALTH-2013-INNOVATION-1, PDE4NPD (no. 602666)", + "TI Pharma grant T4-302" ], "sc:name": "PDEStrIAn", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "vu.nl", diff --git a/data/pdid/pdidbioschemas.jsonld b/data/pdid/pdidbioschemas.jsonld index 2471e7631ac4a..709c53dfeb8f1 100644 --- a/data/pdid/pdidbioschemas.jsonld +++ b/data/pdid/pdidbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lukasz Kurgan", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": "pubmed:26504143", "sc:description": "Database of molecular-level putative protein-drug interactions in the structural human proteome.", "sc:license": "Other", "sc:name": "PDID", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://biomine.cs.vcu.edu/servers/PDID/index.php" } \ No newline at end of file diff --git a/data/pdiviz/pdivizbioschemas.jsonld b/data/pdiviz/pdivizbioschemas.jsonld index b0941a76314b1..e809480dedcba 100644 --- a/data/pdiviz/pdivizbioschemas.jsonld +++ b/data/pdiviz/pdivizbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Plugin for the PyMOL molecular visualization system that is specifically designed to visualize protein-DNA interfaces in three dimensions. PDIviz detects the interface of protein-DNA complexes by calculating the buried surface area directly in PyMOL.", "sc:name": "PDIviz", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://melolab.org/mbl/pdiviz" diff --git a/data/pdmclass/pdmclassbioschemas.jsonld b/data/pdmclass/pdmclassbioschemas.jsonld index a1c9cb6c85772..6a71ecd8b8db6 100644 --- a/data/pdmclass/pdmclassbioschemas.jsonld +++ b/data/pdmclass/pdmclassbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "James W. MacDonald", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression.", "sc:license": "Artistic-2.0", "sc:name": "pdmclass", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pdmclass.html", "sc:version": "1.46.0" diff --git a/data/pdzpepint/pdzpepintbioschemas.jsonld b/data/pdzpepint/pdzpepintbioschemas.jsonld index b7d5ef6bc0d96..f2f2da4c24610 100644 --- a/data/pdzpepint/pdzpepintbioschemas.jsonld +++ b/data/pdzpepint/pdzpepintbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PDZPepInt", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://modpepint.informatik.uni-freiburg.de/PDZPepInt/Input.jsp", "sc:version": "1.0.0" diff --git a/data/pe_filter/pe_filterbioschemas.jsonld b/data/pe_filter/pe_filterbioschemas.jsonld index c6b7d7853312f..0bb43eb8b704f 100644 --- a/data/pe_filter/pe_filterbioschemas.jsonld +++ b/data/pe_filter/pe_filterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Split sorted fasta sequences paired end into two seperate fasta files.", "sc:name": "pe_filter", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://bioweb.pasteur.fr/packages/pack@FastqProcessing@0.38.1", "sc:version": "0.01" diff --git a/data/peak2bed/peak2bedbioschemas.jsonld b/data/peak2bed/peak2bedbioschemas.jsonld index 98420c38419ea..b7b870b60c83c 100644 --- a/data/peak2bed/peak2bedbioschemas.jsonld +++ b/data/peak2bed/peak2bedbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "peak2bed", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/peak2bed/peak2bed/1.0", "sc:version": "1.0" diff --git a/data/peakanalyzer/peakanalyzerbioschemas.jsonld b/data/peakanalyzer/peakanalyzerbioschemas.jsonld index afe320c430db6..d28eda4e5ffcd 100644 --- a/data/peakanalyzer/peakanalyzerbioschemas.jsonld +++ b/data/peakanalyzer/peakanalyzerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A set of utilities for the automated processing and annotation of genome-wide signal enrichment peaks derived through functional genomics techniques", "sc:name": "PeakAnalyzer", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.bioinformatics.org/peakanalyzer/wiki/" } \ No newline at end of file diff --git a/data/peakc/peakcbioschemas.jsonld b/data/peakc/peakcbioschemas.jsonld index 96b574ae36e2f..3850671b77632 100644 --- a/data/peakc/peakcbioschemas.jsonld +++ b/data/peakc/peakcbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "peakC", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/deWitLab/peakC" } \ No newline at end of file diff --git a/data/peakcalling_findpeaks/peakcalling_findpeaksbioschemas.jsonld b/data/peakcalling_findpeaks/peakcalling_findpeaksbioschemas.jsonld index 680665fcacdf4..e2c49e94f880e 100644 --- a/data/peakcalling_findpeaks/peakcalling_findpeaksbioschemas.jsonld +++ b/data/peakcalling_findpeaks/peakcalling_findpeaksbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Peak Finder/Analysis application for the ChIP-Seq.", "sc:name": "peakcalling_findpeaks", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.htslib.org/", "sc:version": "4.0.9.2" diff --git a/data/peaklink/peaklinkbioschemas.jsonld b/data/peaklink/peaklinkbioschemas.jsonld index 8db3cc06d1fce..69d8d5b125a46 100644 --- a/data/peaklink/peaklinkbioschemas.jsonld +++ b/data/peaklink/peaklinkbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Uses information in both the time and frequency domain as inputs to a non-linear support vector machine (SVM) classifier. The PL algorithm first removes candidate corresponding peaks with excessively large elution time shifts, then calculates the correlation between a pair of candidate peaks after removing noise. Then a SVM classifier is trained and applied for differentiating corresponding and non-corresponding peptide peaks.", "sc:name": "PeakLink", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://compgenomics.utsa.edu/zgroup/PeakLink/" } \ No newline at end of file diff --git a/data/peakquant/peakquantbioschemas.jsonld b/data/peakquant/peakquantbioschemas.jsonld index 146f96e0fd724..3fcce8d23ae2f 100644 --- a/data/peakquant/peakquantbioschemas.jsonld +++ b/data/peakquant/peakquantbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Serves as an integrated platform for several Proteomics tools and provides an easily operated graphical user interface.", "sc:name": "PeakQuant", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ruhr-uni-bochum.de/mpc/software/PeakQuant/index.html.de" diff --git a/data/peakseq/peakseqbioschemas.jsonld b/data/peakseq/peakseqbioschemas.jsonld index 5861540bec41a..caa57303cad23 100644 --- a/data/peakseq/peakseqbioschemas.jsonld +++ b/data/peakseq/peakseqbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments.", "sc:name": "PeakSeq", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://info.gersteinlab.org/PeakSeq" } \ No newline at end of file diff --git a/data/peaktrace/peaktracebioschemas.jsonld b/data/peaktrace/peaktracebioschemas.jsonld index a8e10fe0f66d2..e80cd858daa65 100644 --- a/data/peaktrace/peaktracebioschemas.jsonld +++ b/data/peaktrace/peaktracebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Alternative basecaller for improving the quality and read length of Sanger DNA sequencing traces. The basecaller works with trace files produced by the ABI 310, 3700, 3100, 3130, 3730, and 3500 DNA sequencers. MegBACE sequencers are also supported.", "sc:name": "PeakTrace", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.peaktrace.com" diff --git a/data/peakzilla/peakzillabioschemas.jsonld b/data/peakzilla/peakzillabioschemas.jsonld index 8ef89d8e3780d..8a3f114561d98 100644 --- a/data/peakzilla/peakzillabioschemas.jsonld +++ b/data/peakzilla/peakzillabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-2.0", "sc:name": "Peakzilla", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/steinmann/peakzilla" } \ No newline at end of file diff --git a/data/peas/peasbioschemas.jsonld b/data/peas/peasbioschemas.jsonld index 10765e1f66adc..3983dad13b166 100644 --- a/data/peas/peasbioschemas.jsonld +++ b/data/peas/peasbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/peas", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Shuhua Xu", - "Li Jin" + "Li Jin", + "Shuhua Xu" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:21565121", diff --git a/data/pease/peasebioschemas.jsonld b/data/pease/peasebioschemas.jsonld index df1ad90fb532e..31c409977b19c 100644 --- a/data/pease/peasebioschemas.jsonld +++ b/data/pease/peasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Automated tool for predicting the epitope for a given antigen structure and an antibody sequence.", "sc:name": "PEASE", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.ofranlab.org/PEASE" } \ No newline at end of file diff --git a/data/peca/pecabioschemas.jsonld b/data/peca/pecabioschemas.jsonld index 1998688370d4b..22efe08b7d243 100644 --- a/data/peca/pecabioschemas.jsonld +++ b/data/peca/pecabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "PECA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PECA.html", "sc:version": "1.10.0" diff --git a/data/pecop/pecopbioschemas.jsonld b/data/pecop/pecopbioschemas.jsonld index 41522005de22c..fcdea605abd41 100644 --- a/data/pecop/pecopbioschemas.jsonld +++ b/data/pecop/pecopbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This server offers a new way to examine positional conservation in protein sequences.", "sc:name": "PeCoP", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioinformatics.org/pecop/" } \ No newline at end of file diff --git a/data/ped/pedbioschemas.jsonld b/data/ped/pedbioschemas.jsonld index b018bde8755a0..7fccc564c813e 100644 --- a/data/ped/pedbioschemas.jsonld +++ b/data/ped/pedbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Repository for pancreatic-derived -omics data. It includes easurements derived from transcriptomics, proteomics, genomics and miRNA profiles from various pancreas-centred reports on a broad range of specimen and experimental types.", "sc:name": "Pancreatic Expression Database (PED)", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.pancreasexpression.org" } \ No newline at end of file diff --git a/data/pedhunter/pedhunterbioschemas.jsonld b/data/pedhunter/pedhunterbioschemas.jsonld index e7468e6cbd9bd..c00164724e2a6 100644 --- a/data/pedhunter/pedhunterbioschemas.jsonld +++ b/data/pedhunter/pedhunterbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/pedhunter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alejandro Schäffer", - "Richa Agarwala" + "Richa Agarwala", + "Alejandro Schäffer" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:9521925", diff --git a/data/pedibd/pedibdbioschemas.jsonld b/data/pedibd/pedibdbioschemas.jsonld index 1667d3997bd85..e76f9cbabcc36 100644 --- a/data/pedibd/pedibdbioschemas.jsonld +++ b/data/pedibd/pedibdbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Infers pairwise Infer identical-by-descent (IBD) and skips haplotype and inheritance construction.", "sc:name": "PEDIBD", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sites.google.com/site/xlxlxlxinli/pedibd" } \ No newline at end of file diff --git a/data/pedican/pedicanbioschemas.jsonld b/data/pedican/pedicanbioschemas.jsonld index 5cc31cc1cccb6..ad5036c8aa403 100644 --- a/data/pedican/pedicanbioschemas.jsonld +++ b/data/pedican/pedicanbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/SREP11435", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pedican", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Database portal", "sc:citation": [ "pubmed:26073932", - "pmcid:PMC4466794", { "@id": "https://doi.org/10.1038/SREP11435" - } + }, + "pmcid:PMC4466794" ], "sc:description": "An online gene resource for pediatric cancers with literature evidence.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "Pedican", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://pedican.bioinfo-minzhao.org/" - }, - { - "@id": "https://doi.org/10.1038/SREP11435", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pedigreejs/pedigreejsbioschemas.jsonld b/data/pedigreejs/pedigreejsbioschemas.jsonld index 2ec4527182c1f..484e2a9713bc5 100644 --- a/data/pedigreejs/pedigreejsbioschemas.jsonld +++ b/data/pedigreejs/pedigreejsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "pedigreejs", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://ccge-boadicea.github.io/pedigreejs/" } \ No newline at end of file diff --git a/data/pedigreesim/pedigreesimbioschemas.jsonld b/data/pedigreesim/pedigreesimbioschemas.jsonld index 5b5db73fd933a..1054e92b12a98 100644 --- a/data/pedigreesim/pedigreesimbioschemas.jsonld +++ b/data/pedigreesim/pedigreesimbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software that generates simulated genetic marker data of individuals in pedigreed populations. A population can consist of either diploid or tetraploid individuals. It can simulate meioses with or without chiasma interference, and in tetraploids it can simulate meioses with two bivalents or one quadrivalent per set of hom(oe)ologous chromosomes.", "sc:name": "PedigreeSim", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.wageningenur.nl/en/show/Software-PedigreeSim.htm" } \ No newline at end of file diff --git a/data/pedisnp/pedisnpbioschemas.jsonld b/data/pedisnp/pedisnpbioschemas.jsonld index 424c2f5726412..b7c5beed0eb55 100644 --- a/data/pedisnp/pedisnpbioschemas.jsonld +++ b/data/pedisnp/pedisnpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Designed to provide an analysis of Single Nucleotide Polymorphism (SNP) data from a pedigree of two generations: two parents with two or more children. I", "sc:name": "pediSNP", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://pevsnerlab.kennedykrieger.org/pediSNP/" } \ No newline at end of file diff --git a/data/pedpeel/pedpeelbioschemas.jsonld b/data/pedpeel/pedpeelbioschemas.jsonld index 3bd552f2cc56f..8ac87ac329fda 100644 --- a/data/pedpeel/pedpeelbioschemas.jsonld +++ b/data/pedpeel/pedpeelbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PedPeel", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mga.bionet.nsc.ru/soft/pedpeel/" } \ No newline at end of file diff --git a/data/pedro/pedrobioschemas.jsonld b/data/pedro/pedrobioschemas.jsonld index 538f0e265e39e..bb9b4079691be 100644 --- a/data/pedro/pedrobioschemas.jsonld +++ b/data/pedro/pedrobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Software and schemata for modelling, capturing and disseminating proteomics experimental data", "sc:name": "PEDRo", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://pedrodownload.man.ac.uk/" } \ No newline at end of file diff --git a/data/pedsys/pedsysbioschemas.jsonld b/data/pedsys/pedsysbioschemas.jsonld index 84c2186d5479a..1518289dd322a 100644 --- a/data/pedsys/pedsysbioschemas.jsonld +++ b/data/pedsys/pedsysbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/pedsys", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Database system developed as a specialized tool for management of genetic, pedigree and demographic data.", "sc:license": "Other", diff --git a/data/peffect/peffectbioschemas.jsonld b/data/peffect/peffectbioschemas.jsonld index a1da594b2a4ab..f144cdd4d5ac3 100644 --- a/data/peffect/peffectbioschemas.jsonld +++ b/data/peffect/peffectbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:contributor": [ "Burkhard Rost", "Alexander von Humboldt foundation through the German Federal Ministry for Education and Research", - "Yana Bromberg", - "Ernst Ludwig Ehrlich Studienwerk" + "Ernst Ludwig Ehrlich Studienwerk", + "Yana Bromberg" ], "sc:description": "Prediction of type III effector proteins from protein sequence.", "sc:funder": [ @@ -27,9 +27,9 @@ "sc:name": "pEffect", "sc:operatingSystem": "Linux", "sc:provider": [ - "RostLab", + "Rutgers University", "Technical University of Munich", - "Rutgers University" + "RostLab" ], "sc:url": "https://rostlab.org/services/peffect/", "sc:version": "0.0.1" diff --git a/data/pegasys/pegasysbioschemas.jsonld b/data/pegasys/pegasysbioschemas.jsonld index 70e03915bcaf7..82b634cb13f5d 100644 --- a/data/pegasys/pegasysbioschemas.jsonld +++ b/data/pegasys/pegasysbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Pegasys is a a flexible, modular and customizable software system that coordinates the execution of multiple biological sequence analysis tools and facilitates the integration of their output. The software allows users to create analysis workflows using a graphical user interface. Adaptors are included for various software tools.", "sc:name": "Pegasys", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.bioextract.org/query/index.jsp" } \ No newline at end of file diff --git a/data/pele/pelebioschemas.jsonld b/data/pele/pelebioschemas.jsonld index 543c470a4cce4..860696c11c729 100644 --- a/data/pele/pelebioschemas.jsonld +++ b/data/pele/pelebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Model the all-atom protein-ligand dynamical interactions.", "sc:name": "PELE", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://pele.bsc.es" } \ No newline at end of file diff --git a/data/penncnv2/penncnv2bioschemas.jsonld b/data/penncnv2/penncnv2bioschemas.jsonld index 6a2dd3848fc97..93be299c1e66a 100644 --- a/data/penncnv2/penncnv2bioschemas.jsonld +++ b/data/penncnv2/penncnv2bioschemas.jsonld @@ -18,10 +18,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:24021380", { "@id": "https://doi.org/10.1093/bioinformatics/btt521" }, - "pubmed:24021380", "pmcid:PMC3834792" ], "sc:description": "A C++ software package for detection of copy number alterations on tumor samples from SNP arrays and NGS data.", diff --git a/data/pennseq/pennseqbioschemas.jsonld b/data/pennseq/pennseqbioschemas.jsonld index fd47f67acc20d..b278195a9a7e4 100644 --- a/data/pennseq/pennseqbioschemas.jsonld +++ b/data/pennseq/pennseqbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "PennSeq is a statistical method that allows each isoform to have its own non-uniform read distribution.", "sc:name": "PennSeq", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sourceforge.net/projects/pennseq/" } \ No newline at end of file diff --git a/data/pep-fold/pep-foldbioschemas.jsonld b/data/pep-fold/pep-foldbioschemas.jsonld index 01192fca9de07..6abb4f9dbf884 100644 --- a/data/pep-fold/pep-foldbioschemas.jsonld +++ b/data/pep-fold/pep-foldbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-1033-9895", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/pep-fold", "@type": "sc:SoftwareApplication", @@ -26,9 +22,13 @@ "sc:name": "PEP-FOLD", "sc:url": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD3", "sc:version": [ - "2.0", - "3.5" + "3.5", + "2.0" ] + }, + { + "@id": "https://orcid.org/0000-0003-1033-9895", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pep-sitefinder/pep-sitefinderbioschemas.jsonld b/data/pep-sitefinder/pep-sitefinderbioschemas.jsonld index 0927ae36da534..d49c88494a3d3 100644 --- a/data/pep-sitefinder/pep-sitefinderbioschemas.jsonld +++ b/data/pep-sitefinder/pep-sitefinderbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-1033-9895", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/pep-sitefinder", "@type": "sc:SoftwareApplication", @@ -22,10 +26,6 @@ "sc:name": "PEP-SiteFinder", "sc:url": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-SiteFinder", "sc:version": "1.0" - }, - { - "@id": "https://orcid.org/0000-0003-1033-9895", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pep2path/pep2pathbioschemas.jsonld b/data/pep2path/pep2pathbioschemas.jsonld index 2c8197ad8baf8..158ae6716f72e 100644 --- a/data/pep2path/pep2pathbioschemas.jsonld +++ b/data/pep2path/pep2pathbioschemas.jsonld @@ -17,12 +17,12 @@ "@id": "https://bio.tools/pep2path", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Suite", - "Desktop application" + "Desktop application", + "Suite" ], "sc:citation": [ - "pmcid:PMC4154637", "pubmed:25188327", + "pmcid:PMC4154637", { "@id": "https://doi.org/10.1371/journal.pcbi.1003822" } @@ -34,9 +34,9 @@ "sc:license": "GPL-3.0", "sc:name": "Pep2Path", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://pep2path.sourceforge.net", "sc:version": "1.1.0" diff --git a/data/pepbindpred/pepbindpredbioschemas.jsonld b/data/pepbindpred/pepbindpredbioschemas.jsonld index 45a7357444b5e..206d1578c4821 100644 --- a/data/pepbindpred/pepbindpredbioschemas.jsonld +++ b/data/pepbindpred/pepbindpredbioschemas.jsonld @@ -17,11 +17,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC3760854", "pubmed:24019881", { "@id": "https://doi.org/10.1371/journal.pone.0072838" - } + }, + "pmcid:PMC3760854" ], "sc:description": "PepBindPred is for users interested in identifying peptide binding regions within a protein sequence, which may bind to a know protein structure. PepBindPred was trained on a set of non-redundant protein sequences containing known peptide binding regions sourced from the ELM database.", "sc:featureList": { @@ -29,9 +29,9 @@ }, "sc:name": "PepBindPred", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php" }, diff --git a/data/pepcoil/pepcoilbioschemas.jsonld b/data/pepcoil/pepcoilbioschemas.jsonld index 9bfa5b204ada8..c8f34fbba2323 100644 --- a/data/pepcoil/pepcoilbioschemas.jsonld +++ b/data/pepcoil/pepcoilbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "Wellcome Trust", + "UK MRC", + "EMBOSS Contributors" ], "sc:description": "Predict coiled coil regions in protein sequences.", "sc:funder": [ "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "pepcoil", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/pepcoil.html", "sc:version": "r6" diff --git a/data/pepdigest/pepdigestbioschemas.jsonld b/data/pepdigest/pepdigestbioschemas.jsonld index 2c987253a0e69..c23f5336c594b 100644 --- a/data/pepdigest/pepdigestbioschemas.jsonld +++ b/data/pepdigest/pepdigestbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", + "EMBOSS Contributors", "UK MRC", "Wellcome Trust", - "EMBOSS Contributors" + "UK BBSRC" ], "sc:description": "Report on protein proteolytic enzyme or reagent cleavage sites.", "sc:funder": [ + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "pepdigest", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/pepdistiller/pepdistillerbioschemas.jsonld b/data/pepdistiller/pepdistillerbioschemas.jsonld index e164ce624c17f..4ed8907e1267c 100644 --- a/data/pepdistiller/pepdistillerbioschemas.jsonld +++ b/data/pepdistiller/pepdistillerbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Ning Li", - "Fuchu He", - "Yunping Zhu" + "Yunping Zhu", + "Fuchu He" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:22623377", diff --git a/data/pepexplorer/pepexplorerbioschemas.jsonld b/data/pepexplorer/pepexplorerbioschemas.jsonld index ecbee0e08dde7..c65191072eba6 100644 --- a/data/pepexplorer/pepexplorerbioschemas.jsonld +++ b/data/pepexplorer/pepexplorerbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1074/mcp.M113.037002", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pepexplorer", "@type": "sc:SoftwareApplication", @@ -35,10 +39,6 @@ { "@id": "http://orcid.org/0000-0002-8228-5374", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1074/mcp.M113.037002", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pepfoot/pepfootbioschemas.jsonld b/data/pepfoot/pepfootbioschemas.jsonld index cf7ccd28ee0d6..ffdf386fd23d3 100644 --- a/data/pepfoot/pepfootbioschemas.jsonld +++ b/data/pepfoot/pepfootbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "LGPL-3.0", "sc:name": "PepFoot", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/jbellamycarter/pepfoot" } \ No newline at end of file diff --git a/data/pepinfo-ebi/pepinfo-ebibioschemas.jsonld b/data/pepinfo-ebi/pepinfo-ebibioschemas.jsonld index acb05397a930f..7aa2048d9dea5 100644 --- a/data/pepinfo-ebi/pepinfo-ebibioschemas.jsonld +++ b/data/pepinfo-ebi/pepinfo-ebibioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "EMBOSS", - "Web Production" + "Web Production", + "EMBOSS" ], "sc:description": "Plot amino acid properties of a protein sequence in parallel.", "sc:name": "pepinfo (EBI)", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/seqstats/emboss_pepinfo/", diff --git a/data/pepinfo/pepinfobioschemas.jsonld b/data/pepinfo/pepinfobioschemas.jsonld index 250f6386921a0..d03e384e14829 100644 --- a/data/pepinfo/pepinfobioschemas.jsonld +++ b/data/pepinfo/pepinfobioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", "EMBOSS Contributors", - "UK BBSRC" + "Wellcome Trust" ], "sc:description": "Plot amino acid properties of a protein sequence in parallel.", "sc:funder": [ @@ -26,8 +26,8 @@ "sc:license": "GPL-3.0", "sc:name": "pepinfo", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ diff --git a/data/pepis/pepisbioschemas.jsonld b/data/pepis/pepisbioschemas.jsonld index ae12bfd2be627..fa7751ecf0ce2 100644 --- a/data/pepis/pepisbioschemas.jsonld +++ b/data/pepis/pepisbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Pipeline that is dedicatedly developed for Polygenic, specifically, Epistatic QTL mapping.", "sc:name": "PEPIS", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioinfo.noble.org/PolyGenic_QTL/" diff --git a/data/pepmapper/pepmapperbioschemas.jsonld b/data/pepmapper/pepmapperbioschemas.jsonld index 9cc2636ed5d2e..6b48481a74a73 100644 --- a/data/pepmapper/pepmapperbioschemas.jsonld +++ b/data/pepmapper/pepmapperbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "PepMapper is a web-based mapping tool developed for the purpose of epitope prediction using a collection of affinity selected peptides (mimotopes) derived from phage display experiments.", "sc:name": "PepMapper", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://informatics.nenu.edu.cn/PepMapper/" } \ No newline at end of file diff --git a/data/pepmmsmimic/pepmmsmimicbioschemas.jsonld b/data/pepmmsmimic/pepmmsmimicbioschemas.jsonld index 2f4b0c94ffa59..c07312588ad51 100644 --- a/data/pepmmsmimic/pepmmsmimicbioschemas.jsonld +++ b/data/pepmmsmimic/pepmmsmimicbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web-oriented tool that, given a peptide three-dimensional structure, is able to automate a multi-conformers three-dimensional similarity search among 17 million of conformers calculated from 3.9 million of commercially available chemicals collected in the MMsINC database.", "sc:name": "pepMMsMIMIC", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "ELIXIR-ITA-PADOVA", diff --git a/data/pepnet/pepnetbioschemas.jsonld b/data/pepnet/pepnetbioschemas.jsonld index c6a52e62fe9fe..a8c485b0997fe 100644 --- a/data/pepnet/pepnetbioschemas.jsonld +++ b/data/pepnet/pepnetbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "EMBOSS Contributors", + "Wellcome Trust", "UK BBSRC", "UK MRC" ], "sc:description": "Draw a helical net for a protein sequence.", "sc:funder": [ - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "pepnet", diff --git a/data/pepnovo/pepnovobioschemas.jsonld b/data/pepnovo/pepnovobioschemas.jsonld index baeedac4c7c00..5313215c77c15 100644 --- a/data/pepnovo/pepnovobioschemas.jsonld +++ b/data/pepnovo/pepnovobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "\"De novo\" sequencing using probabilistic network modeling.", "sc:name": "PepNovo", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://proteomics.ucsd.edu/ProteoSAFe/" } \ No newline at end of file diff --git a/data/pepper/pepperbioschemas.jsonld b/data/pepper/pepperbioschemas.jsonld index fa6e6ebfdad69..4fdacef34aa8b 100644 --- a/data/pepper/pepperbioschemas.jsonld +++ b/data/pepper/pepperbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Plugin which finds meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization.", "sc:name": "Pepper", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.issb.genopole.fr/Technology/pepper-cytoscape-app" } \ No newline at end of file diff --git a/data/peppsy/peppsybioschemas.jsonld b/data/peppsy/peppsybioschemas.jsonld index 9b0694d2fdd47..9918a4f34c4d3 100644 --- a/data/peppsy/peppsybioschemas.jsonld +++ b/data/peppsy/peppsybioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:author": [ - "Thomas Darde", - "Olivier Sallou" + "Olivier Sallou", + "Thomas Darde" ], "sc:contributor": [ "Olivier Collin", @@ -23,9 +23,9 @@ "sc:description": "A gene expression-based prioritization system to help investigators to determine in which human tissues they should look for an unseen protein.", "sc:name": "PepPSy", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://peppsy.genouest.org" } \ No newline at end of file diff --git a/data/peppy/peppybioschemas.jsonld b/data/peppy/peppybioschemas.jsonld index 46846137c2157..2b185cc84521a 100644 --- a/data/peppy/peppybioschemas.jsonld +++ b/data/peppy/peppybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A software that identifies new proteins and aberrant protein forms withing proteomic data.", "sc:name": "Peppy", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.geneffects.com/peppy/" } \ No newline at end of file diff --git a/data/pepquery/pepquerybioschemas.jsonld b/data/pepquery/pepquerybioschemas.jsonld index 62bbfe92520fd..d9dfcf8515cb4 100644 --- a/data/pepquery/pepquerybioschemas.jsonld +++ b/data/pepquery/pepquerybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/PepQuery", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Gitter", - "PepQuery Google Group" + "PepQuery Google Group", + "Gitter" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:30610011", @@ -20,8 +20,8 @@ "sc:name": "PepQuery", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.pepquery.org/" } \ No newline at end of file diff --git a/data/pepr/peprbioschemas.jsonld b/data/pepr/peprbioschemas.jsonld index a8ef843fe66fa..85193778368a6 100644 --- a/data/pepr/peprbioschemas.jsonld +++ b/data/pepr/peprbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PePr", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://sartorlab.ccmb.med.umich.edu/node/6" } \ No newline at end of file diff --git a/data/pepserve/pepservebioschemas.jsonld b/data/pepserve/pepservebioschemas.jsonld index 682a7430b0bdd..3ea19f05dc3be 100644 --- a/data/pepserve/pepservebioschemas.jsonld +++ b/data/pepserve/pepservebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for peptide analysis, clustering and visualization.", "sc:name": "PepServe", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioserver-1.bioacademy.gr/Bioserver/PepServe/" } \ No newline at end of file diff --git a/data/pepshell/pepshellbioschemas.jsonld b/data/pepshell/pepshellbioschemas.jsonld index 04d12c4e02823..70e48e3080ffa 100644 --- a/data/pepshell/pepshellbioschemas.jsonld +++ b/data/pepshell/pepshellbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Pepshell", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/compomics/pepshell", diff --git a/data/pepstat/pepstatbioschemas.jsonld b/data/pepstat/pepstatbioschemas.jsonld index 073afcb773951..325632b16fcff 100644 --- a/data/pepstat/pepstatbioschemas.jsonld +++ b/data/pepstat/pepstatbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "pepStat", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pepStat.html", "sc:version": "1.8.0" diff --git a/data/pepstats-ebi/pepstats-ebibioschemas.jsonld b/data/pepstats-ebi/pepstats-ebibioschemas.jsonld index 5983b38c7c7be..fac7a21375885 100644 --- a/data/pepstats-ebi/pepstats-ebibioschemas.jsonld +++ b/data/pepstats-ebi/pepstats-ebibioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "EMBOSS", - "Web Production" + "Web Production", + "EMBOSS" ], "sc:description": "Calculate statistics of protein properties.", "sc:name": "pepstats (EBI)", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/seqstats/emboss_pepstats/", diff --git a/data/pepstats/pepstatsbioschemas.jsonld b/data/pepstats/pepstatsbioschemas.jsonld index 4053beeb70dc1..97f4569df33b5 100644 --- a/data/pepstats/pepstatsbioschemas.jsonld +++ b/data/pepstats/pepstatsbioschemas.jsonld @@ -13,9 +13,9 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "UK BBSRC", "UK MRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Calculate statistics of protein properties.", "sc:funder": [ @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "pepstats", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/pepstr/pepstrbioschemas.jsonld b/data/pepstr/pepstrbioschemas.jsonld index 1444be70c0f4e..84b952e561c30 100644 --- a/data/pepstr/pepstrbioschemas.jsonld +++ b/data/pepstr/pepstrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PepStr", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/pepstr/" } \ No newline at end of file diff --git a/data/pepsweetener/pepsweetenerbioschemas.jsonld b/data/pepsweetener/pepsweetenerbioschemas.jsonld index 1828f50163f2d..bbd55e6f2a4a5 100644 --- a/data/pepsweetener/pepsweetenerbioschemas.jsonld +++ b/data/pepsweetener/pepsweetenerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Manual annotation of MS data for intact glycopeptides. It displays an interactive map of all theoretical glycopeptides that match the molecular masses of queried precursor ions. Ion matching can be performed in two modes: simple when the search space spans the combination of all tryptic peptides including N-glycosites in the human proteome, and advanced when the search space is custom-built by specifying peptides and glycans.", "sc:name": "PepSweetener", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://glycoproteome.expasy.org/pepsweetener/app/" } \ No newline at end of file diff --git a/data/peptideatlas/peptideatlasbioschemas.jsonld b/data/peptideatlas/peptideatlasbioschemas.jsonld index d9ac5e84e1ad5..c4725cdb43480 100644 --- a/data/peptideatlas/peptideatlasbioschemas.jsonld +++ b/data/peptideatlas/peptideatlasbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PeptideAtlas peptide database", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.peptideatlas.org" } \ No newline at end of file diff --git a/data/peptidelocator/peptidelocatorbioschemas.jsonld b/data/peptidelocator/peptidelocatorbioschemas.jsonld index 3fb763d3e5e10..c728fc915118c 100644 --- a/data/peptidelocator/peptidelocatorbioschemas.jsonld +++ b/data/peptidelocator/peptidelocatorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "For users interested in identifying bioactive peptides within a protein sequence. PeptideLocator was trained on a set of non-redundant protein sequences conatining known bioactive peptides.", "sc:name": "PeptideLocator", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/biopred.php" diff --git a/data/peptidemass/peptidemassbioschemas.jsonld b/data/peptidemass/peptidemassbioschemas.jsonld index bedcc064d0452..e35eff696d5a0 100644 --- a/data/peptidemass/peptidemassbioschemas.jsonld +++ b/data/peptidemass/peptidemassbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Cleaves a protein sequence with a chosen enzyme and computes masses of the generated peptides.", "sc:name": "PeptideMass", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://us.expasy.org/tools/peptide-mass.html" } \ No newline at end of file diff --git a/data/peptideshaker/peptideshakerbioschemas.jsonld b/data/peptideshaker/peptideshakerbioschemas.jsonld index 1642b66ef0a2b..3f77569e1539c 100644 --- a/data/peptideshaker/peptideshakerbioschemas.jsonld +++ b/data/peptideshaker/peptideshakerbioschemas.jsonld @@ -12,14 +12,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dominik Kopczynsk", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data!", "sc:name": "PeptideShaker", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "BioInfra.Prot", "sc:url": "http://compomics.github.io/projects/peptide-shaker.html", diff --git a/data/peptimapper/peptimapperbioschemas.jsonld b/data/peptimapper/peptimapperbioschemas.jsonld index 60983405766e8..0d34f48249a7e 100644 --- a/data/peptimapper/peptimapperbioschemas.jsonld +++ b/data/peptimapper/peptimapperbioschemas.jsonld @@ -20,18 +20,18 @@ "sc:additionalType": "Web service", "sc:citation": [ "pubmed:30654742", - "pmcid:PMC6337836", { "@id": "https://doi.org/10.1186/s12864-019-5431-9" - } + }, + "pmcid:PMC6337836" ], "sc:description": "Proteogenomics workflow for the expert annotation of eukaryotic genomes.", "sc:featureList": [ { - "@id": "edam:operation_3643" + "@id": "edam:operation_2929" }, { - "@id": "edam:operation_2929" + "@id": "edam:operation_3643" }, { "@id": "edam:operation_3644" @@ -40,9 +40,9 @@ "sc:license": "GPL-3.0", "sc:name": "Peptimapper", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://hub.docker.com/r/dockerprotim/peptimapper/", "sc:version": "1.0" diff --git a/data/peptizer/peptizerbioschemas.jsonld b/data/peptizer/peptizerbioschemas.jsonld index f67dff30a1722..c655d5d4b54f0 100644 --- a/data/peptizer/peptizerbioschemas.jsonld +++ b/data/peptizer/peptizerbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/peptizer", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": "pubmed:18667410", "sc:description": "Automating manual validation of MS/MS search results.", "sc:name": "Peptizer", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "https://github.com/compomics/peptizer", diff --git a/data/pepvac/pepvacbioschemas.jsonld b/data/pepvac/pepvacbioschemas.jsonld index a2cf53dba88d5..7d3fd39298bef 100644 --- a/data/pepvac/pepvacbioschemas.jsonld +++ b/data/pepvac/pepvacbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PEPVAC is a tool to assist in the development of multi-epitope vaccines. It is optimized for this task by predicting peptides with the ability to bind to several human leukocyte antigens that have similar peptide binding specificity.", "sc:name": "PEPVAC", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://imed.med.ucm.es/PEPVAC/" } \ No newline at end of file diff --git a/data/pepwheel/pepwheelbioschemas.jsonld b/data/pepwheel/pepwheelbioschemas.jsonld index 6db4db1151311..53ec6f32fd5c2 100644 --- a/data/pepwheel/pepwheelbioschemas.jsonld +++ b/data/pepwheel/pepwheelbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK BBSRC", "Wellcome Trust", - "UK MRC" + "EMBOSS Contributors", + "UK MRC", + "UK BBSRC" ], "sc:description": "Draw a helical wheel diagram for a protein sequence.", "sc:funder": [ - "Wellcome Trust", "UK MRC", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "pepwheel", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/pepwindow-ebi/pepwindow-ebibioschemas.jsonld b/data/pepwindow-ebi/pepwindow-ebibioschemas.jsonld index ff6760b11dd4d..9ce48a0234d93 100644 --- a/data/pepwindow-ebi/pepwindow-ebibioschemas.jsonld +++ b/data/pepwindow-ebi/pepwindow-ebibioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "EMBOSS", - "Web Production" + "Web Production", + "EMBOSS" ], "sc:description": "Draw a hydropathy plot for a protein sequence.", "sc:name": "pepwindow (EBI)", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/seqstats/emboss_pepwindow/", diff --git a/data/pepwindow/pepwindowbioschemas.jsonld b/data/pepwindow/pepwindowbioschemas.jsonld index 6a9f759e5439b..65c57b55fa4d7 100644 --- a/data/pepwindow/pepwindowbioschemas.jsonld +++ b/data/pepwindow/pepwindowbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "Wellcome Trust", + "EMBOSS Contributors", "UK BBSRC", - "EMBOSS Contributors" + "Wellcome Trust", + "UK MRC" ], "sc:description": "Draw a hydropathy plot for a protein sequence.", "sc:funder": [ "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "pepwindow", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/pepwindowall/pepwindowallbioschemas.jsonld b/data/pepwindowall/pepwindowallbioschemas.jsonld index 7b95478bc8dcb..4aa60638b2841 100644 --- a/data/pepwindowall/pepwindowallbioschemas.jsonld +++ b/data/pepwindowall/pepwindowallbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK MRC", - "UK BBSRC", "EMBOSS Contributors", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Draw Kyte-Doolittle hydropathy plot for a protein alignment.", "sc:funder": [ - "UK MRC", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "pepwindowall", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/pepxml2excel/pepxml2excelbioschemas.jsonld b/data/pepxml2excel/pepxml2excelbioschemas.jsonld index 3b308e2db8896..31561e37c87ba 100644 --- a/data/pepxml2excel/pepxml2excelbioschemas.jsonld +++ b/data/pepxml2excel/pepxml2excelbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "pepXML2Excel", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ms-utils.org/pepXML2Excel.html" } \ No newline at end of file diff --git a/data/pepxmltab/bioconda_pepxmltab.yaml b/data/pepxmltab/bioconda_pepxmltab.yaml index f4f5a2c39dcd3..46d9602575e16 100644 --- a/data/pepxmltab/bioconda_pepxmltab.yaml +++ b/data/pepxmltab/bioconda_pepxmltab.yaml @@ -5,7 +5,6 @@ description: Parsing pepXML files based one XML package. The package tries to ha home: https://bioconductor.org/packages/3.10/bioc/html/pepXMLTab.html identifiers: - biotools:pepxmltab -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-pepxmltab summary: Parsing pepXML files and filter based on peptide FDR. diff --git a/data/pepxmltab/pepxmltabbioschemas.jsonld b/data/pepxmltab/pepxmltabbioschemas.jsonld index 3992f80a1b5ec..eb52fd7f841e7 100644 --- a/data/pepxmltab/pepxmltabbioschemas.jsonld +++ b/data/pepxmltab/pepxmltabbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "pepXMLTab", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pepXMLTab.html", "sc:version": "1.8.0" diff --git a/data/per_viewer/per_viewerbioschemas.jsonld b/data/per_viewer/per_viewerbioschemas.jsonld index d33d113c905c4..599371b2c29df 100644 --- a/data/per_viewer/per_viewerbioschemas.jsonld +++ b/data/per_viewer/per_viewerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Unlicense", "sc:name": "PER viewer", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://per.broadinstitute.org" } \ No newline at end of file diff --git a/data/pergola-web/pergola-webbioschemas.jsonld b/data/pergola-web/pergola-webbioschemas.jsonld index 00e79b7d7f841..f4cd747b538fc 100644 --- a/data/pergola-web/pergola-webbioschemas.jsonld +++ b/data/pergola-web/pergola-webbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKZ414", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Pergola-web", "@type": "sc:SoftwareApplication", @@ -17,15 +21,15 @@ "Julia Ponomarenko" ], "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": [ + "pubmed:31106365", + "pmcid:PMC6602478", { "@id": "https://doi.org/10.1093/NAR/GKZ414" - }, - "pmcid:PMC6602478", - "pubmed:31106365" + } ], "sc:description": "Web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards.", "sc:featureList": [ @@ -33,24 +37,20 @@ "@id": "edam:operation_3359" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_0335" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_0337" } ], "sc:license": "GPL-3.0", "sc:name": "Pergola-web", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://pergola.crg.eu/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ414", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pergola/pergolabioschemas.jsonld b/data/pergola/pergolabioschemas.jsonld index bd9d27c705203..b4a8a3a3c4734 100644 --- a/data/pergola/pergolabioschemas.jsonld +++ b/data/pergola/pergolabioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0003-2065-6202", - "@type": "schema:Person" + "@id": "https://doi.org/10.1186/s12859-016-1416-8", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/pergola", @@ -27,11 +27,11 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC5210299", "pubmed:28049428", { "@id": "https://doi.org/10.1186/s12859-016-1416-8" - } + }, + "pmcid:PMC5210299" ], "sc:description": "Linkage mapping tool for polyploids.", "sc:featureList": { @@ -40,16 +40,16 @@ "sc:license": "GPL-3.0", "sc:name": "Pergola", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://CRAN.R-project.org/package=pergola", "sc:version": "1.1.0" }, { - "@id": "https://doi.org/10.1186/s12859-016-1416-8", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0003-2065-6202", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/periscope/periscopebioschemas.jsonld b/data/periscope/periscopebioschemas.jsonld index bc0110bcaa642..4aa5b5f6e8285 100644 --- a/data/periscope/periscopebioschemas.jsonld +++ b/data/periscope/periscopebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Periscope", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://lightning.med.monash.edu/periscope/" } \ No newline at end of file diff --git a/data/peroxibase/peroxibasebioschemas.jsonld b/data/peroxibase/peroxibasebioschemas.jsonld index 195ec77ecc65a..5ebe62ca17946 100644 --- a/data/peroxibase/peroxibasebioschemas.jsonld +++ b/data/peroxibase/peroxibasebioschemas.jsonld @@ -23,11 +23,11 @@ "@id": "edam:topic_0623" }, "sc:citation": [ - "pmcid:PMC3531118", + "pubmed:23180785", { "@id": "https://doi.org/10.1093/nar/gks1083" }, - "pubmed:23180785" + "pmcid:PMC3531118" ], "sc:description": "Sequences from peroxidase superfamilies with annotation on putative functions and transcription regulation.", "sc:featureList": { @@ -35,8 +35,8 @@ }, "sc:name": "PeroxiBase peroxidase family database", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://peroxibase.toulouse.inra.fr/" diff --git a/data/peroxisomedb/peroxisomedbbioschemas.jsonld b/data/peroxisomedb/peroxisomedbbioschemas.jsonld index f788fc73ad1fc..d3b146e7f990a 100644 --- a/data/peroxisomedb/peroxisomedbbioschemas.jsonld +++ b/data/peroxisomedb/peroxisomedbbioschemas.jsonld @@ -9,54 +9,54 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkp935", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/peroxisomedb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Aurora Pujol", - "Agatha Schlüter" + "Agatha Schlüter", + "Aurora Pujol" ], "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ + "pubmed:19892824", "pmcid:PMC2808949", { "@id": "https://doi.org/10.1093/nar/gkp935" - }, - "pubmed:19892824" + } ], "sc:description": "Complete peroxisomal proteome of H. sapiens and S. cerevisiae, as well as 35 newly sequenced eukaryotic genomes. Version 2.0 integrates the peroxisomal metabolome of whole microbody familiy by the new incorporation of the glycosome proteomes of trypanosomatids and the glyoxysome proteome of A. thaliana. The database includes phylogenetic trees and tools to capture kinetic information from Brenda, CheBI and Sabio-RK databases and selected bibliographic references.", "sc:featureList": [ { - "@id": "edam:operation_0554" + "@id": "edam:operation_0324" }, { - "@id": "edam:operation_3092" + "@id": "edam:operation_0477" }, { - "@id": "edam:operation_0324" + "@id": "edam:operation_3092" }, { "@id": "edam:operation_3431" }, { - "@id": "edam:operation_0477" + "@id": "edam:operation_0554" } ], "sc:license": "Unlicense", "sc:name": "PeroxisomeDB", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.peroxisomeDB.org" - }, - { - "@id": "https://doi.org/10.1093/nar/gkp935", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/personal_genome_browser/personal_genome_browserbioschemas.jsonld b/data/personal_genome_browser/personal_genome_browserbioschemas.jsonld index 2a9501f608610..795b207a46813 100644 --- a/data/personal_genome_browser/personal_genome_browserbioschemas.jsonld +++ b/data/personal_genome_browser/personal_genome_browserbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool allows on to visualize functions of genetic variants.", "sc:name": "Personal Genome Browser", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.pgbrowser.org/" } \ No newline at end of file diff --git a/data/perturbatr/perturbatrbioschemas.jsonld b/data/perturbatr/perturbatrbioschemas.jsonld index 9922007c8e595..bb07a1040e120 100644 --- a/data/perturbatr/perturbatrbioschemas.jsonld +++ b/data/perturbatr/perturbatrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "perturbatr", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/perturbatr.html", "sc:version": "1.0.0" diff --git a/data/pesi_ws/pesi_wsbioschemas.jsonld b/data/pesi_ws/pesi_wsbioschemas.jsonld index 4e0cf0a6da459..d3f1db7926484 100644 --- a/data/pesi_ws/pesi_wsbioschemas.jsonld +++ b/data/pesi_ws/pesi_wsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "As a user or developer you can use the PESI webservice to feed your own application with standard PESI taxonomy.", "sc:name": "PESI WS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.eu-nomen.eu/portal/webservices.php", "sc:version": "1" diff --git a/data/pespotdb/pespotdbbioschemas.jsonld b/data/pespotdb/pespotdbbioschemas.jsonld index a92f57e87af4f..2f209b56e6c8b 100644 --- a/data/pespotdb/pespotdbbioschemas.jsonld +++ b/data/pespotdb/pespotdbbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-9528-6018", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1016/j.celrep.2013.03.001", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pespotdb", "@type": "sc:SoftwareApplication", @@ -19,31 +27,23 @@ "sc:author": "Stefano Costa", "sc:citation": [ "pmcid:PMC4110347", - "pubmed:21740962", - "pubmed:23545499", { "@id": "https://doi.org/10.1016/j.celrep.2013.03.001" - } + }, + "pubmed:21740962", + "pubmed:23545499" ], "sc:contributor": [ - "Martina Carducci", - "Michele Tinti" + "Michele Tinti", + "Martina Carducci" ], "sc:description": "Web resource designed to provide a central repository for the storage and the analysis of data on domain peptide recognition obtained with interaction assays exploiting peptide chip technology.", "sc:name": "PespotDB", "sc:provider": [ - "ELIXIR-ITA-TORVERGATA", - "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" + "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy", + "ELIXIR-ITA-TORVERGATA" ], "sc:url": "http://mint.bio.uniroma2.it/PepspotDB" - }, - { - "@id": "http://orcid.org/0000-0002-9528-6018", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1016/j.celrep.2013.03.001", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pest/pestbioschemas.jsonld b/data/pest/pestbioschemas.jsonld index 9ea09fc86e6e3..ac01bf90bbaad 100644 --- a/data/pest/pestbioschemas.jsonld +++ b/data/pest/pestbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Not licensed", "sc:name": "PEST", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.pesthomepage.org" } \ No newline at end of file diff --git a/data/petfold_and_petcofold/petfold_and_petcofoldbioschemas.jsonld b/data/petfold_and_petcofold/petfold_and_petcofoldbioschemas.jsonld index c361b0b21ad97..186b1c67fdc3e 100644 --- a/data/petfold_and_petcofold/petfold_and_petcofoldbioschemas.jsonld +++ b/data/petfold_and_petcofold/petfold_and_petcofoldbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The PETfold and PETcofold web servers for the analysis of multiple RNA sequences for common RNA structure and for RNA-RNA interaction sites. Analysis is based on probablistic evolutionary an thermodynamic models.", "sc:name": "PETfold and PETcofold", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://rth.dk/resources/petfold/" } \ No newline at end of file diff --git a/data/pevosoar/pevosoarbioschemas.jsonld b/data/pevosoar/pevosoarbioschemas.jsonld index 39be4456b31b3..fd707e2b8dd2c 100644 --- a/data/pevosoar/pevosoarbioschemas.jsonld +++ b/data/pevosoar/pevosoarbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "pevoSOAR", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sts.bioe.uic.edu/pevosoar/" } \ No newline at end of file diff --git a/data/pez/pezbioschemas.jsonld b/data/pez/pezbioschemas.jsonld index f48302d25342f..8bbaf833a46b3 100644 --- a/data/pez/pezbioschemas.jsonld +++ b/data/pez/pezbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "R package that permits measurement, modelling, and simulation of phylogenetic structure in ecological data.", "sc:name": "pez", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/willpearse/pez" diff --git a/data/pfam/pfambioschemas.jsonld b/data/pfam/pfambioschemas.jsonld index 91f2a5fb2ac21..8749337ca230c 100644 --- a/data/pfam/pfambioschemas.jsonld +++ b/data/pfam/pfambioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/pfam", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", "Web application", + "Database portal", "Web API" ], "sc:description": "Database which contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.", "sc:license": "CC0-1.0", "sc:name": "Pfam", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "Identifiers.org", "sc:url": "http://pfam.xfam.org/" diff --git a/data/pfamscan_api/pfamscan_apibioschemas.jsonld b/data/pfamscan_api/pfamscan_apibioschemas.jsonld index 46c8e6edb422d..36f756b5e9d5d 100644 --- a/data/pfamscan_api/pfamscan_apibioschemas.jsonld +++ b/data/pfamscan_api/pfamscan_apibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "This tool is used to search a FASTA sequence against a library of Pfam HMM.", "sc:name": "PfamScan API", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/pfa/pfamscan_rest", diff --git a/data/pflexana/pflexanabioschemas.jsonld b/data/pflexana/pflexanabioschemas.jsonld index d616bf6da384f..ed5a5e4fdf9b7 100644 --- a/data/pflexana/pflexanabioschemas.jsonld +++ b/data/pflexana/pflexanabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "pFlexAna", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bigbird.comp.nus.edu.sg/pmwiki/farm/motion/index.php?n=Site.ProteinFlexibility" } \ No newline at end of file diff --git a/data/pfmpred/pfmpredbioschemas.jsonld b/data/pfmpred/pfmpredbioschemas.jsonld index 2d6f870eff98b..538a6f8b08841 100644 --- a/data/pfmpred/pfmpredbioschemas.jsonld +++ b/data/pfmpred/pfmpredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Developed for predicting mitochondrial proteins of malaria parasite Plasmodium falciparum . All models were trained and tested on 175 proteins (40 mitochondrial & 135 non-mitochondrial proteins) and evaluated using five-fold cross validation.", "sc:name": "PFMpred", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/pfmpred/" } \ No newline at end of file diff --git a/data/pfond/pfondbioschemas.jsonld b/data/pfond/pfondbioschemas.jsonld index d0640c71d3e55..70b19f9d70315 100644 --- a/data/pfond/pfondbioschemas.jsonld +++ b/data/pfond/pfondbioschemas.jsonld @@ -22,10 +22,10 @@ "Web service" ], "sc:citation": [ + "pubmed:23920006", { "@id": "https://doi.org/10.2196/resprot.2675" }, - "pubmed:23920006", "pmcid:PMC3742411" ], "sc:description": "Portal for Families Overcoming Neurodevelopmental Disorders (PFOND) provides a structured web interface for the information sharing with individuals struggling with the consequences of rare developmental disorders.", @@ -34,9 +34,9 @@ }, "sc:name": "PFOND", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://pfond.cmmt.ubc.ca/index.html" } diff --git a/data/pfp-go/pfp-gobioschemas.jsonld b/data/pfp-go/pfp-gobioschemas.jsonld index edc6d0dcb89f1..2f5874ca5ba79 100644 --- a/data/pfp-go/pfp-gobioschemas.jsonld +++ b/data/pfp-go/pfp-gobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Sequence similarity-based protein function prediction server designed to predict GO annotations for a query sequence beyond what can be found by conventional database search such as BLAST.", "sc:name": "PFP", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://kiharalab.org/web/pfp.php" } \ No newline at end of file diff --git a/data/pfp-pred/pfp-predbioschemas.jsonld b/data/pfp-pred/pfp-predbioschemas.jsonld index cc5d869bbc44d..0424673082317 100644 --- a/data/pfp-pred/pfp-predbioschemas.jsonld +++ b/data/pfp-pred/pfp-predbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PFP-Pred", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/PFP-Pred/", "sc:version": "2.0" diff --git a/data/pfp/pfpbioschemas.jsonld b/data/pfp/pfpbioschemas.jsonld index 55ddc81a9eac8..c75d3b56aa9b3 100644 --- a/data/pfp/pfpbioschemas.jsonld +++ b/data/pfp/pfpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces.", "sc:name": "PFP", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://pfp.technion.ac.il/index.html" } \ No newline at end of file diff --git a/data/pfstats/pfstatsbioschemas.jsonld b/data/pfstats/pfstatsbioschemas.jsonld index cb2dbfd119030..5223de69aa036 100644 --- a/data/pfstats/pfstatsbioschemas.jsonld +++ b/data/pfstats/pfstatsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "PFSTATS is a set of programs and scripts devoted to analyze protein families using simple statistics.", "sc:name": "PFSTATS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.biocomp.icb.ufmg.br/biocomp/?page_id=119" diff --git a/data/pftools/pftoolsbioschemas.jsonld b/data/pftools/pftoolsbioschemas.jsonld index 374e92cbb8d2d..28d4365d8cae3 100644 --- a/data/pftools/pftoolsbioschemas.jsonld +++ b/data/pftools/pftoolsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The pftools are a collection of programs to build, calibrate, and search biological sequences with generalized profiles. Generalized profiles are an extension of position specific scoring matrices by including position specific scores for insertions and deletions. They correspond to a matrix representation of a multiple sequence alignment that can be used to search distant homologous sequences and precisely align sequences to the model.", "sc:name": "pftools", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://web.expasy.org/pftools/" } \ No newline at end of file diff --git a/data/pga/pgabioschemas.jsonld b/data/pga/pgabioschemas.jsonld index 4066626c5b00f..97995eda84ff7 100644 --- a/data/pga/pgabioschemas.jsonld +++ b/data/pga/pgabioschemas.jsonld @@ -30,19 +30,19 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0121" + "@id": "edam:topic_3571" }, { "@id": "edam:topic_0219" }, { - "@id": "edam:topic_3571" + "@id": "edam:topic_0121" }, { - "@id": "edam:topic_3520" + "@id": "edam:topic_3170" }, { - "@id": "edam:topic_3170" + "@id": "edam:topic_3520" }, { "@id": "edam:topic_3366" @@ -52,38 +52,38 @@ } ], "sc:citation": [ - "pmcid:PMC4912784", + "pubmed:27316337", { "@id": "https://doi.org/10.1186/s12859-016-1133-3" }, - "pubmed:27316337" + "pmcid:PMC4912784" ], "sc:description": "This package provides functions for construction of customized protein databases based on RNA-Seq data with/without genome guided, database searching, post-processing and report generation. This kind of customized protein database includes both the reference database (such as Refseq or ENSEMBL) and the novel peptide sequences form RNA-Seq data.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_3680" }, { - "@id": "edam:operation_3680" + "@id": "edam:operation_3431" } ], "sc:license": "GPL-2.0", "sc:name": "PGA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PGA.html", "sc:version": "1.4.0" }, - { - "@id": "http://orcid.org/0000-0003-2261-3150", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-016-1133-3", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-2261-3150", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pgca/pgcabioschemas.jsonld b/data/pgca/pgcabioschemas.jsonld index 3a2e42c436451..af437dd892dfa 100644 --- a/data/pgca/pgcabioschemas.jsonld +++ b/data/pgca/pgcabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0177569", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pgca", "@type": "sc:SoftwareApplication", @@ -28,16 +32,12 @@ "sc:license": "GPL-2.0", "sc:name": "pgca", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pgca.html", "sc:version": "1.4.0" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0177569", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pgd/pgdbioschemas.jsonld b/data/pgd/pgdbioschemas.jsonld index 5a186b118cb46..e9429808f5c2e 100644 --- a/data/pgd/pgdbioschemas.jsonld +++ b/data/pgd/pgdbioschemas.jsonld @@ -27,10 +27,10 @@ "@id": "edam:operation_0474" }, { - "@id": "edam:operation_1844" + "@id": "edam:operation_0249" }, { - "@id": "edam:operation_0249" + "@id": "edam:operation_1844" }, { "@id": "edam:operation_0479" @@ -42,9 +42,9 @@ "sc:license": "Apache-2.0", "sc:name": "The Protein Geometry Database (PGD)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://pgd.cgrb.oregonstate.edu/" }, diff --git a/data/pgenn/pgennbioschemas.jsonld b/data/pgenn/pgennbioschemas.jsonld index 113e8133c0334..73ee3c9649b83 100644 --- a/data/pgenn/pgennbioschemas.jsonld +++ b/data/pgenn/pgennbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "System specifically designed for plant gene normalization. This website enables user search gene normalization information by keywords, a list of PMIDs, or UniProt ACs in the database. The results (Gene names and corresponding UniProt ACs) are displayed in sortable tables with text evidence and downloadable for further research.", "sc:name": "pGenN", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://biotm.cis.udel.edu/gn/" } \ No newline at end of file diff --git a/data/pgltools-chromatin/pgltools-chromatinbioschemas.jsonld b/data/pgltools-chromatin/pgltools-chromatinbioschemas.jsonld index c37351d6ac746..0f04c57507228 100644 --- a/data/pgltools-chromatin/pgltools-chromatinbioschemas.jsonld +++ b/data/pgltools-chromatin/pgltools-chromatinbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1186/s12859-017-1621-0", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0002-6274-1571", + "@type": "schema:Person" }, { "@id": "https://bio.tools/pgltools-chromatin", @@ -22,10 +22,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:28388874", + "pmcid:PMC5384132", { "@id": "https://doi.org/10.1186/s12859-017-1621-0" - }, - "pmcid:PMC5384132" + } ], "sc:description": "Pgltools is a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.", "sc:featureList": { @@ -34,14 +34,14 @@ "sc:license": "BSD-3-Clause", "sc:name": "pgltools", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/billgreenwald/pgltools" }, { - "@id": "http://orcid.org/0000-0002-6274-1571", - "@type": "schema:Person" + "@id": "https://doi.org/10.1186/s12859-017-1621-0", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pgltools/pgltoolsbioschemas.jsonld b/data/pgltools/pgltoolsbioschemas.jsonld index 3603c1d32c8d2..98cfa83ba4aa8 100644 --- a/data/pgltools/pgltoolsbioschemas.jsonld +++ b/data/pgltools/pgltoolsbioschemas.jsonld @@ -19,19 +19,19 @@ "biotools:primaryContact": "William W. Greenwald", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5384132", "pubmed:28388874", { "@id": "https://doi.org/10.1186/s12859-017-1621-0" - }, - "pmcid:PMC5384132" + } ], "sc:description": "Manipulation of Hi-C peak and other chromatin interaction data.", "sc:featureList": [ { - "@id": "edam:operation_3222" + "@id": "edam:operation_2403" }, { - "@id": "edam:operation_2403" + "@id": "edam:operation_3222" } ], "sc:license": "BSD-3-Clause", diff --git a/data/pgm/pgmbioschemas.jsonld b/data/pgm/pgmbioschemas.jsonld index 535de4a5e5f2e..f8f7f8186a754 100644 --- a/data/pgm/pgmbioschemas.jsonld +++ b/data/pgm/pgmbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PGM", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.agbase.msstate.edu/tools/pgm/", "sc:version": "1.1" diff --git a/data/pgp/pgpbioschemas.jsonld b/data/pgp/pgpbioschemas.jsonld index a83ca4572aebd..1d7b5f7be7a7b 100644 --- a/data/pgp/pgpbioschemas.jsonld +++ b/data/pgp/pgpbioschemas.jsonld @@ -11,14 +11,14 @@ "@id": "https://bio.tools/pgp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Daniel Arend", - "Matthias Lange" + "Matthias Lange", + "Daniel Arend" ], "sc:additionalType": "Library", "sc:contributor": [ + "European Commission within the transPlant project", "German Federal Ministry of Education and Research within the German-Plant-Phenotyping Network", "Astrid Junker", - "European Commission within the transPlant project", "Uwe Scholz", "Leibniz Institute of Plant Genetics and Crop Plant Research as infrastructural service" ], @@ -31,13 +31,13 @@ "sc:license": "CC-BY-4.0", "sc:name": "Plant Genomics and Phenomics Research Data Repository (PGP)", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": [ - "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben", - "ipk" + "ipk", + "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben" ], "sc:url": "http://edal-pgp.ipk-gatersleben.de/" } \ No newline at end of file diff --git a/data/pgql/pgqlbioschemas.jsonld b/data/pgql/pgqlbioschemas.jsonld index 721f3a52304f2..2203ce5542f22 100644 --- a/data/pgql/pgqlbioschemas.jsonld +++ b/data/pgql/pgqlbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software tool in particular for analyzing gene expression time courses. It allows its user to interactively define linear HMM queries on time course data using rectangular graphical widgets called probabilistic time boxes. The analysis is fully interactive and the graphical display shows the time courses along with the graphical query. Afterwards the results can be submitted to gPROF directly.", "sc:name": "pGQL", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinformatics.rutgers.edu/Software/pGQL/" } \ No newline at end of file diff --git a/data/pgrnafinder/pgrnafinderbioschemas.jsonld b/data/pgrnafinder/pgrnafinderbioschemas.jsonld index bd05fb21f4a3b..b865ffa7c9b35 100644 --- a/data/pgrnafinder/pgrnafinderbioschemas.jsonld +++ b/data/pgrnafinder/pgrnafinderbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/pgrnafinder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Zhou Songyang", - "Zhiming Dai" + "Zhiming Dai", + "Zhou Songyang" ], "sc:additionalType": "Command-line tool", "sc:description": "Web-based tool to design distance independent paired-gRNA.", "sc:name": "pgRNAFinder", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/xiexiaowei/pgRNAFinder" } \ No newline at end of file diff --git a/data/pgs_classify/pgs_classifybioschemas.jsonld b/data/pgs_classify/pgs_classifybioschemas.jsonld index a9b5f1deb2f10..a94f67f777cc1 100644 --- a/data/pgs_classify/pgs_classifybioschemas.jsonld +++ b/data/pgs_classify/pgs_classifybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A new features selection method to improve classification performances in imbalanced data sets.", "sc:name": "Peculiar Genes Selection (PGS)", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/mbeccuti/PGS" } \ No newline at end of file diff --git a/data/pgsea/bioconda_pgsea.yaml b/data/pgsea/bioconda_pgsea.yaml index 4884a0fd07c4f..28ef6371374a9 100644 --- a/data/pgsea/bioconda_pgsea.yaml +++ b/data/pgsea/bioconda_pgsea.yaml @@ -3,7 +3,6 @@ description: Parametric Analysis of Gene Set Enrichment home: https://bioconductor.org/packages/3.10/bioc/html/PGSEA.html identifiers: - biotools:pgsea -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-pgsea diff --git a/data/pgsea/pgseabioschemas.jsonld b/data/pgsea/pgseabioschemas.jsonld index 17f1622d07d9f..c7d6853534cd2 100644 --- a/data/pgsea/pgseabioschemas.jsonld +++ b/data/pgsea/pgseabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "PGSEA", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PGSEA.html", diff --git a/data/pgx/pgxbioschemas.jsonld b/data/pgx/pgxbioschemas.jsonld index aee728ff2fca1..df80ffc72737c 100644 --- a/data/pgx/pgxbioschemas.jsonld +++ b/data/pgx/pgxbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Proteogenomic intregration of mass spectrometry (MS) proteomics data with next generation sequencing (NGS) by mapping identified peptides onto their putative genomic coordinates.", "sc:name": "PGx", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://pgx.fenyolab.org/" } \ No newline at end of file diff --git a/data/phaedra/phaedrabioschemas.jsonld b/data/phaedra/phaedrabioschemas.jsonld index bbe517cf62dd7..efd7806e76c15 100644 --- a/data/phaedra/phaedrabioschemas.jsonld +++ b/data/phaedra/phaedrabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-2.0", "sc:name": "PHAEDRA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.nactem.ac.uk/PHAEDRA/" } \ No newline at end of file diff --git a/data/phageterm/phagetermbioschemas.jsonld b/data/phageterm/phagetermbioschemas.jsonld index 0c1d0ca6bcc6a..7fa83fd5382d1 100644 --- a/data/phageterm/phagetermbioschemas.jsonld +++ b/data/phageterm/phagetermbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Julian Garneau", - "David Bikard", - "Marc Monot" + "Marc Monot", + "David Bikard" ], "sc:additionalType": "Command-line tool", "sc:description": "Determining Bacteriophage Termini and Packaging using NGS data.", "sc:license": "CC-BY-4.0", "sc:name": "PhageTerm", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/phageterm/" } \ No newline at end of file diff --git a/data/phaistos/phaistosbioschemas.jsonld b/data/phaistos/phaistosbioschemas.jsonld index 879ca85b6afdd..d012e09329f97 100644 --- a/data/phaistos/phaistosbioschemas.jsonld +++ b/data/phaistos/phaistosbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Phaistos", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "binf.ku.dk", "sc:url": "http://www.phaistos.org/", diff --git a/data/phantasus/phantasusbioschemas.jsonld b/data/phantasus/phantasusbioschemas.jsonld index dd9961ac14faa..840a6ce684584 100644 --- a/data/phantasus/phantasusbioschemas.jsonld +++ b/data/phantasus/phantasusbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "phantasus", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/phantasus.html", "sc:version": "1.0.2" diff --git a/data/phantompeakqualtools/phantompeakqualtoolsbioschemas.jsonld b/data/phantompeakqualtools/phantompeakqualtoolsbioschemas.jsonld index 13cf95ccc0b80..9cb0fb9277d14 100644 --- a/data/phantompeakqualtools/phantompeakqualtoolsbioschemas.jsonld +++ b/data/phantompeakqualtools/phantompeakqualtoolsbioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Anshul Kundaje", "edam:has_input": [ { - "@id": "edam:data_1383" + "@id": "edam:data_0906" }, { - "@id": "edam:data_0906" + "@id": "edam:data_1383" } ], "edam:has_output": { @@ -30,10 +30,10 @@ }, "sc:additionalType": "Suite", "sc:citation": [ - "pmcid:PMC3931556", { "@id": "https://doi.org/10.1534/g3.113.008680" }, + "pmcid:PMC3931556", "pubmed:3931556" ], "sc:description": "This package computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.", diff --git a/data/pharmacogx/pharmacogxbioschemas.jsonld b/data/pharmacogx/pharmacogxbioschemas.jsonld index e3f27823e576f..662b6024dd104 100644 --- a/data/pharmacogx/pharmacogxbioschemas.jsonld +++ b/data/pharmacogx/pharmacogxbioschemas.jsonld @@ -24,8 +24,8 @@ "sc:license": "Artistic-2.0", "sc:name": "PharmacoGx", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PharmacoGx.html", diff --git a/data/pharmagist/pharmagistbioschemas.jsonld b/data/pharmagist/pharmagistbioschemas.jsonld index b70bcabc91296..c236e88f08aea 100644 --- a/data/pharmagist/pharmagistbioschemas.jsonld +++ b/data/pharmagist/pharmagistbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PharmaGist is a web server for detecting pharmacophores or the spatial arrangement of features that enables a molecule to interact with a specific target receptor. Users input a set of structures of molecules that bind with the receptor for outputs of candidate pharmacophores that can be used in rational drug design.", "sc:name": "PharmaGist", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/PharmaGist" } \ No newline at end of file diff --git a/data/pharmgkb/pharmgkbbioschemas.jsonld b/data/pharmgkb/pharmgkbbioschemas.jsonld index 7d64ac02a6335..5367bef47da92 100644 --- a/data/pharmgkb/pharmgkbbioschemas.jsonld +++ b/data/pharmgkb/pharmgkbbioschemas.jsonld @@ -23,29 +23,29 @@ "@id": "edam:data_0916" }, "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0625" + "@id": "edam:topic_0202" }, { - "@id": "edam:topic_0202" + "@id": "edam:topic_2815" }, { "@id": "edam:topic_0208" }, { - "@id": "edam:topic_2815" + "@id": "edam:topic_0625" } ], "sc:citation": [ - "pubmed:22992668", { "@id": "https://doi.org/10.1038/clpt.2012.96" }, - "pmcid:PMC3660037" + "pmcid:PMC3660037", + "pubmed:22992668" ], "sc:description": "Database on the impact of human genetic variations on drug response. PharmGKB curates primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways.", "sc:featureList": { diff --git a/data/pharmmapper-drug/pharmmapper-drugbioschemas.jsonld b/data/pharmmapper-drug/pharmmapper-drugbioschemas.jsonld index 63516453b9830..db7b33030ace2 100644 --- a/data/pharmmapper-drug/pharmmapper-drugbioschemas.jsonld +++ b/data/pharmmapper-drug/pharmmapper-drugbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkx374", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/pharmmapper-drug", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web service", "sc:citation": [ + "pubmed:28472422", + "pmcid:PMC5793840", { "@id": "https://doi.org/10.1093/nar/gkx374" - }, - "pubmed:28472422", - "pmcid:PMC5793840" + } ], "sc:description": "Potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database.", "sc:featureList": { @@ -31,6 +27,10 @@ "sc:name": "PharmMapper", "sc:url": "http://lilab.ecust.edu.cn/pharmmapper/", "sc:version": "2017" + }, + { + "@id": "https://doi.org/10.1093/nar/gkx374", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phase/phasebioschemas.jsonld b/data/phase/phasebioschemas.jsonld index 411ab2ae96dd9..d4b499ead89ef 100644 --- a/data/phase/phasebioschemas.jsonld +++ b/data/phase/phasebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "PHASE", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://stephenslab.uchicago.edu/software.html#phase" } \ No newline at end of file diff --git a/data/phasebook/phasebookbioschemas.jsonld b/data/phasebook/phasebookbioschemas.jsonld index 535c204430dda..522b71e18ec59 100644 --- a/data/phasebook/phasebookbioschemas.jsonld +++ b/data/phasebook/phasebookbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-1637-1706", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/phasebook", "@type": "sc:SoftwareApplication", @@ -22,10 +26,6 @@ "sc:name": "PHASEBOOK", "sc:operatingSystem": "Linux", "sc:url": "http://www.giga.ulg.ac.be/cms/c_20703/en/unit-of-animal-genomics-software" - }, - { - "@id": "http://orcid.org/0000-0003-1637-1706", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/phaser/phaserbioschemas.jsonld b/data/phaser/phaserbioschemas.jsonld index fba77fe191439..cd2208e030718 100644 --- a/data/phaser/phaserbioschemas.jsonld +++ b/data/phaser/phaserbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "A program for phasing macromolecular crystal structures with maximum likelihood methods.", "sc:name": "Phaser", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://www.phaser.cimr.cam.ac.uk", diff --git a/data/phast/phastbioschemas.jsonld b/data/phast/phastbioschemas.jsonld index ec01f239bbfe7..7925d372076b8 100644 --- a/data/phast/phastbioschemas.jsonld +++ b/data/phast/phastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PHAST (PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views.", "sc:name": "PHAST", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://phast.wishartlab.com/" } \ No newline at end of file diff --git a/data/phaster/phasterbioschemas.jsonld b/data/phaster/phasterbioschemas.jsonld index 0600e699df735..e7ddf926e04b7 100644 --- a/data/phaster/phasterbioschemas.jsonld +++ b/data/phaster/phasterbioschemas.jsonld @@ -9,15 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkw387", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/phaster", "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:27141966", { "@id": "https://doi.org/10.1093/nar/gkw387" }, + "pubmed:27141966", "pmcid:PMC4987931" ], "sc:description": "PHASTER (PHAge Search Tool Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids.", @@ -27,15 +31,11 @@ "sc:license": "Other", "sc:name": "PHASTER", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://phaster.ca/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkw387", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phat/phatbioschemas.jsonld b/data/phat/phatbioschemas.jsonld index 9b497d7ba441e..431225461d041 100644 --- a/data/phat/phatbioschemas.jsonld +++ b/data/phat/phatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "PHAT", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/chgibb/PHAT", "sc:version": "0.10.1-beta.1" diff --git a/data/phd-snp/phd-snpbioschemas.jsonld b/data/phd-snp/phd-snpbioschemas.jsonld index 6c44f4c1da294..f2f4db7a04fd7 100644 --- a/data/phd-snp/phd-snpbioschemas.jsonld +++ b/data/phd-snp/phd-snpbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/phd-snp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Emidio Capriotti", - "Rita Casadio" + "Rita Casadio", + "Emidio Capriotti" ], "sc:additionalType": "Web application", "sc:description": "Support Vector Machines based Predictor of human Deleterious Single Nucleotide Polymorphisms.", "sc:name": "PhD-SNP", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", "sc:url": "http://snps.biofold.org/phd-snp/", diff --git a/data/phd-snpg/phd-snpgbioschemas.jsonld b/data/phd-snpg/phd-snpgbioschemas.jsonld index 1d95196d13b25..1ca69b927fa9e 100644 --- a/data/phd-snpg/phd-snpgbioschemas.jsonld +++ b/data/phd-snpg/phd-snpgbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkx369", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0002-2323-0963", "@type": "schema:Person" @@ -17,15 +21,15 @@ "@id": "https://bio.tools/phd-snpg", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": [ "pubmed:28482034", - "pmcid:PMC5570245", { "@id": "https://doi.org/10.1093/nar/gkx369" - } + }, + "pmcid:PMC5570245" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-2323-0963" @@ -33,18 +37,14 @@ "sc:description": "A binary classifier for predicting pathogenic variants in coding and non-coding regions.", "sc:featureList": [ { - "@id": "edam:operation_3227" + "@id": "edam:operation_3661" }, { - "@id": "edam:operation_3661" + "@id": "edam:operation_3227" } ], "sc:name": "PhD-SNPg", "sc:url": "http://snps.biofold.org/phd-snpg" - }, - { - "@id": "https://doi.org/10.1093/nar/gkx369", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phdcleav/phdcleavbioschemas.jsonld b/data/phdcleav/phdcleavbioschemas.jsonld index fa0655b863b22..9eb6300c83ee2 100644 --- a/data/phdcleav/phdcleavbioschemas.jsonld +++ b/data/phdcleav/phdcleavbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Webserver to predict Dicer cleavage sites in pre-miRNA. Dicer, an RNase III enzyme, plays vital role in RNA interference pathway, processes both pre-miRNAs (precursor microRNAs) and double-stranded (ds) RNAs to generate effector molecules. Thus it is very important to know true Dicer processing sites in the pre-miRNA molecules to understand the RNA interference pathway.", "sc:name": "PHDcleav", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/phdcleav/" } \ No newline at end of file diff --git a/data/phdhtm/phdhtmbioschemas.jsonld b/data/phdhtm/phdhtmbioschemas.jsonld index f2af800925306..b8d2025d0e440 100644 --- a/data/phdhtm/phdhtmbioschemas.jsonld +++ b/data/phdhtm/phdhtmbioschemas.jsonld @@ -20,13 +20,13 @@ "sc:license": "GPL-2.0", "sc:name": "PHDhtm", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ - "RostLab", - "EMBL Heidelberg" + "EMBL Heidelberg", + "RostLab" ], "sc:url": "http://ppopen.informatik.tu-muenchen.de/", "sc:version": "1.0.42" diff --git a/data/pheatmap/pheatmapbioschemas.jsonld b/data/pheatmap/pheatmapbioschemas.jsonld index 55ce3d8ddac04..54f64a2f4037b 100644 --- a/data/pheatmap/pheatmapbioschemas.jsonld +++ b/data/pheatmap/pheatmapbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A package for drawing pretty heatmaps in R. The ordinary heatmap function in R has several drawbacks when it comes to producing publication quality heatmaps. It is hard to produce pictures with consistent text, cell and overall sizes and shapes. The function pheatmap tries to alleviate the problems by offering more fine grained control over heatmap dimensions and appearance.", "sc:name": "pheatmap", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "ELIXIR-EE", diff --git a/data/pheg/phegbioschemas.jsonld b/data/pheg/phegbioschemas.jsonld index f727ecea6b82d..6d475d25f19b4 100644 --- a/data/pheg/phegbioschemas.jsonld +++ b/data/pheg/phegbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Accurate prediction of human essential genes using only nucleotide composition and association information.", "sc:name": "Pheg", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://cefg.uestc.edu.cn/Pheg/" } \ No newline at end of file diff --git a/data/phegenex/phegenexbioschemas.jsonld b/data/phegenex/phegenexbioschemas.jsonld index a29d34f390fed..78aec23d5e4f1 100644 --- a/data/phegenex/phegenexbioschemas.jsonld +++ b/data/phegenex/phegenexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PheGenEx", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://phegenex-umh.cs.umn.edu:8080/PheGenEx/" } \ No newline at end of file diff --git a/data/phen-gen/phen-genbioschemas.jsonld b/data/phen-gen/phen-genbioschemas.jsonld index d68355670f1fc..0702d6763ba79 100644 --- a/data/phen-gen/phen-genbioschemas.jsonld +++ b/data/phen-gen/phen-genbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Combines patients' disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders.", "sc:name": "Phen-Gen", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://phen-gen.org/" } \ No newline at end of file diff --git a/data/phenetic/pheneticbioschemas.jsonld b/data/phenetic/pheneticbioschemas.jsonld index 8bc312762d158..739d4134fb51c 100644 --- a/data/phenetic/pheneticbioschemas.jsonld +++ b/data/phenetic/pheneticbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Infer the molecular mechanism driving your expression phenotype.", "sc:name": "PheNetic", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/phenetic/#/index", diff --git a/data/phenetic_eqtl/phenetic_eqtlbioschemas.jsonld b/data/phenetic_eqtl/phenetic_eqtlbioschemas.jsonld index fb149bcb05729..dc59a920d4392 100644 --- a/data/phenetic_eqtl/phenetic_eqtlbioschemas.jsonld +++ b/data/phenetic_eqtl/phenetic_eqtlbioschemas.jsonld @@ -15,13 +15,13 @@ "sc:license": "GPL-2.0", "sc:name": "PheNetic eQTL", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "ugent.be", - "Ghent University" + "Ghent University", + "ugent.be" ], "sc:url": "http://bioinformatics.intec.ugent.be/phenetic_eqtl/index.html", "sc:version": "1" diff --git a/data/phenobook/phenobookbioschemas.jsonld b/data/phenobook/phenobookbioschemas.jsonld index 960e036e7dab1..75196a5c89b38 100644 --- a/data/phenobook/phenobookbioschemas.jsonld +++ b/data/phenobook/phenobookbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/gigascience/giw019", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/phenobook", "@type": "sc:SoftwareApplication", @@ -31,11 +27,15 @@ }, "sc:name": "Phenobook", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://getphenobook.com/" + }, + { + "@id": "https://doi.org/10.1093/gigascience/giw019", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phenodigm/phenodigmbioschemas.jsonld b/data/phenodigm/phenodigmbioschemas.jsonld index 8134f2b383400..482ab2523775d 100644 --- a/data/phenodigm/phenodigmbioschemas.jsonld +++ b/data/phenodigm/phenodigmbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Jules Jacobsen", "sc:additionalType": "Database portal", "sc:citation": [ + "pmcid:PMC3649640", + "pubmed:23660285", { "@id": "https://doi.org/10.1093/DATABASE/BAT025" - }, - "pmcid:PMC3649640", - "pubmed:23660285" + } ], "sc:description": "Analyzing curated annotations to associate animal models with human diseases.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "PhenoDigm", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://www.sanger.ac.uk/science/tools/phenodigm" } diff --git a/data/phenodis/phenodisbioschemas.jsonld b/data/phenodis/phenodisbioschemas.jsonld index 7469d1a68d773..ba25a35d1dcde 100644 --- a/data/phenodis/phenodisbioschemas.jsonld +++ b/data/phenodis/phenodisbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13023-018-0765-y", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/PhenoDis", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr. Andreas Ruepp", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ - "pubmed:29370821", "pmcid:PMC5785853", + "pubmed:29370821", { "@id": "https://doi.org/10.1186/s13023-018-0765-y" } @@ -27,23 +31,19 @@ "sc:description": "Database for phenotypic characterization of rare cardiac diseases.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_3196" } ], "sc:name": "PhenoDis", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://mips.helmholtz-muenchen.de/phenodis/" - }, - { - "@id": "https://doi.org/10.1186/s13023-018-0765-y", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phenodist/phenodistbioschemas.jsonld b/data/phenodist/phenodistbioschemas.jsonld index 7e4e70c240836..360c624a48c07 100644 --- a/data/phenodist/phenodistbioschemas.jsonld +++ b/data/phenodist/phenodistbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-14-336", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/phenodist", "@type": "sc:SoftwareApplication", @@ -20,40 +24,37 @@ "@id": "edam:data_2855" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0085" + "@id": "edam:topic_2229" }, { "@id": "edam:topic_3523" }, { - "@id": "edam:topic_3336" + "@id": "edam:topic_0085" }, { "@id": "edam:topic_2259" }, { - "@id": "edam:topic_2229" + "@id": "edam:topic_3336" } ], "sc:citation": [ { "@id": "https://doi.org/10.1186/1471-2105-14-336" }, - "pubmed:24256072", - "pmcid:PMC4225524" + "pmcid:PMC4225524", + "pubmed:24256072" ], "sc:description": "This tool is designed for measuring phenotypic distance in image-based high-throughput screening, in order to identify strong phenotypes and to group treatments into functional clusters.", "sc:featureList": [ { - "@id": "edam:operation_3432" - }, - { - "@id": "edam:operation_2238" + "@id": "edam:operation_3443" }, { "@id": "edam:operation_2436" @@ -62,7 +63,10 @@ "@id": "edam:operation_0300" }, { - "@id": "edam:operation_3443" + "@id": "edam:operation_2238" + }, + { + "@id": "edam:operation_3432" } ], "sc:license": "GPL-2.0", @@ -74,10 +78,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/phenoDist.html", "sc:version": "1.22.0" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-14-336", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phenoforecaster/phenoforecasterbioschemas.jsonld b/data/phenoforecaster/phenoforecasterbioschemas.jsonld index c1f771e614e17..ec25dee7d3796 100644 --- a/data/phenoforecaster/phenoforecasterbioschemas.jsonld +++ b/data/phenoforecaster/phenoforecasterbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Isaac W Park", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6426163", { "@id": "https://doi.org/10.1002/aps3.1230" }, - "pubmed:30937222", - "pmcid:PMC6426163" + "pubmed:30937222" ], "sc:description": "Software package for the prediction of flowering phenology.", "sc:featureList": { diff --git a/data/phenogeneranker/phenogenerankerbioschemas.jsonld b/data/phenogeneranker/phenogenerankerbioschemas.jsonld index 1682cd2e06aa2..59f7b399884f1 100644 --- a/data/phenogeneranker/phenogenerankerbioschemas.jsonld +++ b/data/phenogeneranker/phenogenerankerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "PhenoGeneRanker", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/bozdaglab/PhenoGeneRanker" diff --git a/data/phenogmm/phenogmmbioschemas.jsonld b/data/phenogmm/phenogmmbioschemas.jsonld index da892e1aada9b..7bda6f39df481 100644 --- a/data/phenogmm/phenogmmbioschemas.jsonld +++ b/data/phenogmm/phenogmmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "PhenoGMM", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/prubbens/PhenoGMM" } \ No newline at end of file diff --git a/data/phenohm/phenohmbioschemas.jsonld b/data/phenohm/phenohmbioschemas.jsonld index 7e68ebf3c97b1..8bc840592479e 100644 --- a/data/phenohm/phenohmbioschemas.jsonld +++ b/data/phenohm/phenohmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "PhenoHM is a human-mouse comparative phenome-genome server that facilitates cross species identification of genes associated with orthologous phenotypes.", "sc:name": "PhenoHM", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://phenome.cchmc.org" diff --git a/data/phenolyzer/phenolyzerbioschemas.jsonld b/data/phenolyzer/phenolyzerbioschemas.jsonld index f66531318dc35..39294a0a2b616 100644 --- a/data/phenolyzer/phenolyzerbioschemas.jsonld +++ b/data/phenolyzer/phenolyzerbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "Phenolyzer", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://phenolyzer.wglab.org/" } \ No newline at end of file diff --git a/data/phenomecentral/phenomecentralbioschemas.jsonld b/data/phenomecentral/phenomecentralbioschemas.jsonld index 89761a65aca47..2aaf3d7c6ecc9 100644 --- a/data/phenomecentral/phenomecentralbioschemas.jsonld +++ b/data/phenomecentral/phenomecentralbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1002/humu.22851", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/phenomecentral", "@type": "sc:SoftwareApplication", @@ -17,39 +21,35 @@ "Web application" ], "sc:citation": [ - "pmcid:PMC5467641", { "@id": "https://doi.org/10.1002/humu.22851" }, + "pmcid:PMC5467641", "pubmed:26251998" ], "sc:description": "Repository for clinicians and scientists working in the rare disorder community. It enables secure sharing of case records by clinicians and rare disease scientists and helps the user to find additional cases of the same unnamed disorder. The repository identifies similar patients in the database based on semantic similarity between clinical features, automatically prioritized genes from whole-exome data, and candidate genes entered by the users.", "sc:featureList": [ { - "@id": "edam:operation_3197" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_2422" } ], "sc:name": "PhenomeCentral", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://phenomecentral.org", "sc:version": "1.1.16" - }, - { - "@id": "https://doi.org/10.1002/humu.22851", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phenomenal/phenomenalbioschemas.jsonld b/data/phenomenal/phenomenalbioschemas.jsonld index 03f3de2d867ff..9185e6d7d8ba6 100644 --- a/data/phenomenal/phenomenalbioschemas.jsonld +++ b/data/phenomenal/phenomenalbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/gigascience/giy149", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/PhenoMeNal", "@type": "sc:SoftwareApplication", @@ -40,10 +44,6 @@ "Windows" ], "sc:url": "https://portal.phenomenal-h2020.eu/home" - }, - { - "@id": "https://doi.org/10.1093/gigascience/giy149", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phenominer/phenominerbioschemas.jsonld b/data/phenominer/phenominerbioschemas.jsonld index 0aac5b5890b6a..50c5d1cc43763 100644 --- a/data/phenominer/phenominerbioschemas.jsonld +++ b/data/phenominer/phenominerbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/DATABASE/BAV104", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-7230-4164", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1093/DATABASE/BAV104", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/phenominer", "@type": "sc:SoftwareApplication", @@ -25,8 +25,8 @@ }, "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:26507285", "pmcid:PMC4622021", + "pubmed:26507285", { "@id": "https://doi.org/10.1093/DATABASE/BAV104" } diff --git a/data/phenomizer/phenomizerbioschemas.jsonld b/data/phenomizer/phenomizerbioschemas.jsonld index 1bea51be23e4d..f63e0709275f4 100644 --- a/data/phenomizer/phenomizerbioschemas.jsonld +++ b/data/phenomizer/phenomizerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Phenomizer", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://compbio.charite.de/phenomizer" } \ No newline at end of file diff --git a/data/phenopath/phenopathbioschemas.jsonld b/data/phenopath/phenopathbioschemas.jsonld index 94f2a825d73d5..4e8a2a0515899 100644 --- a/data/phenopath/phenopathbioschemas.jsonld +++ b/data/phenopath/phenopathbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Apache-2.0", "sc:name": "phenopath", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/phenopath.html", "sc:version": "1.4.0" diff --git a/data/phenopred/phenopredbioschemas.jsonld b/data/phenopred/phenopredbioschemas.jsonld index c6f355b15ae70..272dcb6b7a1fb 100644 --- a/data/phenopred/phenopredbioschemas.jsonld +++ b/data/phenopred/phenopredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PhenoPred", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.phenopred.org/" } \ No newline at end of file diff --git a/data/phenoscanner/phenoscannerbioschemas.jsonld b/data/phenoscanner/phenoscannerbioschemas.jsonld index 58ce7ca09403a..ed21dd2edb4b5 100644 --- a/data/phenoscanner/phenoscannerbioschemas.jsonld +++ b/data/phenoscanner/phenoscannerbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/PhenoScanner", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Web API", "Database portal", - "Command-line tool" + "Command-line tool", + "Web API", + "Web application" ], "sc:description": "Database of human genotype-phenotype associations.", "sc:license": "Unlicense", "sc:name": "PhenoScanner", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.phenoscanner.medschl.cam.ac.uk/", "sc:version": "2" diff --git a/data/phenosim/phenosimbioschemas.jsonld b/data/phenosim/phenosimbioschemas.jsonld index 8ac0cf4986c80..a3d4ad4fdd4ff 100644 --- a/data/phenosim/phenosimbioschemas.jsonld +++ b/data/phenosim/phenosimbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool to add phenotypes to simulated genotypes It reads the output of coalescent simulators and simulates a qualitative or quantitative phenotype according to user-defined parameters.", "sc:name": "phenosim", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://evoplant.uni-hohenheim.de/downloads/" diff --git a/data/phenotator/phenotatorbioschemas.jsonld b/data/phenotator/phenotatorbioschemas.jsonld index c6c2a5c8044f1..365397deeb70e 100644 --- a/data/phenotator/phenotatorbioschemas.jsonld +++ b/data/phenotator/phenotatorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Phenotator", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://wwwdev.ebi.ac.uk/fgpt/phenotator/", diff --git a/data/phenotest/phenotestbioschemas.jsonld b/data/phenotest/phenotestbioschemas.jsonld index e4ddeb762bd1d..974b56a5c3b1d 100644 --- a/data/phenotest/phenotestbioschemas.jsonld +++ b/data/phenotest/phenotestbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "phenoTest", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/phenoTest.html", "sc:version": "1.28.0" diff --git a/data/phenotypesimulator/phenotypesimulatorbioschemas.jsonld b/data/phenotypesimulator/phenotypesimulatorbioschemas.jsonld index 3f38c1111e953..0a985fe3c3dc2 100644 --- a/data/phenotypesimulator/phenotypesimulatorbioschemas.jsonld +++ b/data/phenotypesimulator/phenotypesimulatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Flexible simulation of phenotypes under different models, including genetic variant and infinitesimal genetic effects (reflecting population structure) as well as non-genetic covariate effects, observational noise and additional correlation effects.", "sc:name": "PhenotypeSimulator", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/PhenotypeSimulator/index.html" } \ No newline at end of file diff --git a/data/phenstat/phenstatbioschemas.jsonld b/data/phenstat/phenstatbioschemas.jsonld index 21e5e890ce714..bc46c26f6f9ba 100644 --- a/data/phenstat/phenstatbioschemas.jsonld +++ b/data/phenstat/phenstatbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0131274", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/phenstat", "@type": "sc:SoftwareApplication", @@ -32,12 +28,16 @@ "sc:license": "Other", "sc:name": "PhenStat", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PhenStat.html", "sc:version": "2.16.0" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0131274", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phenx_toolkit/phenx_toolkitbioschemas.jsonld b/data/phenx_toolkit/phenx_toolkitbioschemas.jsonld index d70374cc4fa26..f27dc2daf15b0 100644 --- a/data/phenx_toolkit/phenx_toolkitbioschemas.jsonld +++ b/data/phenx_toolkit/phenx_toolkitbioschemas.jsonld @@ -18,8 +18,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5507752", "pubmed:28079902", + "pmcid:PMC5507752", { "@id": "https://doi.org/10.1038/gim.2016.199" } @@ -39,9 +39,9 @@ "sc:license": "CC-BY-NC-4.0", "sc:name": "PhenX Toolkit", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.phenxtoolkit.org/" } diff --git a/data/phesant/phesantbioschemas.jsonld b/data/phesant/phesantbioschemas.jsonld index ea59004d59281..15ae69f45273f 100644 --- a/data/phesant/phesantbioschemas.jsonld +++ b/data/phesant/phesantbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/ije/dyx204", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/phesant", "@type": "sc:SoftwareApplication", @@ -24,22 +28,18 @@ "sc:description": "PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank.", "sc:featureList": [ { - "@id": "edam:operation_2403" + "@id": "edam:operation_3208" }, { - "@id": "edam:operation_3208" + "@id": "edam:operation_2403" } ], "sc:name": "PHESANT", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/MRCIEU/PHESANT" - }, - { - "@id": "https://doi.org/10.1093/ije/dyx204", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phever/pheverbioschemas.jsonld b/data/phever/pheverbioschemas.jsonld index e108b604241df..231f70926d1bb 100644 --- a/data/phever/pheverbioschemas.jsonld +++ b/data/phever/pheverbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database that provides accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. It is a database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. It offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families.", "sc:name": "PhEVER", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://pbil.univ-lyon1.fr/databases/phever/help.html" } \ No newline at end of file diff --git a/data/phewas/phewasbioschemas.jsonld b/data/phewas/phewasbioschemas.jsonld index 165a88e27776e..1f5d6c5cec4d7 100644 --- a/data/phewas/phewasbioschemas.jsonld +++ b/data/phewas/phewasbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Analyze many phenotypes compared to a single genetic variant (or other attribute). This method was originally described using electronic medical record (EMR) data from EMR-linked in the Vanderbilt DNA biobank, BioVU, but can also be applied to other richly phenotyped sets. ::DEVELOPER Biomedical Language Processing Lab.", "sc:name": "PheWAS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://phewascatalog.org/" } \ No newline at end of file diff --git a/data/phewas_clinical/phewas_clinicalbioschemas.jsonld b/data/phewas_clinical/phewas_clinicalbioschemas.jsonld index 73e4306d321d7..4479c6db1b6ee 100644 --- a/data/phewas_clinical/phewas_clinicalbioschemas.jsonld +++ b/data/phewas_clinical/phewas_clinicalbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects.", "sc:name": "PheWAS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/PheWAS/PheWAS" } \ No newline at end of file diff --git a/data/phi-base/phi-basebioschemas.jsonld b/data/phi-base/phi-basebioschemas.jsonld index 4f5761a7e2a1a..dfa6487690cf8 100644 --- a/data/phi-base/phi-basebioschemas.jsonld +++ b/data/phi-base/phi-basebioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKW1089", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/phi-base", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:27915230", - "pmcid:PMC5210566", { "@id": "https://doi.org/10.1093/NAR/GKW1089" - } + }, + "pmcid:PMC5210566", + "pubmed:27915230" ], "sc:description": "PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "PHI-base", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.phi-base.org/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKW1089", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/philr/philrbioschemas.jsonld b/data/philr/philrbioschemas.jsonld index 3d8bd169b578e..72152da4a4694 100644 --- a/data/philr/philrbioschemas.jsonld +++ b/data/philr/philrbioschemas.jsonld @@ -20,11 +20,11 @@ "Library" ], "sc:citation": [ + "pmcid:PMC5328592", "pubmed:28198697", { "@id": "https://doi.org/10.7554/eLife.21887" - }, - "pmcid:PMC5328592" + } ], "sc:description": "Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). It specifically allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.", "sc:featureList": { @@ -34,8 +34,8 @@ "sc:name": "philr", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/philr.html", "sc:version": "1.0.0" diff --git a/data/phire/phirebioschemas.jsonld b/data/phire/phirebioschemas.jsonld index 3e733f721dd5f..d44bb2aba7391 100644 --- a/data/phire/phirebioschemas.jsonld +++ b/data/phire/phirebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Phage In silico Regulatory Elements (PHIRE) is a standalone program in Visual Basic which performs a string-based search on bacteriophage genome sequences discovering and extracting blocks displaying sequence similarity corresponding to conserved regulatory elements contained within these genomes.", "sc:name": "PHIRE", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.biw.kuleuven.be/logt/PHIRE.htm" } \ No newline at end of file diff --git a/data/phisite/phisitebioschemas.jsonld b/data/phisite/phisitebioschemas.jsonld index 675f55edb628f..ea6ae6e58333e 100644 --- a/data/phisite/phisitebioschemas.jsonld +++ b/data/phisite/phisitebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of gene regulation in bacteriophages. It collects experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from bacteriophages belonging to Siphoviridae, Myoviridae and Podoviridae families. The database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (EMBL, UniProt, NCBI taxonomy database, NCBI Genome, ICTVdb, PubMed Central).", "sc:name": "phiSITE", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.phisite.org" } \ No newline at end of file diff --git a/data/phlawd/phlawdbioschemas.jsonld b/data/phlawd/phlawdbioschemas.jsonld index e20594b7187f8..f63b6e5674da0 100644 --- a/data/phlawd/phlawdbioschemas.jsonld +++ b/data/phlawd/phlawdbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Program written in C++ that constructs datasets from NCBI data (GenBank). This uses the megaphylogeny method to construct extremely large datasets, but is convenient for small ones too.", "sc:name": "PHLAWD", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://phlawd.net/" } \ No newline at end of file diff --git a/data/phmmer/phmmerbioschemas.jsonld b/data/phmmer/phmmerbioschemas.jsonld index ed732fcb05410..5ee75cb4f869a 100644 --- a/data/phmmer/phmmerbioschemas.jsonld +++ b/data/phmmer/phmmerbioschemas.jsonld @@ -10,13 +10,17 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0001-8626-2148", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/nar/gkv397", + "@type": "sc:CreativeWork" }, { "@id": "https://doi.org/10.1093/bioinformatics/btw305", "@type": "sc:CreativeWork" }, + { + "@id": "http://orcid.org/0000-0001-8626-2148", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/phmmer", "@type": "sc:SoftwareApplication", @@ -27,30 +31,30 @@ "@id": "edam:data_3671" }, "edam:has_output": [ - { - "@id": "edam:data_2085" - }, { "@id": "edam:data_3028" }, { "@id": "edam:data_1394" + }, + { + "@id": "edam:data_2085" } ], "sc:additionalType": [ - "Web service", - "Command-line tool" + "Command-line tool", + "Web service" ], "sc:citation": [ - "pubmed:25943547", - "pmcid:PMC4489315", - "pmcid:PMC5013910", { - "@id": "https://doi.org/10.1093/nar/gkv397" + "@id": "https://doi.org/10.1093/bioinformatics/btw305" }, { - "@id": "https://doi.org/10.1093/bioinformatics/btw305" + "@id": "https://doi.org/10.1093/nar/gkv397" }, + "pmcid:PMC5013910", + "pmcid:PMC4489315", + "pubmed:25943547", "pubmed:27256311" ], "sc:description": "Search a protein sequence against a protein database using HMMER.", @@ -59,26 +63,22 @@ "@id": "edam:operation_2421" }, { - "@id": "edam:operation_3460" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0292" + "@id": "edam:operation_3460" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_0292" } ], "sc:name": "PHMMER", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.ebi.ac.uk/metagenomics/sequence-search/search/phmmer", "sc:version": "2.23.0" - }, - { - "@id": "https://doi.org/10.1093/nar/gkv397", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phobius/phobiusbioschemas.jsonld b/data/phobius/phobiusbioschemas.jsonld index 9d6f46c438da5..1a4460a1f5d24 100644 --- a/data/phobius/phobiusbioschemas.jsonld +++ b/data/phobius/phobiusbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Predict transmembrane topology and signal peptides from the amino acid sequence of a protein.", "sc:name": "Phobius", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ "EMBL-EBI", diff --git a/data/phobius_api/phobius_apibioschemas.jsonld b/data/phobius_api/phobius_apibioschemas.jsonld index aa2fe8e627a9f..2d1b129ab84d7 100644 --- a/data/phobius_api/phobius_apibioschemas.jsonld +++ b/data/phobius_api/phobius_apibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Transmembrane topology and signal peptides prediction from the amino acid sequence of a protein.", "sc:name": "Phobius API", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/pfa/phobius_rest", "sc:version": "1" diff --git a/data/phobos/phobosbioschemas.jsonld b/data/phobos/phobosbioschemas.jsonld index 7e27f822936fb..793020b2a394a 100644 --- a/data/phobos/phobosbioschemas.jsonld +++ b/data/phobos/phobosbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Phobos", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ruhr-uni-bochum.de/spezzoo/cm/cm_phobos.htm", "sc:version": "3.3.12" diff --git a/data/phos3d/phos3dbioschemas.jsonld b/data/phos3d/phos3dbioschemas.jsonld index 162bd45c3b737..477c5b5215f7b 100644 --- a/data/phos3d/phos3dbioschemas.jsonld +++ b/data/phos3d/phos3dbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Phos3D", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://phos3d.mpimp-golm.mpg.de/" } \ No newline at end of file diff --git a/data/phosfer/phosferbioschemas.jsonld b/data/phosfer/phosferbioschemas.jsonld index 8f1f2727d3b4e..2e602d00f65d8 100644 --- a/data/phosfer/phosferbioschemas.jsonld +++ b/data/phosfer/phosferbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PHOSFER", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://saphire.usask.ca/saphire/phosfer/index.html" } \ No newline at end of file diff --git a/data/phosfinder/phosfinderbioschemas.jsonld b/data/phosfinder/phosfinderbioschemas.jsonld index ec2a2b391b13e..ac1e39c02a2fb 100644 --- a/data/phosfinder/phosfinderbioschemas.jsonld +++ b/data/phosfinder/phosfinderbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A web server for the identification of phosphate-binding sites on protein structures.", "sc:name": "Phosfinder", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "ELIXIR-ITA-TORVERGATA", "sc:url": "http://phosfinder.bio.uniroma2.it", diff --git a/data/phosida/phosidabioschemas.jsonld b/data/phosida/phosidabioschemas.jsonld index 61a7ede28f6f1..d008f2eb12299 100644 --- a/data/phosida/phosidabioschemas.jsonld +++ b/data/phosida/phosidabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The database manages posttranslational modification sites of various species ranging from bacteria to human. It contains phosphorylated, N-glycosylated or acetylated sites. All sites are obtained from high-resolution mass spectrometric data. The database is comprised of three main components: the database environment, the prediction platform and the toolkit section.", "sc:name": "PHOSIDA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.phosida.com" } \ No newline at end of file diff --git a/data/phosnetconstruct/phosnetconstructbioschemas.jsonld b/data/phosnetconstruct/phosnetconstructbioschemas.jsonld index f909ac482c867..c50f00de7f472 100644 --- a/data/phosnetconstruct/phosnetconstructbioschemas.jsonld +++ b/data/phosnetconstruct/phosnetconstructbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool to predict novel phosphorylation networks based on the preference of certain kinase families to phosphorylate specific functional protein families (domains). It identifies the potentially phosphorylated proteins from a given set of proteins and predicts target kinases which in turn would phosphorylate these identified phosphoproteins based on their domain compositions.", "sc:name": "PhosNetConstruct", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.nii.ac.in/phosnetconstruct.html" } \ No newline at end of file diff --git a/data/phosphat/phosphatbioschemas.jsonld b/data/phosphat/phosphatbioschemas.jsonld index 9faeb5295d5ed..fb5c90d1d375e 100644 --- a/data/phosphat/phosphatbioschemas.jsonld +++ b/data/phosphat/phosphatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide properties, their annotated biological function as well as the experimental and analytical context is given. For a majority of peptides, the actual annotated mass spectrum is displayed in interactive manner.", "sc:name": "PhosPhAt", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://phosphat.mpimp-golm.mpg.de/" } \ No newline at end of file diff --git a/data/phospho3d/phospho3dbioschemas.jsonld b/data/phospho3d/phospho3dbioschemas.jsonld index 5381257397455..5afd459bd1ea2 100644 --- a/data/phospho3d/phospho3dbioschemas.jsonld +++ b/data/phospho3d/phospho3dbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/phospho3d", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Andreas Zanzoni", - "Allegra Via" + "Allegra Via", + "Andreas Zanzoni" ], "sc:additionalType": "Database portal", "sc:description": "Database of three-dimensional structures of phosphorylation sites which stores information retrieved from the Phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural comparison procedure providing clues for the identification of new putative phosphorylation sites.", "sc:name": "Phospho3d", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "ELIXIR-ITA-SAPIENZA", diff --git a/data/phosphoelm/phosphoelmbioschemas.jsonld b/data/phosphoelm/phosphoelmbioschemas.jsonld index 9651e37831645..e43f870c9c919 100644 --- a/data/phosphoelm/phosphoelmbioschemas.jsonld +++ b/data/phosphoelm/phosphoelmbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-0657-5166", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1093/nar/gkq1104", "@type": "sc:CreativeWork" @@ -42,11 +38,11 @@ "@id": "edam:topic_0601" }, "sc:citation": [ - "pmcid:PMC3013696", - "pubmed:21062810", { "@id": "https://doi.org/10.1093/nar/gkq1104" - } + }, + "pubmed:21062810", + "pmcid:PMC3013696" ], "sc:description": "Experimentally verified phosphorylation sites in eukaryotic proteins.", "sc:featureList": { @@ -54,11 +50,15 @@ }, "sc:name": "PhosphoELM database", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://phospho.elm.eu.org/" + }, + { + "@id": "http://orcid.org/0000-0003-0657-5166", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/phosphonormalizer/phosphonormalizerbioschemas.jsonld b/data/phosphonormalizer/phosphonormalizerbioschemas.jsonld index 2af6dd23e117d..6e16daf203d7c 100644 --- a/data/phosphonormalizer/phosphonormalizerbioschemas.jsonld +++ b/data/phosphonormalizer/phosphonormalizerbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "phosphonormalizer", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/phosphonormalizer.html", "sc:version": "1.4.0" diff --git a/data/phosphopick/phosphopickbioschemas.jsonld b/data/phosphopick/phosphopickbioschemas.jsonld index c333f08916e09..dbea17b844e5a 100644 --- a/data/phosphopick/phosphopickbioschemas.jsonld +++ b/data/phosphopick/phosphopickbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Method for predicting kinase substrates using cellular context information, and is currently able to make predictions for 59 human kinases.", "sc:name": "PhosphoPICK", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioinf.scmb.uq.edu.au/phosphopick/phosphopick" } \ No newline at end of file diff --git a/data/phosphopredict/phosphopredictbioschemas.jsonld b/data/phosphopredict/phosphopredictbioschemas.jsonld index 45995c463996f..fdc27b7a690b2 100644 --- a/data/phosphopredict/phosphopredictbioschemas.jsonld +++ b/data/phosphopredict/phosphopredictbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Novel bioinformatics approach to predict kinase-specific phosphorylation substrates and sites in the human proteome by combining informative protein sequence and functional features to build the prediction models using random forest (RF).", "sc:name": "PhosphoPredict", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://phosphopredict.erc.monash.edu/" } \ No newline at end of file diff --git a/data/phosphortholog/phosphorthologbioschemas.jsonld b/data/phosphortholog/phosphorthologbioschemas.jsonld index a50da205883c4..741f8ad72fa5d 100644 --- a/data/phosphortholog/phosphorthologbioschemas.jsonld +++ b/data/phosphortholog/phosphorthologbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12864-015-1820-X", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/phosphortholog", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jean Yee Hwa Yang", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:26283093", { "@id": "https://doi.org/10.1186/S12864-015-1820-X" }, + "pubmed:26283093", "pmcid:PMC4539857" ], "sc:description": "Cross-species mapping of orthologous protein post-translational modifications.", @@ -32,11 +28,15 @@ "sc:license": "GPL-1.0", "sc:name": "PhosphOrtholog", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.phosphortholog.com/" + }, + { + "@id": "https://doi.org/10.1186/S12864-015-1820-X", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phosphositeplus/phosphositeplusbioschemas.jsonld b/data/phosphositeplus/phosphositeplusbioschemas.jsonld index dff280d96f2fb..e5d8ac9d8d9ab 100644 --- a/data/phosphositeplus/phosphositeplusbioschemas.jsonld +++ b/data/phosphositeplus/phosphositeplusbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Online systems biology resource providing comprehensive info and tools to study protein post-translational modification in man and mouse.", "sc:name": "PhosphoSitePlus", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.phosphosite.org" diff --git a/data/phosphosvm/phosphosvmbioschemas.jsonld b/data/phosphosvm/phosphosvmbioschemas.jsonld index db169ebe97173..350dff6dd151e 100644 --- a/data/phosphosvm/phosphosvmbioschemas.jsonld +++ b/data/phosphosvm/phosphosvmbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Web server for prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine.", "sc:name": "PhosphoSVM", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sysbio.unl.edu/PhosphoSVM/" } \ No newline at end of file diff --git a/data/phossnp/phossnpbioschemas.jsonld b/data/phossnp/phossnpbioschemas.jsonld index 0c390cae88531..cd0ca38677018 100644 --- a/data/phossnp/phossnpbioschemas.jsonld +++ b/data/phossnp/phossnpbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/phossnp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jian Ren", "Zhaolei Zhang", - "Yu Xue" + "Yu Xue", + "Jian Ren" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:19995808", "sc:description": "A database of phosphorylation-related SNP (phosSNP) which are non-synonymous SNP (nsSNP) that affect the protein phosphorylation status. Using an in-house developed kinase-specific phosphorylation site predictor (GPS 2.0), we computationally detected that �_70% of the reported nsSNPs are potential phosSNPs.", "sc:name": "PhosSNP", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://phossnp.biocuckoo.org/" } \ No newline at end of file diff --git a/data/phostryp/phostrypbioschemas.jsonld b/data/phostryp/phostrypbioschemas.jsonld index 457a9fb83cdd9..60924c9e9bbc3 100644 --- a/data/phostryp/phostrypbioschemas.jsonld +++ b/data/phostryp/phostrypbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PhosTryp", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-TORVERGATA", "sc:url": "http://phostryp.bio.uniroma2.it", diff --git a/data/phplabware/phplabwarebioschemas.jsonld b/data/phplabware/phplabwarebioschemas.jsonld index aef53d94b6bd5..2ba554365eba0 100644 --- a/data/phplabware/phplabwarebioschemas.jsonld +++ b/data/phplabware/phplabwarebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It is a web-driven database management system. Data-entry takes place in forms, which can be altered using phplabware’s plugin mechanism. Search results can be output in reports, which are generated based on simple HTML templates. The (php-based) plugin mechanism allows for easy and fast adaptation of phplabware to any specific needs.", "sc:name": "PhpLabWare", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://phplabware.sourceforge.net/", "sc:version": "0.63" diff --git a/data/phpred/phpredbioschemas.jsonld b/data/phpred/phpredbioschemas.jsonld index 1765cc9e98423..84d8b58425cbc 100644 --- a/data/phpred/phpredbioschemas.jsonld +++ b/data/phpred/phpredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-server which was developed to identify the phage proteins located in host cell based on the sequence information.", "sc:name": "PHPred", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://lin.uestc.edu.cn/server/PHPred" } \ No newline at end of file diff --git a/data/phred/phredbioschemas.jsonld b/data/phred/phredbioschemas.jsonld index 5786f3678b012..ec6d332867556 100644 --- a/data/phred/phredbioschemas.jsonld +++ b/data/phred/phredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.", "sc:name": "Phred", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.phrap.org/phredphrapconsed.html" diff --git a/data/phredphrapconsed/phredphrapconsedbioschemas.jsonld b/data/phredphrapconsed/phredphrapconsedbioschemas.jsonld index cbbe06f2a2fba..f30555c22d9a6 100644 --- a/data/phredphrapconsed/phredphrapconsedbioschemas.jsonld +++ b/data/phredphrapconsed/phredphrapconsedbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "Phred Phrap Consed Cross match", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.phrap.org/phredphrapconsed.html" } \ No newline at end of file diff --git a/data/phuser/phuserbioschemas.jsonld b/data/phuser/phuserbioschemas.jsonld index 3225026a9a002..97caeba660ee7 100644 --- a/data/phuser/phuserbioschemas.jsonld +++ b/data/phuser/phuserbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "PHUSER", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.cbs.dtu.dk/services/phuser/" } \ No newline at end of file diff --git a/data/phy-mer/phy-merbioschemas.jsonld b/data/phy-mer/phy-merbioschemas.jsonld index 1ed6b2aaec5c6..a1d564e95e20b 100644 --- a/data/phy-mer/phy-merbioschemas.jsonld +++ b/data/phy-mer/phy-merbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Novel alignment-free and reference-independent mitochondrial haplogroup classifier.", "sc:name": "Phy-Mer", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/danielnavarrogomez/phy-mer" diff --git a/data/phycas/phycasbioschemas.jsonld b/data/phycas/phycasbioschemas.jsonld index ac52ad85b170a..c47574eb0770a 100644 --- a/data/phycas/phycasbioschemas.jsonld +++ b/data/phycas/phycasbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Python application for carrying out phylogenetic analyses. It is also a C++ and Python library that can be used to create new applications or to extend the current functionality.", "sc:name": "Phycas", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://hydrodictyon.eeb.uconn.edu/projects/phycas/index.php/Phycas_Home" } \ No newline at end of file diff --git a/data/phyd3/phyd3bioschemas.jsonld b/data/phyd3/phyd3bioschemas.jsonld index 5608e670ebbba..5ceab7877e1e8 100644 --- a/data/phyd3/phyd3bioschemas.jsonld +++ b/data/phyd3/phyd3bioschemas.jsonld @@ -21,8 +21,8 @@ "sc:license": "GPL-3.0", "sc:name": "PhyD3", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "VIB", "sc:url": "https://phyd3.bits.vib.be", diff --git a/data/phyinformr/phyinformrbioschemas.jsonld b/data/phyinformr/phyinformrbioschemas.jsonld index 32976c4686067..88555eda68f1d 100644 --- a/data/phyinformr/phyinformrbioschemas.jsonld +++ b/data/phyinformr/phyinformrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12862-016-0837-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/phyinformr", "@type": "sc:SoftwareApplication", @@ -17,11 +21,11 @@ }, "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5134231", + "pubmed:27905871", { "@id": "https://doi.org/10.1186/S12862-016-0837-3" }, - "pubmed:27905871" + "pmcid:PMC5134231" ], "sc:description": "Open source software package that performs rapid calculation of phylogenetic information content using the latest advances in phylogenetic informativeness based theory.", "sc:featureList": { @@ -29,16 +33,12 @@ }, "sc:name": "PhyInformR", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://carolinafishes.github.io/software/phyinformR/" }, - { - "@id": "https://doi.org/10.1186/S12862-016-0837-3", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-0863-2283", "@type": "schema:Person" diff --git a/data/phyleasprog/phyleasprogbioschemas.jsonld b/data/phyleasprog/phyleasprogbioschemas.jsonld index db3e3d7cb3fb3..d8989694c053e 100644 --- a/data/phyleasprog/phyleasprogbioschemas.jsonld +++ b/data/phyleasprog/phyleasprogbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "PhyleasProg is a web server for evolutionary analyses. Users input a list of Ensembl protein IDs and a list of species as inputs.", "sc:name": "PhyleasProg", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://phyleasprog.inra.fr" diff --git a/data/phylemon/phylemonbioschemas.jsonld b/data/phylemon/phylemonbioschemas.jsonld index f4d64409d8190..66ac603e0b7cc 100644 --- a/data/phylemon/phylemonbioschemas.jsonld +++ b/data/phylemon/phylemonbioschemas.jsonld @@ -15,14 +15,14 @@ "sc:description": "Suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It is conceived as a response to the increasing demand of molecular sequence analyses for experts and non-experts users.", "sc:name": "Phylemon", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "cipf.es", "Computational Genomics Department. Prince Felipe Research Center (CIPF)", - "http://bioinfo.cipf.es" + "http://bioinfo.cipf.es", + "cipf.es" ], "sc:url": "http://phylemon.bioinfo.cipf.es/", "sc:version": "2" diff --git a/data/phylip/phylipbioschemas.jsonld b/data/phylip/phylipbioschemas.jsonld index 3d0f2c24709db..f670b665a8c4c 100644 --- a/data/phylip/phylipbioschemas.jsonld +++ b/data/phylip/phylipbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "PHYLIP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://evolution.genetics.washington.edu/phylip.html" } \ No newline at end of file diff --git a/data/phylo-mlogo/phylo-mlogobioschemas.jsonld b/data/phylo-mlogo/phylo-mlogobioschemas.jsonld index fd702ae250f78..b4b92a0de2265 100644 --- a/data/phylo-mlogo/phylo-mlogobioschemas.jsonld +++ b/data/phylo-mlogo/phylo-mlogobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Interactive multiple-logo visualization tool for large-number sequence alignments which allows the user to visualize the global profile of whole multiple sequence alignment and to hierarchically visualize homologous logos of each clade simultaneously.", "sc:name": "Phylo-mLogo", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://cg1.iis.sinica.edu.tw/new/phylomlogo/" } \ No newline at end of file diff --git a/data/phylo-node/phylo-nodebioschemas.jsonld b/data/phylo-node/phylo-nodebioschemas.jsonld index b2bed20a7ab85..bd88e99d4080a 100644 --- a/data/phylo-node/phylo-nodebioschemas.jsonld +++ b/data/phylo-node/phylo-nodebioschemas.jsonld @@ -15,8 +15,8 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5391935", "pubmed:28410421", + "pmcid:PMC5391935", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0175480" } @@ -28,9 +28,9 @@ "sc:license": "MIT", "sc:name": "phylo-node", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/dohalloran/phylo-node" }, diff --git a/data/phylo/phylobioschemas.jsonld b/data/phylo/phylobioschemas.jsonld index 3b0a3cc9bb04d..0a9dd5098deb7 100644 --- a/data/phylo/phylobioschemas.jsonld +++ b/data/phylo/phylobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Human-based computing framework applying “crowd sourcing” techniques to solve the Multiple Sequence Alignment (MSA) problem. The key idea is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context.", "sc:name": "Phylo", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://phylo.cs.mcgill.ca/" diff --git a/data/phylobot/phylobotbioschemas.jsonld b/data/phylobot/phylobotbioschemas.jsonld index fb664b36551cc..90fb06f9274c8 100644 --- a/data/phylobot/phylobotbioschemas.jsonld +++ b/data/phylobot/phylobotbioschemas.jsonld @@ -18,11 +18,11 @@ ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:27472806", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1004976" }, - "pmcid:PMC4966924" + "pmcid:PMC4966924", + "pubmed:27472806" ], "sc:description": "A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.", "sc:featureList": [ diff --git a/data/phylodome/phylodomebioschemas.jsonld b/data/phylodome/phylodomebioschemas.jsonld index 03156ebfc82ea..6fce1b53a256d 100644 --- a/data/phylodome/phylodomebioschemas.jsonld +++ b/data/phylodome/phylodomebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.", "sc:name": "PhyloDome", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://mendel.imp.ac.at/PhyloDome/" } \ No newline at end of file diff --git a/data/phylodyn/phylodynbioschemas.jsonld b/data/phylodyn/phylodynbioschemas.jsonld index 0b32af7c75e3e..51ec1d89e8e15 100644 --- a/data/phylodyn/phylodynbioschemas.jsonld +++ b/data/phylodyn/phylodynbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Michael Karcher", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5466693", + "pubmed:27801980", { "@id": "https://doi.org/10.1111/1755-0998.12630" }, - "pubmed:27801980" + "pmcid:PMC5466693" ], "sc:description": "Phylodynamic simulation and inference.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "phylodyn", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/mdkarcher/phylodyn" } diff --git a/data/phylogenetics_at_jst/phylogenetics_at_jstbioschemas.jsonld b/data/phylogenetics_at_jst/phylogenetics_at_jstbioschemas.jsonld index f1d5410f59818..8ac43dccee098 100644 --- a/data/phylogenetics_at_jst/phylogenetics_at_jstbioschemas.jsonld +++ b/data/phylogenetics_at_jst/phylogenetics_at_jstbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Computerized tools (\"workflows\") to process large amounts of data from cross-disciplinary sources as well as tools for designing and running workflows.", "sc:name": "Phylogenetics_AT_JST", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/PasqualeInfn/JST", "sc:version": "1" diff --git a/data/phylogeny_io/phylogeny_iobioschemas.jsonld b/data/phylogeny_io/phylogeny_iobioschemas.jsonld index cc9a54fdf53df..c1c88102af420 100644 --- a/data/phylogeny_io/phylogeny_iobioschemas.jsonld +++ b/data/phylogeny_io/phylogeny_iobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-4369-1019", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1093/NAR/GKZ356", "@type": "sc:CreativeWork" @@ -25,32 +21,36 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31114886", + "pmcid:PMC6602505", { "@id": "https://doi.org/10.1093/NAR/GKZ356" - }, - "pubmed:31114886", - "pmcid:PMC6602505" + } ], "sc:description": "Interactive web-based visualization and sharing of phylogenetic trees.", "sc:featureList": [ { - "@id": "edam:operation_0326" + "@id": "edam:operation_0558" }, { - "@id": "edam:operation_3478" + "@id": "edam:operation_0326" }, { - "@id": "edam:operation_0558" + "@id": "edam:operation_3478" } ], "sc:license": "MIT", "sc:name": "phylogeny IO", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://phylogeny.io" + }, + { + "@id": "https://orcid.org/0000-0003-4369-1019", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/phylogeoref/phylogeorefbioschemas.jsonld b/data/phylogeoref/phylogeorefbioschemas.jsonld index 91c1ddf95e45f..125e478871d31 100644 --- a/data/phylogeoref/phylogeorefbioschemas.jsonld +++ b/data/phylogeoref/phylogeorefbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Java library for producing rich kmls containing phylogenetic data that can be rendered in google earth web browser. In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms (e.g. species, populations), which is discovered through molecular sequencing data and morphological data matrices.", "sc:name": "PhyloGeoRef", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/kdiverson/phyloGeoRef" } \ No newline at end of file diff --git a/data/phylogibbs/phylogibbsbioschemas.jsonld b/data/phylogibbs/phylogibbsbioschemas.jsonld index 9d7b34c4c2a60..32b137cd9fddd 100644 --- a/data/phylogibbs/phylogibbsbioschemas.jsonld +++ b/data/phylogibbs/phylogibbsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.", "sc:name": "Phylogibbs", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.phylogibbs.unibas.ch" } \ No newline at end of file diff --git a/data/phyloligo/phyloligobioschemas.jsonld b/data/phyloligo/phyloligobioschemas.jsonld index 769b69f74dcdf..0f723ffcdaaf4 100644 --- a/data/phyloligo/phyloligobioschemas.jsonld +++ b/data/phyloligo/phyloligobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Identify contaminant or untargeted organism sequences in genome assemblies.", "sc:name": "PhylOligo", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/itsmeludo/Phyloligo/" } \ No newline at end of file diff --git a/data/phylomad/phylomadbioschemas.jsonld b/data/phylomad/phylomadbioschemas.jsonld index a5554441fbc8f..151e71222edff 100644 --- a/data/phylomad/phylomadbioschemas.jsonld +++ b/data/phylomad/phylomadbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "PhyloMAd", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/duchene/phylomad" diff --git a/data/phylommand/phylommandbioschemas.jsonld b/data/phylommand/phylommandbioschemas.jsonld index 3f98c83f6a1c6..9a66ca6c8d2e7 100644 --- a/data/phylommand/phylommandbioschemas.jsonld +++ b/data/phylommand/phylommandbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "GPL-3.0", "sc:name": "Phylommand", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/mr-y/phylommand" } \ No newline at end of file diff --git a/data/phylopars/phyloparsbioschemas.jsonld b/data/phylopars/phyloparsbioschemas.jsonld index df6793fd8bd46..50e850e717f44 100644 --- a/data/phylopars/phyloparsbioschemas.jsonld +++ b/data/phylopars/phyloparsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Allows for easy, efficient estimation of metabolic parameters as inferred from observations on species that are phylogenetically related.", "sc:name": "PhyloPars", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.ibi.vu.nl/programs/phylopars/" diff --git a/data/phylopat/phylopatbioschemas.jsonld b/data/phylopat/phylopatbioschemas.jsonld index 7f052161f6143..0e1023349c78e 100644 --- a/data/phylopat/phylopatbioschemas.jsonld +++ b/data/phylopat/phylopatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Webserver which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. The output can be saved in HTML, Excel or plain text format for further analysis. Output is linked to the FatiGO web interface creating easy access to functional information.", "sc:name": "PhyloPat", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.cmbi.ru.nl/phylopat" diff --git a/data/phylopdb/phylopdbbioschemas.jsonld b/data/phylopdb/phylopdbbioschemas.jsonld index dc855d55a8250..65546d58d3c86 100644 --- a/data/phylopdb/phylopdbbioschemas.jsonld +++ b/data/phylopdb/phylopdbbioschemas.jsonld @@ -21,11 +21,11 @@ "Database portal" ], "sc:citation": [ - "pubmed:24771669", - "pmcid:PMC4000467", { "@id": "https://doi.org/10.1093/database/bau036" - } + }, + "pubmed:24771669", + "pmcid:PMC4000467" ], "sc:description": "Phylogenetic Oligonucleotide Probe Database. Provides a convivial and easy-to-use web interface to browse both regular and explorative 16S rRNA-targeted probes.", "sc:featureList": { diff --git a/data/phyloprofil/phyloprofilbioschemas.jsonld b/data/phyloprofil/phyloprofilbioschemas.jsonld index b9eafee41c239..d6e647ecc9a7b 100644 --- a/data/phyloprofil/phyloprofilbioschemas.jsonld +++ b/data/phyloprofil/phyloprofilbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "PhyloProfil", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/BIONF/phyloprofile" } \ No newline at end of file diff --git a/data/phyloprofile/phyloprofilebioschemas.jsonld b/data/phyloprofile/phyloprofilebioschemas.jsonld index 2b76a81ca468a..35e5ed79a1294 100644 --- a/data/phyloprofile/phyloprofilebioschemas.jsonld +++ b/data/phyloprofile/phyloprofilebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "PhyloProfile", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/BIONF/phyloprofile" } \ No newline at end of file diff --git a/data/phylopythias/phylopythiasbioschemas.jsonld b/data/phylopythias/phylopythiasbioschemas.jsonld index 79a96b90326dd..d4282167a14ec 100644 --- a/data/phylopythias/phylopythiasbioschemas.jsonld +++ b/data/phylopythias/phylopythiasbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Alice McHardy", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4748697", { "@id": "https://doi.org/10.7717/peerj.1603" }, - "pubmed:26870609" + "pubmed:26870609", + "pmcid:PMC4748697" ], "sc:description": "PhyloPythiaS+ allows the analysis of Gb-sized metagenomes with inexpensive hardware and recovery of species or genera-level bins with low error rates in a fully automated fashion.", "sc:featureList": { diff --git a/data/phyloseq/phyloseqbioschemas.jsonld b/data/phyloseq/phyloseqbioschemas.jsonld index 0040efee2438b..9a2dab0580c14 100644 --- a/data/phyloseq/phyloseqbioschemas.jsonld +++ b/data/phyloseq/phyloseqbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0061217", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/phyloseq", "@type": "sc:SoftwareApplication", @@ -20,8 +16,8 @@ "@id": "http://orcid.org/0000-0001-8879-3954" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pubmed:23630581", @@ -33,25 +29,29 @@ "sc:description": "Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_3431" }, { "@id": "edam:operation_2945" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_0337" } ], "sc:license": "GPL-3.0", "sc:name": "phyloseq", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/phyloseq.html", "sc:version": "1.19.1" }, + { + "@id": "https://doi.org/10.1371/journal.pone.0061217", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0001-8879-3954", "@type": "schema:Person" diff --git a/data/phylosift/phylosiftbioschemas.jsonld b/data/phylosift/phylosiftbioschemas.jsonld index 267886451805d..bb93a3ae6ae7a 100644 --- a/data/phylosift/phylosiftbioschemas.jsonld +++ b/data/phylosift/phylosiftbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/phylosift", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Suite" + "Suite", + "Command-line tool" ], "sc:description": "Suite of software tools to conduct phylogenetic analysis of genomes and metagenomes. Using a reference database of protein sequences, PhyloSift can scan new sequences against that data for homologs and identify phylogentic relationships of the new sequence compared to the database sequences.", "sc:license": "GPL-3.0", diff --git a/data/phylosim/phylosimbioschemas.jsonld b/data/phylosim/phylosimbioschemas.jsonld index e3514a5cb9231..004309494e74f 100644 --- a/data/phylosim/phylosimbioschemas.jsonld +++ b/data/phylosim/phylosimbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R.", "sc:name": "PhyloSim", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.ebi.ac.uk/goldman-srv/phylosim/" } \ No newline at end of file diff --git a/data/phylotar/phylotarbioschemas.jsonld b/data/phylotar/phylotarbioschemas.jsonld index d820890bcf36b..b171c8dcf676b 100644 --- a/data/phylotar/phylotarbioschemas.jsonld +++ b/data/phylotar/phylotarbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Dominic J. Bennett", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6027284", + "pubmed:29874797", { "@id": "https://doi.org/10.3390/life8020020" - }, - "pmcid:PMC6027284", - "pubmed:29874797" + } ], "sc:description": "An automated pipeline for retrieving orthologous DNA sequences from GenBank in R.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "MIT", "sc:name": "phylotaR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/ropensci/phylotaR" }, diff --git a/data/phylotol/phylotolbioschemas.jsonld b/data/phylotol/phylotolbioschemas.jsonld index 70086b33ae34e..0d268c023e90b 100644 --- a/data/phylotol/phylotolbioschemas.jsonld +++ b/data/phylotol/phylotolbioschemas.jsonld @@ -17,16 +17,16 @@ "@id": "https://bio.tools/PhyloToL", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "L. A. Katz", - "Mario Cerón-Romero" + "Mario Cerón-Romero", + "L. A. Katz" ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:31062861", + "pmcid:PMC6657734", { "@id": "https://doi.org/10.1093/MOLBEV/MSZ103" - }, - "pmcid:PMC6657734", - "pubmed:31062861" + } ], "sc:description": "A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes.", "sc:featureList": [ diff --git a/data/phylotrac/phylotracbioschemas.jsonld b/data/phylotrac/phylotracbioschemas.jsonld index f2d6b9af808c5..c6ec2b973d48b 100644 --- a/data/phylotrac/phylotracbioschemas.jsonld +++ b/data/phylotrac/phylotracbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PhyloTrac", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.phylotrac.org/" } \ No newline at end of file diff --git a/data/phylotu/phylotubioschemas.jsonld b/data/phylotu/phylotubioschemas.jsonld index 6dcada79250a2..8c9e7f68272cb 100644 --- a/data/phylotu/phylotubioschemas.jsonld +++ b/data/phylotu/phylotubioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Identifies microbial operational taxonomic units (OTUs) from metagenomic data.", "sc:name": "PhylOTU", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/sharpton/PhylOTU" diff --git a/data/phyloviz/phylovizbioschemas.jsonld b/data/phyloviz/phylovizbioschemas.jsonld index e569df36faa37..836ad90bbf04b 100644 --- a/data/phyloviz/phylovizbioschemas.jsonld +++ b/data/phyloviz/phylovizbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/PHYLOViZ", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:description": "Scalable data integration and visualization for multiple phylogenetic inference methods.", "sc:license": "GPL-3.0", diff --git a/data/phylowood/phylowoodbioschemas.jsonld b/data/phylowood/phylowoodbioschemas.jsonld index 18afb47b089cd..674a24b298c98 100644 --- a/data/phylowood/phylowoodbioschemas.jsonld +++ b/data/phylowood/phylowoodbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btt635", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/phylowood", "@type": "sc:SoftwareApplication", @@ -31,11 +27,15 @@ }, "sc:name": "Phylowood", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://mlandis.github.io/phylowood/" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btt635", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phyluce/phylucebioschemas.jsonld b/data/phyluce/phylucebioschemas.jsonld index 0ec7d75698da1..192b15fd52f2c 100644 --- a/data/phyluce/phylucebioschemas.jsonld +++ b/data/phyluce/phylucebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes.", "sc:name": "PHYLUCE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://phyluce.readthedocs.org/en/latest/" } \ No newline at end of file diff --git a/data/phyml/phymlbioschemas.jsonld b/data/phyml/phymlbioschemas.jsonld index 7ba71d16300d2..5bd5c2a1ee187 100644 --- a/data/phyml/phymlbioschemas.jsonld +++ b/data/phyml/phymlbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Stephane Guindon", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:author": "Stephane Guindon", "sc:description": "Phylogenetic estimation software using Maximum Likelihood", "sc:license": "GPL-2.0", "sc:name": "PhyML", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.atgc-montpellier.fr/phyml/" } \ No newline at end of file diff --git a/data/phymyco-db/phymyco-dbbioschemas.jsonld b/data/phymyco-db/phymyco-dbbioschemas.jsonld index e7fc50c257e27..7f2c43f68b80e 100644 --- a/data/phymyco-db/phymyco-dbbioschemas.jsonld +++ b/data/phymyco-db/phymyco-dbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Phymyco-DB", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "GenOuest", "sc:url": "http://phymycodb.genouest.org/" diff --git a/data/phyre/phyrebioschemas.jsonld b/data/phyre/phyrebioschemas.jsonld index e9b6a5fbb327a..a6f9d174232ee 100644 --- a/data/phyre/phyrebioschemas.jsonld +++ b/data/phyre/phyrebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Major update to the original Phyre server. The new system is designed around the idea that you have a protein sequence/gene and want to predict its three-dimensional (3D) structure. It uses the alignment of hidden Markov models via HHsearch1 to significantly improve accuracy of alignment and detection rate.", "sc:name": "Phyre", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index" } \ No newline at end of file diff --git a/data/phyrerisk/phyreriskbioschemas.jsonld b/data/phyrerisk/phyreriskbioschemas.jsonld index e172ddc11aa3f..28804415c1bd4 100644 --- a/data/phyrerisk/phyreriskbioschemas.jsonld +++ b/data/phyrerisk/phyreriskbioschemas.jsonld @@ -15,30 +15,30 @@ "biotools:primaryContact": "Alessia David", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:31075275", + "pmcid:PMC6597944", { "@id": "https://doi.org/10.1016/J.JMB.2019.04.043" - }, - "pubmed:31075275", - "pmcid:PMC6597944" + } ], "sc:description": "Dynamic web application that enables the exploration and mapping of genetic variants onto experimental and predicted structures of proteins and protein complexes.", "sc:featureList": [ { - "@id": "edam:operation_0302" + "@id": "edam:operation_3227" }, { - "@id": "edam:operation_0331" + "@id": "edam:operation_0302" }, { - "@id": "edam:operation_3227" + "@id": "edam:operation_0331" } ], "sc:license": "Unlicense", "sc:name": "PhyreRisk", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://phyrerisk.bc.ic.ac.uk" }, diff --git a/data/phyrex/phyrexbioschemas.jsonld b/data/phyrex/phyrexbioschemas.jsonld index 8334013427fd6..efa136e31cb4e 100644 --- a/data/phyrex/phyrexbioschemas.jsonld +++ b/data/phyrex/phyrexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Program for reconstructing ancestral gene expression profiles and sequence data on a given phylogenetic tree. The program uses a Minimum Evolution algorithm to reconstruct the gene expression profiles and a combination of BaseML and ClustalW to reconstruct the ancestral sequences.", "sc:name": "Phyrex", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.rossnes.org/phyrex/" diff --git a/data/physbinder/physbinderbioschemas.jsonld b/data/physbinder/physbinderbioschemas.jsonld index deb4f2593effe..2e78a5e95ebfc 100644 --- a/data/physbinder/physbinderbioschemas.jsonld +++ b/data/physbinder/physbinderbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkt288", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/physbinder", "@type": "sc:SoftwareApplication", @@ -24,10 +28,10 @@ }, "sc:citation": [ "pmcid:PMC3692127", - "pubmed:23620286", { "@id": "https://doi.org/10.1093/nar/gkt288" - } + }, + "pubmed:23620286" ], "sc:description": "Biophysical identification of transcription factor binding sites.", "sc:featureList": { @@ -42,10 +46,6 @@ "sc:provider": "ugent.be", "sc:url": "http://bioit.dmbr.ugent.be/physbinder/", "sc:version": "1.1" - }, - { - "@id": "https://doi.org/10.1093/nar/gkt288", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/physiolibrary/physiolibrarybioschemas.jsonld b/data/physiolibrary/physiolibrarybioschemas.jsonld index ef9a41a0bdde0..40d328ea2ae16 100644 --- a/data/physiolibrary/physiolibrarybioschemas.jsonld +++ b/data/physiolibrary/physiolibrarybioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "Physiolibrary", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "matfyz.cz", "sc:url": "http://www.physiolibrary.org", diff --git a/data/physortr/physortrbioschemas.jsonld b/data/physortr/physortrbioschemas.jsonld index e040950480fea..d80951a2f6ee9 100644 --- a/data/physortr/physortrbioschemas.jsonld +++ b/data/physortr/physortrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.7717/peerj.2038", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/physortr", "@type": "sc:SoftwareApplication", @@ -17,10 +21,10 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4868591", { "@id": "https://doi.org/10.7717/peerj.2038" }, + "pmcid:PMC4868591", "pubmed:27190724" ], "sc:description": "PhySortR is an R package that can be used for the sorting of phylogenetic trees.", @@ -39,10 +43,6 @@ { "@id": "http://orcid.org/0000-0002-3729-8176", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.7717/peerj.2038", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phytb/phytbbioschemas.jsonld b/data/phytb/phytbbioschemas.jsonld index eff567ca215ad..a37549332e0cc 100644 --- a/data/phytb/phytbbioschemas.jsonld +++ b/data/phytb/phytbbioschemas.jsonld @@ -9,25 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-015-0603-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/phytb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Coll F", "Benavente ED", - "Clark TG", - "Coll F" + "Clark TG" ], "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:25968323", - "pmcid:PMC4429496", { "@id": "https://doi.org/10.1186/S12859-015-0603-3" - } + }, + "pmcid:PMC4429496", + "pubmed:25968323" ], "sc:description": "Phylogenetic tree visualisation and sample positioning for M. tuberculosis.", "sc:featureList": { @@ -40,6 +36,10 @@ "Linux" ], "sc:url": "https://sourceforge.net/projects/phylotrack/" + }, + { + "@id": "https://doi.org/10.1186/S12859-015-0603-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phytotypedb/phytotypedbbioschemas.jsonld b/data/phytotypedb/phytotypedbbioschemas.jsonld index 2375c90f3130e..9b7cc8c2fc602 100644 --- a/data/phytotypedb/phytotypedbbioschemas.jsonld +++ b/data/phytotypedb/phytotypedbbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/database/bay125", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/PhytoTypeDB", "@type": "sc:SoftwareApplication", @@ -22,18 +18,18 @@ ], "sc:citation": [ "pmcid:PMC6301341", + "pubmed:30576486", { "@id": "https://doi.org/10.1093/database/bay125" - }, - "pubmed:30576486" + } ], "sc:description": "Database of plant protein inter-cultivar variability and function.", "sc:featureList": [ { - "@id": "edam:operation_0267" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_0267" }, { "@id": "edam:operation_3196" @@ -42,10 +38,14 @@ "sc:name": "PhytoTypeDB", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://phytotypedb.bio.unipd.it/" + }, + { + "@id": "https://doi.org/10.1093/database/bay125", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/phytozome/phytozomebioschemas.jsonld b/data/phytozome/phytozomebioschemas.jsonld index 9b275ed966f1e..2f79da6e1361b 100644 --- a/data/phytozome/phytozomebioschemas.jsonld +++ b/data/phytozome/phytozomebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Comparative hub for plant genome and gene family data and analysis.", "sc:name": "Phytozome", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.phytozome.net/" } \ No newline at end of file diff --git a/data/pi/pibioschemas.jsonld b/data/pi/pibioschemas.jsonld index 1bbe0f80150c6..85c26a021b8e6 100644 --- a/data/pi/pibioschemas.jsonld +++ b/data/pi/pibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "Pi", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Pi.html", "sc:version": "1.0.0" diff --git a/data/pi2pe/pi2pebioschemas.jsonld b/data/pi2pe/pi2pebioschemas.jsonld index 113a8cb4251e9..ffb64e63a01ac 100644 --- a/data/pi2pe/pi2pebioschemas.jsonld +++ b/data/pi2pe/pi2pebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PI2PE", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://pipe.scs.fsu.edu/" } \ No newline at end of file diff --git a/data/pia/piabioschemas.jsonld b/data/pia/piabioschemas.jsonld index 70bc84bd92b3a..5f04266a3f97c 100644 --- a/data/pia/piabioschemas.jsonld +++ b/data/pia/piabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-7522-4007", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/pia", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "@id": "http://orcid.org/0000-0001-7522-4007" }, "sc:additionalType": [ + "Command-line tool", "Library", "Web application", - "Desktop application", - "Command-line tool" + "Desktop application" ], "sc:author": { "@id": "http://orcid.org/0000-0001-7522-4007" @@ -33,13 +29,17 @@ "sc:license": "BSD-3-Clause", "sc:name": "PIA - Protein Inference Algorithms", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "BioInfra.Prot", "sc:url": "https://mpc-bioinformatics.github.io/pia/", "sc:version": "1.3.0" + }, + { + "@id": "http://orcid.org/0000-0001-7522-4007", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/piage/piagebioschemas.jsonld b/data/piage/piagebioschemas.jsonld index a7a6e067e870a..104a7a2300a28 100644 --- a/data/piage/piagebioschemas.jsonld +++ b/data/piage/piagebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Perform estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects.", "sc:name": "PIAGE", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html" } \ No newline at end of file diff --git a/data/piana/pianabioschemas.jsonld b/data/piana/pianabioschemas.jsonld index 475717ba8db61..70a0d2ccd5b55 100644 --- a/data/piana/pianabioschemas.jsonld +++ b/data/piana/pianabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Software framework that facilitates the work with protein interaction networks by 1) integrating data from multiple sources in a centralized database, 2) providing a library that handles all operations related with the network and 3) automating the analysis of protein-protein interactions networks.", "sc:name": "PIANA", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "upf.edu", diff --git a/data/piano/pianobioschemas.jsonld b/data/piano/pianobioschemas.jsonld index 0f2ba50e3f6b4..2033251fa070a 100644 --- a/data/piano/pianobioschemas.jsonld +++ b/data/piano/pianobioschemas.jsonld @@ -24,15 +24,15 @@ "@id": "http://orcid.org/0000-0003-4153-5354" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC3632109", + "pubmed:23444143", { "@id": "https://doi.org/10.1093/nar/gkt111" - }, - "pubmed:23444143" + } ], "sc:description": "Performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, this package contains functions for combining the results of multiple runs of gene set analyses.", "sc:featureList": { @@ -41,9 +41,9 @@ "sc:license": "GPL-2.0", "sc:name": "piano", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/piano.html", "sc:version": "1.14.4" diff --git a/data/pica/picabioschemas.jsonld b/data/pica/picabioschemas.jsonld index 80b4dbb6258ac..c39247402fe07 100644 --- a/data/pica/picabioschemas.jsonld +++ b/data/pica/picabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-2216-4295", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1186/1471-2105-16-S14-S1", "@type": "sc:CreativeWork" @@ -25,10 +29,10 @@ "sc:additionalType": "Command-line tool", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0797" + "@id": "edam:topic_3174" }, { - "@id": "edam:topic_3174" + "@id": "edam:topic_0797" } ], "sc:citation": [ @@ -55,10 +59,6 @@ }, "sc:url": "https://github.com/univieCUBE/PICA", "sc:version": "1" - }, - { - "@id": "http://orcid.org/0000-0003-2216-4295", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/picard_arrg/picard_arrgbioschemas.jsonld b/data/picard_arrg/picard_arrgbioschemas.jsonld index a2a948f06d576..955d97af3b26b 100644 --- a/data/picard_arrg/picard_arrgbioschemas.jsonld +++ b/data/picard_arrg/picard_arrgbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Add or Replace Read Groups in an input BAM or SAM file.", "sc:name": "picard_arrg", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://broadinstitute.github.io/picard/", "sc:version": "1.56.0" diff --git a/data/picard_bamindexstats/picard_bamindexstatsbioschemas.jsonld b/data/picard_bamindexstats/picard_bamindexstatsbioschemas.jsonld index 5b96ca9dd9ea5..383e3452d938c 100644 --- a/data/picard_bamindexstats/picard_bamindexstatsbioschemas.jsonld +++ b/data/picard_bamindexstats/picard_bamindexstatsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Generate Bam Index Stats for a provided BAM file.", "sc:name": "picard_bamindexstats", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://broadinstitute.github.io/picard/", "sc:version": "1.56.0" diff --git a/data/picard_fastqtosam/picard_fastqtosambioschemas.jsonld b/data/picard_fastqtosam/picard_fastqtosambioschemas.jsonld index b915a67725891..fa2c9277e513f 100644 --- a/data/picard_fastqtosam/picard_fastqtosambioschemas.jsonld +++ b/data/picard_fastqtosam/picard_fastqtosambioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Create an unaligned BAM file.", "sc:name": "picard_fastqtosam", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://broadinstitute.github.io/picard/", diff --git a/data/picard_reordersam/picard_reordersambioschemas.jsonld b/data/picard_reordersam/picard_reordersambioschemas.jsonld index 2abbf20815277..35b4168a80d93 100644 --- a/data/picard_reordersam/picard_reordersambioschemas.jsonld +++ b/data/picard_reordersam/picard_reordersambioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is not the same as sorting as done by the SortSam tool, which sorts by either coordinate values or query name. The ordering in ReorderSam is based on exact name matching of contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are not included in the output.", "sc:name": "picard_reordersam", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://broadinstitute.github.io/picard/", diff --git a/data/picard_replacesamheader/picard_replacesamheaderbioschemas.jsonld b/data/picard_replacesamheader/picard_replacesamheaderbioschemas.jsonld index dd68084a264c9..84e840a4a1302 100644 --- a/data/picard_replacesamheader/picard_replacesamheaderbioschemas.jsonld +++ b/data/picard_replacesamheader/picard_replacesamheaderbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Replace Sam Header with the header from another sam file. The tool does not do any significant validation, so it's up to the user to make sure that the elements in the header are relevant and that the new header has all the required things.", "sc:name": "picard_replacesamheader", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://broadinstitute.github.io/picard/", "sc:version": "1.56.0" diff --git a/data/picard_samtofastq/picard_samtofastqbioschemas.jsonld b/data/picard_samtofastq/picard_samtofastqbioschemas.jsonld index d4dc8f5a12c9e..fa14e148a1b5d 100644 --- a/data/picard_samtofastq/picard_samtofastqbioschemas.jsonld +++ b/data/picard_samtofastq/picard_samtofastqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Create a FASTQ file.", "sc:name": "picard_samtofastq", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://broadinstitute.github.io/picard/", "sc:version": "1.56.1" diff --git a/data/picard_tools/picard_toolsbioschemas.jsonld b/data/picard_tools/picard_toolsbioschemas.jsonld index 7e4e9e1dea2a4..0e1a11554fb72 100644 --- a/data/picard_tools/picard_toolsbioschemas.jsonld +++ b/data/picard_tools/picard_toolsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "Picard", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/broadinstitute/picard", "sc:version": "2.17.x" diff --git a/data/picardasmetrics/picardasmetricsbioschemas.jsonld b/data/picardasmetrics/picardasmetricsbioschemas.jsonld index a4d2574abc530..11202d0b260ff 100644 --- a/data/picardasmetrics/picardasmetricsbioschemas.jsonld +++ b/data/picardasmetrics/picardasmetricsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Reports high-level measures of alignment based on a provided sam or bam file.", "sc:name": "picardasmetrics", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://broadinstitute.github.io/picard/", "sc:version": "1.56.0" diff --git a/data/picardgcbiasmetrics/picardgcbiasmetricsbioschemas.jsonld b/data/picardgcbiasmetrics/picardgcbiasmetricsbioschemas.jsonld index d1c4ddbf88de1..1820f8251720d 100644 --- a/data/picardgcbiasmetrics/picardgcbiasmetricsbioschemas.jsonld +++ b/data/picardgcbiasmetrics/picardgcbiasmetricsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This Galaxy tool uses Picard to report detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.", "sc:name": "picardgcbiasmetrics", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://broadinstitute.github.io/picard/", "sc:version": "1.56.0" diff --git a/data/picardhsmetrics/picardhsmetricsbioschemas.jsonld b/data/picardhsmetrics/picardhsmetricsbioschemas.jsonld index 4985e8210e5ea..2ef8ab7f4ece6 100644 --- a/data/picardhsmetrics/picardhsmetricsbioschemas.jsonld +++ b/data/picardhsmetrics/picardhsmetricsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "For targeted resequencing data.", "sc:name": "picardhsmetrics", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://broadinstitute.github.io/picard/", diff --git a/data/pickgene/pickgenebioschemas.jsonld b/data/pickgene/pickgenebioschemas.jsonld index 93b3707550b8a..68e69483f2fb8 100644 --- a/data/pickgene/pickgenebioschemas.jsonld +++ b/data/pickgene/pickgenebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "pickgene", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pickgene.html", diff --git a/data/pickle/picklebioschemas.jsonld b/data/pickle/picklebioschemas.jsonld index e0013dea10241..13dec290504a2 100644 --- a/data/pickle/picklebioschemas.jsonld +++ b/data/pickle/picklebioschemas.jsonld @@ -9,34 +9,34 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1752-0509-7-96", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pickle", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Nicholas Moschonas", - "Maria Klapa" + "Maria Klapa", + "Nicholas Moschonas" ], "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ - "pubmed:24088582", - "pubmed:29023571", "pmcid:PMC5638325", { "@id": "https://doi.org/10.1186/1752-0509-7-96" - } + }, + "pubmed:24088582", + "pubmed:29023571" ], "sc:description": "A human protein-protein interaction meta-database employing primary dataset integration via genetic information ontology, which allows the integrated network to be reversibly normalized to any level of genetic reference without loss of source information and enables primary PPI dataset cross-checking.", "sc:name": "PICKLE", "sc:operatingSystem": "Windows", "sc:url": "http://www.pickle.gr", "sc:version": "2.5" - }, - { - "@id": "https://doi.org/10.1186/1752-0509-7-96", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/picmi/picmibioschemas.jsonld b/data/picmi/picmibioschemas.jsonld index 8e4deeafa31b7..e1809977504a9 100644 --- a/data/picmi/picmibioschemas.jsonld +++ b/data/picmi/picmibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool to map nucleotide and amino acid variations on genomes and on all gene isoforms.", "sc:name": "PICMI", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "ELIXIR-ITA-SAPIENZA", diff --git a/data/picr/picrbioschemas.jsonld b/data/picr/picrbioschemas.jsonld index 30b8b74555302..7303bf51f6912 100644 --- a/data/picr/picrbioschemas.jsonld +++ b/data/picr/picrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Protein Identifier Cross Reference service to map proteins by identifiers and sequence.", "sc:name": "PICR", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/picr/", diff --git a/data/pics/picsbioschemas.jsonld b/data/pics/picsbioschemas.jsonld index 08eff5e4b8f24..86260cb435ea4 100644 --- a/data/pics/picsbioschemas.jsonld +++ b/data/pics/picsbioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-4728-2343", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/pics", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Renan Sauteraud", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:20528864", "sc:contributor": { @@ -29,12 +25,16 @@ "sc:license": "Artistic-2.0", "sc:name": "PICS", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PICS.html", "sc:version": "2.18.0" + }, + { + "@id": "http://orcid.org/0000-0003-4728-2343", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pictar/pictarbioschemas.jsonld b/data/pictar/pictarbioschemas.jsonld index 6dd054698d4c0..83ed33262e1ad 100644 --- a/data/pictar/pictarbioschemas.jsonld +++ b/data/pictar/pictarbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "PAlgorithm for the identification of microRNA targets.", "sc:name": "PicTar", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://pictar.mdc-berlin.de/" } \ No newline at end of file diff --git a/data/picturedrocks/picturedrocksbioschemas.jsonld b/data/picturedrocks/picturedrocksbioschemas.jsonld index d980a501a67e8..b2b702943185b 100644 --- a/data/picturedrocks/picturedrocksbioschemas.jsonld +++ b/data/picturedrocks/picturedrocksbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "PicturedRocks", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://github.com/umangv/picturedrocks" } \ No newline at end of file diff --git a/data/pidna/pidnabioschemas.jsonld b/data/pidna/pidnabioschemas.jsonld index 8fd39b5430136..0eb2a32f0f0f5 100644 --- a/data/pidna/pidnabioschemas.jsonld +++ b/data/pidna/pidnabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PiDNA", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://dna.bime.ntu.edu.tw/pidna" } \ No newline at end of file diff --git a/data/pie/piebioschemas.jsonld b/data/pie/piebioschemas.jsonld index b39b543439db2..2fc7f77b54464 100644 --- a/data/pie/piebioschemas.jsonld +++ b/data/pie/piebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "PIE the search", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.ncbi.nlm.nih.gov/CBBresearch/Wilbur/IRET/PIE/" } \ No newline at end of file diff --git a/data/pifs/pifsbioschemas.jsonld b/data/pifs/pifsbioschemas.jsonld index 0ea99e9264c28..dbc39852eeb1e 100644 --- a/data/pifs/pifsbioschemas.jsonld +++ b/data/pifs/pifsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Excel encoded application (compatible with OpenOffice Calc) that includes various graphical and numerical outputs which allow NGS practitioners to assessing and comparing the precision in allele frequency estimation for both pool and diploid individual SNP data under various sampling, coverage and experimental error designs.", "sc:name": "PIFs", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www1.montpellier.inra.fr/CBGP/software/PoolSeqUtils/" } \ No newline at end of file diff --git a/data/pigengene/pigengenebioschemas.jsonld b/data/pigengene/pigengenebioschemas.jsonld index 8110562a55341..b639c690d63b0 100644 --- a/data/pigengene/pigengenebioschemas.jsonld +++ b/data/pigengene/pigengenebioschemas.jsonld @@ -20,11 +20,11 @@ "Library" ], "sc:citation": [ - "pmcid:PMC5353782", { "@id": "https://doi.org/10.1186/s12920-017-0253-6" }, - "pubmed:28298217" + "pubmed:28298217", + "pmcid:PMC5353782" ], "sc:description": "This package infers biological signatures from gene expression profiles using data from one platform, and evaluate them on a different one. It also identifies clusters of highly coexpressed genes using coexpression network analysis, summarizing the biological information of each module in an eigengene, learning a Bayesian network that models the probabilistic dependencies between modules, and building a decision tree based on the expression of eigengenes.", "sc:featureList": { @@ -33,20 +33,20 @@ "sc:license": "GPL-2.0", "sc:name": "Pigengene", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Pigengene.html", "sc:version": "1.0.0" }, - { - "@id": "https://doi.org/10.1186/s12920-017-0253-6", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0001-5902-6238", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/s12920-017-0253-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pileline/pilelinebioschemas.jsonld b/data/pileline/pilelinebioschemas.jsonld index eca4061e9e127..af92162febac8 100644 --- a/data/pileline/pilelinebioschemas.jsonld +++ b/data/pileline/pilelinebioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-12-31", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-4146-0551", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/pileline", "@type": "sc:SoftwareApplication", @@ -16,33 +24,25 @@ "@id": "http://orcid.org/0000-0002-4146-0551" }, "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": [ - "pubmed:21261974", + "pmcid:PMC3037855", { "@id": "https://doi.org/10.1186/1471-2105-12-31" }, - "pmcid:PMC3037855" + "pubmed:21261974" ], "sc:description": "Fexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments. PileLineGUI adds a graphical interface.", "sc:license": "LGPL-2.1", "sc:name": "PileLine", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://sing.ei.uvigo.es/pileline/index.php/Main_Page" - }, - { - "@id": "http://orcid.org/0000-0002-4146-0551", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-12-31", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pileup2cov/pileup2covbioschemas.jsonld b/data/pileup2cov/pileup2covbioschemas.jsonld index 9bef4abf21758..ba19dc4a60486 100644 --- a/data/pileup2cov/pileup2covbioschemas.jsonld +++ b/data/pileup2cov/pileup2covbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Convert a .mpileup file into a SynTView .coverage file.", "sc:name": "pileup2cov", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://bioweb.pasteur.fr/packages/pack@SynTViewTools@0.0.1", "sc:version": "0.0.1" diff --git a/data/pileup_to_vcf/pileup_to_vcfbioschemas.jsonld b/data/pileup_to_vcf/pileup_to_vcfbioschemas.jsonld index 2260e19969807..4a5f2c971debd 100644 --- a/data/pileup_to_vcf/pileup_to_vcfbioschemas.jsonld +++ b/data/pileup_to_vcf/pileup_to_vcfbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Convert a pileup to VCF with filtering.", "sc:name": "pileup_to_vcf", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf", diff --git a/data/pilon/pilonbioschemas.jsonld b/data/pilon/pilonbioschemas.jsonld index d61e03e4a49a4..01d543cb12bb8 100644 --- a/data/pilon/pilonbioschemas.jsonld +++ b/data/pilon/pilonbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.", "sc:name": "pilon", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.broadinstitute.org/software/pilon/", "sc:version": "v1.16" diff --git a/data/pimp/pimpbioschemas.jsonld b/data/pimp/pimpbioschemas.jsonld index b21048eb41aa4..a7bfb06e54485 100644 --- a/data/pimp/pimpbioschemas.jsonld +++ b/data/pimp/pimpbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "PiMP", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://polyomics.mvls.gla.ac.uk/" } \ No newline at end of file diff --git a/data/pims_lims/pims_limsbioschemas.jsonld b/data/pims_lims/pims_limsbioschemas.jsonld index a6e7779934a3d..aff03bc2cfab0 100644 --- a/data/pims_lims/pims_limsbioschemas.jsonld +++ b/data/pims_lims/pims_limsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chris Morris", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:author": "Chris Morris (STFC)", "sc:description": "Laboratory Information Management System (LIMS) to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes.", "sc:name": "PiMS LIMS", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "STFC", "sc:url": "https://www.limswiki.org/index.php/PiMS", diff --git a/data/pina/pinabioschemas.jsonld b/data/pina/pinabioschemas.jsonld index 63931affd5c60..f805cd19ae380 100644 --- a/data/pina/pinabioschemas.jsonld +++ b/data/pina/pinabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. Moreover, it provides a variety of built-in tools to filter and analyze the network for gaining insight into the network.", "sc:name": "PINA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://omics.bjcancer.org/pina/" diff --git a/data/pinalog/pinalogbioschemas.jsonld b/data/pinalog/pinalogbioschemas.jsonld index 8aeb6122befa6..53a3c867f3272 100644 --- a/data/pinalog/pinalogbioschemas.jsonld +++ b/data/pinalog/pinalogbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Protein-protein interaction(PPI) network alignment method aiming to map similar parts of PPI networks in terms of protein similarity (by both sequence and function) and the local network similarity. It incorporates not only sequence similarity and topological similarity of proteins in the equivalencing process but also uses the function similarity of protein pairs.", "sc:name": "PINALOG", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.sbg.bio.ic.ac.uk/~pinalog/index.html" } \ No newline at end of file diff --git a/data/pindel/pindelbioschemas.jsonld b/data/pindel/pindelbioschemas.jsonld index 5391bf9e0de16..401ff0c145e3c 100644 --- a/data/pindel/pindelbioschemas.jsonld +++ b/data/pindel/pindelbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btp394", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/pindel", "@type": "sc:SoftwareApplication", @@ -37,11 +33,11 @@ }, "sc:author": "Kai Ye", "sc:citation": [ - "pubmed:19561018", - "pmcid:PMC2781750", { "@id": "https://doi.org/10.1093/bioinformatics/btp394" - } + }, + "pubmed:19561018", + "pmcid:PMC2781750" ], "sc:description": "A pattern growth approach to detect break points of large deletions and medium sized insertions from paired end short reads.", "sc:featureList": { @@ -51,9 +47,9 @@ "sc:license": "Unlicense", "sc:name": "Pindel", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:softwareHelp": [ { @@ -64,6 +60,10 @@ } ], "sc:url": "http://gmt.genome.wustl.edu/packages/pindel/" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btp394", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ping/pingbioschemas.jsonld b/data/ping/pingbioschemas.jsonld index b0ca905088588..10de1e8c26e6c 100644 --- a/data/ping/pingbioschemas.jsonld +++ b/data/ping/pingbioschemas.jsonld @@ -14,15 +14,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Renan Sauteraud", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC3290535", + "pubmed:22393380", { "@id": "https://doi.org/10.1371/journal.pone.0032095" - }, - "pubmed:22393380" + } ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-4728-2343" @@ -34,9 +34,9 @@ "sc:license": "Artistic-2.0", "sc:name": "PING", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PING.html", "sc:version": "2.18.0" diff --git a/data/pingo/pingobioschemas.jsonld b/data/pingo/pingobioschemas.jsonld index 2472a49b59ebb..f3c7207e8fd13 100644 --- a/data/pingo/pingobioschemas.jsonld +++ b/data/pingo/pingobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories.", "sc:name": "PiNGO", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "PSB", "sc:url": "http://www.psb.ugent.be/esb/PiNGO/Home.html", diff --git a/data/pingpongpro/pingpongprobioschemas.jsonld b/data/pingpongpro/pingpongprobioschemas.jsonld index d3958da3c1733..caa73b3f68718 100644 --- a/data/pingpongpro/pingpongprobioschemas.jsonld +++ b/data/pingpongpro/pingpongprobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "PingPongPro", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/suhrig/pingpongpro" } \ No newline at end of file diff --git a/data/pinmol/pinmolbioschemas.jsonld b/data/pinmol/pinmolbioschemas.jsonld index 621a408d750aa..47159f316c827 100644 --- a/data/pinmol/pinmolbioschemas.jsonld +++ b/data/pinmol/pinmolbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "PinMol", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://bratulab.wordpress.com/software/", "sc:version": "beta 1.0" diff --git a/data/pinpor/pinporbioschemas.jsonld b/data/pinpor/pinporbioschemas.jsonld index 94f6488ae2678..e4e9d1bc8a726 100644 --- a/data/pinpor/pinporbioschemas.jsonld +++ b/data/pinpor/pinporbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Machine-learning predictor to ascertain which newly observed INDELs are likely to be pathogenic.", "sc:name": "PinPor", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://watson.compbio.iupui.edu/pinpor/" diff --git a/data/pinsplus/pinsplusbioschemas.jsonld b/data/pinsplus/pinsplusbioschemas.jsonld index a18d6a5b5ce99..928709859dc93 100644 --- a/data/pinsplus/pinsplusbioschemas.jsonld +++ b/data/pinsplus/pinsplusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "LGPL-3.0", "sc:name": "PINSPlus", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://bioinformatics.cse.unr.edu/software/PINSPlus/", "sc:version": "2.0.0" diff --git a/data/pint/bioconda_pint.yaml b/data/pint/bioconda_pint.yaml index cd47f156c832a..97a21c98e5134 100644 --- a/data/pint/bioconda_pint.yaml +++ b/data/pint/bioconda_pint.yaml @@ -4,7 +4,6 @@ description: Pairwise data integration for functional genomics, including tools home: https://bioconductor.org/packages/3.10/bioc/html/pint.html identifiers: - biotools:pint -- doi:10.1038/nmeth.3252 license: BSD_2_clause + file LICENSE license_file: LICENSE name: bioconductor-pint diff --git a/data/pint/pintbioschemas.jsonld b/data/pint/pintbioschemas.jsonld index 56fbca14d3f83..f7418f5875877 100644 --- a/data/pint/pintbioschemas.jsonld +++ b/data/pint/pintbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "BSD-4-Clause", "sc:name": "pint", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pint.html", diff --git a/data/pint_pathways/pint_pathwaysbioschemas.jsonld b/data/pint_pathways/pint_pathwaysbioschemas.jsonld index 82391c9dabe0e..a32fb4a5e28ec 100644 --- a/data/pint_pathways/pint_pathwaysbioschemas.jsonld +++ b/data/pint_pathways/pint_pathwaysbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Pathway INtegration Tool (PINT) allows integration and annotation of systems biology markup language (SBML) files from a variety of sources. Gene list files are also accepted.", "sc:name": "PINT", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://csb2.ym.edu.tw/pint/" } \ No newline at end of file diff --git a/data/pinta/pintabioschemas.jsonld b/data/pinta/pintabioschemas.jsonld index 69eb0e28c06c4..66bd3b16e21ee 100644 --- a/data/pinta/pintabioschemas.jsonld +++ b/data/pinta/pintabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web tool for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. It is available for 5 species (human, mouse, rat, worm and yeast).", "sc:name": "PINTA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.esat.kuleuven.be/pinta/" } \ No newline at end of file diff --git a/data/pintron/pintronbioschemas.jsonld b/data/pintron/pintronbioschemas.jsonld index 936860ecfcd1b..8ffe58fe5590a 100644 --- a/data/pintron/pintronbioschemas.jsonld +++ b/data/pintron/pintronbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Raffaella Rizzi", - "Paola Bonizzoni", - "Yuri Pirola" + "Yuri Pirola", + "Paola Bonizzoni" ], "sc:additionalType": "Command-line tool", "sc:description": "A pipeline for gene-structure prediction based on spliced alignment of transcript sequences (ESTs and mRNAs) against a genomic sequence.", "sc:license": "AGPL-3.0", "sc:name": "PIntron", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-BICOCCA", "sc:url": "http://pintron.algolab.eu/", diff --git a/data/pints/pintsbioschemas.jsonld b/data/pints/pintsbioschemas.jsonld index 9c54ee9afa608..f5d235f130752 100644 --- a/data/pints/pintsbioschemas.jsonld +++ b/data/pints/pintsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/pints", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rob Russell", - "Yvonne Lara" + "Yvonne Lara", + "Rob Russell" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:12595245", diff --git a/data/pipasic/pipasicbioschemas.jsonld b/data/pipasic/pipasicbioschemas.jsonld index 7a4ee0f02005f..a14c168b70567 100644 --- a/data/pipasic/pipasicbioschemas.jsonld +++ b/data/pipasic/pipasicbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework.", "sc:name": "Pipasic", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sourceforge.net/projects/pipasic/" } \ No newline at end of file diff --git a/data/pipealign/pipealignbioschemas.jsonld b/data/pipealign/pipealignbioschemas.jsonld index e98e456607c98..750a8a7b38b4a 100644 --- a/data/pipealign/pipealignbioschemas.jsonld +++ b/data/pipealign/pipealignbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "PipeAlign2", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.lbgi.fr/pipealign" } \ No newline at end of file diff --git a/data/pipeline_pilot/pipeline_pilotbioschemas.jsonld b/data/pipeline_pilot/pipeline_pilotbioschemas.jsonld index dc42b8be48e2e..68d0c2a68aba8 100644 --- a/data/pipeline_pilot/pipeline_pilotbioschemas.jsonld +++ b/data/pipeline_pilot/pipeline_pilotbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Analysis and workflow development of Next Generation Sequencing and gene expression.", "sc:name": "Pipeline Pilot", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://accelrys.com/products/pipeline-pilot/component-collections.html" } \ No newline at end of file diff --git a/data/pipelinedog/pipelinedogbioschemas.jsonld b/data/pipelinedog/pipelinedogbioschemas.jsonld index 1be1fbffc55b2..561d1f7387cb7 100644 --- a/data/pipelinedog/pipelinedogbioschemas.jsonld +++ b/data/pipelinedog/pipelinedogbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/pipelinedog", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jinchuan Xing", - "Yazhou Sun" + "Yazhou Sun", + "Jinchuan Xing" ], "sc:additionalType": "Command-line tool", "sc:description": "Simple and flexible graphic pipeline construction and maintenance tool.", "sc:name": "PipelineDog", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.npmjs.com/package/pipelinedog" } \ No newline at end of file diff --git a/data/piphillin/piphillinbioschemas.jsonld b/data/piphillin/piphillinbioschemas.jsonld index a5f17030a2d4e..03dcbd8333c5f 100644 --- a/data/piphillin/piphillinbioschemas.jsonld +++ b/data/piphillin/piphillinbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0166104", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/piphillin", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:27820856", + "pmcid:PMC5098786", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0166104" - }, - "pmcid:PMC5098786" + } ], "sc:description": "Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "Piphillin", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://secondgenome.com/solutions/resources/data-analysis-tools/piphillin/" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0166104", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pipred/pipredbioschemas.jsonld b/data/pipred/pipredbioschemas.jsonld index 7eb44985fd5fb..9cdf2649a0ade 100644 --- a/data/pipred/pipredbioschemas.jsonld +++ b/data/pipred/pipredbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/S41598-019-43189-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/PiPred", "@type": "sc:SoftwareApplication", @@ -44,6 +40,10 @@ "Mac" ], "sc:url": "https://github.com/labstructbioinf/PiPred" + }, + { + "@id": "https://doi.org/10.1038/S41598-019-43189-4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pipsa/pipsabioschemas.jsonld b/data/pipsa/pipsabioschemas.jsonld index 0a5e27e6dd6c9..e1e25a779bcd1 100644 --- a/data/pipsa/pipsabioschemas.jsonld +++ b/data/pipsa/pipsabioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Compute and analyze the pairwise similarity of 3D interaction property fields for a set of proteins.", "sc:name": "PIPSA", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://pipsa.h-its.org/pipsa/" diff --git a/data/piqmie/piqmiebioschemas.jsonld b/data/piqmie/piqmiebioschemas.jsonld index 2530ad2c7043d..55d9ab78d6e48 100644 --- a/data/piqmie/piqmiebioschemas.jsonld +++ b/data/piqmie/piqmiebioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "http://orcid.org/0000-0003-1711-7961", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1093/nar/gku478", - "@type": "sc:CreativeWork" - }, { "@id": "https://doi.org/10.1371/journal.pone.0170762", "@type": "sc:CreativeWork" @@ -25,23 +21,23 @@ "@id": "https://bio.tools/piqmie", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Roland Kanaar", { "@id": "http://orcid.org/0000-0003-1711-7961" - } + }, + "Roland Kanaar" ], "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4086067", - "pmcid:PMC5325209", + { + "@id": "https://doi.org/10.1371/journal.pone.0170762" + }, "pubmed:28234898", - "pubmed:24861615", + "pmcid:PMC5325209", { "@id": "https://doi.org/10.1093/nar/gku478" }, - { - "@id": "https://doi.org/10.1371/journal.pone.0170762" - } + "pubmed:24861615", + "pmcid:PMC4086067" ], "sc:description": "Proteomics Identifications & Quantitations Data Management & Integration Service (PIQMIe) is a web server for semi-quantitative proteomics data management and analysis.", "sc:license": "GPL-3.0", @@ -49,6 +45,10 @@ "sc:operatingSystem": "Linux", "sc:url": "http://piqmie.biotools.nl/", "sc:version": "1.0" + }, + { + "@id": "https://doi.org/10.1093/nar/gku478", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pir/pirbioschemas.jsonld b/data/pir/pirbioschemas.jsonld index 63dc0be7bdb22..af48ca212bf07 100644 --- a/data/pir/pirbioschemas.jsonld +++ b/data/pir/pirbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Integrated protein informatics resource for genomic, proteomic and systems biology research.", "sc:name": "PIR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://pir.georgetown.edu/" } \ No newline at end of file diff --git a/data/pirsf/pirsfbioschemas.jsonld b/data/pirsf/pirsfbioschemas.jsonld index 1ba41722c3ef0..83245fef282de 100644 --- a/data/pirsf/pirsfbioschemas.jsonld +++ b/data/pirsf/pirsfbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The classification system is based on whole proteins rather than on the component domains therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains.", "sc:name": "PIRSF whole-protein classification database", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml" diff --git a/data/pita/pitabioschemas.jsonld b/data/pita/pitabioschemas.jsonld index b745f95a35654..3b7019e369300 100644 --- a/data/pita/pitabioschemas.jsonld +++ b/data/pita/pitabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PITA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/thornton-srv/databases/pita/", diff --git a/data/pitufo/pitufobioschemas.jsonld b/data/pitufo/pitufobioschemas.jsonld index 1f6006134b23a..b51b34f6b7e8d 100644 --- a/data/pitufo/pitufobioschemas.jsonld +++ b/data/pitufo/pitufobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Java software to find minimal sets of precursors of target compounds in a metabolic network.", "sc:name": "PITUFO", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sites.google.com/site/pitufosoftware" } \ No newline at end of file diff --git a/data/pixie/pixiebioschemas.jsonld b/data/pixie/pixiebioschemas.jsonld index 85f57e9c713f9..628f79d96d3ee 100644 --- a/data/pixie/pixiebioschemas.jsonld +++ b/data/pixie/pixiebioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/pixie", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Thomas Metz", - "Erin Baker" + "Erin Baker", + "Thomas Metz" ], "sc:additionalType": "Command-line tool", "sc:description": "Algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association.", "sc:name": "PIXiE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/PNNL-Comp-Mass-Spec/PIXiE" } \ No newline at end of file diff --git a/data/pizsa/pizsabioschemas.jsonld b/data/pizsa/pizsabioschemas.jsonld index 1d66645d138a3..d56c7e1cfb590 100644 --- a/data/pizsa/pizsabioschemas.jsonld +++ b/data/pizsa/pizsabioschemas.jsonld @@ -22,10 +22,10 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC6602501", { "@id": "https://doi.org/10.1093/NAR/GKZ368" }, + "pmcid:PMC6602501", "pubmed:31114890" ], "sc:description": "Protein Interaction Z-Score Assessment.", @@ -34,18 +34,18 @@ "@id": "edam:operation_2492" }, { - "@id": "edam:operation_0272" + "@id": "edam:operation_0321" }, { - "@id": "edam:operation_0321" + "@id": "edam:operation_0272" } ], "sc:license": "Unlicense", "sc:name": "PIZSA", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://cospi.iiserpune.ac.in/pizsa" } diff --git a/data/pkgdeptools/bioconda_pkgdeptools.yaml b/data/pkgdeptools/bioconda_pkgdeptools.yaml index fed17016c183f..9d2f900e65fd5 100644 --- a/data/pkgdeptools/bioconda_pkgdeptools.yaml +++ b/data/pkgdeptools/bioconda_pkgdeptools.yaml @@ -8,7 +8,6 @@ description: This package provides tools for computing and analyzing dependency home: https://bioconductor.org/packages/3.10/bioc/html/pkgDepTools.html identifiers: - biotools:pkgdeptools -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-pkgdeptools diff --git a/data/pklfilemerger/pklfilemergerbioschemas.jsonld b/data/pklfilemerger/pklfilemergerbioschemas.jsonld index 5dc30c03a912d..2462fcb67aefb 100644 --- a/data/pklfilemerger/pklfilemergerbioschemas.jsonld +++ b/data/pklfilemerger/pklfilemergerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Merges individual Q-TOF .pkl files into a single file for database searching.", "sc:name": "PklFileMerger", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.uib.no/en/rg/probe/66698/pklfilemerger" diff --git a/data/pknotsrg/pknotsrgbioschemas.jsonld b/data/pknotsrg/pknotsrgbioschemas.jsonld index 3d49f1f272a68..60e711f0790b7 100644 --- a/data/pknotsrg/pknotsrgbioschemas.jsonld +++ b/data/pknotsrg/pknotsrgbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server for single sequence RNA secondary structure prediction including pseudoknots, source code, binary executable, and web service available.", "sc:name": "pknotsRG", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/" } \ No newline at end of file diff --git a/data/pla/plabioschemas.jsonld b/data/pla/plabioschemas.jsonld index a9fe0db19c708..01d18c3d8db09 100644 --- a/data/pla/plabioschemas.jsonld +++ b/data/pla/plabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Piecewise-constant and Low-rank Approximation for Multi-sample aCGH Data Analysis.", "sc:name": "PLA", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinformatics.ust.hk/Software.html" } \ No newline at end of file diff --git a/data/plaac/plaacbioschemas.jsonld b/data/plaac/plaacbioschemas.jsonld index 6f0d1822afb16..b7b714f05a744 100644 --- a/data/plaac/plaacbioschemas.jsonld +++ b/data/plaac/plaacbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Search protein sequences to identify candidate prion subsequences using a hidden-Markov model (HMM) algorithm.", "sc:name": "PLAAC", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://plaac.wi.mit.edu/" diff --git a/data/plabipd/plabipdbioschemas.jsonld b/data/plabipd/plabipdbioschemas.jsonld index 6e77c958e124a..f1895c609eacd 100644 --- a/data/plabipd/plabipdbioschemas.jsonld +++ b/data/plabipd/plabipdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "PlabiPD currently hosts data functional annotation of plant genomes using the MapMan Annotation, it also offers a webservice \"Mercator\" to automatically annotate and classify plant FASTA sequence in bulk submission. Also to visualize Plant expression data on metabolic maps.", "sc:name": "PlabiPD", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "fzj", "sc:url": "https://plabipd.de" diff --git a/data/placnetw/placnetwbioschemas.jsonld b/data/placnetw/placnetwbioschemas.jsonld index 039b47bc11787..981b92e77205b 100644 --- a/data/placnetw/placnetwbioschemas.jsonld +++ b/data/placnetw/placnetwbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Fernando de la Cruz", "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:description": "Web-based tool for plasmid reconstruction from bacterial genomes.", "sc:license": "MIT", "sc:name": "PLACNETw", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://castillo.dicom.unican.es/upload/" } \ No newline at end of file diff --git a/data/plan2l/plan2lbioschemas.jsonld b/data/plan2l/plan2lbioschemas.jsonld index ca5e6cb3501c5..a0a6c21afceef 100644 --- a/data/plan2l/plan2lbioschemas.jsonld +++ b/data/plan2l/plan2lbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A web based tool that integrates text mining and information extraction techniques to access useful information for analyzing genetic, cellular and molecular aspects of Arabidposis thaliana.", "sc:name": "PLAN2L", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://zope.bioinfo.cnio.es/plan2l" } \ No newline at end of file diff --git a/data/plandbaffy/plandbaffybioschemas.jsonld b/data/plandbaffy/plandbaffybioschemas.jsonld index 75d2756171440..2f21e1f2c6cd9 100644 --- a/data/plandbaffy/plandbaffybioschemas.jsonld +++ b/data/plandbaffy/plandbaffybioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PLANdbAffy", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://affymetrix2.bioinf.fbb.msu.ru" } \ No newline at end of file diff --git a/data/planet/planetbioschemas.jsonld b/data/planet/planetbioschemas.jsonld index 4ca0638d3c58f..1b53a16566b4a 100644 --- a/data/planet/planetbioschemas.jsonld +++ b/data/planet/planetbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "PlaNET", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/wvictor14/planet" } \ No newline at end of file diff --git a/data/plannet/plannetbioschemas.jsonld b/data/plannet/plannetbioschemas.jsonld index aafc69a1a4aa5..3cce8a469c60b 100644 --- a/data/plannet/plannetbioschemas.jsonld +++ b/data/plannet/plannetbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Homology-based predicted interactome for multiple planarian transcriptomes.", "sc:name": "PlanNET", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://compgen.bio.ub.edu/PlanNET" } \ No newline at end of file diff --git a/data/plantaligdb/plantaligdbbioschemas.jsonld b/data/plantaligdb/plantaligdbbioschemas.jsonld index 3cb2e19431baa..33ed34f3ab3c0 100644 --- a/data/plantaligdb/plantaligdbbioschemas.jsonld +++ b/data/plantaligdb/plantaligdbbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "PlantAligDB", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://plantaligdb.portugene.com" } \ No newline at end of file diff --git a/data/plantcv_v2/plantcv_v2bioschemas.jsonld b/data/plantcv_v2/plantcv_v2bioschemas.jsonld index 2ac69b74e7e91..66d517ff7a3c5 100644 --- a/data/plantcv_v2/plantcv_v2bioschemas.jsonld +++ b/data/plantcv_v2/plantcv_v2bioschemas.jsonld @@ -9,12 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.7717/peerj.4088", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/plantcv_v2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Noah Fahlgren", - "Malia A. Gehan" + "Malia A. Gehan", + "Noah Fahlgren" ], "sc:additionalType": "Library", "sc:citation": [ @@ -35,10 +39,6 @@ "Windows" ], "sc:url": "https://github.com/danforthcenter/plantcv-v2-paper" - }, - { - "@id": "https://doi.org/10.7717/peerj.4088", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/plantgsea/plantgseabioschemas.jsonld b/data/plantgsea/plantgseabioschemas.jsonld index 39b31d790d004..441edfb2c34f3 100644 --- a/data/plantgsea/plantgseabioschemas.jsonld +++ b/data/plantgsea/plantgseabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "PlantGSEA is a tool for gene set enrichment analysis in plants.", "sc:name": "PlantGSEA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://structuralbiology.cau.edu.cn/PlantGSEA" diff --git a/data/plantmetabolomics/plantmetabolomicsbioschemas.jsonld b/data/plantmetabolomics/plantmetabolomicsbioschemas.jsonld index aab5c65a09e78..e9056ce6fb59c 100644 --- a/data/plantmetabolomics/plantmetabolomicsbioschemas.jsonld +++ b/data/plantmetabolomics/plantmetabolomicsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An NSF-funded multi-institutional project developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes.", "sc:name": "PlantMetabolomics", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://plantmetabolomics.vrac.iastate.edu/ver2/" } \ No newline at end of file diff --git a/data/plantnatsdb/plantnatsdbbioschemas.jsonld b/data/plantnatsdb/plantnatsdbbioschemas.jsonld index 6e4ea9135453e..e4e73823f223e 100644 --- a/data/plantnatsdb/plantnatsdbbioschemas.jsonld +++ b/data/plantnatsdb/plantnatsdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. Plant Natural Antisense Transcripts DataBase is a platform for annotating and discovering NATs by integrating various data sources.", "sc:name": "PlantNATsDB", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bis.zju.edu.cn/pnatdb/" diff --git a/data/plantpan/plantpanbioschemas.jsonld b/data/plantpan/plantpanbioschemas.jsonld index 1db91ca6b2fbb..ec4220323be3d 100644 --- a/data/plantpan/plantpanbioschemas.jsonld +++ b/data/plantpan/plantpanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Database-assisted system for recognizing combinatorial cis-regulatory elements with distance constraint in plant co-expressed genes.", "sc:name": "PlantPAN", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://plantpan2.itps.ncku.edu.tw/" } \ No newline at end of file diff --git a/data/plantphos/plantphosbioschemas.jsonld b/data/plantphos/plantphosbioschemas.jsonld index e929a3c4f67cb..fba1a957fa41f 100644 --- a/data/plantphos/plantphosbioschemas.jsonld +++ b/data/plantphos/plantphosbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PlantPhos", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://csb.cse.yzu.edu.tw/PlantPhos/" } \ No newline at end of file diff --git a/data/plantpis/plantpisbioschemas.jsonld b/data/plantpis/plantpisbioschemas.jsonld index b78bd31ada700..4893f00c4dfc9 100644 --- a/data/plantpis/plantpisbioschemas.jsonld +++ b/data/plantpis/plantpisbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "It is a web querying system for a database collecting plant protease inhibitors data. Protease inhibitors in plants are naturally occurring proteins that inhibit the function of endogenous and exogenous proteases. PlantPIs contains information extracted principally from MEROPS database, filtered, annotated and compared with data stored in other protein and gene public databases, using both automated techniques and domain expert evaluations.", "sc:name": "PlantPIs", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://plantpis.ba.itb.cnr.it/" } \ No newline at end of file diff --git a/data/plantrgs/plantrgsbioschemas.jsonld b/data/plantrgs/plantrgsbioschemas.jsonld index 09aef3b1378b6..353d7f2bb3a0e 100644 --- a/data/plantrgs/plantrgsbioschemas.jsonld +++ b/data/plantrgs/plantrgsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "PlantRGS is a web server for identification of most suitable candidate reference gene(s) for quantitative gene expression studies in plants. PlantRGS identifies the most suitable reference genes with minimum expression variance across the selected experimental conditions based on microarray data.", "sc:name": "PlantRGS", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.nipgr.res.in/PlantRGS/", diff --git a/data/plantsdb/plantsdbbioschemas.jsonld b/data/plantsdb/plantsdbbioschemas.jsonld index ef2fe024055b8..3b81de4e5c82e 100644 --- a/data/plantsdb/plantsdbbioschemas.jsonld +++ b/data/plantsdb/plantsdbbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/plantsdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Heidrun Gundlach", - "Klaus Mayer" + "Klaus Mayer", + "Heidrun Gundlach" ], "sc:additionalType": "Database portal", "sc:description": "Structured and interconnected genome and gene data for 12 major plant species ranging from model organisms like Arabidopsis to important crops, like wheat. Additionally it provides a platform for integrative and comparative plant genome research for which specialized online tools such as Crows Nest, a comparative map viewer or an RNAseqExpression Browser.", "sc:name": "PlantsDB", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "hmgu", diff --git a/data/planttfcat/planttfcatbioschemas.jsonld b/data/planttfcat/planttfcatbioschemas.jsonld index 1c8f5d8c2e76d..2419eee5d65f8 100644 --- a/data/planttfcat/planttfcatbioschemas.jsonld +++ b/data/planttfcat/planttfcatbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-14-321", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/planttfcat", "@type": "sc:SoftwareApplication", @@ -22,8 +18,8 @@ { "@id": "https://doi.org/10.1186/1471-2105-14-321" }, - "pubmed:24219505", - "pmcid:PMC4225725" + "pmcid:PMC4225725", + "pubmed:24219505" ], "sc:description": "An online plant transcription factor and transcriptional regulator categorization and analysis tool.", "sc:featureList": { @@ -32,10 +28,14 @@ "sc:name": "PlantTFcat", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://plantgrn.noble.org/PlantTFcat/" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-321", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/planttfdb/planttfdbbioschemas.jsonld b/data/planttfdb/planttfdbbioschemas.jsonld index 354147a8d2651..fe7e8f85822e7 100644 --- a/data/planttfdb/planttfdbbioschemas.jsonld +++ b/data/planttfdb/planttfdbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, search using a sequence identifier, or query using BLAST.", "sc:name": "PlantTFDB", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://plntfdb.bio.uni-potsdam.de/v1.0/" diff --git a/data/plasmidspades/plasmidspadesbioschemas.jsonld b/data/plasmidspades/plasmidspadesbioschemas.jsonld index b7214864db6e7..a6260c95a9af9 100644 --- a/data/plasmidspades/plasmidspadesbioschemas.jsonld +++ b/data/plasmidspades/plasmidspadesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Genome assembler for plasmids.", "sc:name": "plasmidspades", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://cab.spbu.ru/software/spades/", "sc:version": "3.9.0" diff --git a/data/plasmodesma/plasmodesmabioschemas.jsonld b/data/plasmodesma/plasmodesmabioschemas.jsonld index b5e014cc194ae..5b596068077f0 100644 --- a/data/plasmodesma/plasmodesmabioschemas.jsonld +++ b/data/plasmodesma/plasmodesmabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "CECILL-1.0", "sc:name": "Plasmodesma", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://plasmodesma.igbmc.science" diff --git a/data/plasmodium_autocount/plasmodium_autocountbioschemas.jsonld b/data/plasmodium_autocount/plasmodium_autocountbioschemas.jsonld index a23c874d9fc82..9b222ebfa0610 100644 --- a/data/plasmodium_autocount/plasmodium_autocountbioschemas.jsonld +++ b/data/plasmodium_autocount/plasmodium_autocountbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Plasmodium Autocount", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.vicbioinformatics.com/software.autocount.shtml" } \ No newline at end of file diff --git a/data/plass/plassbioschemas.jsonld b/data/plass/plassbioschemas.jsonld index f5f0f65e1b01f..f1d6f752b2281 100644 --- a/data/plass/plassbioschemas.jsonld +++ b/data/plass/plassbioschemas.jsonld @@ -9,19 +9,15 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-8637-6719", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/Plass", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "http://orcid.org/0000-0001-9642-8244" + "@id": "http://orcid.org/0000-0001-8781-9753" }, { - "@id": "http://orcid.org/0000-0001-8781-9753" + "@id": "http://orcid.org/0000-0001-9642-8244" } ], "sc:additionalType": "Command-line tool", @@ -48,12 +44,16 @@ ] }, { - "@id": "http://orcid.org/0000-0001-9642-8244", + "@id": "http://orcid.org/0000-0001-8637-6719", "@type": "schema:Person" }, { "@id": "http://orcid.org/0000-0001-8781-9753", "@type": "schema:Person" + }, + { + "@id": "http://orcid.org/0000-0001-9642-8244", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/plast/plastbioschemas.jsonld b/data/plast/plastbioschemas.jsonld index a09cc5c86a953..8497b847cc9b8 100644 --- a/data/plast/plastbioschemas.jsonld +++ b/data/plast/plastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CECILL-2.0", "sc:name": "Plast", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "GenOuest", "sc:url": "http://www.irisa.fr/symbiose/projects/plast/", diff --git a/data/plastid/plastidbioschemas.jsonld b/data/plastid/plastidbioschemas.jsonld index c79d40c056f61..a84c4a5dcf753 100644 --- a/data/plastid/plastidbioschemas.jsonld +++ b/data/plastid/plastidbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:27875984", { "@id": "https://doi.org/10.1186/S12864-016-3278-X" }, - "pmcid:PMC5120557" + "pmcid:PMC5120557", + "pubmed:27875984" ], "sc:description": "Nucleotide-resolution analysis of next-generation sequencing and genomics data.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "Plastid", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://plastid.readthedocs.io/en/latest/" } diff --git a/data/plastid_genome_annotator/plastid_genome_annotatorbioschemas.jsonld b/data/plastid_genome_annotator/plastid_genome_annotatorbioschemas.jsonld index 963c27c4b41e4..8d855e0c9b94e 100644 --- a/data/plastid_genome_annotator/plastid_genome_annotatorbioschemas.jsonld +++ b/data/plastid_genome_annotator/plastid_genome_annotatorbioschemas.jsonld @@ -18,8 +18,8 @@ { "@id": "https://doi.org/10.1186/s13007-019-0435-7" }, - "pubmed:31139240", - "pmcid:PMC6528300" + "pmcid:PMC6528300", + "pubmed:31139240" ], "sc:description": "Software package for rapid, accurate, and flexible batch annotation of plastomes.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "Plastid Genome Annotator", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/quxiaojian/PGA" }, diff --git a/data/plata/platabioschemas.jsonld b/data/plata/platabioschemas.jsonld index a47b8f27b78c6..ba0c54d40b0f4 100644 --- a/data/plata/platabioschemas.jsonld +++ b/data/plata/platabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Python scripts for the analyses and visualization of probe level Affymetrix exon array data.", "sc:name": "PLATA", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://sandberg.cmb.ki.se/plata/" diff --git a/data/platecore/platecorebioschemas.jsonld b/data/platecore/platecorebioschemas.jsonld index b5940397436e2..5533695275da3 100644 --- a/data/platecore/platecorebioschemas.jsonld +++ b/data/platecore/platecorebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Errol Strain", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Provides basic S4 data structures and routines for analyzing plate based flow cytometry data.", "sc:license": "Artistic-2.0", "sc:name": "plateCore", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/plateCore.html", "sc:version": "1.32.0" diff --git a/data/plato_plugin_for_autocomplete_on_ontologies/plato_plugin_for_autocomplete_on_ontologiesbioschemas.jsonld b/data/plato_plugin_for_autocomplete_on_ontologies/plato_plugin_for_autocomplete_on_ontologiesbioschemas.jsonld index 1a065bcaeb142..93732a91af64a 100644 --- a/data/plato_plugin_for_autocomplete_on_ontologies/plato_plugin_for_autocomplete_on_ontologiesbioschemas.jsonld +++ b/data/plato_plugin_for_autocomplete_on_ontologies/plato_plugin_for_autocomplete_on_ontologiesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "General-use embeddable JavaScript widget used for browsing and searching ontologies. It is generically configurable for use with any ontology served by the Ontology Lookup Service (OLS). It’s features include the ability to visualise matching ontology terms in their rightful place in the tree, and to expand and collapse nodes as desired.", "sc:name": "PLATO Plugin for Autocomplete on Ontologies", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://wwwdev.ebi.ac.uk/fgpt/PLATOdemo/", diff --git a/data/plaza_dicots/plaza_dicotsbioschemas.jsonld b/data/plaza_dicots/plaza_dicotsbioschemas.jsonld index 7f90712db198b..d7e5a56005e24 100644 --- a/data/plaza_dicots/plaza_dicotsbioschemas.jsonld +++ b/data/plaza_dicots/plaza_dicotsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Access point for plant comparative genomics.", "sc:name": "PLAZA dicots", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "PSB", "sc:url": "http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/", diff --git a/data/plaza_monocots/plaza_monocotsbioschemas.jsonld b/data/plaza_monocots/plaza_monocotsbioschemas.jsonld index 32948a1132ccb..5e385a438c17e 100644 --- a/data/plaza_monocots/plaza_monocotsbioschemas.jsonld +++ b/data/plaza_monocots/plaza_monocotsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Access point for plant comparative genomics.", "sc:name": "PLAZA monocots", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "PSB", "sc:url": "http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_monocots/", diff --git a/data/plecdom/plecdombioschemas.jsonld b/data/plecdom/plecdombioschemas.jsonld index 7bf1de55c0f66..2575f8a81efd1 100644 --- a/data/plecdom/plecdombioschemas.jsonld +++ b/data/plecdom/plecdombioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.", "sc:name": "PLecDom", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.nipgr.res.in/plecdom.html" diff --git a/data/plek/plekbioschemas.jsonld b/data/plek/plekbioschemas.jsonld index b948dbc59a2db..28b3891d15c77 100644 --- a/data/plek/plekbioschemas.jsonld +++ b/data/plek/plekbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Junying Zhan", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4177586", "pubmed:25239089", { "@id": "https://doi.org/10.1186/1471-2105-15-311" - }, - "pmcid:PMC4177586" + } ], "sc:description": "Tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme.", "sc:featureList": [ diff --git a/data/plethy/plethybioschemas.jsonld b/data/plethy/plethybioschemas.jsonld index 2d839e777ebaf..740af5ad08aa9 100644 --- a/data/plethy/plethybioschemas.jsonld +++ b/data/plethy/plethybioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "plethy", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/plethy.html", diff --git a/data/plexdb/plexdbbioschemas.jsonld b/data/plexdb/plexdbbioschemas.jsonld index 93864619446bc..7edb6b53395e0 100644 --- a/data/plexdb/plexdbbioschemas.jsonld +++ b/data/plexdb/plexdbbioschemas.jsonld @@ -18,16 +18,16 @@ { "@id": "https://doi.org/10.1093/nar/gkr938" }, - "pubmed:22084198", - "pmcid:PMC3245067" + "pmcid:PMC3245067", + "pubmed:22084198" ], "sc:description": "Unified gene expression resource for plants and plant pathogens. It is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.", "sc:featureList": [ { - "@id": "edam:operation_0314" + "@id": "edam:operation_3232" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_0314" }, { "@id": "edam:operation_3196" @@ -36,15 +36,15 @@ "@id": "edam:operation_0313" }, { - "@id": "edam:operation_3232" + "@id": "edam:operation_2495" } ], "sc:license": "Other", "sc:name": "PLEXdb", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.plexdb.org/" }, diff --git a/data/plgem/plgembioschemas.jsonld b/data/plgem/plgembioschemas.jsonld index ca94d9f123258..4baaa09e9c7ae 100644 --- a/data/plgem/plgembioschemas.jsonld +++ b/data/plgem/plgembioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-4542-9970", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-5-203", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/plgem", "@type": "sc:SoftwareApplication", @@ -16,8 +24,8 @@ "@id": "http://orcid.org/0000-0003-4542-9970" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pubmed:15606915", @@ -34,19 +42,11 @@ "sc:name": "plgem", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/plgem.html", "sc:version": "1.46.0" - }, - { - "@id": "http://orcid.org/0000-0003-4542-9970", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-5-203", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/plier/bioconda_plier.yaml b/data/plier/bioconda_plier.yaml index 5f595082f68a7..0b5db5fb3cc41 100644 --- a/data/plier/bioconda_plier.yaml +++ b/data/plier/bioconda_plier.yaml @@ -5,7 +5,6 @@ description: The PLIER (Probe Logarithmic Error Intensity Estimate) method produ home: https://bioconductor.org/packages/3.10/bioc/html/plier.html identifiers: - biotools:plier -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-plier diff --git a/data/plier/plierbioschemas.jsonld b/data/plier/plierbioschemas.jsonld index c7c1137312f9a..475ba88fe3e80 100644 --- a/data/plier/plierbioschemas.jsonld +++ b/data/plier/plierbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Crispin Miller", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The Probe Logarithmic Error Intensity Estimate method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.", "sc:license": "GPL-2.0", "sc:name": "plier", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/plier.html", "sc:version": "1.44.0" diff --git a/data/plink-ss/plink-ssbioschemas.jsonld b/data/plink-ss/plink-ssbioschemas.jsonld index bc24f10983d2a..2086b58f7cc37 100644 --- a/data/plink-ss/plink-ssbioschemas.jsonld +++ b/data/plink-ss/plink-ssbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "High-throughput mass spectrometry method for precise identification of disulfide-linked peptides.", "sc:name": "pLink-SS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://pfind.ict.ac.cn/software/pLink/2014/pLink-SS.html" } \ No newline at end of file diff --git a/data/plink/plinkbioschemas.jsonld b/data/plink/plinkbioschemas.jsonld index ebe67a9620c58..f829567536d4d 100644 --- a/data/plink/plinkbioschemas.jsonld +++ b/data/plink/plinkbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-2.0", "sc:name": "PLINK", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://zzz.bwh.harvard.edu/plink/" } \ No newline at end of file diff --git a/data/plip/plipbioschemas.jsonld b/data/plip/plipbioschemas.jsonld index 74037287f75ed..57fba003c2c05 100644 --- a/data/plip/plipbioschemas.jsonld +++ b/data/plip/plipbioschemas.jsonld @@ -31,11 +31,11 @@ "@id": "edam:topic_0128" }, "sc:citation": [ - "pmcid:PMC4489249", + "pubmed:25873628", { "@id": "https://doi.org/10.1093/nar/gkv315" }, - "pubmed:25873628" + "pmcid:PMC4489249" ], "sc:description": "Protein-Ligand Interaction Profiler. Analysis of non-covalent interactions (hydrogen bonds, water bridges, salt bridges, halogen bonds, hydrophobic interactions, π-stacking, π-cation interactions, metal complexes) in atom-level detail in protein-ligand complexes from PDB files.", "sc:featureList": { diff --git a/data/plmla/plmlabioschemas.jsonld b/data/plmla/plmlabioschemas.jsonld index 542f30eb34d08..95913aaafb8f5 100644 --- a/data/plmla/plmlabioschemas.jsonld +++ b/data/plmla/plmlabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "PLMLA is an in silico online tool for prediction of potential lysine methylation and lysine acetylation from protein sequences.", "sc:name": "PLMLA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioinfo.ncu.edu.cn/inquiries_PLMLA.aspx" } \ No newline at end of file diff --git a/data/plnseq/plnseqbioschemas.jsonld b/data/plnseq/plnseqbioschemas.jsonld index c63e557789469..82b36ad666300 100644 --- a/data/plnseq/plnseqbioschemas.jsonld +++ b/data/plnseq/plnseqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Package which conducts differential expression (DE) analysis using high throughput RNA-seq read count data generated from correlated samples.", "sc:name": "PLNseq", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://homepage.fudan.edu.cn/zhangh/softwares/plnseq/" } \ No newline at end of file diff --git a/data/plntfdb/plntfdbbioschemas.jsonld b/data/plntfdb/plntfdbbioschemas.jsonld index d721a3ca044c9..692d42f25311e 100644 --- a/data/plntfdb/plntfdbbioschemas.jsonld +++ b/data/plntfdb/plntfdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Plant Transcription Factor Database is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and annotated. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online.", "sc:name": "PlnTFDB", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://plntfdb.bio.uni-potsdam.de/" } \ No newline at end of file diff --git a/data/ploc_bal-meuk/ploc_bal-meukbioschemas.jsonld b/data/ploc_bal-meuk/ploc_bal-meukbioschemas.jsonld index 60abf3e9560e4..6d775029e1c75 100644 --- a/data/ploc_bal-meuk/ploc_bal-meukbioschemas.jsonld +++ b/data/ploc_bal-meuk/ploc_bal-meukbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Unlicense", "sc:name": "pLoc_bal-mEuk", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.jci-bioinfo.cn/pLoc_bal-mEuk/" diff --git a/data/plot/plotbioschemas.jsonld b/data/plot/plotbioschemas.jsonld index c1e4ef82c8049..79aaf3a02418e 100644 --- a/data/plot/plotbioschemas.jsonld +++ b/data/plot/plotbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Plot some information from a list of transcripts.", "sc:name": "plot", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/plotcon/plotconbioschemas.jsonld b/data/plotcon/plotconbioschemas.jsonld index 3838bcb00ab76..c0abd177a466b 100644 --- a/data/plotcon/plotconbioschemas.jsonld +++ b/data/plotcon/plotconbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "UK MRC", - "Wellcome Trust", - "EMBOSS Contributors" + "UK BBSRC", + "EMBOSS Contributors", + "Wellcome Trust" ], "sc:description": "Plot conservation of a sequence alignment.", "sc:funder": [ @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "plotcon", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/plotgenomecoverage/plotgenomecoveragebioschemas.jsonld b/data/plotgenomecoverage/plotgenomecoveragebioschemas.jsonld index 9f8660ccdc579..8bee35231dabd 100644 --- a/data/plotgenomecoverage/plotgenomecoveragebioschemas.jsonld +++ b/data/plotgenomecoverage/plotgenomecoveragebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Get the coverage of a genome.", "sc:name": "plotgenomecoverage", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/plotibd/plotibdbioschemas.jsonld b/data/plotibd/plotibdbioschemas.jsonld index 9d09d07711eb2..4068c26f30687 100644 --- a/data/plotibd/plotibdbioschemas.jsonld +++ b/data/plotibd/plotibdbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1159/000334083", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/plotibd", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:22189471", - "pmcid:PMC3267995", { "@id": "https://doi.org/10.1159/000334083" - } + }, + "pubmed:22189471", + "pmcid:PMC3267995" ], "sc:description": "plotIBD is a perl script to assist with plotting sampled inheritance vectors in pedigrees", "sc:featureList": { @@ -32,6 +28,10 @@ "sc:operatingSystem": "Linux", "sc:url": "http://faculty.washington.edu/wijsman/software.shtml", "sc:version": "20111108" + }, + { + "@id": "https://doi.org/10.1159/000334083", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/plotorf/plotorfbioschemas.jsonld b/data/plotorf/plotorfbioschemas.jsonld index 845cabb6162e8..fb84f1657e2dc 100644 --- a/data/plotorf/plotorfbioschemas.jsonld +++ b/data/plotorf/plotorfbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", + "UK MRC", "UK BBSRC", - "EMBOSS Contributors", - "UK MRC" + "EMBOSS Contributors" ], "sc:description": "Plot potential open reading frames in a nucleotide sequence.", "sc:funder": [ - "UK BBSRC", "UK MRC", + "UK BBSRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "plotorf", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/plpe/bioconda_plpe.yaml b/data/plpe/bioconda_plpe.yaml index b264bc78a90d2..e82cbb41b7645 100644 --- a/data/plpe/bioconda_plpe.yaml +++ b/data/plpe/bioconda_plpe.yaml @@ -3,7 +3,6 @@ description: This package performs tests for paired high-throughput data. home: https://bioconductor.org/packages/3.10/bioc/html/PLPE.html identifiers: - biotools:plpe -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-plpe diff --git a/data/plpe/plpebioschemas.jsonld b/data/plpe/plpebioschemas.jsonld index 77f5c5a58165a..c99fc6c3d302d 100644 --- a/data/plpe/plpebioschemas.jsonld +++ b/data/plpe/plpebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "PLPE", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PLPE.html", "sc:version": "1.34.0" diff --git a/data/plrs/plrsbioschemas.jsonld b/data/plrs/plrsbioschemas.jsonld index 47a06970412ed..4afcbb340e033 100644 --- a/data/plrs/plrsbioschemas.jsonld +++ b/data/plrs/plrsbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "plrs", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/plrs.html", "sc:version": "1.14.0" diff --git a/data/pluma/plumabioschemas.jsonld b/data/pluma/plumabioschemas.jsonld index 2e234106a6013..a454e218cc03c 100644 --- a/data/pluma/plumabioschemas.jsonld +++ b/data/pluma/plumabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis.", "sc:name": "PluMA", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://biorg.cis.fiu.edu/pluma/" } \ No newline at end of file diff --git a/data/pluri-iq/pluri-iqbioschemas.jsonld b/data/pluri-iq/pluri-iqbioschemas.jsonld index 118f12315f2b2..920a09c73375d 100644 --- a/data/pluri-iq/pluri-iqbioschemas.jsonld +++ b/data/pluri-iq/pluri-iqbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-1172-4018", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1016/j.stemcr.2017.06.006", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/pluri-iq", "@type": "sc:SoftwareApplication", @@ -39,6 +31,14 @@ "sc:name": "Pluri-IQ", "sc:operatingSystem": "Windows", "sc:url": "http://www.cnbc.pt/equipment/microscopyUnit.asp#divImageAnalysis" + }, + { + "@id": "https://doi.org/10.1016/j.stemcr.2017.06.006", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-1172-4018", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pluripred/pluripredbioschemas.jsonld b/data/pluripred/pluripredbioschemas.jsonld index 4e521ae0d32be..b203e4882728a 100644 --- a/data/pluripred/pluripredbioschemas.jsonld +++ b/data/pluripred/pluripredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Predicting proteins responsible for pluripotency for mouse as well as human but here we construct this server using data of the mouse.", "sc:name": "PluriPred", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bicresources.jcbose.ac.in/ssaha4/pluripred/" } \ No newline at end of file diff --git a/data/plw/plwbioschemas.jsonld b/data/plw/plwbioschemas.jsonld index 3462dfc086c64..d7d61e6c3dd80 100644 --- a/data/plw/plwbioschemas.jsonld +++ b/data/plw/plwbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-9-156", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/plw", "@type": "sc:SoftwareApplication", @@ -35,12 +31,16 @@ "sc:license": "GPL-2.0", "sc:name": "plw", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/plw.html", "sc:version": "1.34.0" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-9-156", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/plyranges/plyrangesbioschemas.jsonld b/data/plyranges/plyrangesbioschemas.jsonld index 39fe3cd4e5d83..55a06fa9a706b 100644 --- a/data/plyranges/plyrangesbioschemas.jsonld +++ b/data/plyranges/plyrangesbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "plyranges", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/plyranges.html", "sc:version": "1.0.3" diff --git a/data/pma/pmabioschemas.jsonld b/data/pma/pmabioschemas.jsonld index b7d9a46774f1d..a289663667c2e 100644 --- a/data/pma/pmabioschemas.jsonld +++ b/data/pma/pmabioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Jessica Da Gama Duarte", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5828362", + "pubmed:29482592", { "@id": "https://doi.org/10.1186/s13104-018-3266-0" }, - "pubmed:29482592" + "pmcid:PMC5828362" ], "sc:description": "Protein Microarray Analyser, a user-friendly tool for data processing and normalization.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:name": "PMA", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/protein-microarray-analyser/" }, diff --git a/data/pmdb/pmdbbioschemas.jsonld b/data/pmdb/pmdbbioschemas.jsonld index 12d045bfc58c3..ed2b63c7fb311 100644 --- a/data/pmdb/pmdbbioschemas.jsonld +++ b/data/pmdb/pmdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool collects three dimensional protein models obtained by structure prediction methods.", "sc:name": "PMDB", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "ELIXIR-ITA-SAPIENZA", "sc:url": "https://bioinformatics.cineca.it/PMDB/" diff --git a/data/pmirkb/pmirkbbioschemas.jsonld b/data/pmirkb/pmirkbbioschemas.jsonld index 04258ce911b8e..9f487511fa617 100644 --- a/data/pmirkb/pmirkbbioschemas.jsonld +++ b/data/pmirkb/pmirkbbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/pmirkb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lingfeng Gou", "Yijun Meng", + "Dijun Chen", "Ming Chen", - "Dijun Chen" + "Lingfeng Gou" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:20719744", "sc:description": "It includes the miRNAs of two model plants, Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Four major functional modules, \"SNPs\", \"Pri-miRNAs\", \"MiR—Tar\", and \"Self-reg\", are provided.", "sc:name": "PmiRKB", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bis.zju.edu.cn/pmirkb/" } \ No newline at end of file diff --git a/data/pmle/pmlebioschemas.jsonld b/data/pmle/pmlebioschemas.jsonld index 86e1e519d057d..fe3342b656759 100644 --- a/data/pmle/pmlebioschemas.jsonld +++ b/data/pmle/pmlebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Estimate the gene flow parameter q for a collection of two or more semi-isolated populations by (pseudo) maximum likelihood using either single or multi locus, haploid or diploid, genotype data. Suitable molecular data types minimally include allozymes, microsatellites, and RFLPs.", "sc:name": "PMLE", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.rannala.org/docs/pmle20.html" } \ No newline at end of file diff --git a/data/pmm/pmmbioschemas.jsonld b/data/pmm/pmmbioschemas.jsonld index d7b7150e0f586..510ef074a813a 100644 --- a/data/pmm/pmmbioschemas.jsonld +++ b/data/pmm/pmmbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "pmm", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pmm.html", diff --git a/data/pmrd/pmrdbioschemas.jsonld b/data/pmrd/pmrdbioschemas.jsonld index be16a5784683a..648f04589e5f8 100644 --- a/data/pmrd/pmrdbioschemas.jsonld +++ b/data/pmrd/pmrdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The database integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. Includes model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc.", "sc:name": "Plant MicroRNA Database (PMRD)", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioinformatics.cau.edu.cn/PMRD" } \ No newline at end of file diff --git a/data/pmsearch/pmsearchbioschemas.jsonld b/data/pmsearch/pmsearchbioschemas.jsonld index b75f01aa3a8f1..6e1b71785bb8f 100644 --- a/data/pmsearch/pmsearchbioschemas.jsonld +++ b/data/pmsearch/pmsearchbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool that utilizes Position Weight Matrices to search for putative Transcription Factor Binding Sites. PMSearch takes Position Frequency Matrices (PFMs) and DNA sequences to initiate a prediction task. The user may upload motifs/matrices (Position Frequency Matrices, PFM or Position Weight Matrices, PWM) or retrieve PFMs from our local dataset as input.", "sc:name": "PMSearch", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://mcube.nju.edu.cn/jwang/lab/soft/PMS/home.html" diff --git a/data/pmut/pmutbioschemas.jsonld b/data/pmut/pmutbioschemas.jsonld index 72416d94c1ae8..bad6be213540c 100644 --- a/data/pmut/pmutbioschemas.jsonld +++ b/data/pmut/pmutbioschemas.jsonld @@ -20,9 +20,9 @@ "@id": "http://orcid.org/0000-0002-2035-7555" }, "sc:additionalType": [ + "Web application", "Command-line tool", - "Web API", - "Web application" + "Web API" ], "sc:description": "Web portal for the annotation of pathological protein variants.", "sc:license": "GPL-3.0", diff --git a/data/pn-bottm/pn-bottmbioschemas.jsonld b/data/pn-bottm/pn-bottmbioschemas.jsonld index ea14cacbc452e..b0cd91f45a386 100644 --- a/data/pn-bottm/pn-bottmbioschemas.jsonld +++ b/data/pn-bottm/pn-bottmbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Other", "sc:name": "PN-BOTTM", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bit.ly/AboutPNBOT" } \ No newline at end of file diff --git a/data/pnns/pnnsbioschemas.jsonld b/data/pnns/pnnsbioschemas.jsonld index 8d4e5ca4dd67f..97ddb30a38150 100644 --- a/data/pnns/pnnsbioschemas.jsonld +++ b/data/pnns/pnnsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "PNNS", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://gaussian.bu.edu/pnns.html" } \ No newline at end of file diff --git a/data/pobo/pobobioschemas.jsonld b/data/pobo/pobobioschemas.jsonld index a86f0588d7b6c..6150a900635bd 100644 --- a/data/pobo/pobobioschemas.jsonld +++ b/data/pobo/pobobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.", "sc:name": "POBO", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://ekhidna.biocenter.helsinki.fi/poxo/pobo/" } \ No newline at end of file diff --git a/data/pocketzebra/pocketzebrabioschemas.jsonld b/data/pocketzebra/pocketzebrabioschemas.jsonld index 2d09f75027462..8cfbfe70d3e1c 100644 --- a/data/pocketzebra/pocketzebrabioschemas.jsonld +++ b/data/pocketzebra/pocketzebrabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "pocketZebra", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://biokinet.belozersky.msu.ru/pocketzebra" } \ No newline at end of file diff --git a/data/poco/pocobioschemas.jsonld b/data/poco/pocobioschemas.jsonld index f45b2b1a0dfcc..92d1ddd8fac73 100644 --- a/data/poco/pocobioschemas.jsonld +++ b/data/poco/pocobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "POCO searches a set of promoters from co-expressed genes for nucleotide patterns that are over-represented.", "sc:name": "POCO", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://ekhidna.biocenter.helsinki.fi/poxo/poco/" diff --git a/data/podkat/bioconda_podkat.yaml b/data/podkat/bioconda_podkat.yaml index 9d987a6b32464..084e2b8ccd364 100644 --- a/data/podkat/bioconda_podkat.yaml +++ b/data/podkat/bioconda_podkat.yaml @@ -9,7 +9,6 @@ description: This package provides an association test that is capable of dealin home: https://bioconductor.org/packages/3.10/bioc/html/podkat.html identifiers: - biotools:podkat -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-podkat diff --git a/data/podkat/podkatbioschemas.jsonld b/data/podkat/podkatbioschemas.jsonld index d4afcf7dad7cb..4fbe4229b6a94 100644 --- a/data/podkat/podkatbioschemas.jsonld +++ b/data/podkat/podkatbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ulrich Bodenhofer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides an association test that is capable of dealing with very rare and even private variants. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest.", "sc:license": "GPL-2.0", "sc:name": "podkat", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/podkat.html", "sc:version": "1.6.0" diff --git a/data/poeas/poeasbioschemas.jsonld b/data/poeas/poeasbioschemas.jsonld index dc99986ba6c90..ccd65765381c9 100644 --- a/data/poeas/poeasbioschemas.jsonld +++ b/data/poeas/poeasbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Plant ontology enrichment analysis server. The server uses a simple list of genes as an input and perform enrichment analysis and provide results in two levels: a table with enrichment results and a visulaization utilitity to generate ontological graphs that can be used in publications.", "sc:name": "POEAS", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://caps.ncbs.res.in/poeas/" } \ No newline at end of file diff --git a/data/poets/poetsbioschemas.jsonld b/data/poets/poetsbioschemas.jsonld index 573b1f0b44567..cd1b726c0f6cf 100644 --- a/data/poets/poetsbioschemas.jsonld +++ b/data/poets/poetsbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "David M. Bassen", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5264316", - "pubmed:28122561", { "@id": "https://doi.org/10.1186/s12918-016-0380-2" - } + }, + "pmcid:PMC5264316", + "pubmed:28122561" ], "sc:description": "Constrained multiobjective optimization approach to estimate biochemical model ensembles in the Julia programming language.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "POETs", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/varnerlab/POETs.jl" }, diff --git a/data/pogos/pogosbioschemas.jsonld b/data/pogos/pogosbioschemas.jsonld index fdf7def2e41f9..1cc27a8ccf927 100644 --- a/data/pogos/pogosbioschemas.jsonld +++ b/data/pogos/pogosbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "pogos", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pogos.html", "sc:version": "1.0.0" diff --git a/data/pointcloudxplore/pointcloudxplorebioschemas.jsonld b/data/pointcloudxplore/pointcloudxplorebioschemas.jsonld index 621d0f64ffd91..083e298ffb991 100644 --- a/data/pointcloudxplore/pointcloudxplorebioschemas.jsonld +++ b/data/pointcloudxplore/pointcloudxplorebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Visualization tool for the PointCloud and Virtual Embryo data sets. It was developed to help biologists understand the relationship between gene expression patterns in three dimensions.", "sc:name": "PointCloudXplore", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=pcx" } \ No newline at end of file diff --git a/data/poissonseq/poissonseqbioschemas.jsonld b/data/poissonseq/poissonseqbioschemas.jsonld index 820dd2cb1489f..b71f93a66c4f0 100644 --- a/data/poissonseq/poissonseqbioschemas.jsonld +++ b/data/poissonseq/poissonseqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A method for normalization, testing, and false discovery rate estimation for RNA-sequencing data.", "sc:name": "PoissonSeq", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/PoissonSeq/index.html" } \ No newline at end of file diff --git a/data/pol3scan/pol3scanbioschemas.jsonld b/data/pol3scan/pol3scanbioschemas.jsonld index f28f81e36c96a..6dbedc6d184e7 100644 --- a/data/pol3scan/pol3scanbioschemas.jsonld +++ b/data/pol3scan/pol3scanbioschemas.jsonld @@ -13,14 +13,14 @@ "biotools:primaryContact": "Prof. Riccardo Percudani", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC523650", - "pubmed:8165140" + "pubmed:8165140", + "pmcid:PMC523650" ], "sc:description": "Identification of Polymerase III-transcribed elements in genomic sequences.", "sc:name": "Pol3scan", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-PARMA", "sc:url": "https://github.com/Percud/Pol3scan.git", diff --git a/data/polbase/polbasebioschemas.jsonld b/data/polbase/polbasebioschemas.jsonld index 00fc22a5ac6db..317eef170fa7b 100644 --- a/data/polbase/polbasebioschemas.jsonld +++ b/data/polbase/polbasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Polbase is a repository of biochemical, genetic, and structural information about DNA Polymerases.", "sc:name": "Polbase", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://polbase.neb.com/" } \ No newline at end of file diff --git a/data/polnet/polnetbioschemas.jsonld b/data/polnet/polnetbioschemas.jsonld index a2f452d57d633..b3a0324bc9c75 100644 --- a/data/polnet/polnetbioschemas.jsonld +++ b/data/polnet/polnetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "LGPL-3.0", "sc:name": "PolNet", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/mobernabeu/polnet" diff --git a/data/poly/polybioschemas.jsonld b/data/poly/polybioschemas.jsonld index 2b071968d3fd5..a7ab72ed906d7 100644 --- a/data/poly/polybioschemas.jsonld +++ b/data/poly/polybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Program for polygenic analysis and power analysis of human quantitative traits. It is convenient to use this to analyze multiple models / traits in large pedigrees.", "sc:name": "POLY", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://csg.sph.umich.edu/chen/public/software/poly/" } \ No newline at end of file diff --git a/data/polyadq/polyadqbioschemas.jsonld b/data/polyadq/polyadqbioschemas.jsonld index 3f72e009b55c2..d30cab93a4527 100644 --- a/data/polyadq/polyadqbioschemas.jsonld +++ b/data/polyadq/polyadqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Program for detection of human polyadenylation signals. To avoid training on possibly flawed data, the development of the program began with a de novo characterization of human mRNA 3′ processing signals. This information was used in training two quadratic discriminant functions that the program uses to evaluate potential polyA signals.", "sc:name": "polyadq", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://cb.utdallas.edu/tools/polyadq/polyadq_form.html" diff --git a/data/polyamotif/polyamotifbioschemas.jsonld b/data/polyamotif/polyamotifbioschemas.jsonld index 9e677654f44cc..eef181bc1616c 100644 --- a/data/polyamotif/polyamotifbioschemas.jsonld +++ b/data/polyamotif/polyamotifbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Predict the 12 main variants of human poly(A) motifs, i.e., AATAAA, ATTAAA, AAAAAG, AAGAAA, TATAAA, AATACA, AGTAAA, ACTAAA, GATAAA, CATAAA, AATATA, and AATAGA.", "sc:name": "PolyAMotif", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://sfb.kaust.edu.sa/Pages/Software.aspx" diff --git a/data/polyapeak/polyapeakbioschemas.jsonld b/data/polyapeak/polyapeakbioschemas.jsonld index 9dac45a773a91..c3f2c40e8915c 100644 --- a/data/polyapeak/polyapeakbioschemas.jsonld +++ b/data/polyapeak/polyapeakbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R package for ranking ChIP-seq peaks with shape information. polyaPeak uses a Bayesian hierarchical model to incorporate the peak shapes in the ranking. The shapes are described by a mixture of multivariate Polya distributions. Real data analyses show that polyaPeak outperforms several popular peak calling software including MACS, CisGenome and PICS.", "sc:name": "PolyaPeak", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://web1.sph.emory.edu/users/hwu30/software/polyaPeak.html" } \ No newline at end of file diff --git a/data/polyclustr/polyclustrbioschemas.jsonld b/data/polyclustr/polyclustrbioschemas.jsonld index 8f36056ae6e2d..cbdae1d96cdef 100644 --- a/data/polyclustr/polyclustrbioschemas.jsonld +++ b/data/polyclustr/polyclustrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "polyClustR", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/syspremed/polyClustR", "sc:version": "0.1.0" diff --git a/data/polydot/polydotbioschemas.jsonld b/data/polydot/polydotbioschemas.jsonld index 216e80a8f53f3..78c896ec0cf1a 100644 --- a/data/polydot/polydotbioschemas.jsonld +++ b/data/polydot/polydotbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK MRC", "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "EMBOSS Contributors" ], "sc:description": "Draw dotplots for all-against-all comparison of a sequence set.", "sc:funder": [ @@ -27,8 +27,8 @@ "sc:name": "polydot", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/polyester/polyesterbioschemas.jsonld b/data/polyester/polyesterbioschemas.jsonld index 57664e830f8cf..f878cab5f2b8f 100644 --- a/data/polyester/polyesterbioschemas.jsonld +++ b/data/polyester/polyesterbioschemas.jsonld @@ -22,9 +22,9 @@ "sc:license": "Artistic-2.0", "sc:name": "polyester", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/polyester.html", "sc:version": "1.10.0" diff --git a/data/polyfit/polyfitbioschemas.jsonld b/data/polyfit/polyfitbioschemas.jsonld index 87527939385e9..e7a3da1ef1ae1 100644 --- a/data/polyfit/polyfitbioschemas.jsonld +++ b/data/polyfit/polyfitbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Conrad Burden", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Add-on to the packages DESeq which ensures the p-value distribution is uniform over the interval [0, 1] for data satisfying the null hypothesis of no differential expression, and uses an adpated Storey-Tibshiran method to calculate q-values.", "sc:license": "GPL-3.0", "sc:name": "Polyfit", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Polyfit.html", "sc:version": "1.8.0" diff --git a/data/polygenicpathways/polygenicpathwaysbioschemas.jsonld b/data/polygenicpathways/polygenicpathwaysbioschemas.jsonld index 788d4b62ad86f..f00f2ad213973 100644 --- a/data/polygenicpathways/polygenicpathwaysbioschemas.jsonld +++ b/data/polygenicpathways/polygenicpathwaysbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The datasets list genes, environmental risk factors and autoantibodies in a number of polygenic diseases and provide KEGG pathway analysis etched out by susceptibility genes. Host/pathogen interactions are also characterised for herpes simplex, helicobacter pylori and the HIV-1/AIDS virus.", "sc:name": "PolygenicPathways", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.polygenicpathways.co.uk" } \ No newline at end of file diff --git a/data/polyhap/polyhapbioschemas.jsonld b/data/polyhap/polyhapbioschemas.jsonld index b56c03f5d0777..520d743f40fa1 100644 --- a/data/polyhap/polyhapbioschemas.jsonld +++ b/data/polyhap/polyhapbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "polyHap is a program for phasing polyploids and copy number regions. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM) and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences.", "sc:name": "polyHap", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.imperial.ac.uk/people/l.coin", "sc:version": "2" diff --git a/data/polymarker/polymarkerbioschemas.jsonld b/data/polymarker/polymarkerbioschemas.jsonld index db4b5713d460d..c2b73c30dde29 100644 --- a/data/polymarker/polymarkerbioschemas.jsonld +++ b/data/polymarker/polymarkerbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/polymarker", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web service" + "Web service", + "Command-line tool" ], "sc:description": "An automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid wheat. PolyMarker generates a multiple alignment between the target SNP sequence and the IWGSC chromosome survey sequences (IWGSC, 2014 ) for each of the three wheat genomes. It then generates a mask with informative positions which are highlighted with respect to the target genome.", "sc:license": "Not licensed", "sc:name": "PolyMarker", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://polymarker.tgac.ac.uk/" } \ No newline at end of file diff --git a/data/polymirts/polymirtsbioschemas.jsonld b/data/polymirts/polymirtsbioschemas.jsonld index f3580084a7de3..425ac6c0dd902 100644 --- a/data/polymirts/polymirtsbioschemas.jsonld +++ b/data/polymirts/polymirtsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Polymorphism in microRNA Target Site (PolymiRTS) is a database of naturally occurring DNA variations in predicted and experimentally identified microRNA (miRNA) target sites. PolymiRTS aims to identify SNPs that might affect miRNA targeting in humans and mice.", "sc:name": "PolymiRTS", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://compbio.uthsc.edu/miRSNP/" } \ No newline at end of file diff --git a/data/polypharmacology_browser/polypharmacology_browserbioschemas.jsonld b/data/polypharmacology_browser/polypharmacology_browserbioschemas.jsonld index fc9373d0f3c79..8bea3fa0e26ab 100644 --- a/data/polypharmacology_browser/polypharmacology_browserbioschemas.jsonld +++ b/data/polypharmacology_browser/polypharmacology_browserbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13321-017-0199-x", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/PolyPharmacology_Browser", "@type": "sc:SoftwareApplication", @@ -18,35 +22,31 @@ ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28270862", "pmcid:PMC5319934", { "@id": "https://doi.org/10.1186/s13321-017-0199-x" - } + }, + "pubmed:28270862" ], "sc:description": "PolyPharmacology Browser (PPB) - Web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data", "sc:featureList": [ - { - "@id": "edam:operation_2929" - }, { "@id": "edam:operation_3501" }, { "@id": "edam:operation_2489" + }, + { + "@id": "edam:operation_2929" } ], "sc:name": "PPB", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://gdbtools.unibe.ch:8080/PPB/" - }, - { - "@id": "https://doi.org/10.1186/s13321-017-0199-x", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/polyphen-2/polyphen-2bioschemas.jsonld b/data/polyphen-2/polyphen-2bioschemas.jsonld index f73e0a75e23e5..a9ee7ed66f6b3 100644 --- a/data/polyphen-2/polyphen-2bioschemas.jsonld +++ b/data/polyphen-2/polyphen-2bioschemas.jsonld @@ -9,51 +9,51 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1002/0471142905.hg0720s76", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/polyphen-2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ivan Adzhubey", "sc:additionalType": "Web application", "sc:citation": [ - { - "@id": "https://doi.org/10.1038/nmeth0410-248" - }, { "@id": "https://doi.org/10.1002/0471142905.hg0720s76" }, "pmcid:PMC2855889", - "pubmed:20354512", "pubmed:23315928", - "pmcid:PMC4480630" + "pmcid:PMC4480630", + "pubmed:20354512", + { + "@id": "https://doi.org/10.1038/nmeth0410-248" + } ], "sc:description": "Polymorphism Phenotyping (PolyPhen) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein.", "sc:featureList": [ { "@id": "edam:operation_3092" }, - { - "@id": "edam:operation_2422" - }, { "@id": "edam:operation_1777" }, { "@id": "edam:operation_0477" + }, + { + "@id": "edam:operation_2422" } ], "sc:license": "Not licensed", "sc:name": "PolyPhen-2", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://genetics.bwh.harvard.edu/pph2/" }, - { - "@id": "https://doi.org/10.1002/0471142905.hg0720s76", - "@type": "sc:CreativeWork" - }, { "@id": "https://doi.org/10.1038/nmeth0410-248", "@type": "sc:CreativeWork" diff --git a/data/polyphred/polyphredbioschemas.jsonld b/data/polyphred/polyphredbioschemas.jsonld index 2ef486509281a..d6802a0049b1e 100644 --- a/data/polyphred/polyphredbioschemas.jsonld +++ b/data/polyphred/polyphredbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/polyphred", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Phil Green", - "Brent Ewing" + "Brent Ewing", + "Phil Green" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:9207020", "sc:description": "UNIX-based tool for sequence trace based genotyping; integrated with Phred/Phrap/Consed (see DNA -- Contig Assembly); free for non-commercial use.", "sc:name": "PolyPhred", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://droog.gs.washington.edu/polyphred/" } \ No newline at end of file diff --git a/data/polyq/polyqbioschemas.jsonld b/data/polyq/polyqbioschemas.jsonld index b77cf91218149..3aa1dd1494cb6 100644 --- a/data/polyq/polyqbioschemas.jsonld +++ b/data/polyq/polyqbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Collection of sequences of all human proteins containing runs of seven or more glutamine residues and their annotated sequences with domain information. It can be interrogated such that the sequence context of polyglutamine repeats in disease and non-disease associated proteins can be investigated.", "sc:name": "PolyQ", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://pxgrid.med.monash.edu.au/polyq" } \ No newline at end of file diff --git a/data/polysearch/polysearchbioschemas.jsonld b/data/polysearch/polysearchbioschemas.jsonld index 05b67d0c60dad..dccda1503c9ca 100644 --- a/data/polysearch/polysearchbioschemas.jsonld +++ b/data/polysearch/polysearchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PolySearch allows users to conduct comprehensive and associative queries, such as given X, find all Y's, where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also identifies, highlights and ranks abstracts, paragraphs or sentences.", "sc:name": "PolySearch", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://wishart.biology.ualberta.ca/polysearch" } \ No newline at end of file diff --git a/data/polysearch2/polysearch2bioschemas.jsonld b/data/polysearch2/polysearch2bioschemas.jsonld index 1edfc0f3882a8..7f0c41216cb10 100644 --- a/data/polysearch2/polysearch2bioschemas.jsonld +++ b/data/polysearch2/polysearch2bioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4489268", "pubmed:25925572", { "@id": "https://doi.org/10.1093/NAR/GKV383" - } + }, + "pmcid:PMC4489268" ], "sc:description": "Significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "PolySearch2", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://polysearch.cs.ualberta.ca/" } diff --git a/data/polyunphased/polyunphasedbioschemas.jsonld b/data/polyunphased/polyunphasedbioschemas.jsonld index 46f03cb94d6a5..c29c968357426 100644 --- a/data/polyunphased/polyunphasedbioschemas.jsonld +++ b/data/polyunphased/polyunphasedbioschemas.jsonld @@ -28,8 +28,8 @@ "sc:license": "GPL-3.0", "sc:name": "Polyunphased", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/abureau/polyUnphased" }, diff --git a/data/polyview-2d/polyview-2dbioschemas.jsonld b/data/polyview-2d/polyview-2dbioschemas.jsonld index cb7f3ef17bcc5..0c4880be39110 100644 --- a/data/polyview-2d/polyview-2dbioschemas.jsonld +++ b/data/polyview-2d/polyview-2dbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Protein structure visualization server can be used to generate amino acid sequence annotations, such as secondary structure, relative solvent accessibility, evolutionary conservation, and physico-chemical property profiles. It can also be used to identify residues involved in protein-protein interactions and highlight other important sites and motifs.", "sc:name": "POLYVIEW-2D", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://polyview.cchmc.org/" diff --git a/data/polyview-mm/polyview-mmbioschemas.jsonld b/data/polyview-mm/polyview-mmbioschemas.jsonld index 71dcb5cd56a76..6be89a01d1d42 100644 --- a/data/polyview-mm/polyview-mmbioschemas.jsonld +++ b/data/polyview-mm/polyview-mmbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "POLYVIEW-MM", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://polyview.cchmc.org/conform.html" } \ No newline at end of file diff --git a/data/pombase/pombasebioschemas.jsonld b/data/pombase/pombasebioschemas.jsonld index 7dccd6a3233d0..e26e548e93223 100644 --- a/data/pombase/pombasebioschemas.jsonld +++ b/data/pombase/pombasebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Comprehensive online database for fission yeast. Contains annotation of genomic sequence and features, comprehensive manual literature curation, genome-wide data sets, and supports sophisticated user-defined queries.", "sc:name": "PomBase", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.pombase.org/" } \ No newline at end of file diff --git a/data/pombase_assembly_converter/pombase_assembly_converterbioschemas.jsonld b/data/pombase_assembly_converter/pombase_assembly_converterbioschemas.jsonld index 70adae09c835f..b2b6bfe20f684 100644 --- a/data/pombase_assembly_converter/pombase_assembly_converterbioschemas.jsonld +++ b/data/pombase_assembly_converter/pombase_assembly_converterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Map your data to the current assembly.", "sc:name": "PomBase assembly converter", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "EMBL-EBI", diff --git a/data/pombase_motif_search/pombase_motif_searchbioschemas.jsonld b/data/pombase_motif_search/pombase_motif_searchbioschemas.jsonld index 393c1b46308fb..1f5e9305f880b 100644 --- a/data/pombase_motif_search/pombase_motif_searchbioschemas.jsonld +++ b/data/pombase_motif_search/pombase_motif_searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Search PomBase protein set for a given motif.", "sc:name": "PomBase Motif search", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ "Sanger Institute", diff --git a/data/pombase_vep/pombase_vepbioschemas.jsonld b/data/pombase_vep/pombase_vepbioschemas.jsonld index 8b9ee4a002870..590b90b62a7de 100644 --- a/data/pombase_vep/pombase_vepbioschemas.jsonld +++ b/data/pombase_vep/pombase_vepbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Upload a set of SNPs in our standard format and export a file containing consequence types.", "sc:name": "PomBase VEP", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://genomebrowser.pombase.org/tools.html", diff --git a/data/pomelo_ii/pomelo_iibioschemas.jsonld b/data/pomelo_ii/pomelo_iibioschemas.jsonld index 751e323a6c354..ed42b0c116e47 100644 --- a/data/pomelo_ii/pomelo_iibioschemas.jsonld +++ b/data/pomelo_ii/pomelo_iibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Pomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of information such as PubMed references, Gene Ontology terms, GO terms, etc.", "sc:name": "Pomelo II", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://pomelo2.bioinfo.cnio.es" } \ No newline at end of file diff --git a/data/pomo/pomobioschemas.jsonld b/data/pomo/pomobioschemas.jsonld index c536a71768cb2..b3252133d4208 100644 --- a/data/pomo/pomobioschemas.jsonld +++ b/data/pomo/pomobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "POMO", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://pomo.cs.tut.fi/", "sc:version": "20140613" diff --git a/data/pon-diso/pon-disobioschemas.jsonld b/data/pon-diso/pon-disobioschemas.jsonld index e12fd452f17b9..df78ba3fff396 100644 --- a/data/pon-diso/pon-disobioschemas.jsonld +++ b/data/pon-diso/pon-disobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A method to predict changes in disorder regions contained in protein caused by amino acid substitutions.", "sc:name": "PON-Diso", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://structure.bmc.lu.se/PON-Diso/", diff --git a/data/pongo/pongobioschemas.jsonld b/data/pongo/pongobioschemas.jsonld index 4e6a8cd5e2e14..bbd2b7f7cbc85 100644 --- a/data/pongo/pongobioschemas.jsonld +++ b/data/pongo/pongobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP.", "sc:name": "PONGO", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://pongo.biocomp.unibo.it/" } \ No newline at end of file diff --git a/data/pool-hmm/pool-hmmbioschemas.jsonld b/data/pool-hmm/pool-hmmbioschemas.jsonld index d0f7bd167b668..e7c85042de36d 100644 --- a/data/pool-hmm/pool-hmmbioschemas.jsonld +++ b/data/pool-hmm/pool-hmmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Estimate allele frequencies and detect selective sweeps, using NGS data from a sample of pooled individuals from the same population.", "sc:name": "Pool-hmm", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://qgsp.jouy.inra.fr/index.php?option=com_content&view=article&id=56&Itemid=63" } \ No newline at end of file diff --git a/data/poolhap2/poolhap2bioschemas.jsonld b/data/poolhap2/poolhap2bioschemas.jsonld index 7afc2993cb382..6d98fe5a572a0 100644 --- a/data/poolhap2/poolhap2bioschemas.jsonld +++ b/data/poolhap2/poolhap2bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Computer program that infers haplotype (or epitype in case of DNA methylation sequencing) from a pool. In its current release, only pathogen sequencing application is implemented. In pathogen studies utilizing next generation sequencing, investigators ofte n collect samples naturally as pools of multiple strains, e.g., when the samples are taken from patients’ blood. To analyze these types of within-host polymorphisms, one would ideally like to determine the haplotypes in the sample.", "sc:name": "PoolHap2", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://code.google.com/p/poolhap2/" diff --git a/data/pooling/poolingbioschemas.jsonld b/data/pooling/poolingbioschemas.jsonld index cd2af4998e599..0378fd2faa862 100644 --- a/data/pooling/poolingbioschemas.jsonld +++ b/data/pooling/poolingbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.", "sc:name": "Pooling", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://alan.cs.gsu.edu/NGS/?q=content/pooling" diff --git a/data/popabc/popabcbioschemas.jsonld b/data/popabc/popabcbioschemas.jsonld index f5810767733eb..390e43194ce1d 100644 --- a/data/popabc/popabcbioschemas.jsonld +++ b/data/popabc/popabcbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Computer package to estimate historical demographic parameters of closely related species/populations (e.g. population size, migration rate, mutation rate, recombination rate, splitting events) within a Isolation with migration model. The software performs coalescent simulation in the framework of approximate Bayesian computation. It can also be used to perform Bayesian model choice to discriminate between different demographic scenarios.", "sc:name": "popABC", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://code.google.com/p/popabc/", "sc:version": "1.0" diff --git a/data/popdel/popdelbioschemas.jsonld b/data/popdel/popdelbioschemas.jsonld index 27352d9eb46a2..b249c30f2eb03 100644 --- a/data/popdel/popdelbioschemas.jsonld +++ b/data/popdel/popdelbioschemas.jsonld @@ -25,8 +25,8 @@ "sc:license": "GPL-3.0", "sc:name": "PopDel", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/kehrlab/PopDel", "sc:version": "1.1.1" diff --git a/data/popgev/popgevbioschemas.jsonld b/data/popgev/popgevbioschemas.jsonld index 21a48f84493b2..88bef77a31657 100644 --- a/data/popgev/popgevbioschemas.jsonld +++ b/data/popgev/popgevbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/popgev", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:26002882", "sc:description": "Web-based browser that can conveniently show the results of population analysis.", "sc:name": "PopGeV", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.soyomics.com/popgev/" diff --git a/data/pophelper/pophelperbioschemas.jsonld b/data/pophelper/pophelperbioschemas.jsonld index 40bd27c41d52c..086409c3f6a6b 100644 --- a/data/pophelper/pophelperbioschemas.jsonld +++ b/data/pophelper/pophelperbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "An R package and web app to analyse and visualize population structure.", "sc:name": "pophelper", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://pophelper.com/" } \ No newline at end of file diff --git a/data/popi/popibioschemas.jsonld b/data/popi/popibioschemas.jsonld index 4077b52c21063..5d5e5a123eaee 100644 --- a/data/popi/popibioschemas.jsonld +++ b/data/popi/popibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "POPI is a SVM-based prediction server using informative physicochemical properties for predicting immunogenicity of binding peptides of MHC class I and II.", "sc:name": "POPI", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://iclab.life.nctu.edu.tw/POPI/", "sc:version": "2.1" diff --git a/data/popisk/popiskbioschemas.jsonld b/data/popisk/popiskbioschemas.jsonld index 06034e9b88b58..79036430bdfe9 100644 --- a/data/popisk/popiskbioschemas.jsonld +++ b/data/popisk/popiskbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Support vector machine and weighted degree string kernel to predict immunogenicity of HLA-A2 binding peptides.", "sc:name": "POPISK", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://140.113.239.45/POPISK/" } \ No newline at end of file diff --git a/data/popitam/popitambioschemas.jsonld b/data/popitam/popitambioschemas.jsonld index f5fc51ccd973e..0611f2c92c36c 100644 --- a/data/popitam/popitambioschemas.jsonld +++ b/data/popitam/popitambioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Searches for unknown post-translational modifications.", "sc:name": "Popitam", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/chernan/popitam" } \ No newline at end of file diff --git a/data/poplddecay/poplddecaybioschemas.jsonld b/data/poplddecay/poplddecaybioschemas.jsonld index 9fbe6f2bfce16..4b92c3f032012 100644 --- a/data/poplddecay/poplddecaybioschemas.jsonld +++ b/data/poplddecay/poplddecaybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "PopLDdecay", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/BGI-shenzhen/PopLDdecay" } \ No newline at end of file diff --git a/data/popoolation/popoolationbioschemas.jsonld b/data/popoolation/popoolationbioschemas.jsonld index e3b6b0a4a7978..cb498bd8ccdfc 100644 --- a/data/popoolation/popoolationbioschemas.jsonld +++ b/data/popoolation/popoolationbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals.", "sc:name": "PoPoolation", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/popoolation/" } \ No newline at end of file diff --git a/data/pops-protease/pops-proteasebioschemas.jsonld b/data/pops-protease/pops-proteasebioschemas.jsonld index 07b633f4e1367..6f61ca574daff 100644 --- a/data/pops-protease/pops-proteasebioschemas.jsonld +++ b/data/pops-protease/pops-proteasebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computational tool for modeling and predicting protease specificity. It provides a novel method for building computational models of protease specificity, which while still being based on these amino acid sequences, can be built from any experimental data or expert knowledge available to the user.", "sc:name": "PoPS", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://pops.csse.monash.edu.au/" } \ No newline at end of file diff --git a/data/popscomp/popscompbioschemas.jsonld b/data/popscomp/popscompbioschemas.jsonld index cbd061f3b4018..e80e565512bbd 100644 --- a/data/popscomp/popscompbioschemas.jsonld +++ b/data/popscomp/popscompbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/popscomp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jens Kleinjung", - "Franca Fraternali" + "Franca Fraternali", + "Jens Kleinjung" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:15980485", diff --git a/data/populationprofiler/populationprofilerbioschemas.jsonld b/data/populationprofiler/populationprofilerbioschemas.jsonld index 9bd44da391ff6..f94c76b43b5cb 100644 --- a/data/populationprofiler/populationprofilerbioschemas.jsonld +++ b/data/populationprofiler/populationprofilerbioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pmcid:PMC4795740", - "pubmed:26987120", { "@id": "https://doi.org/10.1371/journal.pone.0151554" - } + }, + "pubmed:26987120" ], "sc:description": "PopulationProfiler is a software tool that reduces per-cell measurements to population statistics. The software imports measurements from a simple text file, visualizes population distributions in a compact and comprehensive way, and can create gates for subpopulation classes based on control samples.", "sc:featureList": { diff --git a/data/porcupine/porcupinebioschemas.jsonld b/data/porcupine/porcupinebioschemas.jsonld index 9321b215e9414..0217517ddea8f 100644 --- a/data/porcupine/porcupinebioschemas.jsonld +++ b/data/porcupine/porcupinebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool that constructs one’s analysis visually and automatically produces analysis code. The graphical representation improves understanding of the performed analysis, while retaining the flexibility of modifying the produced code manually to custom needs.", "sc:name": "Porcupine", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://timvanmourik.github.io/Porcupine/" } \ No newline at end of file diff --git a/data/porelogo/porelogobioschemas.jsonld b/data/porelogo/porelogobioschemas.jsonld index b512f7e9e5bea..35e6b50762719 100644 --- a/data/porelogo/porelogobioschemas.jsonld +++ b/data/porelogo/porelogobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An automated tool for the visualization of sequence and conservation of pore-lining residues in transmembrane protein structures.", "sc:name": "PoreLogo", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/thornton-srv/software/PoreLogo/", diff --git a/data/poretools/poretoolsbioschemas.jsonld b/data/poretools/poretoolsbioschemas.jsonld index 9468e0297c186..2743c3d782fa4 100644 --- a/data/poretools/poretoolsbioschemas.jsonld +++ b/data/poretools/poretoolsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.", "sc:name": "Poretools", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/arq5x/poretools" } \ No newline at end of file diff --git a/data/porewalker/porewalkerbioschemas.jsonld b/data/porewalker/porewalkerbioschemas.jsonld index 968ccbf4d6692..f6abaa7fc1d2a 100644 --- a/data/porewalker/porewalkerbioschemas.jsonld +++ b/data/porewalker/porewalkerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A fully automated method designed to detect and characterise transmembrane protein channels from their 3D structure.", "sc:name": "PoreWalker", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/thornton-srv/software/PoreWalker/", diff --git a/data/porgy/porgybioschemas.jsonld b/data/porgy/porgybioschemas.jsonld index 5f4b9594d63d0..1d9df1d70b803 100644 --- a/data/porgy/porgybioschemas.jsonld +++ b/data/porgy/porgybioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "LGPL-3.0", "sc:name": "PORGY", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://porgy.labri.fr/" } \ No newline at end of file diff --git a/data/porter/porterbioschemas.jsonld b/data/porter/porterbioschemas.jsonld index a87c1a246b7e8..8c0312c60f640 100644 --- a/data/porter/porterbioschemas.jsonld +++ b/data/porter/porterbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/s41598-019-48786-x", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Porter", "@type": "sc:SoftwareApplication", @@ -21,22 +17,26 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:31451723", + "pmcid:PMC6710256", { "@id": "https://doi.org/10.1038/s41598-019-48786-x" - }, - "pubmed:31451723", - "pmcid:PMC6710256" + } ], "sc:description": "Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes", "sc:license": "CC-BY-NC-SA-4.0", "sc:name": "Porter", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://distilldeep.ucd.ie/porter/", "sc:version": "5" + }, + { + "@id": "https://doi.org/10.1038/s41598-019-48786-x", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/porter5/porter5bioschemas.jsonld b/data/porter5/porter5bioschemas.jsonld index a6bc12486adb6..96bfb978783b6 100644 --- a/data/porter5/porter5bioschemas.jsonld +++ b/data/porter5/porter5bioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "Porter5", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://distilldeep.ucd.ie/porter/", "sc:version": "5" diff --git a/data/portrait/portraitbioschemas.jsonld b/data/portrait/portraitbioschemas.jsonld index 095ecea6c842e..ebcc2c4458923 100644 --- a/data/portrait/portraitbioschemas.jsonld +++ b/data/portrait/portraitbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/portrait", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:19653905", "sc:description": "Algorithm for identifying non-coding RNAs on a transcriptome context.", "sc:name": "PORTRAIT", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bioinformatics.org/portrait/" } \ No newline at end of file diff --git a/data/posa/posabioschemas.jsonld b/data/posa/posabioschemas.jsonld index d85b873ed0526..c9d88ed123af8 100644 --- a/data/posa/posabioschemas.jsonld +++ b/data/posa/posabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "POSA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://posa.godziklab.org/" } \ No newline at end of file diff --git a/data/possum-cis/possum-cisbioschemas.jsonld b/data/possum-cis/possum-cisbioschemas.jsonld index d242c3e03b118..ef1e5dc73600d 100644 --- a/data/possum-cis/possum-cisbioschemas.jsonld +++ b/data/possum-cis/possum-cisbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predict cis-elements in DNA sequences using the standard method of Position Specific Scoring Matrices. It measures the resemblance of every sequence fragment to the chosen cis-element matrices by calculating log-likelihood ratio scores (base e), and returns high-scoring sequence fragments.", "sc:name": "Possum", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://zlab.bu.edu/~mfrith/possum/" } \ No newline at end of file diff --git a/data/possum-pssm/possum-pssmbioschemas.jsonld b/data/possum-pssm/possum-pssmbioschemas.jsonld index 18be3184d2096..83b710e45781a 100644 --- a/data/possum-pssm/possum-pssmbioschemas.jsonld +++ b/data/possum-pssm/possum-pssmbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/possum-pssm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jiangning Song", - "Trevor Lithgow" + "Trevor Lithgow", + "Jiangning Song" ], "sc:additionalType": "Web application", "sc:description": "Bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.", "sc:name": "POSSUM", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://possum.erc.monash.edu/" } \ No newline at end of file diff --git a/data/possum/possumbioschemas.jsonld b/data/possum/possumbioschemas.jsonld index 105d442c7e53b..a151d8c3a6d4f 100644 --- a/data/possum/possumbioschemas.jsonld +++ b/data/possum/possumbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PoSSuM", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://possum.cbrc.jp/PoSSuM/" } \ No newline at end of file diff --git a/data/possumsearch/possumsearchbioschemas.jsonld b/data/possumsearch/possumsearchbioschemas.jsonld index 739a687fb5a56..0b047eb128e72 100644 --- a/data/possumsearch/possumsearchbioschemas.jsonld +++ b/data/possumsearch/possumsearchbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:operatingSystem": "Linux", "sc:provider": [ "Bielefeld university", - "CeBiTec", - "BiBiServ" + "BiBiServ", + "CeBiTec" ], "sc:url": "https://bibiserv.cebitec.uni-bielefeld.de/possumsearch", "sc:version": "1" diff --git a/data/possumsearch2/possumsearch2bioschemas.jsonld b/data/possumsearch2/possumsearch2bioschemas.jsonld index 23db7d1a8e631..f16bb54c89fe2 100644 --- a/data/possumsearch2/possumsearch2bioschemas.jsonld +++ b/data/possumsearch2/possumsearch2bioschemas.jsonld @@ -18,13 +18,13 @@ "sc:description": "Significant speedup of database searches with HMMs by search space reduction with PSSM family models.", "sc:name": "PoSSuMsearch2", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ + "CeBiTec", "Bielefeld University", - "BiBiServ", - "CeBiTec" + "BiBiServ" ], "sc:url": "https://bibiserv.cebitec.uni-bielefeld.de/possumsearch2", "sc:version": "2" diff --git a/data/post/postbioschemas.jsonld b/data/post/postbioschemas.jsonld index 104080cadad38..43470e587dbf6 100644 --- a/data/post/postbioschemas.jsonld +++ b/data/post/postbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "POST", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/POST.html", "sc:version": "1.4.0" diff --git a/data/postman/postmanbioschemas.jsonld b/data/postman/postmanbioschemas.jsonld index 37baf9b45bed3..f95fb8541b7ba 100644 --- a/data/postman/postmanbioschemas.jsonld +++ b/data/postman/postmanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Post-translational modification software.", "sc:name": "POSTMan", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.uib.no/en/rg/probe/65847/postman" } \ No newline at end of file diff --git a/data/potterswheel/potterswheelbioschemas.jsonld b/data/potterswheel/potterswheelbioschemas.jsonld index 3d66b0c83d5ad..c422e9bda681f 100644 --- a/data/potterswheel/potterswheelbioschemas.jsonld +++ b/data/potterswheel/potterswheelbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "MATLAB toolbox for mechanistic mathematical modeling. It allows reaction network or ordinary differential equation (ODE) based modeling.", "sc:name": "PottersWheel", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.potterswheel.de/" } \ No newline at end of file diff --git a/data/power/powerbioschemas.jsonld b/data/power/powerbioschemas.jsonld index 5de8ed0a547a0..66708998f9014 100644 --- a/data/power/powerbioschemas.jsonld +++ b/data/power/powerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Phylogenetic Web Repeater (POWER) allows users to perform phylogenetic analysis using the PHYLIP package. The POWER pipeline can start with processing either multiple sequence alignments (MSA) or can proceed directly with aligned sequences.", "sc:name": "POWER", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://power.nhri.org.tw/" } \ No newline at end of file diff --git a/data/powerexplorer/powerexplorerbioschemas.jsonld b/data/powerexplorer/powerexplorerbioschemas.jsonld index 5ffd0a76ba224..9010906d93596 100644 --- a/data/powerexplorer/powerexplorerbioschemas.jsonld +++ b/data/powerexplorer/powerexplorerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "PowerExplorer", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PowerExplorer.html", "sc:version": "1.0.1" diff --git a/data/powerfit/powerfitbioschemas.jsonld b/data/powerfit/powerfitbioschemas.jsonld index c2134c6b569d4..167bf9911ed89 100644 --- a/data/powerfit/powerfitbioschemas.jsonld +++ b/data/powerfit/powerfitbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Apache-2.0", "sc:name": "PowerFit web portal", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "Utrecht University", "sc:url": "http://milou.science.uu.nl/services/POWERFIT", diff --git a/data/powergwasinteraction/powergwasinteractionbioschemas.jsonld b/data/powergwasinteraction/powergwasinteractionbioschemas.jsonld index d5d7897c4de76..3891d935254a6 100644 --- a/data/powergwasinteraction/powergwasinteractionbioschemas.jsonld +++ b/data/powergwasinteraction/powergwasinteractionbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Code for approximate power calculations for identification of gene x gene and gene x environment interactions in genomewide association studies using a two-stage analysis.", "sc:name": "powerGWASinteraction", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://kooperberg.fhcrc.org/soft.html" } \ No newline at end of file diff --git a/data/powergxe/powergxebioschemas.jsonld b/data/powergxe/powergxebioschemas.jsonld index c826d8cf112fe..ac99abbdfe931 100644 --- a/data/powergxe/powergxebioschemas.jsonld +++ b/data/powergxe/powergxebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "SAS Macro for power calculations for genetic association tests exploiting gene-environment interaction.", "sc:name": "PowerGxE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.hsph.harvard.edu/peter-kraft/software/" } \ No newline at end of file diff --git a/data/powertcr/powertcrbioschemas.jsonld b/data/powertcr/powertcrbioschemas.jsonld index a89bc9937d555..aac042ee99330 100644 --- a/data/powertcr/powertcrbioschemas.jsonld +++ b/data/powertcr/powertcrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "powerTCR", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/powerTCR.html", "sc:version": "1.0.0" diff --git a/data/poxo/poxobioschemas.jsonld b/data/poxo/poxobioschemas.jsonld index 5f1344bf95c6e..7057ef074ad09 100644 --- a/data/poxo/poxobioschemas.jsonld +++ b/data/poxo/poxobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "POXO", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.bioinfo.biocenter.helsinki.fi/poxo" } \ No newline at end of file diff --git a/data/ppa-pred/ppa-predbioschemas.jsonld b/data/ppa-pred/ppa-predbioschemas.jsonld index 05d66f8716e43..705158e441c6b 100644 --- a/data/ppa-pred/ppa-predbioschemas.jsonld +++ b/data/ppa-pred/ppa-predbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Server which helps you in predicting the binding affinity of protein-protein complex of your interest.", "sc:name": "PPA-Pred", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.iitm.ac.in/bioinfo/PPA_Pred/" } \ No newline at end of file diff --git a/data/ppb/ppbbioschemas.jsonld b/data/ppb/ppbbioschemas.jsonld index 24f40657f3f74..7fb6fbea96438 100644 --- a/data/ppb/ppbbioschemas.jsonld +++ b/data/ppb/ppbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PPB", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://gdbtools.unibe.ch:8080/PPB/" } \ No newline at end of file diff --git a/data/ppfold/ppfoldbioschemas.jsonld b/data/ppfold/ppfoldbioschemas.jsonld index 0c46c2345c11b..d05554e83666c 100644 --- a/data/ppfold/ppfoldbioschemas.jsonld +++ b/data/ppfold/ppfoldbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PPfold", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "birc.au.dk", "sc:url": "http://www.daimi.au.dk/~compbio/pfold/downloads.html#release", diff --git a/data/ppi/ppibioschemas.jsonld b/data/ppi/ppibioschemas.jsonld index a32793f615e0d..bdf431975aec8 100644 --- a/data/ppi/ppibioschemas.jsonld +++ b/data/ppi/ppibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This server classifies a protein-protein complex concerning its interaction type into permanent, transient or crystal artifact. The discrimination is performed using two characteristics of the protein-protein complex derived from its structure: the hydrophobicity of the interface and the quotient of interface area ratios, which takes the symmetry of the protein-protein interface into account.", "sc:name": "PPI", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "University of Hamburg - Center for Bioinformatics", "sc:url": "http://proteinsplus.zbh.uni-hamburg.de/#ppi" diff --git a/data/ppicompare/ppicomparebioschemas.jsonld b/data/ppicompare/ppicomparebioschemas.jsonld index 6a988c08f6c81..59d0decff1e90 100644 --- a/data/ppicompare/ppicomparebioschemas.jsonld +++ b/data/ppicompare/ppicomparebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "PPICompare", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://sourceforge.net/projects/ppicompare/" } \ No newline at end of file diff --git a/data/ppicurator/ppicuratorbioschemas.jsonld b/data/ppicurator/ppicuratorbioschemas.jsonld index 9849ccd349479..15ed56c476062 100644 --- a/data/ppicurator/ppicuratorbioschemas.jsonld +++ b/data/ppicurator/ppicuratorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "PPICurator", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://ppicurator.hupo.org.cn/" } \ No newline at end of file diff --git a/data/ppiexp/ppiexpbioschemas.jsonld b/data/ppiexp/ppiexpbioschemas.jsonld index 52e05ef46447a..10fbbb117ed6e 100644 --- a/data/ppiexp/ppiexpbioschemas.jsonld +++ b/data/ppiexp/ppiexpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "PPIExp", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.fgvis.com/expressvis/PPIExp", "sc:version": "1.0" diff --git a/data/ppim/ppimbioschemas.jsonld b/data/ppim/ppimbioschemas.jsonld index eee13f8be59ce..b48b95c46cac8 100644 --- a/data/ppim/ppimbioschemas.jsonld +++ b/data/ppim/ppimbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:26620522", "pmcid:PMC4734591", { "@id": "https://doi.org/10.1104/pp.15.01821" - } + }, + "pubmed:26620522" ], "sc:description": "Protein-Protein Interaction database for Maize.", "sc:featureList": { diff --git a/data/ppinfer/ppinferbioschemas.jsonld b/data/ppinfer/ppinferbioschemas.jsonld index 0cc4fd66e697c..a725097af4caf 100644 --- a/data/ppinfer/ppinferbioschemas.jsonld +++ b/data/ppinfer/ppinferbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "PPInfer", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PPInfer.html", "sc:version": "1.6.0" diff --git a/data/ppipre/ppiprebioschemas.jsonld b/data/ppipre/ppiprebioschemas.jsonld index aff46e10feae2..234c84d2af397 100644 --- a/data/ppipre/ppiprebioschemas.jsonld +++ b/data/ppipre/ppiprebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predicting protein-protein interactions by combining heterogeneous features.", "sc:name": "ppiPre", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://cran.r-project.org/src/contrib/Archive/ppiPre/" } \ No newline at end of file diff --git a/data/ppisearch/ppisearchbioschemas.jsonld b/data/ppisearch/ppisearchbioschemas.jsonld index b7e8250c37325..11013fa1cbb68 100644 --- a/data/ppisearch/ppisearchbioschemas.jsonld +++ b/data/ppisearch/ppisearchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.", "sc:name": "PPISearch", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://gemdock.life.nctu.edu.tw/ppisearch/" } \ No newline at end of file diff --git a/data/ppistats/ppistatsbioschemas.jsonld b/data/ppistats/ppistatsbioschemas.jsonld index bb40ba568b1ff..d7f7e22aafae8 100644 --- a/data/ppistats/ppistatsbioschemas.jsonld +++ b/data/ppistats/ppistatsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "ppiStats", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ppiStats.html", "sc:version": "1.40.0" diff --git a/data/ppisurv/ppisurvbioschemas.jsonld b/data/ppisurv/ppisurvbioschemas.jsonld index 96ffb608ddeca..9a52f2a8ca5c8 100644 --- a/data/ppisurv/ppisurvbioschemas.jsonld +++ b/data/ppisurv/ppisurvbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PPISURV", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.bioprofiling.de/GEO/PPISURV/ppisurv.html" } \ No newline at end of file diff --git a/data/ppixpress/ppixpressbioschemas.jsonld b/data/ppixpress/ppixpressbioschemas.jsonld index c88f7414f11fa..ea07dd22dd94f 100644 --- a/data/ppixpress/ppixpressbioschemas.jsonld +++ b/data/ppixpress/ppixpressbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PPIXpress", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sourceforge.net/projects/ppixpress/" } \ No newline at end of file diff --git a/data/ppms/ppmsbioschemas.jsonld b/data/ppms/ppmsbioschemas.jsonld index 9793acdcd7de0..c85a126b97914 100644 --- a/data/ppms/ppmsbioschemas.jsonld +++ b/data/ppms/ppmsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Tool for finding common substructures of the two proteins.", "sc:name": "PPMs", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://sites.google.com/site/guofeics/ppms-online-document" } \ No newline at end of file diff --git a/data/pppbenchmark/pppbenchmarkbioschemas.jsonld b/data/pppbenchmark/pppbenchmarkbioschemas.jsonld index 25ac93164ee65..1c108a025a883 100644 --- a/data/pppbenchmark/pppbenchmarkbioschemas.jsonld +++ b/data/pppbenchmark/pppbenchmarkbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btp191", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-4327-3730", "@type": "schema:Person" @@ -35,10 +31,10 @@ }, "sc:citation": [ "pmcid:PMC2687945", + "pubmed:19478005", { "@id": "https://doi.org/10.1093/bioinformatics/btp191" - }, - "pubmed:19478005" + } ], "sc:description": "Promoter prediction program evaluation.", "sc:featureList": { @@ -46,13 +42,17 @@ }, "sc:name": "PPPbenchmark", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/pppbenchmark", "sc:version": "1.3" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btp191", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pprint/pprintbioschemas.jsonld b/data/pprint/pprintbioschemas.jsonld index 266c0f535ed36..54557a3b0333d 100644 --- a/data/pprint/pprintbioschemas.jsonld +++ b/data/pprint/pprintbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-server for predicting RNA-binding residues of a protein.", "sc:name": "Pprint", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/pprint/" } \ No newline at end of file diff --git a/data/pps/ppsbioschemas.jsonld b/data/pps/ppsbioschemas.jsonld index e5eb4e7f01cb9..ac0524d126fae 100644 --- a/data/pps/ppsbioschemas.jsonld +++ b/data/pps/ppsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "PPS (PTMs Peptide Scanner) is a novel software to reveal known or highly potential PTM sites in eukaryotic proteins.", "sc:name": "PPS", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://pps.biocuckoo.org/", "sc:version": "1.0" diff --git a/data/ppsc/ppscbioschemas.jsonld b/data/ppsc/ppscbioschemas.jsonld index 1d50f34656ddf..91b5f13ec86b5 100644 --- a/data/ppsc/ppscbioschemas.jsonld +++ b/data/ppsc/ppscbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Prediction of protein stability changes.", "sc:name": "PPSC", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "bils.se", "sc:url": "http://structure.bmc.lu.se/PPSC/", diff --git a/data/ppus/ppusbioschemas.jsonld b/data/ppus/ppusbioschemas.jsonld index 25ae661fb54e9..cd7dffeaf4b15 100644 --- a/data/ppus/ppusbioschemas.jsonld +++ b/data/ppus/ppusbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Online tool to predict pseudouridine sites recognized by pseudouridine synthase in RNA.", "sc:name": "PPUS", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://lyh.pkmu.cn/ppus/" } \ No newline at end of file diff --git a/data/ppv_npv/ppv_npvbioschemas.jsonld b/data/ppv_npv/ppv_npvbioschemas.jsonld index 9c1d5a63e8de3..0088e0eb4e1ce 100644 --- a/data/ppv_npv/ppv_npvbioschemas.jsonld +++ b/data/ppv_npv/ppv_npvbioschemas.jsonld @@ -20,8 +20,8 @@ { "@id": "https://doi.org/10.1186/S41512-017-0017-Y" }, - "pmcid:PMC6460848", - "pubmed:31093546" + "pubmed:31093546", + "pmcid:PMC6460848" ], "sc:description": "Novel method for interrogating receiver operating characteristic curves for assessing prognostic tests.", "sc:featureList": [ @@ -35,19 +35,19 @@ "sc:license": "Unlicense", "sc:name": "PPV NPV", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://d4ta.link/ppvnpv/" }, - { - "@id": "https://orcid.org/0000-0002-8734-7335", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/S41512-017-0017-Y", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-8734-7335", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pqsfinder/pqsfinderbioschemas.jsonld b/data/pqsfinder/pqsfinderbioschemas.jsonld index 3610578887d32..74914bcaa5bc3 100644 --- a/data/pqsfinder/pqsfinderbioschemas.jsonld +++ b/data/pqsfinder/pqsfinderbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jiri Hon", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The main functionality of the this package is to detect DNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, this package is able to detect sequences responsible for G4s folded from imperfect G-runs containing bulges or mismatches and as such is more sensitive than competing algorithms.", "sc:license": "BSD-4-Clause", "sc:name": "pqsfinder", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pqsfinder.html", diff --git a/data/prada/bioconda_prada.yaml b/data/prada/bioconda_prada.yaml index ff37d3e50219b..31e0a3a71b3b2 100644 --- a/data/prada/bioconda_prada.yaml +++ b/data/prada/bioconda_prada.yaml @@ -5,7 +5,6 @@ description: Tools for analysing and navigating data from high-throughput phenot home: https://bioconductor.org/packages/3.10/bioc/html/prada.html identifiers: - biotools:prada -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-prada diff --git a/data/praline/pralinebioschemas.jsonld b/data/praline/pralinebioschemas.jsonld index cbc85a92a6fa0..1143ae44a50e7 100644 --- a/data/praline/pralinebioschemas.jsonld +++ b/data/praline/pralinebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.", "sc:name": "PRALINE", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://ibivu.cs.vu.nl/programs/pralinewww/" } \ No newline at end of file diff --git a/data/praline_2/praline_2bioschemas.jsonld b/data/praline_2/praline_2bioschemas.jsonld index 042e917a2f192..a56db9b2e6b96 100644 --- a/data/praline_2/praline_2bioschemas.jsonld +++ b/data/praline_2/praline_2bioschemas.jsonld @@ -14,8 +14,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:author": { "@id": "https://orcid.org/0000-0002-7971-6209" @@ -24,8 +24,8 @@ "sc:license": "GPL-2.0", "sc:name": "PRALINE 2", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ibivu/PRALINE", "sc:version": [ diff --git a/data/pram/prambioschemas.jsonld b/data/pram/prambioschemas.jsonld index 80526de81ad5e..3b4d62443eb23 100644 --- a/data/pram/prambioschemas.jsonld +++ b/data/pram/prambioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "PRAM", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://bioconductor.org/packages/pram" diff --git a/data/prank/prankbioschemas.jsonld b/data/prank/prankbioschemas.jsonld index f4991d201022b..ee777fd37e547 100644 --- a/data/prank/prankbioschemas.jsonld +++ b/data/prank/prankbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PRANK", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://wasabiapp.org/software/prank/" } \ No newline at end of file diff --git a/data/prank_api/prank_apibioschemas.jsonld b/data/prank_api/prank_apibioschemas.jsonld index b02dc1bca137e..65c76ed3505f4 100644 --- a/data/prank_api/prank_apibioschemas.jsonld +++ b/data/prank_api/prank_apibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It’s based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences.", "sc:name": "PRANK API", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/msa/prank_rest", "sc:version": "1" diff --git a/data/prankweb/prankwebbioschemas.jsonld b/data/prankweb/prankwebbioschemas.jsonld index 6ec5b44729d13..c2459300a3aea 100644 --- a/data/prankweb/prankwebbioschemas.jsonld +++ b/data/prankweb/prankwebbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1093/NAR/GKZ424", "@type": "sc:CreativeWork" }, + { + "@id": "https://orcid.org/0000-0003-4679-0557", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/PrankWeb", "@type": "sc:SoftwareApplication", @@ -24,36 +28,32 @@ "Web service" ], "sc:citation": [ - "pmcid:PMC6602436", - "pubmed:31114880", { "@id": "https://doi.org/10.1093/NAR/GKZ424" - } + }, + "pubmed:31114880", + "pmcid:PMC6602436" ], "sc:description": "Web application for protein-ligand binding sites analysis and visualization | This repositary contains PrankWeb web application.", "sc:featureList": [ { - "@id": "edam:operation_0482" + "@id": "edam:operation_2575" }, { - "@id": "edam:operation_0445" + "@id": "edam:operation_0482" }, { - "@id": "edam:operation_2575" + "@id": "edam:operation_0445" } ], "sc:license": "Apache-2.0", "sc:name": "PrankWeb", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://prankweb.cz/" - }, - { - "@id": "https://orcid.org/0000-0003-4679-0557", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/praptorx_property/praptorx_propertybioschemas.jsonld b/data/praptorx_property/praptorx_propertybioschemas.jsonld index 5f3a5deecd91a..6d3a87644ede4 100644 --- a/data/praptorx_property/praptorx_propertybioschemas.jsonld +++ b/data/praptorx_property/praptorx_propertybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web server predicting structure property of a protein sequence without using any template information.", "sc:name": "PRaptorX Property", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://raptorx2.uchicago.edu/StructurePropertyPred/predict/" diff --git a/data/pratt/prattbioschemas.jsonld b/data/pratt/prattbioschemas.jsonld index 9a5fe0bf4671f..2409b209bc411 100644 --- a/data/pratt/prattbioschemas.jsonld +++ b/data/pratt/prattbioschemas.jsonld @@ -13,8 +13,8 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "Inge Jonassen", - "Web Production" + "Web Production", + "Inge Jonassen" ], "sc:description": "Discover patterns in unaligned protein sequences.", "sc:name": "Pratt", @@ -24,8 +24,8 @@ "Mac" ], "sc:provider": [ - "EMBL-EBI", - "University of Bergen" + "University of Bergen", + "EMBL-EBI" ], "sc:url": "http://www.ebi.ac.uk/Tools/pfa/pratt/", "sc:version": "1" diff --git a/data/prbr/prbrbioschemas.jsonld b/data/prbr/prbrbioschemas.jsonld index 292132b9545ad..6f520376957b6 100644 --- a/data/prbr/prbrbioschemas.jsonld +++ b/data/prbr/prbrbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Identify RNA-binding residues from protein sequences which combines a hybrid feature with the enriched random forest (ERF) algorithm.", "sc:name": "PRBR", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cbi.seu.edu.cn/PRBR/" } \ No newline at end of file diff --git a/data/prcbench/prcbenchbioschemas.jsonld b/data/prcbench/prcbenchbioschemas.jsonld index 52a0807b1920f..5ac36c7626d42 100644 --- a/data/prcbench/prcbenchbioschemas.jsonld +++ b/data/prcbench/prcbenchbioschemas.jsonld @@ -15,27 +15,27 @@ "biotools:primaryContact": "Takaya Saito", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5408773", { "@id": "https://doi.org/10.1093/bioinformatics/btw570" }, + "pmcid:PMC5408773", "pubmed:27591081" ], "sc:description": "The package provides a testing workbench for evaluating precision-recall curves under various conditions in R.", "sc:featureList": [ { - "@id": "edam:operation_2238" + "@id": "edam:operation_2428" }, { - "@id": "edam:operation_2428" + "@id": "edam:operation_2238" } ], "sc:license": "GPL-3.0", "sc:name": "prcbench", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ii.uib.no", "sc:url": "https://cran.r-project.org/package=prcbench", diff --git a/data/prdos/prdosbioschemas.jsonld b/data/prdos/prdosbioschemas.jsonld index c30ec1f5a85c1..4e38d82c0828a 100644 --- a/data/prdos/prdosbioschemas.jsonld +++ b/data/prdos/prdosbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PrDOS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://prdos.hgc.jp/cgi-bin/top.cgi" } \ No newline at end of file diff --git a/data/prebs/prebsbioschemas.jsonld b/data/prebs/prebsbioschemas.jsonld index c1a19b63aae34..133d46a9ecf0c 100644 --- a/data/prebs/prebsbioschemas.jsonld +++ b/data/prebs/prebsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0126545", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/prebs", "@type": "sc:SoftwareApplication", @@ -22,30 +18,34 @@ "Library" ], "sc:citation": [ + "pubmed:25966034", { "@id": "https://doi.org/10.1371/journal.pone.0126545" }, - "pmcid:PMC4429080", - "pubmed:25966034" + "pmcid:PMC4429080" ], "sc:description": "This package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.", "sc:featureList": [ { - "@id": "edam:operation_2424" + "@id": "edam:operation_0335" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_2424" } ], "sc:license": "Artistic-2.0", "sc:name": "prebs", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/prebs.html", "sc:version": "1.14.0" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0126545", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/preciseprimer/preciseprimerbioschemas.jsonld b/data/preciseprimer/preciseprimerbioschemas.jsonld index 91bd882d84b3b..c1a821dcb5384 100644 --- a/data/preciseprimer/preciseprimerbioschemas.jsonld +++ b/data/preciseprimer/preciseprimerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries.", "sc:name": "PrecisePrimer", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/PrecisePrimer/" } \ No newline at end of file diff --git a/data/precog/precogbioschemas.jsonld b/data/precog/precogbioschemas.jsonld index feb5a5b6eaa3d..d74912b3f0d8d 100644 --- a/data/precog/precogbioschemas.jsonld +++ b/data/precog/precogbioschemas.jsonld @@ -17,10 +17,10 @@ ], "sc:author": "Luciano Fernandez", "sc:contributor": [ + "Olga Kourtchenko", "Anders Blomberg", "Martin Zackrisson", - "Jonas Warringer", - "Olga Kourtchenko" + "Jonas Warringer" ], "sc:description": "Tool developed to automate visualization, analysis and exploration of complex and highly resolved microbial growth data, as well as standardized extraction of the fitness components it contains. It is hope that this tool will promote simplicity, transparency and standardization in microbial growth phenomics, and provide a portal with the standalone software and online tools so that other microbiology labs can easily upload, assess and visualize their growth data.", "sc:name": "PRECOG", diff --git a/data/pred-gpcr/pred-gpcrbioschemas.jsonld b/data/pred-gpcr/pred-gpcrbioschemas.jsonld index ced045dca0bf1..5bc376783c248 100644 --- a/data/pred-gpcr/pred-gpcrbioschemas.jsonld +++ b/data/pred-gpcr/pred-gpcrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles.", "sc:name": "PRED-GPCR", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://athina.biol.uoa.gr/bioinformatics/PRED-GPCR/" } \ No newline at end of file diff --git a/data/pred-signal/pred-signalbioschemas.jsonld b/data/pred-signal/pred-signalbioschemas.jsonld index 239f59cbde5b0..9e3a95f762158 100644 --- a/data/pred-signal/pred-signalbioschemas.jsonld +++ b/data/pred-signal/pred-signalbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PRED-SIGNAL is a tool that takes a protein sequence as input and predicts the signal peptides of archaea", "sc:name": "PRED-SIGNAL", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.compgen.org/tools/PRED-SIGNAL", "sc:version": "1.1" diff --git a/data/pred-tat/pred-tatbioschemas.jsonld b/data/pred-tat/pred-tatbioschemas.jsonld index a14e7cbbafffb..fb472ee979b85 100644 --- a/data/pred-tat/pred-tatbioschemas.jsonld +++ b/data/pred-tat/pred-tatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PRED-TAT is a tool that takes a protein sequence as input and discriminating Sec from Tat signal peptides and predicting their cleavage sites.", "sc:name": "PRED-TAT", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.compgen.org/tools/PRED-TAT", "sc:version": "1.1" diff --git a/data/pred-tmbb/pred-tmbbbioschemas.jsonld b/data/pred-tmbb/pred-tmbbbioschemas.jsonld index 9a5cd4adb54ea..08c23e3215531 100644 --- a/data/pred-tmbb/pred-tmbbbioschemas.jsonld +++ b/data/pred-tmbb/pred-tmbbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.", "sc:name": "PRED-TMBB", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinformatics.biol.uoa.gr/PRED-TMBB/" } \ No newline at end of file diff --git a/data/pred-tmbb2/pred-tmbb2bioschemas.jsonld b/data/pred-tmbb2/pred-tmbb2bioschemas.jsonld index f67a89bd84cba..b150ba9cfd9db 100644 --- a/data/pred-tmbb2/pred-tmbb2bioschemas.jsonld +++ b/data/pred-tmbb2/pred-tmbb2bioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-4935-2325", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/pred-tmbb2", "@type": "sc:SoftwareApplication", @@ -25,6 +21,10 @@ "sc:name": "PRED-TMBB2", "sc:url": "http://www.compgen.org/tools/PRED-TMBB2", "sc:version": "1.1" + }, + { + "@id": "http://orcid.org/0000-0003-4935-2325", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/preda/predabioschemas.jsonld b/data/preda/predabioschemas.jsonld index 6a5b729b4a027..ff46fb67d81ab 100644 --- a/data/preda/predabioschemas.jsonld +++ b/data/preda/predabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "PREDA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PREDA.html", "sc:version": "1.20.0" diff --git a/data/predcsf/predcsfbioschemas.jsonld b/data/predcsf/predcsfbioschemas.jsonld index 1e9ac51888d21..d103b398a0d8e 100644 --- a/data/predcsf/predcsfbioschemas.jsonld +++ b/data/predcsf/predcsfbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PredCSF", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/PredCSF/" } \ No newline at end of file diff --git a/data/preddimer/preddimerbioschemas.jsonld b/data/preddimer/preddimerbioschemas.jsonld index 5ed449298f46f..3d459c179d6e1 100644 --- a/data/preddimer/preddimerbioschemas.jsonld +++ b/data/preddimer/preddimerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "PREDDIMER reconstructs putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal α-helices.", "sc:name": "PREDDIMER", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://model.nmr.ru/preddimer/" } \ No newline at end of file diff --git a/data/predector/predectorbioschemas.jsonld b/data/predector/predectorbioschemas.jsonld index e24fe94aaee78..f67de00b52c1b 100644 --- a/data/predector/predectorbioschemas.jsonld +++ b/data/predector/predectorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool designed for biologists, its main function is to search for the cis-elements (nucleotides) that regulate the genes for a bacteria specie, assuming that one usually consider that a cis sequence regulates a gene if it is oriented in the same direction and if it is localized in a user-specified interval regarding to the beginning of the gene.", "sc:name": "Predector", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.montefiore.ulg.ac.be/~hiard/PreDetector/PreDetector.php" diff --git a/data/predgpi/predgpibioschemas.jsonld b/data/predgpi/predgpibioschemas.jsonld index c263768cf447c..6bfccc5703663 100644 --- a/data/predgpi/predgpibioschemas.jsonld +++ b/data/predgpi/predgpibioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/predgpi", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Andrea Pierleoni", "Rita Casadio", - "Pier Luigi Martelli", - "Andrea Pierleoni" + "Pier Luigi Martelli" ], "sc:additionalType": "Web application", "sc:description": "Prediction system for GPI-anchored proteins.", "sc:name": "PredGPI", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "ELIXIR-ITA-BOLOGNA", diff --git a/data/predhydroxy/predhydroxybioschemas.jsonld b/data/predhydroxy/predhydroxybioschemas.jsonld index cd056f6b30215..06e62be70d584 100644 --- a/data/predhydroxy/predhydroxybioschemas.jsonld +++ b/data/predhydroxy/predhydroxybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Web service which is constructed to predict the proline and lysine hydroxylation sites based on position weight amino acids composition, 8 high-quality amino acid indices and support vector machine.", "sc:name": "PredHydroxy", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioinfo.ncu.edu.cn/PredHydroxy.aspx" diff --git a/data/predictionet/predictionetbioschemas.jsonld b/data/predictionet/predictionetbioschemas.jsonld index 3d2a65a99e286..543764af782bd 100644 --- a/data/predictionet/predictionetbioschemas.jsonld +++ b/data/predictionet/predictionetbioschemas.jsonld @@ -31,19 +31,19 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:22096235", { "@id": "https://doi.org/10.1093/nar/gkr1050" }, - "pmcid:PMC3245161", - "pubmed:22096235" + "pmcid:PMC3245161" ], "sc:description": "Set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases.", "sc:license": "Artistic-2.0", "sc:name": "predictionet", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/predictionet.html", "sc:version": "1.20.0" diff --git a/data/predictivenetworks/predictivenetworksbioschemas.jsonld b/data/predictivenetworks/predictivenetworksbioschemas.jsonld index 2d0e4ab1eb258..5fb341d498193 100644 --- a/data/predictivenetworks/predictivenetworksbioschemas.jsonld +++ b/data/predictivenetworks/predictivenetworksbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model.", "sc:name": "PredictiveNetworks", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://compbio.dfci.harvard.edu/predictivenetworks//" diff --git a/data/predictnls/predictnlsbioschemas.jsonld b/data/predictnls/predictnlsbioschemas.jsonld index aa973186d4df6..0fbcc89e5dcae 100644 --- a/data/predictnls/predictnlsbioschemas.jsonld +++ b/data/predictnls/predictnlsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/embo-reports/kvd092", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/predictnls", "@type": "sc:SoftwareApplication", @@ -37,10 +33,10 @@ "sc:author": "Murat Cokol", "sc:citation": [ "pubmed:11258480", - "pmcid:PMC1083765", { "@id": "https://doi.org/10.1093/embo-reports/kvd092" - } + }, + "pmcid:PMC1083765" ], "sc:contributor": [ "Rajesh Nair", @@ -49,10 +45,10 @@ "sc:description": "Prediction and analysis of nuclear localization signals.", "sc:featureList": [ { - "@id": "edam:operation_2489" + "@id": "edam:operation_3092" }, { - "@id": "edam:operation_3092" + "@id": "edam:operation_2489" } ], "sc:isAccessibleForFree": true, @@ -60,14 +56,18 @@ "sc:name": "PredictNLS", "sc:operatingSystem": "Linux", "sc:provider": [ - "Columbia University", - "RostLab" + "RostLab", + "Columbia University" ], "sc:softwareHelp": { "@id": "https://rostlab.org/owiki/index.php/PredictNLS" }, "sc:url": "https://www.rostlab.org/owiki/index.php/PredictNLS", "sc:version": "1.0.18" + }, + { + "@id": "https://doi.org/10.1093/embo-reports/kvd092", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/predictpa/predictpabioschemas.jsonld b/data/predictpa/predictpabioschemas.jsonld index 727beb3bfe986..26b438f3e3ffd 100644 --- a/data/predictpa/predictpabioschemas.jsonld +++ b/data/predictpa/predictpabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Bayesian network model that integrates genomic, transcriptomic and proteomic data to predict protein abundance. Specifically, by using expression, sequence and interaction data, we effectively link transcriptional information with post-transcriptional and protein translational data.", "sc:name": "PredictPA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinf.scmb.uq.edu.au:8080/proteinabundance/" } \ No newline at end of file diff --git a/data/predictprotein/predictproteinbioschemas.jsonld b/data/predictprotein/predictproteinbioschemas.jsonld index b0ba90b2442e8..8cd5aa04078fb 100644 --- a/data/predictprotein/predictproteinbioschemas.jsonld +++ b/data/predictprotein/predictproteinbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail.", "sc:name": "PredictProtein", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ppopen.rostlab.org" } \ No newline at end of file diff --git a/data/predictprotein_open/predictprotein_openbioschemas.jsonld b/data/predictprotein_open/predictprotein_openbioschemas.jsonld index b0171b87ba1fc..c60fe0a72a05e 100644 --- a/data/predictprotein_open/predictprotein_openbioschemas.jsonld +++ b/data/predictprotein_open/predictprotein_openbioschemas.jsonld @@ -17,17 +17,17 @@ "Guy Yachdav" ], "sc:contributor": [ - "Alexander von Humboldt foundation through the German Ministry for Research and Education", + "Edda Kloppmann", "Laszlo Kajan", - "Edda Kloppmann" + "Alexander von Humboldt foundation through the German Ministry for Research and Education" ], "sc:description": "Prediction of various aspects of protein structure and function. A user may submit a query to the server without registration.", "sc:funder": "Alexander von Humboldt foundation through the German Ministry for Research and Education", "sc:license": "CC-BY-4.0", "sc:name": "PredictProtein Open", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": [ diff --git a/data/predictsnp/predictsnpbioschemas.jsonld b/data/predictsnp/predictsnpbioschemas.jsonld index 04e2fa222c55a..5a15337ecb5c6 100644 --- a/data/predictsnp/predictsnpbioschemas.jsonld +++ b/data/predictsnp/predictsnpbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/predictsnp", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": [ - "Jaroslav Bendl", + "Jan Brezovsky", "Jiri Damborsky", - "Ondrej Salanda", "Jan Stourac", - "Jan Brezovsky" + "Ondrej Salanda", + "Jaroslav Bendl" ], "sc:contributor": [ "Eric D. Wieben", @@ -29,16 +29,16 @@ "sc:description": "A consensus classifier that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database.", "sc:name": "PredictSNP", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ + "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories", - "Masaryk University, Brno, Czech Republic", "Mayo Clinic, Rochester, New York, United States of America", - "Brno University of Technology, Brno, Czech Republic", - "International Centre for Clinical Research, Brno, Czech Republic" + "Masaryk University, Brno, Czech Republic", + "Brno University of Technology, Brno, Czech Republic" ], "sc:url": "http://loschmidt.chemi.muni.cz/predictsnp", "sc:version": "1.0" diff --git a/data/predictsnp2/predictsnp2bioschemas.jsonld b/data/predictsnp2/predictsnp2bioschemas.jsonld index 1671f03572697..a7f92521ef252 100644 --- a/data/predictsnp2/predictsnp2bioschemas.jsonld +++ b/data/predictsnp2/predictsnp2bioschemas.jsonld @@ -13,37 +13,37 @@ "sc:additionalType": "Web application", "sc:author": [ "Jan Stourac", - "Jan Brezovsky", + "Jaroslav Bendl", "Milos Musil", - "Jiri Damborsky", - "Jaroslav Bendl" + "Jan Brezovsky", + "Jiri Damborsky" ], "sc:contributor": [ "Jaroslav Zendulka", - "Czech Ministry of Education of the Czech Republic (LO1214 and LQ1605; http://www.msmt.cz)", "CESNET and the CERIT Scientific Cloud (LM2015042 and LM2015085; http://www.msmt.cz)", - "Research and Application of Advanced Methods in ICT (FIT-S-14-2299; http://www.fit.vutbr.cz/)", "European Union Framework Programme (REGPOT 316345; ec.europa.eu/research)", - "European Commission within the Research Infrastructures programme of Horizon 2020" + "Research and Application of Advanced Methods in ICT (FIT-S-14-2299; http://www.fit.vutbr.cz/)", + "European Commission within the Research Infrastructures programme of Horizon 2020", + "Czech Ministry of Education of the Czech Republic (LO1214 and LQ1605; http://www.msmt.cz)" ], "sc:description": "A consensus classifier that combines five of the top performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect of SNPs within the human genome. The obtained results are provided together with annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg, UCSC and Ensembl databases.", "sc:funder": [ - "Czech Ministry of Education of the Czech Republic (LO1214 and LQ1605; http://www.msmt.cz)", - "European Union Framework Programme (REGPOT 316345; ec.europa.eu/research)", "Research and Application of Advanced Methods in ICT (FIT-S-14-2299; http://www.fit.vutbr.cz/)", + "Czech Ministry of Education of the Czech Republic (LO1214 and LQ1605; http://www.msmt.cz)", "CESNET and the CERIT Scientific Cloud (LM2015042 and LM2015085; http://www.msmt.cz)", + "European Union Framework Programme (REGPOT 316345; ec.europa.eu/research)", "European Commission within the Research Infrastructures programme of Horizon 2020" ], "sc:name": "PredictSNP2", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "Brno University of Technology, Brno, Czech Republic", - "International Centre for Clinical Research, Brno, Czech Republic", "Masaryk University, Brno, Czech Republic", + "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories" ], "sc:url": "http://loschmidt.chemi.muni.cz/predictsnp2", diff --git a/data/predikin/predikinbioschemas.jsonld b/data/predikin/predikinbioschemas.jsonld index 9d3910f47d92e..47339c2fdef70 100644 --- a/data/predikin/predikinbioschemas.jsonld +++ b/data/predikin/predikinbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation", "sc:name": "Predikin", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://predikin.biosci.uq.edu.au" } \ No newline at end of file diff --git a/data/preditor/preditorbioschemas.jsonld b/data/preditor/preditorbioschemas.jsonld index f4e7bfecbd574..35a4563e68a48 100644 --- a/data/preditor/preditorbioschemas.jsonld +++ b/data/preditor/preditorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions.", "sc:name": "PREDITOR", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://wishart.biology.ualberta.ca/shiftor/cgi-bin/preditor_current.py" } \ No newline at end of file diff --git a/data/predrem/predrembioschemas.jsonld b/data/predrem/predrembioschemas.jsonld index 2c2cf9dc07552..25ba288580cdc 100644 --- a/data/predrem/predrembioschemas.jsonld +++ b/data/predrem/predrembioschemas.jsonld @@ -19,10 +19,10 @@ "sc:additionalType": "Database portal", "sc:citation": [ "pmcid:PMC4343075", + "pubmed:25725063", { "@id": "https://doi.org/10.1093/database/bav007" - }, - "pubmed:25725063" + } ], "sc:description": "Database of Dna REgulatory Motifs and motifs modules predicted from DNase I hypersensitive sites in 349 human cell and tissue samples.", "sc:featureList": { @@ -30,9 +30,9 @@ }, "sc:name": "PreDREM", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://server.cs.ucf.edu/predrem/" } diff --git a/data/predtm/predtmbioschemas.jsonld b/data/predtm/predtmbioschemas.jsonld index 18ab2f85656e2..4e5b2931e0b1a 100644 --- a/data/predtm/predtmbioschemas.jsonld +++ b/data/predtm/predtmbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PredTM", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ELIXIR-SI-hackathon", "sc:url": "http://transpred.ki.si", diff --git a/data/predus/predusbioschemas.jsonld b/data/predus/predusbioschemas.jsonld index 50f3f40ec1143..208f4d8c09f96 100644 --- a/data/predus/predusbioschemas.jsonld +++ b/data/predus/predusbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PredUs", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PredUs" } \ No newline at end of file diff --git a/data/predyflexy/predyflexybioschemas.jsonld b/data/predyflexy/predyflexybioschemas.jsonld index 3e462581da400..37775205794fb 100644 --- a/data/predyflexy/predyflexybioschemas.jsonld +++ b/data/predyflexy/predyflexybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Predict local protein structures and protein flexibility from its sequence. Results can be visualized at the amino acid level through a table and graphics.", "sc:name": "PredyFlexy", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/" } \ No newline at end of file diff --git a/data/preg/pregbioschemas.jsonld b/data/preg/pregbioschemas.jsonld index 4864eebb68368..d089da3e51ee5 100644 --- a/data/preg/pregbioschemas.jsonld +++ b/data/preg/pregbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "UK MRC", "EMBOSS Contributors", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC", + "UK BBSRC" ], "sc:description": "Regular expression search of protein sequence(s).", "sc:funder": [ @@ -27,12 +27,12 @@ "sc:name": "preg", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/preg.html", "sc:version": "r6" diff --git a/data/prelude_fugue/prelude_fuguebioschemas.jsonld b/data/prelude_fugue/prelude_fuguebioschemas.jsonld index e1331ff4ebb50..de52cde0127d0 100644 --- a/data/prelude_fugue/prelude_fuguebioschemas.jsonld +++ b/data/prelude_fugue/prelude_fuguebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predict the local structure of a protein in terms of backbone dihedral angle domains, identify sequence regions that form early during folding, and locate structural weaknesses, defined as regions whose sequence is not optimal with respect to the tertiary fold.", "sc:name": "Prelude Fugue", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://babylone.ulb.ac.be/Prelude_and_Fugue/" } \ No newline at end of file diff --git a/data/premer-cg/premer-cgbioschemas.jsonld b/data/premer-cg/premer-cgbioschemas.jsonld index 19f0e45c5bcc0..7ec63e5a9eb9c 100644 --- a/data/premer-cg/premer-cgbioschemas.jsonld +++ b/data/premer-cg/premer-cgbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PrEMeR-CG", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioserv.mps.ohio-state.edu/premer/" } \ No newline at end of file diff --git a/data/premeta/premetabioschemas.jsonld b/data/premeta/premetabioschemas.jsonld index cd28176b19d7c..1943c67a73ecf 100644 --- a/data/premeta/premetabioschemas.jsonld +++ b/data/premeta/premetabioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12864-017-3573-1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/premeta", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Zheng-Zheng Tang", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5310051", + "pubmed:28196472", { "@id": "https://doi.org/10.1186/s12864-017-3573-1" }, - "pubmed:28196472" + "pmcid:PMC5310051" ], "sc:description": "Facilitates the exchange of information between four software packages for meta-analysis of rare-variant associations: MASS, RAREMETAL, MetaSKAT, and seqMeta.", "sc:featureList": { @@ -33,6 +29,10 @@ "sc:name": "PreMeta", "sc:operatingSystem": "Linux", "sc:url": "http://dlin.web.unc.edu/software/premeta/" + }, + { + "@id": "https://doi.org/10.1186/s12864-017-3573-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/preopdb/preopdbbioschemas.jsonld b/data/preopdb/preopdbbioschemas.jsonld index 486a56addbf50..570b8df2509d1 100644 --- a/data/preopdb/preopdbbioschemas.jsonld +++ b/data/preopdb/preopdbbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "The Prokaryotic Operon DataBase constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more than 1200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved.", "sc:name": "PreOpDB", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://biocomputo2.ibt.unam.mx/OperonPredictor/" } \ No newline at end of file diff --git a/data/prep_suite/prep_suitebioschemas.jsonld b/data/prep_suite/prep_suitebioschemas.jsonld index a14a2c2e447f5..a530e37332209 100644 --- a/data/prep_suite/prep_suitebioschemas.jsonld +++ b/data/prep_suite/prep_suitebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.", "sc:name": "PREP Suite", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://prep.unl.edu/" } \ No newline at end of file diff --git a/data/prepareannotation/prepareannotationbioschemas.jsonld b/data/prepareannotation/prepareannotationbioschemas.jsonld index 2d68d26fe1f0e..a6030bd32d03e 100644 --- a/data/prepareannotation/prepareannotationbioschemas.jsonld +++ b/data/prepareannotation/prepareannotationbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Prepares Annotation file: clusterizes, filters exon and sorts annotations.", "sc:name": "prepareannotation", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/prephappy/prephappybioschemas.jsonld b/data/prephappy/prephappybioschemas.jsonld index 8b23246c0e204..15cedb88e264c 100644 --- a/data/prephappy/prephappybioschemas.jsonld +++ b/data/prephappy/prephappybioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Prephappy is a tool to help prepare input files for the haplotype reconstruction program HAPPY.", "sc:name": "Prephappy", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://valdarlab.unc.edu/prephappy.html", "sc:version": "20130226" diff --git a/data/preppi/preppibioschemas.jsonld b/data/preppi/preppibioschemas.jsonld index ec024e60dd72c..50b108f29dc4b 100644 --- a/data/preppi/preppibioschemas.jsonld +++ b/data/preppi/preppibioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Database of predicted and experimentally determined protein-protein interactions (PPI) for yeast and human. Predicted interactions in the database are determined using a Bayesian framework that combines structural, functional, evolutionary and expression information.", "sc:name": "PrePPI", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bhapp.c2b2.columbia.edu/PrePPI/" diff --git a/data/preprocesscore/bioconda_preprocesscore.yaml b/data/preprocesscore/bioconda_preprocesscore.yaml index 333f73a81c5f6..a2ccb88922d8c 100644 --- a/data/preprocesscore/bioconda_preprocesscore.yaml +++ b/data/preprocesscore/bioconda_preprocesscore.yaml @@ -3,7 +3,6 @@ description: A library of core preprocessing routines. home: https://bioconductor.org/packages/3.10/bioc/html/preprocessCore.html identifiers: - biotools:preprocesscore -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-preprocesscore diff --git a/data/presartools/presartoolsbioschemas.jsonld b/data/presartools/presartoolsbioschemas.jsonld index 609977994fca5..600a5079cecdc 100644 --- a/data/presartools/presartoolsbioschemas.jsonld +++ b/data/presartools/presartoolsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Generate design/target file and archive for SARTools inputs.", "sc:name": "presartools", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/PF2-pasteur-fr/SARTools", "sc:version": "0.1.0" diff --git a/data/preseq/preseqbioschemas.jsonld b/data/preseq/preseqbioschemas.jsonld index 09dc3df5c2a71..7b1376394822f 100644 --- a/data/preseq/preseqbioschemas.jsonld +++ b/data/preseq/preseqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This package is aimed at predicting and number of distinct reads and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.", "sc:name": "preseq", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://smithlabresearch.org/software/preseq/" } \ No newline at end of file diff --git a/data/press/pressbioschemas.jsonld b/data/press/pressbioschemas.jsonld index 9e647dc5b1c17..887feac7132c4 100644 --- a/data/press/pressbioschemas.jsonld +++ b/data/press/pressbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "P.R.E.S.S. (Protein Residue-Level Structural Statistics) is an R-package developed to allow researchers to get access to and manipulate on a large set of statistical data on protein residue-level structural properties such as residue-level virtual bond lengths, virtual bond angles, and virtual torsion angles.", "sc:name": "P.R.E.S.S.", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://orion.math.iastate.edu/press/presspage/P.R.E.S.S..html", diff --git a/data/prettyplot/prettyplotbioschemas.jsonld b/data/prettyplot/prettyplotbioschemas.jsonld index cf9b3a85805b1..e5a59a2f985a6 100644 --- a/data/prettyplot/prettyplotbioschemas.jsonld +++ b/data/prettyplot/prettyplotbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", + "EMBOSS Contributors", "Wellcome Trust", - "UK MRC", - "EMBOSS Contributors" + "UK BBSRC", + "UK MRC" ], "sc:description": "Draw a sequence alignment with pretty formatting.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "prettyplot", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/prettyplot.html", "sc:version": "r6" diff --git a/data/prettyplot_ws_husar/prettyplot_ws_husarbioschemas.jsonld b/data/prettyplot_ws_husar/prettyplot_ws_husarbioschemas.jsonld index 011ccdcb04861..0d0467d6d9518 100644 --- a/data/prettyplot_ws_husar/prettyplot_ws_husarbioschemas.jsonld +++ b/data/prettyplot_ws_husar/prettyplot_ws_husarbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Reads in a set of aligned DNA or protein sequences. It displays them graphically, with conserved regions highlighted in various ways.", "sc:name": "prettyplot WS (husar)", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/prettyplot.html", "sc:version": "1" diff --git a/data/prettyseq/prettyseqbioschemas.jsonld b/data/prettyseq/prettyseqbioschemas.jsonld index 86be565239a0d..fd64abf8c89e7 100644 --- a/data/prettyseq/prettyseqbioschemas.jsonld +++ b/data/prettyseq/prettyseqbioschemas.jsonld @@ -19,20 +19,20 @@ ], "sc:description": "Write a nucleotide sequence and its translation to file.", "sc:funder": [ - "UK BBSRC", "UK MRC", + "UK BBSRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "prettyseq", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/prettyseq.html", "sc:version": "r6" diff --git a/data/prex/prexbioschemas.jsonld b/data/prex/prexbioschemas.jsonld index 412c3e01c0552..65b9e6ec409b0 100644 --- a/data/prex/prexbioschemas.jsonld +++ b/data/prex/prexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Database of peroxiredoxin (Prx or PRDX) protein sequences unambiguously classified into one of six distinct subfamilies. Subfamily members were identified using the Deacon Active Site Profiler (DASP) bioinformatics tool to focus in on functionally relevant sequence fragments surrounding key residues required for protein activity. Searches of this database can be conducted by protein annotation, accession number, PDB ID, organism name or protein sequence.", "sc:name": "PREX", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.csb.wfu.edu/prex/" diff --git a/data/prgdb/prgdbbioschemas.jsonld b/data/prgdb/prgdbbioschemas.jsonld index 096c8e5f6cf8b..76bd39f40e675 100644 --- a/data/prgdb/prgdbbioschemas.jsonld +++ b/data/prgdb/prgdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database provides a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16,000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. Data can be examined using different query tools.", "sc:name": "Plant Resistance Genes database (prgdb)", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.prgdb.org" } \ No newline at end of file diff --git a/data/priam_search/priam_searchbioschemas.jsonld b/data/priam_search/priam_searchbioschemas.jsonld index ffbc8d47bc5bb..c667320d2e620 100644 --- a/data/priam_search/priam_searchbioschemas.jsonld +++ b/data/priam_search/priam_searchbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/priam_search", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", "Database portal", + "Web application", "Command-line tool" ], "sc:author": "Thomas Bernard", @@ -25,10 +25,10 @@ "Windows" ], "sc:provider": [ - "Lyon 1 University", + "Pole Rhone-Alpin de Bioinformatique", "INRA", "univ-lyon1.fr", - "Pole Rhone-Alpin de Bioinformatique" + "Lyon 1 University" ], "sc:url": "http://priam.prabi.fr/REL_MAR15/index_mar15.html" } \ No newline at end of file diff --git a/data/price/pricebioschemas.jsonld b/data/price/pricebioschemas.jsonld index dd1b8d92656af..ebbcc8702beb2 100644 --- a/data/price/pricebioschemas.jsonld +++ b/data/price/pricebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "PRICE uses paired-read information to iteratively increase the size of existing contigs.", "sc:name": "PRICE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://derisilab.ucsf.edu/software/price/index.html" } \ No newline at end of file diff --git a/data/pridb/pridbbioschemas.jsonld b/data/pridb/pridbbioschemas.jsonld index c687bf924b51a..9ae3530c6aa1d 100644 --- a/data/pridb/pridbbioschemas.jsonld +++ b/data/pridb/pridbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of protein-RNA interfaces extracted from complexes in the Protein Data Bank (PDB). It is designed to facilitate detailed analyses of individual protein-RNA complexes and their interfaces, in addition to automated generation of user-defined data sets of protein-RNA interfaces for statistical analyses and machine learning applications.", "sc:name": "PRIDB", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bindr.gdcb.iastate.edu/PRIDB" } \ No newline at end of file diff --git a/data/pride/pridebioschemas.jsonld b/data/pride/pridebioschemas.jsonld index fd5bad7c9b3a9..5c07eaa84ab39 100644 --- a/data/pride/pridebioschemas.jsonld +++ b/data/pride/pridebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays.", "sc:name": "PRIDE", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ "EMBL-EBI Databases", diff --git a/data/pride_converter/pride_converterbioschemas.jsonld b/data/pride_converter/pride_converterbioschemas.jsonld index 112f6d2bfefce..a3f70eb17e9e3 100644 --- a/data/pride_converter/pride_converterbioschemas.jsonld +++ b/data/pride_converter/pride_converterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Converts mass spectrometry data from most common data formats into valid PRIDE XML for submission to the publicly available PRIDE database. It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service.", "sc:name": "PRIDE Converter", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/PRIDE-Toolsuite/pride-converter-2", diff --git a/data/pride_toolsuite/pride_toolsuitebioschemas.jsonld b/data/pride_toolsuite/pride_toolsuitebioschemas.jsonld index eecf1028a59a6..bcb7558d05a74 100644 --- a/data/pride_toolsuite/pride_toolsuitebioschemas.jsonld +++ b/data/pride_toolsuite/pride_toolsuitebioschemas.jsonld @@ -11,14 +11,14 @@ "@id": "https://bio.tools/pride_toolsuite", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Suite" + "Suite", + "Desktop application" ], "sc:description": "A selection of tools and libraries for interacting with data in PRIDE.", "sc:name": "PRIDE Toolsuite", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/PRIDE-Toolsuite" } \ No newline at end of file diff --git a/data/prifi/prifibioschemas.jsonld b/data/prifi/prifibioschemas.jsonld index 5eaadbd6ec0ac..e6a49f11d7671 100644 --- a/data/prifi/prifibioschemas.jsonld +++ b/data/prifi/prifibioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PriFi", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://services.birc.au.dk/prifi/" } \ No newline at end of file diff --git a/data/primaclade/primacladebioschemas.jsonld b/data/primaclade/primacladebioschemas.jsonld index 4d3d210c852a7..e383c33189946 100644 --- a/data/primaclade/primacladebioschemas.jsonld +++ b/data/primaclade/primacladebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Accepts a multiple species nucleotide alignment file as input, iteratively runs the Primer3 application for each sequence, and then collates the results to identify a set of polymerase chain reaction (PCR) primers that will bind across the alignment.", "sc:name": "Primaclade", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://primaclade.org/cgi-bin/primaclade.cgi" } \ No newline at end of file diff --git a/data/primer/primerbioschemas.jsonld b/data/primer/primerbioschemas.jsonld index f8fa7e4dab44d..4ffb78ccd2ca0 100644 --- a/data/primer/primerbioschemas.jsonld +++ b/data/primer/primerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predicts potential protein-binding nucleotides in the RNA sequence.", "sc:name": "Primer", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bclab.inha.ac.kr/primer/" } \ No newline at end of file diff --git a/data/primer3/primer3bioschemas.jsonld b/data/primer3/primer3bioschemas.jsonld index d22ffc303909e..1c729db1014f7 100644 --- a/data/primer3/primer3bioschemas.jsonld +++ b/data/primer3/primer3bioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Primer3", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://primer3.ut.ee/", diff --git a/data/primer3plus/primer3plusbioschemas.jsonld b/data/primer3plus/primer3plusbioschemas.jsonld index fda4bf527a62e..2215ca457994a 100644 --- a/data/primer3plus/primer3plusbioschemas.jsonld +++ b/data/primer3plus/primer3plusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Primer3Plus is an enhanced web interface to the popular Primer3 PCR primer design program.", "sc:name": "Primer3Plus", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi" } \ No newline at end of file diff --git a/data/primerbank/primerbankbioschemas.jsonld b/data/primerbank/primerbankbioschemas.jsonld index af6a714731a2a..a6368d2c2e273 100644 --- a/data/primerbank/primerbankbioschemas.jsonld +++ b/data/primerbank/primerbankbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PrimerBank", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://pga.mgh.harvard.edu/primerbank/" } \ No newline at end of file diff --git a/data/primerdesign-m/primerdesign-mbioschemas.jsonld b/data/primerdesign-m/primerdesign-mbioschemas.jsonld index c0ffc5d91eb99..30d992871d6a3 100644 --- a/data/primerdesign-m/primerdesign-mbioschemas.jsonld +++ b/data/primerdesign-m/primerdesign-mbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Primer design for highly variable sets of aligned sequences. It includes design requirements for next-generation sequences (NGS) including 454 sequences. It can also be used for primer and probe design for PCR, Sanger sequencing, and other systems with custom barcodes and DNA handles for universal primer annealing. The tool will design several alternative primer sets, whenever possible.", "sc:name": "PrimerDesign-M", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html" } \ No newline at end of file diff --git a/data/primerize-2d/primerize-2dbioschemas.jsonld b/data/primerize-2d/primerize-2dbioschemas.jsonld index 0139850666e0e..00dbf0f5a2cd7 100644 --- a/data/primerize-2d/primerize-2dbioschemas.jsonld +++ b/data/primerize-2d/primerize-2dbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Automated primer design for RNA multidimensional chemical mapping .", "sc:name": "Primerize-2D", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://primerize.stanford.edu/primerize2d/" } \ No newline at end of file diff --git a/data/primerize/primerizebioschemas.jsonld b/data/primerize/primerizebioschemas.jsonld index e5c92e46d8b11..21c89c380c404 100644 --- a/data/primerize/primerizebioschemas.jsonld +++ b/data/primerize/primerizebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Primerize is a Web Server for primer designs of DNA sequence PCR assembly. Primerize is optimized to reduce primer boundaries mispriming, is designed for fixed sequences of RNA problems, and passed wide and stringent tests.", "sc:name": "Primerize", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://primerize.stanford.edu/", diff --git a/data/primers4clades/primers4cladesbioschemas.jsonld b/data/primers4clades/primers4cladesbioschemas.jsonld index e0f11267b8831..9f45613dedba5 100644 --- a/data/primers4clades/primers4cladesbioschemas.jsonld +++ b/data/primers4clades/primers4cladesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Primers4clades is a web server that uses phylogenetic trees to design primers to amplify novel sequences from across species using metagenomic DNA or from uncharacterized organisms. Beginning with a set of non-aligned protein coding genes, primers4clades aligns the sequences, computes a neighbor-joining tree and designs lineage specific primers for the user selected species or sequence clusters.", "sc:name": "primers4clades", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://maya.ccg.unam.mx/primers4clades/" } \ No newline at end of file diff --git a/data/primersearch/primersearchbioschemas.jsonld b/data/primersearch/primersearchbioschemas.jsonld index 62d465b1d94a0..a29a02033636e 100644 --- a/data/primersearch/primersearchbioschemas.jsonld +++ b/data/primersearch/primersearchbioschemas.jsonld @@ -12,22 +12,22 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "EMBOSS Contributors", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Search DNA sequences for matches with primer pairs.", "sc:funder": [ "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "primersearch", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ diff --git a/data/primerselect/primerselectbioschemas.jsonld b/data/primerselect/primerselectbioschemas.jsonld index c656925878266..c004e29582e0c 100644 --- a/data/primerselect/primerselectbioschemas.jsonld +++ b/data/primerselect/primerselectbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Program that computes the AES score for each position in a genome given a random primer 5′ tag.", "sc:name": "PrimerSelect", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.gis.a-star.edu.sg/pathchip/" } \ No newline at end of file diff --git a/data/primerseq/primerseqbioschemas.jsonld b/data/primerseq/primerseqbioschemas.jsonld index 4216f38cd00d8..44bf958d884b8 100644 --- a/data/primerseq/primerseqbioschemas.jsonld +++ b/data/primerseq/primerseqbioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC4411361", + "pubmed:24747190", { "@id": "https://doi.org/10.1016/j.gpb.2014.04.001" - }, - "pmcid:PMC4411361", - "pubmed:24747190" + } ], "sc:description": "PrimerSeq designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data.", "sc:featureList": { @@ -26,8 +26,8 @@ }, "sc:name": "PrimerSeq", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://primerseq.sourceforge.net/", "sc:version": "1.1.12" diff --git a/data/primerstation/primerstationbioschemas.jsonld b/data/primerstation/primerstationbioschemas.jsonld index 493ea068744b7..7894eac9c08bc 100644 --- a/data/primerstation/primerstationbioschemas.jsonld +++ b/data/primerstation/primerstationbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PrimerStation is a multiplex genomic PCR primer design tool specific for the human genome.", "sc:name": "PrimerStation", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://ps.cb.k.u-tokyo.ac.jp/" } \ No newline at end of file diff --git a/data/primersuite/primersuitebioschemas.jsonld b/data/primersuite/primersuitebioschemas.jsonld index c34f7707e85bf..e48db352cf36a 100644 --- a/data/primersuite/primersuitebioschemas.jsonld +++ b/data/primersuite/primersuitebioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Jennifer Lu", "sc:additionalType": "Suite", "sc:citation": [ + "pubmed:28117430", "pmcid:PMC5259761", { "@id": "https://doi.org/10.1038/srep41328" - }, - "pubmed:28117430" + } ], "sc:description": "High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "PrimerSuite", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.primer-suite.com/" } diff --git a/data/primerxl/primerxlbioschemas.jsonld b/data/primerxl/primerxlbioschemas.jsonld index 09a03ec5f188d..e8ccbbfd99889 100644 --- a/data/primerxl/primerxlbioschemas.jsonld +++ b/data/primerxl/primerxlbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "primerXL", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.primerxl.org/" } \ No newline at end of file diff --git a/data/primo/primobioschemas.jsonld b/data/primo/primobioschemas.jsonld index fbc01864dcca9..15b637d022b65 100644 --- a/data/primo/primobioschemas.jsonld +++ b/data/primo/primobioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Özlem Tastan Bishop", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC5113968", + "pubmed:27855192", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0166698" - }, - "pmcid:PMC5113968", - "pubmed:27855192" + } ], "sc:description": "An Interactive Homology Modeling Pipeline", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "PRIMO", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://primo.rubi.ru.ac.za/" diff --git a/data/princces/princcesbioschemas.jsonld b/data/princces/princcesbioschemas.jsonld index 0a59253e1c5ec..c2771d0dbb597 100644 --- a/data/princces/princcesbioschemas.jsonld +++ b/data/princces/princcesbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/princces", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:citation": "pubmed:26409191", "sc:description": "Computer program for the automatic visualization of voids in proteins or protein complexes. The input of the program is the PDB (Protein Data Bank) file of the structure.", diff --git a/data/prince/princebioschemas.jsonld b/data/prince/princebioschemas.jsonld index cda57083f5e14..0c5434702e94f 100644 --- a/data/prince/princebioschemas.jsonld +++ b/data/prince/princebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web server which analyzes the structural features and physicochemical properties of the protein-RNA interface.", "sc:name": "PRince", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html" diff --git a/data/princess/princessbioschemas.jsonld b/data/princess/princessbioschemas.jsonld index 97c1ee4b5bfbe..64c9f60b9e50a 100644 --- a/data/princess/princessbioschemas.jsonld +++ b/data/princess/princessbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Feng Chen", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:28065902", "pmcid:PMC5860394", { "@id": "https://doi.org/10.1093/bioinformatics/btw758" - }, - "pubmed:28065902" + } ], "sc:description": "Privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:license": "Other", "sc:name": "PRINCESS", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/achenfengb/PRINCESS_opensource" }, diff --git a/data/princeton_tigress/princeton_tigressbioschemas.jsonld b/data/princeton_tigress/princeton_tigressbioschemas.jsonld index f7ec495f65115..6b183a7015047 100644 --- a/data/princeton_tigress/princeton_tigressbioschemas.jsonld +++ b/data/princeton_tigress/princeton_tigressbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Automated refinement method that intends to refine an input protein structure by addressing both sampling and selection.", "sc:name": "Princeton_TIGRESS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://atlas.princeton.edu/refinement/" } \ No newline at end of file diff --git a/data/prinseq/prinseqbioschemas.jsonld b/data/prinseq/prinseqbioschemas.jsonld index b4e5e04b59eae..9d5fdadd36eae 100644 --- a/data/prinseq/prinseqbioschemas.jsonld +++ b/data/prinseq/prinseqbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "PRINSEQ", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://edwards.sdsu.edu/prinseq" diff --git a/data/prints/printsbioschemas.jsonld b/data/prints/printsbioschemas.jsonld index 3adef3d7557dc..fd4e74435cc42 100644 --- a/data/prints/printsbioschemas.jsonld +++ b/data/prints/printsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A compendium of protein fingerprints, or group of conserved motifs used to characterise a protein family.", "sc:name": "PRINTS protein motif fingerprint database", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/" } \ No newline at end of file diff --git a/data/printsextract/printsextractbioschemas.jsonld b/data/printsextract/printsextractbioschemas.jsonld index ecd74bb3fa424..576a887ec527c 100644 --- a/data/printsextract/printsextractbioschemas.jsonld +++ b/data/printsextract/printsextractbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "UK MRC", + "EMBOSS Contributors", + "Wellcome Trust" ], "sc:description": "Extract data from PRINTS database for use by pscan.", "sc:funder": [ + "UK MRC", "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "printsextract", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/printsextract.html", "sc:version": "r6" diff --git a/data/priority/prioritybioschemas.jsonld b/data/priority/prioritybioschemas.jsonld index 72390eea05d96..47cb6c42fecd6 100644 --- a/data/priority/prioritybioschemas.jsonld +++ b/data/priority/prioritybioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "PRIORITY is a tool for de novo motif discovery in the context of transcription factor (TF) binding sites. It implements a new approach to motif discovery in which informative priors over sequence positions are used to guide the search.", "sc:name": "PRIORITY", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.cs.duke.edu/~amink/software/priority/", "sc:version": "2.1.0" diff --git a/data/prism-ppi/prism-ppibioschemas.jsonld b/data/prism-ppi/prism-ppibioschemas.jsonld index faac4c0ce75b4..bf33c8d6916b7 100644 --- a/data/prism-ppi/prism-ppibioschemas.jsonld +++ b/data/prism-ppi/prism-ppibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Fast and accurate prediction of protein-protein interactions (PPIs).", "sc:name": "PRISM", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://cosbi.ku.edu.tr/prism/" } \ No newline at end of file diff --git a/data/prism_3/prism_3bioschemas.jsonld b/data/prism_3/prism_3bioschemas.jsonld index 77b718aad469d..3e50eeffcae28 100644 --- a/data/prism_3/prism_3bioschemas.jsonld +++ b/data/prism_3/prism_3bioschemas.jsonld @@ -19,10 +19,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC5570231", - "pubmed:28460067", { "@id": "https://doi.org/10.1093/NAR/GKX320" - } + }, + "pubmed:28460067" ], "sc:description": "PRediction Informatics for Secondary Metabolomes. Prediction of genetically encoded natural product structures based on microbial genomes. It takes a microbial genome sequence as input, identifies biosynthetic gene clusters, and generates combinatorial libraries of structure predictions.", "sc:featureList": { diff --git a/data/prismatic/prismaticbioschemas.jsonld b/data/prismatic/prismaticbioschemas.jsonld index b1ba859f9574d..68e074e862126 100644 --- a/data/prismatic/prismaticbioschemas.jsonld +++ b/data/prismatic/prismaticbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s40679-017-0048-z", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/prismatic", "@type": "sc:SoftwareApplication", @@ -38,10 +42,6 @@ "Windows" ], "sc:url": "http://prism-em.com/" - }, - { - "@id": "https://doi.org/10.1186/s40679-017-0048-z", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/prize/bioconda_prize.yaml b/data/prize/bioconda_prize.yaml index 0cf6e892ea113..86320614fb58e 100644 --- a/data/prize/bioconda_prize.yaml +++ b/data/prize/bioconda_prize.yaml @@ -11,7 +11,6 @@ description: The high throughput studies often produce large amounts of numerous home: https://bioconductor.org/packages/3.10/bioc/html/Prize.html identifiers: - biotools:prize -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-prize summary: 'Prize: an R package for prioritization estimation based on analytic hierarchy diff --git a/data/prize/prizebioschemas.jsonld b/data/prize/prizebioschemas.jsonld index 93ab6e80ff8ce..4795eaf27c11d 100644 --- a/data/prize/prizebioschemas.jsonld +++ b/data/prize/prizebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Daryanaz Dargahi", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This tool offers a novel approach to narrow down long lists of candidates by prioritizing them based on how well they meet the research goal. It organizes and analyzes complex decisions where multiple criteria are involved. The technique structures problems into a hierarchy of elements, and helps to specify numerical weights representing the relative importance of each element.", "sc:license": "Artistic-2.0", "sc:name": "Prize", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Prize.html", "sc:version": "1.5.1" diff --git a/data/prmepred/prmepredbioschemas.jsonld b/data/prmepred/prmepredbioschemas.jsonld index b5767dc6de0a9..3d88dc7fb1d6c 100644 --- a/data/prmepred/prmepredbioschemas.jsonld +++ b/data/prmepred/prmepredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Protein arginine methylation prediction tool.", "sc:name": "PRmePRed", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioinfo.icgeb.res.in/PRmePRed/" } \ No newline at end of file diff --git a/data/prn/prnbioschemas.jsonld b/data/prn/prnbioschemas.jsonld index ac99fbee87a6f..a2b871048392d 100644 --- a/data/prn/prnbioschemas.jsonld +++ b/data/prn/prnbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.5951.2", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-3413-5977", "@type": "schema:Person" @@ -25,11 +21,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:25844159", + "pmcid:PMC4367516", { "@id": "https://doi.org/10.12688/F1000RESEARCH.5951.2" - }, - "pmcid:PMC4367516", - "pubmed:25844159" + } ], "sc:description": "Preprints of the R-fMRI Network. A community funded preprint hosting service. Provides free-submission and free hosting of manuscripts for resting state functional magnetic resonance imaging (R-fMRI) and neuroscience related studies.", "sc:featureList": { @@ -37,6 +33,10 @@ }, "sc:name": "PRN", "sc:url": "http://rfmri.org/PRN" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.5951.2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pro-bs/pro-bsbioschemas.jsonld b/data/pro-bs/pro-bsbioschemas.jsonld index 8cfe1b99a1ea4..e259405a8a888 100644 --- a/data/pro-bs/pro-bsbioschemas.jsonld +++ b/data/pro-bs/pro-bsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Tool for predicting the binding sites for the given proteins.", "sc:name": "Pro-BS", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sites.google.com/site/guofeics/pro-bs" } \ No newline at end of file diff --git a/data/pro-coffee/pro-coffeebioschemas.jsonld b/data/pro-coffee/pro-coffeebioschemas.jsonld index 91a246c13ce4a..26f7359439aed 100644 --- a/data/pro-coffee/pro-coffeebioschemas.jsonld +++ b/data/pro-coffee/pro-coffeebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Pro-Coffee", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://tcoffee.crg.cat/apps/tcoffee/do:procoffee" } \ No newline at end of file diff --git a/data/pro-maya/pro-mayabioschemas.jsonld b/data/pro-maya/pro-mayabioschemas.jsonld index 755f032873bc8..da7d45bafee08 100644 --- a/data/pro-maya/pro-mayabioschemas.jsonld +++ b/data/pro-maya/pro-mayabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predict the protein stability free energy difference (ΔG), arising from a single-site amino acid substitution compared to the wild-type, denoted as ΔΔG.", "sc:name": "Pro-Maya", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bental.tau.ac.il/ProMaya/" } \ No newline at end of file diff --git a/data/pro/probioschemas.jsonld b/data/pro/probioschemas.jsonld index 9a65a6fa673e1..ab70725f82115 100644 --- a/data/pro/probioschemas.jsonld +++ b/data/pro/probioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "The Protein Ontology", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://pir.georgetown.edu/pro" } \ No newline at end of file diff --git a/data/proabc/proabcbioschemas.jsonld b/data/proabc/proabcbioschemas.jsonld index fc4288b8c3454..dcf513a766eee 100644 --- a/data/proabc/proabcbioschemas.jsonld +++ b/data/proabc/proabcbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predictor of Antibody-Antigen interactions based on the Random Forest Algorithm. User submitted sequences are automatically aligned and annotated according to their source organism and germline families.", "sc:name": "proABC", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "ELIXIR-ITA-SAPIENZA", "sc:url": "http://www.biocomputing.it/proABC", diff --git a/data/probamr/probamrbioschemas.jsonld b/data/probamr/probamrbioschemas.jsonld index 3e02a0c8575f6..b340673ca4d11 100644 --- a/data/probamr/probamrbioschemas.jsonld +++ b/data/probamr/probamrbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "proBAMr", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/proBAMr.html", diff --git a/data/probcons/probconsbioschemas.jsonld b/data/probcons/probconsbioschemas.jsonld index b188cb4664d10..2a298f7d35ef8 100644 --- a/data/probcons/probconsbioschemas.jsonld +++ b/data/probcons/probconsbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "ProbCons", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://probcons.stanford.edu/" } \ No newline at end of file diff --git a/data/probcons_ws_jabaws/probcons_ws_jabawsbioschemas.jsonld b/data/probcons_ws_jabaws/probcons_ws_jabawsbioschemas.jsonld index 455197820c3c2..7673dfc6127de 100644 --- a/data/probcons_ws_jabaws/probcons_ws_jabawsbioschemas.jsonld +++ b/data/probcons_ws_jabaws/probcons_ws_jabawsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Tool for progressive protein multiple sequence alignment based on probabilistic consistency.", "sc:name": "Probcons WS (jabaws)", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.compbio.dundee.ac.uk/jabaws/", "sc:version": "1" diff --git a/data/probe/probebioschemas.jsonld b/data/probe/probebioschemas.jsonld index ac188c6a600ca..838240f772cf5 100644 --- a/data/probe/probebioschemas.jsonld +++ b/data/probe/probebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "Protein Binding Evaluation (PROBE)", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://pallab.serc.iisc.ernet.in/probe" } \ No newline at end of file diff --git a/data/probelynx/probelynxbioschemas.jsonld b/data/probelynx/probelynxbioschemas.jsonld index be1ea96f7f960..c40aaea348105 100644 --- a/data/probelynx/probelynxbioschemas.jsonld +++ b/data/probelynx/probelynxbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Using current releases of genomic sequence data, this tool allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and the tool reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.", "sc:name": "ProbeLynx", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.pathogenomics.ca/probelynx" } \ No newline at end of file diff --git a/data/probematch/probematchbioschemas.jsonld b/data/probematch/probematchbioschemas.jsonld index 284cb2bedc784..49cd4f328d0c4 100644 --- a/data/probematch/probematchbioschemas.jsonld +++ b/data/probematch/probematchbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A program that matches a large set of oligonucleotide sequences against a genome database using gapped alignments.", "sc:name": "ProbeMatch", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.cs.wisc.edu/%7Ejignesh/probematch/" } \ No newline at end of file diff --git a/data/prober-chem/prober-chembioschemas.jsonld b/data/prober-chem/prober-chembioschemas.jsonld index a0e0a0ab90245..dc62351529a32 100644 --- a/data/prober-chem/prober-chembioschemas.jsonld +++ b/data/prober-chem/prober-chembioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/j.cels.2017.04.007", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/prober-chem", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lior Pachter", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5758053", - "pubmed:28501650", { "@id": "https://doi.org/10.1016/j.cels.2017.04.007" - } + }, + "pubmed:28501650", + "pmcid:PMC5758053" ], "sc:description": "PROBer is a program to quantify chemical modification profiles for a general set of sequencing-based ‘toeprinting’ assays, which aim at probing RNA structures (DMS/SHAPE-seq), detecting RNA modifications (Pseudo-seq), and investigating RNA-protein interactions (iCLIP).", "sc:featureList": { @@ -37,6 +33,10 @@ ], "sc:url": "http://pachterlab.github.io/PROBer/", "sc:version": "0.3.1" + }, + { + "@id": "https://doi.org/10.1016/j.cels.2017.04.007", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/probias/probiasbioschemas.jsonld b/data/probias/probiasbioschemas.jsonld index 3433da4772bdc..9e10861cb59af 100644 --- a/data/probias/probiasbioschemas.jsonld +++ b/data/probias/probiasbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "It is a novel sensitive method for the detection of user-defined compositional bias in biological sequences.\nIt automatically searches a user-supplied protein sequence for segments that contain unusually dense clusters of user-specified amino acid types and computes analytical estimates of the statistical significance of each cluster.", "sc:name": "ProBias", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://lcg.rit.albany.edu/bias/" diff --git a/data/probis-ligands/probis-ligandsbioschemas.jsonld b/data/probis-ligands/probis-ligandsbioschemas.jsonld index d87a0cf6753ee..153e1376a544c 100644 --- a/data/probis-ligands/probis-ligandsbioschemas.jsonld +++ b/data/probis-ligands/probis-ligandsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "ProBiS is a web server for predicting ligands by similarity in binding sites.", "sc:name": "ProBiS-ligands", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://probis.cmm.ki.si/ligands" diff --git a/data/probis/probisbioschemas.jsonld b/data/probis/probisbioschemas.jsonld index ffee24ea5f7d3..8b220d3c494d3 100644 --- a/data/probis/probisbioschemas.jsonld +++ b/data/probis/probisbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server which detects protein binding sites based on local structural alignments. Algorithms have been parallelized to allow for faster computing against the PDB. Pre-calculated protein similarity profiles for over 29,000 non-redundant proteins are also available.", "sc:name": "ProBiS", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://probis.cmm.ki.si" } \ No newline at end of file diff --git a/data/problm/problmbioschemas.jsonld b/data/problm/problmbioschemas.jsonld index a9a9ab81369b9..22c9a999cdbf1 100644 --- a/data/problm/problmbioschemas.jsonld +++ b/data/problm/problmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Webserver that creates a combined protein-membrane complex when given a membrane protein (helical or beta-barrel) and bilayer lipid membrane (POPC, POPE or artificial).", "sc:name": "ProBLM", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://compbio.clemson.edu/sapp/problm_webserver/" } \ No newline at end of file diff --git a/data/probrna/probrnabioschemas.jsonld b/data/probrna/probrnabioschemas.jsonld index d714997a44306..1b770df74872a 100644 --- a/data/probrna/probrnabioschemas.jsonld +++ b/data/probrna/probrnabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Produce features found to be related to both the secondary and tertiary structures of the RNAs.", "sc:name": "ProbRNA", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://hkbic.cuhk.edu.hk/software/probrna" } \ No newline at end of file diff --git a/data/process/bioconda_process.yaml b/data/process/bioconda_process.yaml index c2c9d9318176d..dcc0d9c61da24 100644 --- a/data/process/bioconda_process.yaml +++ b/data/process/bioconda_process.yaml @@ -3,7 +3,6 @@ description: A package for processing protein mass spectrometry data. home: https://bioconductor.org/packages/3.10/bioc/html/PROcess.html identifiers: - biotools:process -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-process summary: Ciphergen SELDI-TOF Processing diff --git a/data/process/processbioschemas.jsonld b/data/process/processbioschemas.jsonld index f55bb27fa045f..43b31c0a32253 100644 --- a/data/process/processbioschemas.jsonld +++ b/data/process/processbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xiaochun Li", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A package for processing protein mass spectrometry data.", "sc:license": "Artistic-2.0", "sc:name": "PROcess", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PROcess.html", "sc:version": "1.50.0" diff --git a/data/procheck/procheckbioschemas.jsonld b/data/procheck/procheckbioschemas.jsonld index 4a5c16382ae49..12943af02e272 100644 --- a/data/procheck/procheckbioschemas.jsonld +++ b/data/procheck/procheckbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Check the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.", "sc:name": "PROCHECK", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/" } \ No newline at end of file diff --git a/data/procksi/procksibioschemas.jsonld b/data/procksi/procksibioschemas.jsonld index cccc6c9bbc7b9..a2ff32835343e 100644 --- a/data/procksi/procksibioschemas.jsonld +++ b/data/procksi/procksibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Multi-layer protein comparison meta-server that computes structure similarities using various information theory measures. It integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. Based on a diverse set of similarity measures computes a consensus similarity profile for the entire protein set. All results can be clustered, visualised, analysed.", "sc:name": "ProCKSI", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.procksi.net/" } \ No newline at end of file diff --git a/data/proclass/proclassbioschemas.jsonld b/data/proclass/proclassbioschemas.jsonld index 5b3a1235b41d4..f3f7164833330 100644 --- a/data/proclass/proclassbioschemas.jsonld +++ b/data/proclass/proclassbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PROCLASS", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/proclass/" } \ No newline at end of file diff --git a/data/procoil/procoilbioschemas.jsonld b/data/procoil/procoilbioschemas.jsonld index cb6552b0f6961..eb59a965b9762 100644 --- a/data/procoil/procoilbioschemas.jsonld +++ b/data/procoil/procoilbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1074/mcp.M110.004994", "@type": "sc:CreativeWork" }, + { + "@id": "http://orcid.org/0000-0001-6859-8828", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/procoil", "@type": "sc:SoftwareApplication", @@ -24,11 +28,11 @@ "Library" ], "sc:citation": [ + "pmcid:PMC3098589", "pubmed:21311038", { "@id": "https://doi.org/10.1074/mcp.M110.004994" - }, - "pmcid:PMC3098589" + } ], "sc:description": "The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.", "sc:featureList": { @@ -38,15 +42,11 @@ "sc:name": "procoil", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/procoil.html", "sc:version": "2.2.0" - }, - { - "@id": "http://orcid.org/0000-0001-6859-8828", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/procon/proconbioschemas.jsonld b/data/procon/proconbioschemas.jsonld index a350663209375..72021ad8e67d9 100644 --- a/data/procon/proconbioschemas.jsonld +++ b/data/procon/proconbioschemas.jsonld @@ -17,10 +17,10 @@ "@id": "https://bio.tools/procon", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "PD Dr. Martin Eisenacher", { "@id": "http://orcid.org/0000-0002-1767-2343" - } + }, + "PD Dr. Martin Eisenacher" ], "sc:additionalType": "Desktop application", "sc:author": [ @@ -34,9 +34,9 @@ "sc:license": "Apache-2.0", "sc:name": "ProCon (Proteomics Conversion Tool)", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.ruhr-uni-bochum.de/mpc/software/ProCon/index.html.en", "sc:version": "0.9.654" diff --git a/data/procona/proconabioschemas.jsonld b/data/procona/proconabioschemas.jsonld index 72ddbd539b8b1..e0131e717c126 100644 --- a/data/procona/proconabioschemas.jsonld +++ b/data/procona/proconabioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David L Gibbs", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Protein co-expression network construction using peptide level data, with statisical analysis. (Journal of Clinical Bioinformatics 2013, 3:11 doi:10.1186/2043-9113-3-11)", "sc:license": "GPL-2.0", "sc:name": "ProCoNA", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ProCoNA.html", diff --git a/data/prodepth/prodepthbioschemas.jsonld b/data/prodepth/prodepthbioschemas.jsonld index 810cc72ca0a04..b6fb80ac26bb7 100644 --- a/data/prodepth/prodepthbioschemas.jsonld +++ b/data/prodepth/prodepthbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Prodepth is an online prediction web server for the accurate prediction of residue depth from protein sequences only. It can be used to accurately identify the burial depth status of amino acid residues in a protein.", "sc:name": "Prodepth", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/Prodepth/" } \ No newline at end of file diff --git a/data/prodesign/prodesignbioschemas.jsonld b/data/prodesign/prodesignbioschemas.jsonld index 689e591730519..2089b0057f03f 100644 --- a/data/prodesign/prodesignbioschemas.jsonld +++ b/data/prodesign/prodesignbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Generate oligonucleotide probes for genes and gene families.", "sc:name": "Prodesign", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.uhnresearch.ca/labs/tillier/software.htm#7" diff --git a/data/prodge/prodgebioschemas.jsonld b/data/prodge/prodgebioschemas.jsonld index f923b1bfada35..e4035a9468085 100644 --- a/data/prodge/prodgebioschemas.jsonld +++ b/data/prodge/prodgebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Protein Domain Gene visualizes existing and suggests novel domaindomain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct.", "sc:name": "ProDGe", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.ra.cs.uni-tuebingen.de/software/ProDGe/index.htm", "sc:version": "20110509" diff --git a/data/prodigy-crystal/prodigy-crystalbioschemas.jsonld b/data/prodigy-crystal/prodigy-crystalbioschemas.jsonld index 40032ac8d3b9c..9665ab6a6213f 100644 --- a/data/prodigy-crystal/prodigy-crystalbioschemas.jsonld +++ b/data/prodigy-crystal/prodigy-crystalbioschemas.jsonld @@ -23,15 +23,15 @@ "Anna Vangone" ], "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:description": "PRODIGY-CRYSTAL (PROtein binDIng enerGY prediction to classify CRYSTALlographic interfaces) is an automatic web server for distinguish crystallographic from biological interfaces in protein complexes.", "sc:license": "Other", "sc:name": "PRODIGY-CRYSTAL", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://bianca.science.uu.nl/prodigy/cryst" diff --git a/data/prodigy-lig/prodigy-ligbioschemas.jsonld b/data/prodigy-lig/prodigy-ligbioschemas.jsonld index d940d14852996..5bec341c301c5 100644 --- a/data/prodigy-lig/prodigy-ligbioschemas.jsonld +++ b/data/prodigy-lig/prodigy-ligbioschemas.jsonld @@ -17,9 +17,9 @@ "@id": "https://bio.tools/PRODIGY-LIG", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", "Command-line tool", - "Web service" + "Web service", + "Web application" ], "sc:author": { "@id": "http://orcid.org/0000-0001-7369-1322" @@ -29,8 +29,8 @@ "sc:name": "PRODIGY-LIG", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ { diff --git a/data/prodigy/prodigybioschemas.jsonld b/data/prodigy/prodigybioschemas.jsonld index 5d7d9ee9c87c3..41e7a8f83cd77 100644 --- a/data/prodigy/prodigybioschemas.jsonld +++ b/data/prodigy/prodigybioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Apache-2.0", "sc:name": "PRODIGY", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": { diff --git a/data/prodom/prodombioschemas.jsonld b/data/prodom/prodombioschemas.jsonld index 5d7edca332683..c3de4349159df 100644 --- a/data/prodom/prodombioschemas.jsonld +++ b/data/prodom/prodombioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ProDom protein domain database", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://prodom.prabi.fr/prodom/current/html/home.php" } \ No newline at end of file diff --git a/data/prodomcg_evoscen/prodomcg_evoscenbioschemas.jsonld b/data/prodomcg_evoscen/prodomcg_evoscenbioschemas.jsonld index 726fb78677a9b..3f2c19e15f10b 100644 --- a/data/prodomcg_evoscen/prodomcg_evoscenbioschemas.jsonld +++ b/data/prodomcg_evoscen/prodomcg_evoscenbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A set of webservices allowing to browse ProDom-CG267 evolutionary scenarios.", "sc:name": "ProdomCG_evoscen", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.health2api.com/?p=10236", "sc:version": "1" diff --git a/data/prodomcg_tree/prodomcg_treebioschemas.jsonld b/data/prodomcg_tree/prodomcg_treebioschemas.jsonld index f732407b2a355..e1382bb8451de 100644 --- a/data/prodomcg_tree/prodomcg_treebioschemas.jsonld +++ b/data/prodomcg_tree/prodomcg_treebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Set of webservices allowing to browse ProDom-CG267 phylogenetic tree.", "sc:name": "ProdomCG_tree", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.health2api.com/?p=10237", "sc:version": "1" diff --git a/data/prodonet/prodonetbioschemas.jsonld b/data/prodonet/prodonetbioschemas.jsonld index 597a3e883807a..59aaf6fda07d3 100644 --- a/data/prodonet/prodonetbioschemas.jsonld +++ b/data/prodonet/prodonetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ProdoNet", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.prodonet.tu-bs.de" } \ No newline at end of file diff --git a/data/prody/prodybioschemas.jsonld b/data/prody/prodybioschemas.jsonld index 7705ae6803357..3d9cb05f36bfa 100644 --- a/data/prody/prodybioschemas.jsonld +++ b/data/prody/prodybioschemas.jsonld @@ -28,8 +28,8 @@ "sc:license": "MIT", "sc:name": "ProDy", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://prody.csb.pitt.edu/" diff --git a/data/prof_sim/prof_simbioschemas.jsonld b/data/prof_sim/prof_simbioschemas.jsonld index c4e9c520e146d..f03bf39e6cff7 100644 --- a/data/prof_sim/prof_simbioschemas.jsonld +++ b/data/prof_sim/prof_simbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A profile-profile comparison program that compares PSI-BLAST profiles.", "sc:name": "prof_sim", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://biozon.org/ftp/software/prof_sim/index.html" } \ No newline at end of file diff --git a/data/profacc/profaccbioschemas.jsonld b/data/profacc/profaccbioschemas.jsonld index b72634a7f0680..d0d8f5a30ee7d 100644 --- a/data/profacc/profaccbioschemas.jsonld +++ b/data/profacc/profaccbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/profacc", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": "Burkhard Rost", "sc:contributor": "Chris Sander", @@ -20,13 +20,13 @@ "sc:license": "GPL-2.0", "sc:name": "PROFacc", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ - "RostLab", - "EMBL Heidelberg" + "EMBL Heidelberg", + "RostLab" ], "sc:url": "http://ppopen.informatik.tu-muenchen.de/", "sc:version": "1.0.42" diff --git a/data/profcom/profcombioschemas.jsonld b/data/profcom/profcombioschemas.jsonld index 453290d34532d..af277c81b8a4c 100644 --- a/data/profcom/profcombioschemas.jsonld +++ b/data/profcom/profcombioschemas.jsonld @@ -18,8 +18,8 @@ "sc:license": "Unlicense", "sc:name": "ProfCom", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://webclu.bio.wzw.tum.de/profcom/" diff --git a/data/profdisis/profdisisbioschemas.jsonld b/data/profdisis/profdisisbioschemas.jsonld index ec96ad02b7a76..fa23c5d55011d 100644 --- a/data/profdisis/profdisisbioschemas.jsonld +++ b/data/profdisis/profdisisbioschemas.jsonld @@ -11,23 +11,23 @@ "@id": "https://bio.tools/profdisis", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": "Yanay Ofran", "sc:citation": "pubmed:17646316", "sc:contributor": [ - "Burkhard Rost", - "Venkatesh Mysore" + "Venkatesh Mysore", + "Burkhard Rost" ], "sc:description": "Prediction of protein-DNA interaction sites identified from sequence.", "sc:license": "GPL-2.0", "sc:name": "PROFdisis", "sc:operatingSystem": "Linux", "sc:provider": [ - "D.E.Shaw Research", "RostLab", - "Columbia University" + "Columbia University", + "D.E.Shaw Research" ], "sc:url": "http://ppopen.informatik.tu-muenchen.de/", "sc:version": "1.0.6" diff --git a/data/profeat/profeatbioschemas.jsonld b/data/profeat/profeatbioschemas.jsonld index 0433da0f10b36..f74d320c08503 100644 --- a/data/profeat/profeatbioschemas.jsonld +++ b/data/profeat/profeatbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1093/nar/gkl305", "@type": "sc:CreativeWork" }, - { - "@id": "https://doi.org/10.1093/nar/gkr284", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/profeat", "@type": "sc:SoftwareApplication", @@ -25,31 +21,35 @@ "Dr. Tao Lin" ], "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ - "pubmed:16845018", - "pubmed:21609959", { - "@id": "https://doi.org/10.1093/nar/gkr284" + "@id": "https://doi.org/10.1093/nar/gkl305" }, - "pubmed:27742592", "pmcid:PMC3125735", + "pubmed:21609959", + "pmcid:PMC1538821", + "pubmed:27742592", { - "@id": "https://doi.org/10.1093/nar/gkl305" + "@id": "https://doi.org/10.1093/nar/gkr284" }, - "pmcid:PMC1538821" + "pubmed:16845018" ], "sc:description": "Tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.", "sc:license": "Unlicense", "sc:name": "PROFEAT", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi" + }, + { + "@id": "https://doi.org/10.1093/nar/gkr284", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/profed/profedbioschemas.jsonld b/data/profed/profedbioschemas.jsonld index cb89249d0a3b1..8398bcd96a008 100644 --- a/data/profed/profedbioschemas.jsonld +++ b/data/profed/profedbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ProFED", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://ebi056.uni-muenster.de:3838/profed/" } \ No newline at end of file diff --git a/data/profhtm/profhtmbioschemas.jsonld b/data/profhtm/profhtmbioschemas.jsonld index b18d548cbce7d..968c7f35f122a 100644 --- a/data/profhtm/profhtmbioschemas.jsonld +++ b/data/profhtm/profhtmbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/profhtm", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:author": "Burkhard Rost", "sc:contributor": "Chris Sander", @@ -20,13 +20,13 @@ "sc:license": "GPL-2.0", "sc:name": "PROFhtm", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": [ - "EMBL Heidelberg", - "RostLab" + "RostLab", + "EMBL Heidelberg" ], "sc:url": "http://ppopen.informatik.tu-muenchen.de/", "sc:version": "1.0.42" diff --git a/data/profia/bioconda_profia.yaml b/data/profia/bioconda_profia.yaml index 6286675d2ac0c..8fea6de21eeb4 100644 --- a/data/profia/bioconda_profia.yaml +++ b/data/profia/bioconda_profia.yaml @@ -12,7 +12,6 @@ description: Flow Injection Analysis coupled to High-Resolution Mass Spectrometr home: https://bioconductor.org/packages/3.10/bioc/html/proFIA.html identifiers: - biotools:profia -- doi:10.1038/nmeth.3252 license: CeCILL name: bioconductor-profia summary: Preprocessing of FIA-HRMS data diff --git a/data/profia/profiabioschemas.jsonld b/data/profia/profiabioschemas.jsonld index 446e5f43012b6..7965f78c5a1f6 100644 --- a/data/profia/profiabioschemas.jsonld +++ b/data/profia/profiabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "CECILL-2.1", "sc:name": "proFIA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/proFIA.html", diff --git a/data/profilescoredist/profilescoredistbioschemas.jsonld b/data/profilescoredist/profilescoredistbioschemas.jsonld index a0728d67c7823..876c6d1dc1288 100644 --- a/data/profilescoredist/profilescoredistbioschemas.jsonld +++ b/data/profilescoredist/profilescoredistbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "MIT", "sc:name": "profileScoreDist", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/profileScoreDist.html", "sc:version": "1.2.0" diff --git a/data/profisis/profisisbioschemas.jsonld b/data/profisis/profisisbioschemas.jsonld index f47dbdea1aaa7..e708ce580dda6 100644 --- a/data/profisis/profisisbioschemas.jsonld +++ b/data/profisis/profisisbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:author": "Yanay Ofran", "sc:citation": "pubmed:17237081", "sc:contributor": [ - "Burkhard Rost", - "Grants RO1-GM63029-01 and R01-GM64633-01 from the National Institutes of Health (NIH)" + "Grants RO1-GM63029-01 and R01-GM64633-01 from the National Institutes of Health (NIH)", + "Burkhard Rost" ], "sc:description": "Prediction of protein-protein interaction sites identified from sequence.", "sc:funder": "Grants RO1-GM63029-01 and R01-GM64633-01 from the National Institutes of Health (NIH)", @@ -26,8 +26,8 @@ "sc:name": "PROFisis", "sc:operatingSystem": "Linux", "sc:provider": [ - "Columbia University", - "RostLab" + "RostLab", + "Columbia University" ], "sc:url": "https://rostlab.org/owiki/index.php/PROFisis", "sc:version": "1.0.11" diff --git a/data/profit/profitbioschemas.jsonld b/data/profit/profitbioschemas.jsonld index 58dd157644306..3655baf57016f 100644 --- a/data/profit/profitbioschemas.jsonld +++ b/data/profit/profitbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK BBSRC", "UK MRC", - "Wellcome Trust" + "EMBOSS Contributors", + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Scan one or more sequences with a simple frequency matrix.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "profit", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/profound/profoundbioschemas.jsonld b/data/profound/profoundbioschemas.jsonld index 6f9603e7da2ff..ae47fd0e5e1f1 100644 --- a/data/profound/profoundbioschemas.jsonld +++ b/data/profound/profoundbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A tool for searching a protein sequence collections with peptide mass maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map.", "sc:name": "ProFound", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://prowl.rockefeller.edu/prowl-cgi/profound.exe" } \ No newline at end of file diff --git a/data/profppikernel/profppikernelbioschemas.jsonld b/data/profppikernel/profppikernelbioschemas.jsonld index f61e8e6a14508..84ef950e5e927 100644 --- a/data/profppikernel/profppikernelbioschemas.jsonld +++ b/data/profppikernel/profppikernelbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool uses an accelerated version of the original profile kernel to train SVM based protein-protein interaction (PPI) prediction models and to predict new PPIs from sequence alone.", "sc:name": "Profppikernel", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://rostlab.org/owiki/index.php/Profppikernel" } \ No newline at end of file diff --git a/data/profsec/profsecbioschemas.jsonld b/data/profsec/profsecbioschemas.jsonld index cab213897faa0..19f22eb4cbf41 100644 --- a/data/profsec/profsecbioschemas.jsonld +++ b/data/profsec/profsecbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "PROFsec", "sc:operatingSystem": "Linux", "sc:provider": [ - "Columbia University", - "RostLab" + "RostLab", + "Columbia University" ], "sc:url": "http://www.predictprotein.org", "sc:version": "1.0.42" diff --git a/data/proftmb/proftmbbioschemas.jsonld b/data/proftmb/proftmbbioschemas.jsonld index 8091895499a0f..aa9a1af1be345 100644 --- a/data/proftmb/proftmbbioschemas.jsonld +++ b/data/proftmb/proftmbbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkl262", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/proftmb", "@type": "sc:SoftwareApplication", @@ -19,8 +23,8 @@ "@id": "edam:data_0896" }, "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:applicationSubCategory": [ { @@ -32,15 +36,15 @@ ], "sc:author": "Henry Bigelow", "sc:citation": [ + "pmcid:PMC1538807", { "@id": "https://doi.org/10.1093/nar/gkl262" }, - "pmcid:PMC1538807", "pubmed:16844988" ], "sc:contributor": [ - "Burkhard Rost", - "grant R01-LM07329-01 from the National Library of Medicine" + "grant R01-LM07329-01 from the National Library of Medicine", + "Burkhard Rost" ], "sc:description": "Per-residue prediction of bacterial transmembrane beta barrels.", "sc:featureList": [ @@ -56,24 +60,20 @@ "sc:license": "GPL-2.0", "sc:name": "PROFtmb", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ - "Columbia University", + "RostLab", "Irvine Cancer Center", - "RostLab" + "Columbia University" ], "sc:softwareHelp": { "@id": "https://rostlab.org/owiki/index.php/Proftmb" }, "sc:url": "http://ppopen.informatik.tu-muenchen.de/", "sc:version": "1.1.12" - }, - { - "@id": "https://doi.org/10.1093/nar/gkl262", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/profunc/profuncbioschemas.jsonld b/data/profunc/profuncbioschemas.jsonld index 88c615468e1d0..29e0b10dcb942 100644 --- a/data/profunc/profuncbioschemas.jsonld +++ b/data/profunc/profuncbioschemas.jsonld @@ -13,16 +13,16 @@ "biotools:primaryContact": "Roman Laskowski", "sc:additionalType": "Web application", "sc:author": [ - "Thornton Group", - "Roman Laskowski" + "Roman Laskowski", + "Thornton Group" ], "sc:contributor": "James Watson", "sc:description": "Protein function prediction.", "sc:name": "ProFunc", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/thornton-srv/databases/profunc", diff --git a/data/progenetix/progenetixbioschemas.jsonld b/data/progenetix/progenetixbioschemas.jsonld index 9af767b4bfd6b..09347e85cd239 100644 --- a/data/progenetix/progenetixbioschemas.jsonld +++ b/data/progenetix/progenetixbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With >30000 cases from >1000 publications, Progenetix is the largest curated database for whole genome copy number profiles. The current dataset contains >20000 chromosomal CGH and >10000 profiles from genomic array experiments. This data covers hundreds of cancer entities.", "sc:name": "Progenetix", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", diff --git a/data/progenomes/progenomesbioschemas.jsonld b/data/progenomes/progenomesbioschemas.jsonld index 80452b1ed2f13..17ba514686c84 100644 --- a/data/progenomes/progenomesbioschemas.jsonld +++ b/data/progenomes/progenomesbioschemas.jsonld @@ -10,26 +10,22 @@ }, "@graph": [ { - "@id": "https://orcid.org/0000-0003-1429-7485", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/NAR/GKW989", + "@type": "sc:CreativeWork" }, { "@id": "http://orcid.org/0000-0001-6831-4557", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1093/NAR/GKW989", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/progenomes", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "https://orcid.org/0000-0003-1429-7485" + "@id": "http://orcid.org/0000-0001-6831-4557" }, { - "@id": "http://orcid.org/0000-0001-6831-4557" + "@id": "https://orcid.org/0000-0003-1429-7485" } ], "sc:additionalType": "Database portal", @@ -47,9 +43,9 @@ "sc:license": "GPL-3.0", "sc:name": "proGenomes", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ "HD-HuB", @@ -57,6 +53,10 @@ ], "sc:url": "http://progenomes.embl.de/", "sc:version": "1" + }, + { + "@id": "https://orcid.org/0000-0003-1429-7485", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/progeny/progenybioschemas.jsonld b/data/progeny/progenybioschemas.jsonld index 2ff98b66affc7..57c8b2932e760 100644 --- a/data/progeny/progenybioschemas.jsonld +++ b/data/progeny/progenybioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-8552-8976", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/progeny", "@type": "sc:SoftwareApplication", @@ -17,11 +21,11 @@ }, "sc:additionalType": "Library", "sc:citation": [ + "pubmed:29295995", "pmcid:PMC5750219", { "@id": "https://doi.org/10.1038/s41467-017-02391-6" - }, - "pubmed:29295995" + } ], "sc:contributor": { "@id": "https://orcid.org/0000-0002-8552-8976" @@ -41,16 +45,12 @@ "sc:version": "1.2.0" }, { - "@id": "https://orcid.org/0000-0002-6862-5221", - "@type": "schema:Person" + "@id": "https://doi.org/10.1038/s41467-017-02391-6", + "@type": "sc:CreativeWork" }, { - "@id": "https://orcid.org/0000-0002-8552-8976", + "@id": "https://orcid.org/0000-0002-6862-5221", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1038/s41467-017-02391-6", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/proglycprot/proglycprotbioschemas.jsonld b/data/proglycprot/proglycprotbioschemas.jsonld index bc62725b06664..1d860c11d79f7 100644 --- a/data/proglycprot/proglycprotbioschemas.jsonld +++ b/data/proglycprot/proglycprotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A manually curated, comprehensive repository of experimentally characterized bacterial and archaeal glycoproteins, generated from an exhaustive literature search.", "sc:name": "ProGlycProt", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.proglycprot.org/" } \ No newline at end of file diff --git a/data/prognoscan/prognoscanbioschemas.jsonld b/data/prognoscan/prognoscanbioschemas.jsonld index c3051d47705da..235da2a3e9d47 100644 --- a/data/prognoscan/prognoscanbioschemas.jsonld +++ b/data/prognoscan/prognoscanbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PrognoScan", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.prognoscan.org/" } \ No newline at end of file diff --git a/data/prohits-viz/prohits-vizbioschemas.jsonld b/data/prohits-viz/prohits-vizbioschemas.jsonld index 84e8deadf1c5f..28aba636a5ac7 100644 --- a/data/prohits-viz/prohits-vizbioschemas.jsonld +++ b/data/prohits-viz/prohits-vizbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "James D R Knight", "sc:additionalType": [ - "Suite", - "Web application" + "Web application", + "Suite" ], "sc:description": "A suite of web-based tools for visualizing and analyzing protein interaction data.", "sc:name": "ProHits-viz", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://prohits-viz.lunenfeld.ca/" } \ No newline at end of file diff --git a/data/proinflam/proinflambioschemas.jsonld b/data/proinflam/proinflambioschemas.jsonld index c36270bac783b..4e9c867f9d72e 100644 --- a/data/proinflam/proinflambioschemas.jsonld +++ b/data/proinflam/proinflambioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ProInflam", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://metabiosys.iiserb.ac.in/proinflam/index.html" } \ No newline at end of file diff --git a/data/projector_2/projector_2bioschemas.jsonld b/data/projector_2/projector_2bioschemas.jsonld index 0899867e0efd9..7916166acaa59 100644 --- a/data/projector_2/projector_2bioschemas.jsonld +++ b/data/projector_2/projector_2bioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Projector 2", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bamics2.cmbi.ru.nl/websoftware/projector2/projector2_start.php" } \ No newline at end of file diff --git a/data/prokaryote-rnaseq/prokaryote-rnaseqbioschemas.jsonld b/data/prokaryote-rnaseq/prokaryote-rnaseqbioschemas.jsonld index 1729c4ff964fa..e73da6f379f0c 100644 --- a/data/prokaryote-rnaseq/prokaryote-rnaseqbioschemas.jsonld +++ b/data/prokaryote-rnaseq/prokaryote-rnaseqbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/prokaryote-rnaseq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alexander Raknes", - "Erik Hjerde" + "Erik Hjerde", + "Alexander Raknes" ], "sc:additionalType": "Workflow", "sc:author": "Alexander Raknes", "sc:description": "Galaxy workflow for the analysis of differential expressed genes between two prokaryote transcriptome datasets.", "sc:name": "Prokaryote RNA sequence analysis workflow", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ELIXIR-NO", "sc:url": "https://galaxy-uit.bioinfo.no/u/ehj000/p/prokaryote-rnaseq-dataset", diff --git a/data/prokka/prokkabioschemas.jsonld b/data/prokka/prokkabioschemas.jsonld index f03642c9ccd33..b29dc1df5fbaa 100644 --- a/data/prokka/prokkabioschemas.jsonld +++ b/data/prokka/prokkabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/prokka", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Torsten Seemann", - "Australia" + "Australia", + "Torsten Seemann" ], "sc:additionalType": "Command-line tool", "sc:author": "Torsten Seemann", @@ -20,12 +20,12 @@ "sc:description": "Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.", "sc:name": "Prokka", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "University of Melbourne, Australia", - "unimelb.edu.au" + "unimelb.edu.au", + "University of Melbourne, Australia" ], "sc:url": "https://github.com/tseemann/prokka", "sc:version": "1" diff --git a/data/prokware/prokwarebioschemas.jsonld b/data/prokware/prokwarebioschemas.jsonld index 043b837d713df..73370e7b0bcb0 100644 --- a/data/prokware/prokwarebioschemas.jsonld +++ b/data/prokware/prokwarebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Investigate protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only.", "sc:name": "ProKware", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://ProKware.mbc.nctu.edu.tw/" } \ No newline at end of file diff --git a/data/proloc-go/proloc-gobioschemas.jsonld b/data/proloc-go/proloc-gobioschemas.jsonld index 6746c348c401e..20e939691fa10 100644 --- a/data/proloc-go/proloc-gobioschemas.jsonld +++ b/data/proloc-go/proloc-gobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "ProLoc-GO is an efficient sequence-based method by mining informative Gene Ontology terms for predicting protein subcellular localization.", "sc:name": "ProLoc-GO", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://140.113.239.45/prolocgo/" } \ No newline at end of file diff --git a/data/proloc/prolocbioschemas.jsonld b/data/proloc/prolocbioschemas.jsonld index 8968325bfbd74..9c7683ff69cf6 100644 --- a/data/proloc/prolocbioschemas.jsonld +++ b/data/proloc/prolocbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-1520-2268", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1371/journal.pcbi.1004920", "@type": "sc:CreativeWork" @@ -24,15 +20,15 @@ "@id": "http://orcid.org/0000-0002-1520-2268" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pmcid:PMC4866734", "pubmed:27175778", { "@id": "https://doi.org/10.1371/journal.pcbi.1004920" - }, - "pmcid:PMC4866734" + } ], "sc:description": "Pattern recognition techniques on quantitiative mass spectrometry data to infer protein sub-cellular localisation.", "sc:featureList": { @@ -41,12 +37,16 @@ "sc:license": "GPL-2.0", "sc:name": "pRoloc", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pRoloc.html", "sc:version": "1.20.1" + }, + { + "@id": "http://orcid.org/0000-0002-1520-2268", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/prolocgui/prolocguibioschemas.jsonld b/data/prolocgui/prolocguibioschemas.jsonld index dfdb4d2c48985..c03718a3aae02 100644 --- a/data/prolocgui/prolocguibioschemas.jsonld +++ b/data/prolocgui/prolocguibioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/prolocgui", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lisa M Breckels", - "Laurent Gatto" + "Laurent Gatto", + "Lisa M Breckels" ], "sc:additionalType": [ "Command-line tool", @@ -22,8 +22,8 @@ "sc:license": "GPL-2.0", "sc:name": "pRolocGUI", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pRolocGUI.html", diff --git a/data/prom/prombioschemas.jsonld b/data/prom/prombioschemas.jsonld index 34492e113591a..732e4fa628e25 100644 --- a/data/prom/prombioschemas.jsonld +++ b/data/prom/prombioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Algorithm which represents the successful integration of a genome scale transcriptional regulatory network with a biochemically detailed metabolic network, bridging two important classes of systems biology models that have rarely been combined quantitatively.", "sc:name": "PROM", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://price.systemsbiology.org/research/prom/" } \ No newline at end of file diff --git a/data/promals3d/promals3dbioschemas.jsonld b/data/promals3d/promals3dbioschemas.jsonld index 79f253c46386c..bac92ced0ed9d 100644 --- a/data/promals3d/promals3dbioschemas.jsonld +++ b/data/promals3d/promals3dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.", "sc:name": "PROMALS3D", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://prodata.swmed.edu/promals3d" } \ No newline at end of file diff --git a/data/promateus/promateusbioschemas.jsonld b/data/promateus/promateusbioschemas.jsonld index 30d7364b10a52..b0d17bebcaf07 100644 --- a/data/promateus/promateusbioschemas.jsonld +++ b/data/promateus/promateusbioschemas.jsonld @@ -11,10 +11,10 @@ "@id": "https://bio.tools/promateus", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dana Reichmann", "Mati Cohen", "Jaimie Prilusky", - "Asaf Carmi" + "Asaf Carmi", + "Dana Reichmann" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:15050833", diff --git a/data/promaya/promayabioschemas.jsonld b/data/promaya/promayabioschemas.jsonld index a80de09f5e025..47761151d240c 100644 --- a/data/promaya/promayabioschemas.jsonld +++ b/data/promaya/promayabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A server for estimating the effect of mutations on protein thermal stability.", "sc:name": "ProMaya", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://bental.tau.ac.il/ProMaya/", diff --git a/data/promex/promexbioschemas.jsonld b/data/promex/promexbioschemas.jsonld index 3732ee538a847..5c48bb5575934 100644 --- a/data/promex/promexbioschemas.jsonld +++ b/data/promex/promexbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A mass spectral library consisting of tryptic peptide product ion spectra generated by liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS). Developed using samples derived from Arabidopsis thaliana and Medicago truncatula. The database serves as a reference and can be used for protein identification in uncharacterized samples. Protein identification is linked to other molecular levels of biological organization such as metabolite, pathway and transcript data.", "sc:name": "ProMEX protein mass spectral library", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://promex.pph.univie.ac.at/promex/" diff --git a/data/promh/promhbioschemas.jsonld b/data/promh/promhbioschemas.jsonld index 863221eacef5f..78f6e3b5f7e71 100644 --- a/data/promh/promhbioschemas.jsonld +++ b/data/promh/promhbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PromH", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.softberry.com/berry.phtml?topic=promhg&group=programs&subgroup=promoter" } \ No newline at end of file diff --git a/data/promiscuous/promiscuousbioschemas.jsonld b/data/promiscuous/promiscuousbioschemas.jsonld index 12ee929f301c1..25c511149cde4 100644 --- a/data/promiscuous/promiscuousbioschemas.jsonld +++ b/data/promiscuous/promiscuousbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "PROMISCUOUS is a database of drugs, including withdrawn or experimental drugs, annotated with drug-protein and protein-protein relationships compiled from public resources via text and data mining including manual curation. Measures of structural similarity for drugs as well as known side-effects can be easily connected to protein-protein interactions to establish and analyse networks responsible for multi-pharmacology.", "sc:name": "PROMISCUOUS", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioinformatics.charite.de/promiscuous" } \ No newline at end of file diff --git a/data/promise/promisebioschemas.jsonld b/data/promise/promisebioschemas.jsonld index cba51dccd6e12..48540889495f5 100644 --- a/data/promise/promisebioschemas.jsonld +++ b/data/promise/promisebioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/promise", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Stan Pounds", - "Xueyuan Cao" + "Xueyuan Cao", + "Stan Pounds" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables.", "sc:license": "GPL-2.0", "sc:name": "PROMISE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PROMISE.html", "sc:version": "1.26.0" diff --git a/data/promk/promkbioschemas.jsonld b/data/promk/promkbioschemas.jsonld index 1696896cfa488..7f62615870e92 100644 --- a/data/promk/promkbioschemas.jsonld +++ b/data/promk/promkbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Method for predicting protein function using Multiple Kernels.", "sc:name": "ProMK", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sites.google.com/site/guoxian85/home/promk" } \ No newline at end of file diff --git a/data/promo/promobioschemas.jsonld b/data/promo/promobioschemas.jsonld index df31d38a56fe9..1460438764ed1 100644 --- a/data/promo/promobioschemas.jsonld +++ b/data/promo/promobioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Unlicense", "sc:name": "PROMO", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://acgt.cs.tau.ac.il/promo/" diff --git a/data/promoser/promoserbioschemas.jsonld b/data/promoser/promoserbioschemas.jsonld index 1b11a26db183d..203099a4b93c8 100644 --- a/data/promoser/promoserbioschemas.jsonld +++ b/data/promoser/promoserbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.", "sc:name": "PromoSer", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://biowulf.bu.edu/zlab/PromoSer/" } \ No newline at end of file diff --git a/data/promost/promostbioschemas.jsonld b/data/promost/promostbioschemas.jsonld index 853fa86bb5f74..f887f1a8635bc 100644 --- a/data/promost/promostbioschemas.jsonld +++ b/data/promost/promostbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.", "sc:name": "ProMoST", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://proteomics.mcw.edu/promost.html" } \ No newline at end of file diff --git a/data/promoter/promoterbioschemas.jsonld b/data/promoter/promoterbioschemas.jsonld index a8e82c96204ab..622a02277085d 100644 --- a/data/promoter/promoterbioschemas.jsonld +++ b/data/promoter/promoterbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Other", "sc:name": "Promoter", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "CBS", diff --git a/data/promotercad/promotercadbioschemas.jsonld b/data/promotercad/promotercadbioschemas.jsonld index 2c0c899f3894c..8e8384ea175c1 100644 --- a/data/promotercad/promotercadbioschemas.jsonld +++ b/data/promotercad/promotercadbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PromoterCAD is a web server for designing synthetic promoters in plants with altered transcriptional regulation. PromoterCAD uses published high-throughput expression and motif data from Arabidopsis thaliana to guide DNA design.", "sc:name": "PromoterCAD", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://promotercad.org/" } \ No newline at end of file diff --git a/data/promoterwise/promoterwisebioschemas.jsonld b/data/promoterwise/promoterwisebioschemas.jsonld index bc1ec4647e211..f7605f4458fb5 100644 --- a/data/promoterwise/promoterwisebioschemas.jsonld +++ b/data/promoterwise/promoterwisebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "PromoterWise", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/psa/promoterwise/", diff --git a/data/prompredict/prompredictbioschemas.jsonld b/data/prompredict/prompredictbioschemas.jsonld index fd4be7d1cf831..d8fb8368b33ec 100644 --- a/data/prompredict/prompredictbioschemas.jsonld +++ b/data/prompredict/prompredictbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PromPredict", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://nucleix.mbu.iisc.ernet.in/prompredict/prompredict.html" } \ No newline at end of file diff --git a/data/prompt/promptbioschemas.jsonld b/data/prompt/promptbioschemas.jsonld index bef39e01462ac..39ca1375436fb 100644 --- a/data/prompt/promptbioschemas.jsonld +++ b/data/prompt/promptbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "PROMPT is a platform independent system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatical data retrieval and integration, a multitude of analysis and comparison algorithms and a full-featured easy to use graphical user interface (GUI) application with an integrated help-system.", "sc:name": "PROMPT", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.geneinfo.eu/prompt/", "sc:version": "0.9.7" diff --git a/data/promzea/promzeabioschemas.jsonld b/data/promzea/promzeabioschemas.jsonld index 506c0c4f3509b..3820a940c88af 100644 --- a/data/promzea/promzeabioschemas.jsonld +++ b/data/promzea/promzeabioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2229-13-42", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/promzea", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Christophe Liseron-Monfils", - "Manish Raizada" + "Manish Raizada", + "Christophe Liseron-Monfils" ], "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC3658923", "pubmed:23497159", { "@id": "https://doi.org/10.1186/1471-2229-13-42" - }, - "pmcid:PMC3658923" + } ], "sc:description": "Perl-based application to discover de novo motifs underlying co-regulated genes in maize, Arabidopsis or rice.", "sc:featureList": { @@ -30,15 +34,11 @@ }, "sc:name": "Promzea", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.promzea.org" - }, - { - "@id": "https://doi.org/10.1186/1471-2229-13-42", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/proovread/proovreadbioschemas.jsonld b/data/proovread/proovreadbioschemas.jsonld index ee82b9d5db98c..db7a7fa5a9b9c 100644 --- a/data/proovread/proovreadbioschemas.jsonld +++ b/data/proovread/proovreadbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Hybrid correction pipeline for SMRT reads, which can be flexibly adapted on existing hardware and infrastructure from a laptop to a high performance computing cluster.", "sc:name": "proovread", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bioinfo.biozentrum.uni-wuerzburg.de/groups/genomics/research/development_of_bioinformatical_tools/" } \ No newline at end of file diff --git a/data/prop/propbioschemas.jsonld b/data/prop/propbioschemas.jsonld index 70e6d18dfc5c2..d888a83b074ab 100644 --- a/data/prop/propbioschemas.jsonld +++ b/data/prop/propbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": [ "Command-line tool", - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:description": "Neural network prediction of arginine and lysine propeptide cleavage sites in eukaryotic protein sequences.", "sc:license": "Other", "sc:name": "ProP", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/ProP/", diff --git a/data/propas/propasbioschemas.jsonld b/data/propas/propasbioschemas.jsonld index 662f6455c6e97..2e96c7d81ff2a 100644 --- a/data/propas/propasbioschemas.jsonld +++ b/data/propas/propasbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/propas", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": "pubmed:22368391", "sc:description": "Calculate the basic property of peptides/proteins. The properties include the Isoelectric point (pI), Mass weight (MW) and Hydrophobicity (Hy). Additionally, amino acid composition of all peptides/proteins in the list was also calculated.", diff --git a/data/proper/properbioschemas.jsonld b/data/proper/properbioschemas.jsonld index 7603bc9eecc1f..f0eef130c325f 100644 --- a/data/proper/properbioschemas.jsonld +++ b/data/proper/properbioschemas.jsonld @@ -18,11 +18,11 @@ "Library" ], "sc:citation": [ + "pubmed:25273110", "pmcid:PMC4287952", { "@id": "https://doi.org/10.1093/bioinformatics/btu640" - }, - "pubmed:25273110" + } ], "sc:description": "This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.", "sc:featureList": { @@ -31,8 +31,8 @@ "sc:license": "GPL-3.0", "sc:name": "PROPER", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PROPER.html", diff --git a/data/prophage_hunter/prophage_hunterbioschemas.jsonld b/data/prophage_hunter/prophage_hunterbioschemas.jsonld index f850a4d265a2d..36efdb2194ebc 100644 --- a/data/prophage_hunter/prophage_hunterbioschemas.jsonld +++ b/data/prophage_hunter/prophage_hunterbioschemas.jsonld @@ -17,11 +17,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6602508", { "@id": "https://doi.org/10.1093/NAR/GKZ380" }, - "pubmed:31114893" + "pubmed:31114893", + "pmcid:PMC6602508" ], "sc:description": "Integrative tool that employs similarity matching within our customized phage parts library and machine learning of prophage genetic features, to score the probability of a prophage being active.", "sc:featureList": { @@ -36,13 +36,13 @@ ], "sc:url": "https://pro-hunter.bgi.com/" }, - { - "@id": "https://orcid.org/0000-0002-0507-7352", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1093/NAR/GKZ380", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-0507-7352", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/prophecy/prophecybioschemas.jsonld b/data/prophecy/prophecybioschemas.jsonld index c149e2953dfee..152d5b76a7c93 100644 --- a/data/prophecy/prophecybioschemas.jsonld +++ b/data/prophecy/prophecybioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Profiling of phenotypic characteristics in yeast.", "sc:name": "PROPHECY", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://prophecy.lundberg.gu.se/" diff --git a/data/prophet/prophetbioschemas.jsonld b/data/prophet/prophetbioschemas.jsonld index ef7f9f3956c4b..50add7782f9d1 100644 --- a/data/prophet/prophetbioschemas.jsonld +++ b/data/prophet/prophetbioschemas.jsonld @@ -13,15 +13,15 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "UK BBSRC", + "EMBOSS Contributors", "UK MRC", - "EMBOSS Contributors" + "UK BBSRC" ], "sc:description": "Scan one or more sequences with a Gribskov or Henikoff profile.", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "prophet", diff --git a/data/propr/proprbioschemas.jsonld b/data/propr/proprbioschemas.jsonld index f96fa558b7772..498b66bde5572 100644 --- a/data/propr/proprbioschemas.jsonld +++ b/data/propr/proprbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "propr", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/propr/index.html", "sc:version": "3.5.1" diff --git a/data/propred/propredbioschemas.jsonld b/data/propred/propredbioschemas.jsonld index f6de7c0b8bb11..20eac044e58d0 100644 --- a/data/propred/propredbioschemas.jsonld +++ b/data/propred/propredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This server allows users to predict MHC class II binders.", "sc:name": "Propred", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/propred/" } \ No newline at end of file diff --git a/data/propred1/propred1bioschemas.jsonld b/data/propred1/propred1bioschemas.jsonld index 47ec691cd25df..91c5c20c7cde4 100644 --- a/data/propred1/propred1bioschemas.jsonld +++ b/data/propred1/propred1bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Online service for identifying the MHC Class-I binding regions in antigens. It implements matrices for 47 MHC Class-I alleles, proteasomal and immunoproteasomal models. The main aim of this server is to help users in identifying the promiscuous regions.", "sc:name": "ProPred1", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/propred1/" } \ No newline at end of file diff --git a/data/props/propsbioschemas.jsonld b/data/props/propsbioschemas.jsonld index 78b658de4b8c9..bce5c7b75600e 100644 --- a/data/props/propsbioschemas.jsonld +++ b/data/props/propsbioschemas.jsonld @@ -32,9 +32,9 @@ "sc:license": "GPL-2.0", "sc:name": "PROPS", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PROPS.html", "sc:version": "1.2.0" diff --git a/data/propsearch/propsearchbioschemas.jsonld b/data/propsearch/propsearchbioschemas.jsonld index 7e62e29ff9aaa..09e2ba3462c1a 100644 --- a/data/propsearch/propsearchbioschemas.jsonld +++ b/data/propsearch/propsearchbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "PROPSEARCH was designed to detect functional and / or structural homologs, if the sequence identity is below about 25%. It uses the amino acid physico-chemical properties, content of bulky residues, content of small residues, average hydrophobicity, average charge a.s.o. and are used as query vector. Sequences in the database are transformed into vectors as well, and the euclidian distance between the query and database sequences is calculated.", "sc:name": "PROPSEARCH", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://abcis.cbs.cnrs.fr/propsearch/" diff --git a/data/proq2/proq2bioschemas.jsonld b/data/proq2/proq2bioschemas.jsonld index 8babc92c348c0..7f95476c8cd69 100644 --- a/data/proq2/proq2bioschemas.jsonld +++ b/data/proq2/proq2bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Neural network based predictor that based on a number of structural features predicts the quality of a protein model. It is optimized to find correct models in contrast to other methods which are optimized to find native structures.", "sc:name": "ProQ2", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioinfo.ifm.liu.se/ProQ2/" } \ No newline at end of file diff --git a/data/prorate/proratebioschemas.jsonld b/data/prorate/proratebioschemas.jsonld index 027e105043f86..0b9e572ba0326 100644 --- a/data/prorate/proratebioschemas.jsonld +++ b/data/prorate/proratebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PRORATE", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/folding/" } \ No newline at end of file diff --git a/data/prorepeat/prorepeatbioschemas.jsonld b/data/prorepeat/prorepeatbioschemas.jsonld index c6ddfa05ea423..f93642ad18dbd 100644 --- a/data/prorepeat/prorepeatbioschemas.jsonld +++ b/data/prorepeat/prorepeatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An integrated curated repository and analysis platform or research on biological characteristics of amino acid tandem repeats.", "sc:name": "ProRepeat", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://prorepeat.bioinformatics.nl:443/dev/f?p=131:1:3958512077619968" } \ No newline at end of file diff --git a/data/prosa-web/prosa-webbioschemas.jsonld b/data/prosa-web/prosa-webbioschemas.jsonld index e13313efc8bfa..b62034126dc00 100644 --- a/data/prosa-web/prosa-webbioschemas.jsonld +++ b/data/prosa-web/prosa-webbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling.", "sc:name": "ProSA-web", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://prosa.services.came.sbg.ac.at/prosa.php" diff --git a/data/prosampler/prosamplerbioschemas.jsonld b/data/prosampler/prosamplerbioschemas.jsonld index c5cc1495eab3c..308721b133bf0 100644 --- a/data/prosampler/prosamplerbioschemas.jsonld +++ b/data/prosampler/prosamplerbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-3.0", "sc:name": "ProSampler", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/zhengchangsulab/prosampler" } \ No newline at end of file diff --git a/data/prosat/prosatbioschemas.jsonld b/data/prosat/prosatbioschemas.jsonld index 332abb218bb6d..2db8e91f47dc0 100644 --- a/data/prosat/prosatbioschemas.jsonld +++ b/data/prosat/prosatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ProSAT+", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://prosat.h-its.org/" } \ No newline at end of file diff --git a/data/prosat2/prosat2bioschemas.jsonld b/data/prosat2/prosat2bioschemas.jsonld index 1fc977bc486c2..7e0ede3678c78 100644 --- a/data/prosat2/prosat2bioschemas.jsonld +++ b/data/prosat2/prosat2bioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Protein Structure Annotation Tool (ProSAT2) is a tool for the visualization of sequence based, residue-specific annotations mapped onto three-dimensional (3D) protein structures", "sc:name": "ProSAT2", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://projects.villa-bosch.de/dbase/ps2/" diff --git a/data/proseq/proseqbioschemas.jsonld b/data/proseq/proseqbioschemas.jsonld index 7375e7013347f..fd0d4bd899f8a 100644 --- a/data/proseq/proseqbioschemas.jsonld +++ b/data/proseq/proseqbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "PROcessor of SEQuences is a program for sequence editing and population genetics analysis. It is quite a convenient tool for sequence handling and preliminary molecular evolution analysis. However, it is recommended to check the results of the analyses by the other software since the program is under development and not all the parts of the program are thoroughly tested and completely reliable", "sc:name": "ProSeq", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://dps.plants.ox.ac.uk/sequencing/proseq.htm", "sc:version": "3.5" diff --git a/data/prosess/prosessbioschemas.jsonld b/data/prosess/prosessbioschemas.jsonld index b66b49243e38f..e2d06b83519f8 100644 --- a/data/prosess/prosessbioschemas.jsonld +++ b/data/prosess/prosessbioschemas.jsonld @@ -11,27 +11,27 @@ "@id": "https://bio.tools/prosess", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mark Berjanskii", "Jianjun (Ben) Zhou", - "Paul Stothard", "Paul Lu", - "Peter Tang", + "Mark Berjanskii", + "Paul Stothard", + "David Wishart", + "Yongjie (Jack) Liang", "Joseph Cruz", + "Cam MacDonell", "Guohui Lin", "You Zhou", - "Yongjie (Jack) Liang", - "Contact Form", - "Cam MacDonell", - "David Wishart" + "Peter Tang", + "Contact Form" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:20460469", "sc:description": "Comprehensive web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy and computational modeling.", "sc:name": "PROSESS", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.prosess.ca" } \ No newline at end of file diff --git a/data/prosextract/prosextractbioschemas.jsonld b/data/prosextract/prosextractbioschemas.jsonld index e1776f0c8be92..b145c88688433 100644 --- a/data/prosextract/prosextractbioschemas.jsonld +++ b/data/prosextract/prosextractbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "Wellcome Trust", "EMBOSS Contributors", "UK BBSRC", - "Wellcome Trust", "UK MRC" ], "sc:description": "Process the PROSITE motif database for use by patmatmotifs.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "prosextract", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/prosight_ptm/prosight_ptmbioschemas.jsonld b/data/prosight_ptm/prosight_ptmbioschemas.jsonld index 51592d0ea11fb..6096f3e10c98a 100644 --- a/data/prosight_ptm/prosight_ptmbioschemas.jsonld +++ b/data/prosight_ptm/prosight_ptmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web portal for PTM search in top-down experiments.", "sc:name": "ProSight PTM", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://prosightptm.northwestern.edu/" } \ No newline at end of file diff --git a/data/prosight_ptm_ion_predictor/prosight_ptm_ion_predictorbioschemas.jsonld b/data/prosight_ptm_ion_predictor/prosight_ptm_ion_predictorbioschemas.jsonld index a3755b4558bd4..74f280216b1d4 100644 --- a/data/prosight_ptm_ion_predictor/prosight_ptm_ion_predictorbioschemas.jsonld +++ b/data/prosight_ptm_ion_predictor/prosight_ptm_ion_predictorbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Generate exact masses for CID/ECD fragments with PTMs.", "sc:name": "ProSight PTM Ion Predictor", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://prosightptm.northwestern.edu/ionpredictor" } \ No newline at end of file diff --git a/data/prosit/prositbioschemas.jsonld b/data/prosit/prositbioschemas.jsonld index 0eb1ce732c865..736a00af89b4e 100644 --- a/data/prosit/prositbioschemas.jsonld +++ b/data/prosit/prositbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Apache-2.0", "sc:name": "Prosit", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.proteomicsdb.org/prosit/" } \ No newline at end of file diff --git a/data/prosite/prositebioschemas.jsonld b/data/prosite/prositebioschemas.jsonld index 7c63e45a7762e..973fe0fbe41fc 100644 --- a/data/prosite/prositebioschemas.jsonld +++ b/data/prosite/prositebioschemas.jsonld @@ -19,23 +19,23 @@ "biotools:primaryContact": "PROSITE helpdesk", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:23161676", - "pmcid:PMC3531220", { "@id": "https://doi.org/10.1093/nar/gks1067" - } + }, + "pubmed:23161676", + "pmcid:PMC3531220" ], "sc:description": "Consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.", "sc:featureList": [ - { - "@id": "edam:operation_0253" - }, { "@id": "edam:operation_0296" }, { "@id": "edam:operation_0361" }, + { + "@id": "edam:operation_0253" + }, { "@id": "edam:operation_2414" } diff --git a/data/prosite_scan_ebi/prosite_scan_ebibioschemas.jsonld b/data/prosite_scan_ebi/prosite_scan_ebibioschemas.jsonld index 1fac48db4b4c1..1602866d226e2 100644 --- a/data/prosite_scan_ebi/prosite_scan_ebibioschemas.jsonld +++ b/data/prosite_scan_ebi/prosite_scan_ebibioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "PROSITE", - "Web Production" + "Web Production", + "PROSITE" ], "sc:description": "Scan a protein against PROSITE or HAMAP patterns and profiles.", "sc:name": "PROSITE Scan (EBI)", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/pfa/ps_scan/", diff --git a/data/prosmos/prosmosbioschemas.jsonld b/data/prosmos/prosmosbioschemas.jsonld index 89b228643f1c6..f93e1b3c9d63d 100644 --- a/data/prosmos/prosmosbioschemas.jsonld +++ b/data/prosmos/prosmosbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections between SSEs, coordinates of SSE start and ends, etc and then retrieves all structures from a database that contain this pattern.", "sc:name": "ProSMoS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://prodata.swmed.edu/ProSMoS/" } \ No newline at end of file diff --git a/data/prosnex/prosnexbioschemas.jsonld b/data/prosnex/prosnexbioschemas.jsonld index e89ed1f287cfa..5e93baff9188c 100644 --- a/data/prosnex/prosnexbioschemas.jsonld +++ b/data/prosnex/prosnexbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKZ390", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0002-3043-0015", "@type": "schema:Person" @@ -21,19 +17,19 @@ "@id": "https://bio.tools/ProSNEx", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Onur Sercinoglu", { "@id": "https://orcid.org/0000-0002-3043-0015" }, - "Rasim Murat Aydinkal", - "Onur Sercinoglu" + "Rasim Murat Aydinkal" ], "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC6602423", + "pubmed:31114881", { "@id": "https://doi.org/10.1093/NAR/GKZ390" - }, - "pmcid:PMC6602423", - "pubmed:31114881" + } ], "sc:description": "Web-based application for exploration and analysis of protein structures using network formalism.", "sc:featureList": [ @@ -41,10 +37,10 @@ "@id": "edam:operation_0272" }, { - "@id": "edam:operation_0244" + "@id": "edam:operation_2950" }, { - "@id": "edam:operation_2950" + "@id": "edam:operation_0244" } ], "sc:license": "Unlicense", @@ -55,6 +51,10 @@ "Mac" ], "sc:url": "http://prosnex-tool.com" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ390", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/prosom/prosombioschemas.jsonld b/data/prosom/prosombioschemas.jsonld index 451748e365a20..4a3c3f1220923 100644 --- a/data/prosom/prosombioschemas.jsonld +++ b/data/prosom/prosombioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Promoter prediction program based on unsupervised clustering of physical properties of DNA.", "sc:name": "ProSOM", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "ugent.be", diff --git a/data/prospect/prospectbioschemas.jsonld b/data/prospect/prospectbioschemas.jsonld index 1501f51164f4d..9f18f9118203c 100644 --- a/data/prospect/prospectbioschemas.jsonld +++ b/data/prospect/prospectbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software of using Ciphergen outcome files to reduce the count of peaks to a biological more interesting subset.", "sc:name": "ProSpect", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://fafner.meb.ki.se/personal/yudpaw/?page_id=13" } \ No newline at end of file diff --git a/data/prospectr/prospectrbioschemas.jsonld b/data/prospectr/prospectrbioschemas.jsonld index 01d39e5623e57..47d7a05f5cdde 100644 --- a/data/prospectr/prospectrbioschemas.jsonld +++ b/data/prospectr/prospectrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This tool can be used to enrich lists of genes found at a suspected disease locus. Given a list of genes, it will return a ranked list ordered by the likelihood of involvement in disease.", "sc:name": "Prospectr", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.genetics.med.ed.ac.uk/prospectr/" } \ No newline at end of file diff --git a/data/prosplicer/prosplicerbioschemas.jsonld b/data/prosplicer/prosplicerbioschemas.jsonld index ccd9a2e43dade..216a327f3174f 100644 --- a/data/prosplicer/prosplicerbioschemas.jsonld +++ b/data/prosplicer/prosplicerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ProSplicer", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://prosplicer.mbc.nctu.edu.tw/" } \ No newline at end of file diff --git a/data/prostar/prostarbioschemas.jsonld b/data/prostar/prostarbioschemas.jsonld index 6d075e3e8b518..c409e88482cc2 100644 --- a/data/prostar/prostarbioschemas.jsonld +++ b/data/prostar/prostarbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Samuel Wieczorek", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:27976474", "sc:description": "This package provides a GUI interface for DAPAR.", "sc:license": "Artistic-2.0", "sc:name": "Prostar", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Prostar.html", "sc:version": "1.6.1" diff --git a/data/prostrip/prostripbioschemas.jsonld b/data/prostrip/prostripbioschemas.jsonld index 9eadb9838e25e..bc2b358e9d9b4 100644 --- a/data/prostrip/prostripbioschemas.jsonld +++ b/data/prostrip/prostripbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server to find the similar structural repeats in a three-dimensional protein structure.", "sc:name": "ProSTRIP", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://cluster.physics.iisc.ernet.in/prostrip/" } \ No newline at end of file diff --git a/data/prot-spam/prot-spambioschemas.jsonld b/data/prot-spam/prot-spambioschemas.jsonld index 4c59bb6f355a9..8423d376b5fbd 100644 --- a/data/prot-spam/prot-spambioschemas.jsonld +++ b/data/prot-spam/prot-spambioschemas.jsonld @@ -19,30 +19,30 @@ "biotools:primaryContact": "Jendrik Schellhorn", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:30535314", { "@id": "https://doi.org/10.1093/gigascience/giy148" }, - "pmcid:PMC6436989", - "pubmed:30535314" + "pmcid:PMC6436989" ], "sc:description": "Alignment-free phylogeny reconstruction based on whole-proteome sequences.", "sc:featureList": [ { - "@id": "edam:operation_0289" + "@id": "edam:operation_3478" }, { "@id": "edam:operation_0557" }, { - "@id": "edam:operation_3478" + "@id": "edam:operation_0289" } ], "sc:license": "Unlicense", "sc:name": "Prot-SpaM", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/jschellh/ProtSpaM" } diff --git a/data/prot2d/prot2dbioschemas.jsonld b/data/prot2d/prot2dbioschemas.jsonld index b64e52f86ff57..43a6f1993bd57 100644 --- a/data/prot2d/prot2dbioschemas.jsonld +++ b/data/prot2d/prot2dbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sebastien Artigaud", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:23986565", "sc:description": "The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments.", "sc:license": "GPL-2.0", "sc:name": "prot2D", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/prot2D.html", diff --git a/data/prot_pi/prot_pibioschemas.jsonld b/data/prot_pi/prot_pibioschemas.jsonld index 0de7246678df5..67a3aee29b49e 100644 --- a/data/prot_pi/prot_pibioschemas.jsonld +++ b/data/prot_pi/prot_pibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Other", "sc:name": "Prot pi", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://www.protpi.ch" diff --git a/data/protchemsi/protchemsibioschemas.jsonld b/data/protchemsi/protchemsibioschemas.jsonld index 9637d5461fe2b..e70269b07aa31 100644 --- a/data/protchemsi/protchemsibioschemas.jsonld +++ b/data/protchemsi/protchemsibioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ProtChemSI", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://pcidb.russelllab.org/" } \ No newline at end of file diff --git a/data/protdcal/protdcalbioschemas.jsonld b/data/protdcal/protdcalbioschemas.jsonld index dd23cc23ac657..4944bf065b4b5 100644 --- a/data/protdcal/protdcalbioschemas.jsonld +++ b/data/protdcal/protdcalbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-015-0586-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/protdcal", "@type": "sc:SoftwareApplication", @@ -24,23 +28,19 @@ "sc:description": "A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins.", "sc:featureList": [ { - "@id": "edam:operation_2403" + "@id": "edam:operation_2406" }, { - "@id": "edam:operation_2406" + "@id": "edam:operation_2403" } ], "sc:name": "ProtDCal", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinf.sce.carleton.ca/ProtDCal/" - }, - { - "@id": "https://doi.org/10.1186/S12859-015-0586-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/protea/proteabioschemas.jsonld b/data/protea/proteabioschemas.jsonld index 5bf0650a64d69..12bedd5b8159c 100644 --- a/data/protea/proteabioschemas.jsonld +++ b/data/protea/proteabioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/protea", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Desktop application" + "Desktop application", + "Web application" ], "sc:citation": "pubmed:19517987", "sc:description": "Software devoted to protein-coding sequences identification. The input is a set of DNA sequences that need not to be aligned. The method takes advantage of the specific substitution pattern of coding sequences together with the consistency of reading frames.", "sc:name": "protea", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinfo.lifl.fr/protea/index.php" } \ No newline at end of file diff --git a/data/protedna/protednabioschemas.jsonld b/data/protedna/protednabioschemas.jsonld index be34d95ed5529..599c3e639ab1f 100644 --- a/data/protedna/protednabioschemas.jsonld +++ b/data/protedna/protednabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ProteDNA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://serv.csbb.ntu.edu.tw/ProteDNA/index.php" } \ No newline at end of file diff --git a/data/protege/protegebioschemas.jsonld b/data/protege/protegebioschemas.jsonld index 3ea05b5fe1967..34523243d052f 100644 --- a/data/protege/protegebioschemas.jsonld +++ b/data/protege/protegebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/protege", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:citation": "pubmed:24771560", "sc:description": "Free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protégé implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats.", diff --git a/data/protegen/protegenbioschemas.jsonld b/data/protegen/protegenbioschemas.jsonld index 0df03c840825e..d80605c3c4b34 100644 --- a/data/protegen/protegenbioschemas.jsonld +++ b/data/protegen/protegenbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Protegen is a web-based database and analysis system that curates, stores and analyzes protective antigens. Protegen includes basic antigen information and experimental evidence curated from peer-reviewed articles. It also includes detailed gene/protein information (e.g. DNA and protein sequences, and COG classification). Different antigen features, such as protein weight and pI, and subcellular localizations of bacterial proteins are precomputed.", "sc:name": "Protegen", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.violinet.org/protegen" } \ No newline at end of file diff --git a/data/protein_cavity_search/protein_cavity_searchbioschemas.jsonld b/data/protein_cavity_search/protein_cavity_searchbioschemas.jsonld index 290b17317ca6e..2bce0b2e3cb47 100644 --- a/data/protein_cavity_search/protein_cavity_searchbioschemas.jsonld +++ b/data/protein_cavity_search/protein_cavity_searchbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Protein Cavity Search is a software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.", "sc:name": "Protein Cavity Search", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://sourceforge.net/projects/cavity-search/", "sc:version": "0.21" diff --git a/data/protein_contacts_atlas/protein_contacts_atlasbioschemas.jsonld b/data/protein_contacts_atlas/protein_contacts_atlasbioschemas.jsonld index aed0ffd6a95c1..9c3e62791278f 100644 --- a/data/protein_contacts_atlas/protein_contacts_atlasbioschemas.jsonld +++ b/data/protein_contacts_atlas/protein_contacts_atlasbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "An interactive resource of non-covalent contacts from over 100,000 publicly available crystal structures in the Protein Data Bank", "sc:name": "Protein Contacts Atlas", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.mrc-lmb.cam.ac.uk/pca/" diff --git a/data/protein_disorder_predictors/protein_disorder_predictorsbioschemas.jsonld b/data/protein_disorder_predictors/protein_disorder_predictorsbioschemas.jsonld index e1b6c90079a47..8af998a0e65b7 100644 --- a/data/protein_disorder_predictors/protein_disorder_predictorsbioschemas.jsonld +++ b/data/protein_disorder_predictors/protein_disorder_predictorsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "List is a list or Protein Disorder Predictors", "sc:name": "Protein Disorder Predictors", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.disprot.org/predictors.php" } \ No newline at end of file diff --git a/data/protein_model_portal/protein_model_portalbioschemas.jsonld b/data/protein_model_portal/protein_model_portalbioschemas.jsonld index 0aa5341d71d8a..562228d3581aa 100644 --- a/data/protein_model_portal/protein_model_portalbioschemas.jsonld +++ b/data/protein_model_portal/protein_model_portalbioschemas.jsonld @@ -24,17 +24,17 @@ { "@id": "https://doi.org/10.1093/database/bat031" }, - "pubmed:23624946", - "pmcid:PMC3889916" + "pmcid:PMC3889916", + "pubmed:23624946" ], "sc:contributor": "SIB Swiss Institute of Bioinformatics", "sc:description": "Developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase.", "sc:featureList": [ { - "@id": "edam:operation_2414" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_2414" }, { "@id": "edam:operation_3431" diff --git a/data/protein_peeling_3_d/protein_peeling_3_dbioschemas.jsonld b/data/protein_peeling_3_d/protein_peeling_3_dbioschemas.jsonld index 4fb548f51ed83..d44921d4aea99 100644 --- a/data/protein_peeling_3_d/protein_peeling_3_dbioschemas.jsonld +++ b/data/protein_peeling_3_d/protein_peeling_3_dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.", "sc:name": "Protein Peeling 3 D", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.dsimb.inserm.fr/dsimb_tools/peeling3/" } \ No newline at end of file diff --git a/data/protein_sequence_logos/protein_sequence_logosbioschemas.jsonld b/data/protein_sequence_logos/protein_sequence_logosbioschemas.jsonld index 3cfe95b863d77..cc64835829847 100644 --- a/data/protein_sequence_logos/protein_sequence_logosbioschemas.jsonld +++ b/data/protein_sequence_logos/protein_sequence_logosbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Protein Sequence Logos", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://rth.dk/resources/plogo/" } \ No newline at end of file diff --git a/data/protein_solubility/protein_solubilitybioschemas.jsonld b/data/protein_solubility/protein_solubilitybioschemas.jsonld index 7ae758f7db171..0847acdaec138 100644 --- a/data/protein_solubility/protein_solubilitybioschemas.jsonld +++ b/data/protein_solubility/protein_solubilitybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/protein_solubility", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Xiaonan Wang", - "Kang Zhou" + "Kang Zhou", + "Xiaonan Wang" ], "sc:additionalType": "Workflow", "sc:citation": "pubmed:31038685", @@ -21,8 +21,8 @@ "sc:name": "protein solubility", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/xiaomizhou616/protein_solubility" } \ No newline at end of file diff --git a/data/protein_spotlight/protein_spotlightbioschemas.jsonld b/data/protein_spotlight/protein_spotlightbioschemas.jsonld index 085a24600ce6a..e5e215790234c 100644 --- a/data/protein_spotlight/protein_spotlightbioschemas.jsonld +++ b/data/protein_spotlight/protein_spotlightbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Protein Spotlight is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics. Spotlight articles describe a specific protein or family of proteins on an informal tone.", "sc:name": "Protein Spotlight", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://web.expasy.org/spotlight/" diff --git a/data/proteinart/proteinartbioschemas.jsonld b/data/proteinart/proteinartbioschemas.jsonld index 2500e4cf934e4..66ed6c9a0d9f8 100644 --- a/data/proteinart/proteinartbioschemas.jsonld +++ b/data/proteinart/proteinartbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "ProteinART is a web tool that uses combinatorial optimization for protein inference from tandem mass spectrometry peptide identifications. It uses a set of confidently identified peptides, peptide detectability, and a protein database to provide the most likely set of identified proteins.", "sc:name": "ProteinART", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://darwin.informatics.indiana.edu/applications/ProteinInference/" diff --git a/data/proteinatlas/proteinatlasbioschemas.jsonld b/data/proteinatlas/proteinatlasbioschemas.jsonld index adec1ad14c48f..dd53d20965dd3 100644 --- a/data/proteinatlas/proteinatlasbioschemas.jsonld +++ b/data/proteinatlas/proteinatlasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "The Human Protein Atlas", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "bils.se", "sc:url": "http://www.proteinatlas.org/" diff --git a/data/proteindbs/proteindbsbioschemas.jsonld b/data/proteindbs/proteindbsbioschemas.jsonld index 7007f498c7941..8df0471e95ca3 100644 --- a/data/proteindbs/proteindbsbioschemas.jsonld +++ b/data/proteindbs/proteindbsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a fast computation time.", "sc:name": "ProteinDBS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://proteindbs.rnet.missouri.edu/" } \ No newline at end of file diff --git a/data/proteindecision/proteindecisionbioschemas.jsonld b/data/proteindecision/proteindecisionbioschemas.jsonld index be1b1cd5da75f..98318794eaa8c 100644 --- a/data/proteindecision/proteindecisionbioschemas.jsonld +++ b/data/proteindecision/proteindecisionbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computer software for identifying protein by serching against protein database with the input Peptide-Mass Fingerprinting Data. It can handle the issues of selecting peaks from mass spectrum, transforming database format, displaying the top ranks of identification result, and detailed information for each ranking.", "sc:name": "ProteinDecision", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://digbio.missouri.edu/ProteinDecision/" } \ No newline at end of file diff --git a/data/proteinguru/proteingurubioschemas.jsonld b/data/proteinguru/proteingurubioschemas.jsonld index f5ef1e837897f..7531e821a679d 100644 --- a/data/proteinguru/proteingurubioschemas.jsonld +++ b/data/proteinguru/proteingurubioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ProteinGuru", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.proteinguru.com" } \ No newline at end of file diff --git a/data/proteinhistorian/proteinhistorianbioschemas.jsonld b/data/proteinhistorian/proteinhistorianbioschemas.jsonld index f4b27f4839ab7..ebc4b55824655 100644 --- a/data/proteinhistorian/proteinhistorianbioschemas.jsonld +++ b/data/proteinhistorian/proteinhistorianbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1002567", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/proteinhistorian", "@type": "sc:SoftwareApplication", @@ -21,24 +17,28 @@ "Web application" ], "sc:citation": [ - "pmcid:PMC3386163", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1002567" }, - "pubmed:22761559" + "pubmed:22761559", + "pmcid:PMC3386163" ], "sc:description": "Identifies enrichment for proteins of different phylogenetic ages in protein sets of interest. Over thirty eukaryotic species are currently supported and other protein attributes can be uploaded to combine with the protein age analysis.", "sc:featureList": [ { - "@id": "edam:operation_0324" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_0324" } ], "sc:license": "GPL-1.0", "sc:name": "ProteinHistorian", "sc:url": "http://lighthouse.ucsf.edu/ProteinHistorian/" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1002567", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/proteininfer/proteininferbioschemas.jsonld b/data/proteininfer/proteininferbioschemas.jsonld index f1fae4b29300c..deee0f1660382 100644 --- a/data/proteininfer/proteininferbioschemas.jsonld +++ b/data/proteininfer/proteininferbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "ProteinInfer is a softwarr for combinatorial perspective of the protein inference problem", "sc:name": "ProteinInfer", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinformatics.ust.hk/proteininfer/" } \ No newline at end of file diff --git a/data/proteinprofiles/proteinprofilesbioschemas.jsonld b/data/proteinprofiles/proteinprofilesbioschemas.jsonld index b4e0f946f6138..fc051918d7c1b 100644 --- a/data/proteinprofiles/proteinprofilesbioschemas.jsonld +++ b/data/proteinprofiles/proteinprofilesbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "proteinProfiles", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/proteinProfiles.html", "sc:version": "1.20.0" diff --git a/data/proteinprospector/proteinprospectorbioschemas.jsonld b/data/proteinprospector/proteinprospectorbioschemas.jsonld index c782a1d162c53..ce45a3c48211d 100644 --- a/data/proteinprospector/proteinprospectorbioschemas.jsonld +++ b/data/proteinprospector/proteinprospectorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ProteinProspector", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://prospector.ucsf.edu" } \ No newline at end of file diff --git a/data/proteinspector/proteinspectorbioschemas.jsonld b/data/proteinspector/proteinspectorbioschemas.jsonld index 8614a736b08f8..83af10e31ccf0 100644 --- a/data/proteinspector/proteinspectorbioschemas.jsonld +++ b/data/proteinspector/proteinspectorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Apache-2.0", "sc:name": "Proteinspector", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "https://bitbucket.org/proteinspector/qc_analysis/", diff --git a/data/proteinsplus/proteinsplusbioschemas.jsonld b/data/proteinsplus/proteinsplusbioschemas.jsonld index 26ddf8fb925c2..7e1ffbefea46c 100644 --- a/data/proteinsplus/proteinsplusbioschemas.jsonld +++ b/data/proteinsplus/proteinsplusbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "ProteinsPlus", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://proteinsplus.zbh.uni-hamburg.de" } \ No newline at end of file diff --git a/data/protemot/protemotbioschemas.jsonld b/data/protemot/protemotbioschemas.jsonld index 3e65728611f65..63778cd186d36 100644 --- a/data/protemot/protemotbioschemas.jsonld +++ b/data/protemot/protemotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Protein motif (Protemot) server predicts protein binding sites based on structural templates automatically extracted from crystal structures of protein-ligand complexes in the PDB.", "sc:name": "Protemot", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://protemot.csbb.ntu.edu.tw/" } \ No newline at end of file diff --git a/data/proteo/proteobioschemas.jsonld b/data/proteo/proteobioschemas.jsonld index 9677d52c9b4f1..4aa110c4fab5e 100644 --- a/data/proteo/proteobioschemas.jsonld +++ b/data/proteo/proteobioschemas.jsonld @@ -14,14 +14,14 @@ "sc:description": "Peptides that were identified, in collaboration, by Spanish National Cancer Research Centre (CNIO) and Centro Nacional de Investigaciones Cardiovasculares (CNIC).\n\nWe interrogate peptides from eight large-scale human proteomics experiments and databases, irrespective of tissue or cell type, for the vast majority of the protein-coding genes in these experiments. The peptide has to be included in at least 2 experiments.", "sc:name": "PROTEO: Peptide evidence for the human genome", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ + "cnio.es", "CNIO", - "CNIC", - "cnio.es" + "CNIC" ], "sc:url": "http://proteo.bioinfo.cnio.es", "sc:version": "1" diff --git a/data/proteoformer/proteoformerbioschemas.jsonld b/data/proteoformer/proteoformerbioschemas.jsonld index 243382ea35097..a8ac92e0d7784 100644 --- a/data/proteoformer/proteoformerbioschemas.jsonld +++ b/data/proteoformer/proteoformerbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-9441-9539", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/proteoformer", "@type": "sc:SoftwareApplication", @@ -26,17 +22,17 @@ ], "sc:additionalType": "Command-line tool", "sc:author": [ - "Elvis Ndah", { "@id": "https://orcid.org/0000-0001-9441-9539" }, { "@id": "https://orcid.org/0000-0003-1677-9533" - } + }, + "Elvis Ndah" ], "sc:contributor": [ - "Alexander Koch", "Sandra Steyaert", + "Alexander Koch", { "@id": "https://orcid.org/0000-0002-7575-2085" } @@ -55,12 +51,16 @@ ] }, { - "@id": "https://orcid.org/0000-0003-1677-9533", + "@id": "https://orcid.org/0000-0001-9441-9539", "@type": "schema:Person" }, { "@id": "https://orcid.org/0000-0002-7575-2085", "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0003-1677-9533", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/proteomatic/proteomaticbioschemas.jsonld b/data/proteomatic/proteomaticbioschemas.jsonld index e4ba875bdc3af..46ebaf65ce582 100644 --- a/data/proteomatic/proteomaticbioschemas.jsonld +++ b/data/proteomatic/proteomaticbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Platform for creating MS/MS data analysis workflows using scripts.", "sc:name": "Proteomatic", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/specht/proteomatic" } \ No newline at end of file diff --git a/data/proteome-pi/proteome-pibioschemas.jsonld b/data/proteome-pi/proteome-pibioschemas.jsonld index 09a869d039ec2..f6c6c7de6cf21 100644 --- a/data/proteome-pi/proteome-pibioschemas.jsonld +++ b/data/proteome-pi/proteome-pibioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0001-8187-1980", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/nar/gkw978", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/proteome-pi", @@ -28,10 +28,10 @@ "sc:additionalType": "Database portal", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0123" + "@id": "edam:topic_0121" }, { - "@id": "edam:topic_0121" + "@id": "edam:topic_0123" }, { "@id": "edam:topic_3520" @@ -62,8 +62,8 @@ "sc:url": "http://isoelectricpointdb.org/" }, { - "@id": "https://doi.org/10.1093/nar/gkw978", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0001-8187-1980", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/proteomedigestsim/proteomedigestsimbioschemas.jsonld b/data/proteomedigestsim/proteomedigestsimbioschemas.jsonld index 2c67f51c839dd..ce41a48be5514 100644 --- a/data/proteomedigestsim/proteomedigestsimbioschemas.jsonld +++ b/data/proteomedigestsim/proteomedigestsimbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R classes for prediction of proteome coverage based on iterative digestion by MED-FASP or similar.", "sc:name": "ProteomeDigestSim", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/jgmeyerucsd/ProteomeDigestSim" } \ No newline at end of file diff --git a/data/proteometools/proteometoolsbioschemas.jsonld b/data/proteometools/proteometoolsbioschemas.jsonld index 315c59f8390a6..86bd4bca5b77b 100644 --- a/data/proteometools/proteometoolsbioschemas.jsonld +++ b/data/proteometools/proteometoolsbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/proteometools", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", "Desktop application", - "Database portal" + "Database portal", + "Library" ], "sc:description": "A project that's aim is to translate the human proteome into molecular and digital tools for drug discovery, personalized medicine and life science research. It offers a repository of synthesized peptides and different tools for analyzing them.", "sc:name": "ProteomeTools", diff --git a/data/proteomexchange/proteomexchangebioschemas.jsonld b/data/proteomexchange/proteomexchangebioschemas.jsonld index 0a613b2b55913..18c78452877dc 100644 --- a/data/proteomexchange/proteomexchangebioschemas.jsonld +++ b/data/proteomexchange/proteomexchangebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This consortium has been set up to provide a globally coordinated submission of mass spectrometry proteomics data to the main existing proteomics repositories, and to encourage optimal data dissemination.", "sc:name": "ProteomeXchange", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.proteomexchange.org/" } \ No newline at end of file diff --git a/data/proteomicsannotationhubdata/bioconda_proteomicsannotationhubdata.yaml b/data/proteomicsannotationhubdata/bioconda_proteomicsannotationhubdata.yaml index 1bd9971c22ee1..7eebe2cc5ece0 100644 --- a/data/proteomicsannotationhubdata/bioconda_proteomicsannotationhubdata.yaml +++ b/data/proteomicsannotationhubdata/bioconda_proteomicsannotationhubdata.yaml @@ -4,7 +4,6 @@ description: These recipes convert a variety and a growing number of public prot home: https://bioconductor.org/packages/3.10/bioc/html/ProteomicsAnnotationHubData.html identifiers: - biotools:proteomicsannotationhubdata -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-proteomicsannotationhubdata summary: Transform public proteomics data resources into Bioconductor Data Structures diff --git a/data/proteomicsannotationhubdata/proteomicsannotationhubdatabioschemas.jsonld b/data/proteomicsannotationhubdata/proteomicsannotationhubdatabioschemas.jsonld index 88be77c6a6598..a4cb3558c9af9 100644 --- a/data/proteomicsannotationhubdata/proteomicsannotationhubdatabioschemas.jsonld +++ b/data/proteomicsannotationhubdata/proteomicsannotationhubdatabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "ProteomicsAnnotationHubData", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ProteomicsAnnotationHubData.html", diff --git a/data/proteomicsdb/proteomicsdbbioschemas.jsonld b/data/proteomicsdb/proteomicsdbbioschemas.jsonld index 0428397ec51ad..c35bcebc27e32 100644 --- a/data/proteomicsdb/proteomicsdbbioschemas.jsonld +++ b/data/proteomicsdb/proteomicsdbbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/proteomicsdb", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:citation": "pubmed:24870543", "sc:description": "Explorable, interactive human proteome database, including MS/MS data.", "sc:name": "ProteomicsDB", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.proteomicsdb.org/" diff --git a/data/proteomirexpress/proteomirexpressbioschemas.jsonld b/data/proteomirexpress/proteomirexpressbioschemas.jsonld index d4d9a85dd426e..a7de2908ef12b 100644 --- a/data/proteomirexpress/proteomirexpressbioschemas.jsonld +++ b/data/proteomirexpress/proteomirexpressbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks.", "sc:name": "ProteoMirExpress", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://jjwanglab.org/proteomirexpress/" } \ No newline at end of file diff --git a/data/proteopedia/proteopediabioschemas.jsonld b/data/proteopedia/proteopediabioschemas.jsonld index 2f1345b50fa6c..9591038569409 100644 --- a/data/proteopedia/proteopediabioschemas.jsonld +++ b/data/proteopedia/proteopediabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Proteopedia", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "Instruct", "sc:url": "http://www.proteopedia.org" diff --git a/data/proteoqc/proteoqcbioschemas.jsonld b/data/proteoqc/proteoqcbioschemas.jsonld index aa4e93514c742..7386864147122 100644 --- a/data/proteoqc/proteoqcbioschemas.jsonld +++ b/data/proteoqc/proteoqcbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "proteoQC", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/proteoQC.html", "sc:version": "1.10.0" diff --git a/data/proteore/proteorebioschemas.jsonld b/data/proteore/proteorebioschemas.jsonld index c2f2673e8a630..44bb4f1f1c2dc 100644 --- a/data/proteore/proteorebioschemas.jsonld +++ b/data/proteore/proteorebioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/ProteoRE", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Workflow" + "Workflow", + "Web application" ], "sc:description": "ProteoRE (Proteomics Research Environment) is a Galaxy-based instance for the functional analysis and the exploration of proteomics and transcriptomics data in biomedical research; ProteoRE comprises 18 tools organized into five subsections for: i) data manipulation; ii) human and iii ) mouse species database annotation; iv) functional analysis; and v) pathway analysis along with graphical representations.", "sc:name": "ProteoRE", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.proteore.org/", "sc:version": "2.0" diff --git a/data/proteosafe/proteosafebioschemas.jsonld b/data/proteosafe/proteosafebioschemas.jsonld index 8475a0ead42ba..86cb17c26eff6 100644 --- a/data/proteosafe/proteosafebioschemas.jsonld +++ b/data/proteosafe/proteosafebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Blind spectral search of tandem mass spectra of peptides.", "sc:name": "ProteoSAFe", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://proteomics.ucsd.edu/ProteoSAFe/" diff --git a/data/proteosign/proteosignbioschemas.jsonld b/data/proteosign/proteosignbioschemas.jsonld index 2a56d085ac3d1..f5fe83a715bfb 100644 --- a/data/proteosign/proteosignbioschemas.jsonld +++ b/data/proteosign/proteosignbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Protein differential expression analysis designed with the end-proteomics user in mind.\nIt aims to fully automate the process of statistically evaluating differential expression in mass spectrometry-based bottom-up (shotgun) quantitative proteomics data by requiring minimal user interaction time and generating publication-quality data plots.", "sc:name": "Proteosign", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioinformatics.med.uoc.gr/ProteoSign/" diff --git a/data/proteowizard/proteowizardbioschemas.jsonld b/data/proteowizard/proteowizardbioschemas.jsonld index 3eeebf0dab569..97236180f29a6 100644 --- a/data/proteowizard/proteowizardbioschemas.jsonld +++ b/data/proteowizard/proteowizardbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "The ProteoWizard Library and Tools are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis.", "sc:name": "ProteoWizard", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://proteowizard.sourceforge.net/" } \ No newline at end of file diff --git a/data/proteoworker/proteoworkerbioschemas.jsonld b/data/proteoworker/proteoworkerbioschemas.jsonld index 22aa8c0c5f7b6..cc9d1fce2c36e 100644 --- a/data/proteoworker/proteoworkerbioschemas.jsonld +++ b/data/proteoworker/proteoworkerbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-9243-5084", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/ProteoWorker", "@type": "sc:SoftwareApplication", @@ -24,11 +20,15 @@ "sc:license": "Proprietary", "sc:name": "ProteoWorker", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://www.proteoworker.com" + }, + { + "@id": "https://orcid.org/0000-0001-9243-5084", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/proteus/proteusbioschemas.jsonld b/data/proteus/proteusbioschemas.jsonld index aa0f901095bb0..3fa76805c06ca 100644 --- a/data/proteus/proteusbioschemas.jsonld +++ b/data/proteus/proteusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An archive of functional signatures in protein termini.", "sc:name": "ProTeus", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.proteus.cs.huji.ac.il/index.php" } \ No newline at end of file diff --git a/data/proteus2/proteus2bioschemas.jsonld b/data/proteus2/proteus2bioschemas.jsonld index 930ca70b909b5..b5a7ceb699b98 100644 --- a/data/proteus2/proteus2bioschemas.jsonld +++ b/data/proteus2/proteus2bioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PROTEUS2", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://wishart.biology.ualberta.ca/proteus2" } \ No newline at end of file diff --git a/data/protfun/protfunbioschemas.jsonld b/data/protfun/protfunbioschemas.jsonld index ce4a984f43948..713728484be46 100644 --- a/data/protfun/protfunbioschemas.jsonld +++ b/data/protfun/protfunbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "Other", "sc:name": "ProtFun", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/ProtFun/", diff --git a/data/protgenerics/bioconda_protgenerics.yaml b/data/protgenerics/bioconda_protgenerics.yaml index 515a06e241ee3..75927f781e35a 100644 --- a/data/protgenerics/bioconda_protgenerics.yaml +++ b/data/protgenerics/bioconda_protgenerics.yaml @@ -3,7 +3,6 @@ description: S4 generic functions needed by Bioconductor proteomics packages. home: https://bioconductor.org/packages/3.10/bioc/html/ProtGenerics.html identifiers: - biotools:protgenerics -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-protgenerics summary: S4 generic functions for Bioconductor proteomics infrastructure diff --git a/data/protgenerics/protgenericsbioschemas.jsonld b/data/protgenerics/protgenericsbioschemas.jsonld index 4eaa8943e02ff..e4cf5142198b0 100644 --- a/data/protgenerics/protgenericsbioschemas.jsonld +++ b/data/protgenerics/protgenericsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laurent Gatto", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "S4 generic functions needed by BioConductor proteomics packages.", "sc:license": "Artistic-2.0", "sc:name": "ProtGenerics", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ProtGenerics.html", "sc:version": "1.6.0" diff --git a/data/proticdb/proticdbbioschemas.jsonld b/data/proticdb/proticdbbioschemas.jsonld index 6639f74fff3ea..808aa898d0d25 100644 --- a/data/proticdb/proticdbbioschemas.jsonld +++ b/data/proticdb/proticdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Proteomic database to store, track, query and compare proteome data.", "sc:name": "PROTICdb", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://pappso.inra.fr/bioinfo/proticdb/" } \ No newline at end of file diff --git a/data/protident/protidentbioschemas.jsonld b/data/protident/protidentbioschemas.jsonld index 65c45a53a3d7c..835e48b53ca93 100644 --- a/data/protident/protidentbioschemas.jsonld +++ b/data/protident/protidentbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ProtIdent", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/Protease/" } \ No newline at end of file diff --git a/data/protinfo/protinfobioschemas.jsonld b/data/protinfo/protinfobioschemas.jsonld index 8c67503cbb1d7..6a47e057f74c8 100644 --- a/data/protinfo/protinfobioschemas.jsonld +++ b/data/protinfo/protinfobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling.", "sc:name": "Protinfo", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://protinfo.compbio.buffalo.edu/" } \ No newline at end of file diff --git a/data/protk/protkbioschemas.jsonld b/data/protk/protkbioschemas.jsonld index 74c7dcf6b44b6..fe6c0d14a5ad6 100644 --- a/data/protk/protkbioschemas.jsonld +++ b/data/protk/protkbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "protk", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/iracooke/protk" } \ No newline at end of file diff --git a/data/protobug/protobugbioschemas.jsonld b/data/protobug/protobugbioschemas.jsonld index 84ee48a18ca6d..03fc783390431 100644 --- a/data/protobug/protobugbioschemas.jsonld +++ b/data/protobug/protobugbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/database/bau122", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/protobug", "@type": "sc:SoftwareApplication", @@ -31,11 +27,15 @@ }, "sc:name": "ProtoBug", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.protobug.cs.huji.ac.il/" + }, + { + "@id": "https://doi.org/10.1093/database/bau122", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/protocolnavigator/protocolnavigatorbioschemas.jsonld b/data/protocolnavigator/protocolnavigatorbioschemas.jsonld index f2ca6810e25bc..a562d4b924ede 100644 --- a/data/protocolnavigator/protocolnavigatorbioschemas.jsonld +++ b/data/protocolnavigator/protocolnavigatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Virtual laboratory environment that promote reproducibility of biological experiments and reuse of experimental data.", "sc:name": "ProtocolNavigator", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://protocolnavigator.org/" } \ No newline at end of file diff --git a/data/protomap/protomapbioschemas.jsonld b/data/protomap/protomapbioschemas.jsonld index 3432c4754a5d8..7bd930aa5b190 100644 --- a/data/protomap/protomapbioschemas.jsonld +++ b/data/protomap/protomapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Recently developed technique to map in vivo substrates of proteolytic events. It uses 1D SDS-PAGE and mass spectrometry to globally identify shifts in gel-migration and corresponding changes in the topography of proteolytic fragments.", "sc:name": "PROTOMAP", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.scripps.edu/chemphys/cravatt/protomap/" } \ No newline at end of file diff --git a/data/protomata/protomatabioschemas.jsonld b/data/protomata/protomatabioschemas.jsonld index 40151f0165b62..edf561b911348 100644 --- a/data/protomata/protomatabioschemas.jsonld +++ b/data/protomata/protomatabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "CECILL-2.0", "sc:name": "Protomata", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "GenOuest", diff --git a/data/protoss/protossbioschemas.jsonld b/data/protoss/protossbioschemas.jsonld index 374c22a6e72fc..7f90666a52cad 100644 --- a/data/protoss/protossbioschemas.jsonld +++ b/data/protoss/protossbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Protoss", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "University of Hamburg - Center for Bioinformatics", "sc:url": "http://proteinsplus.zbh.uni-hamburg.de/#protoss" diff --git a/data/protparam/protparambioschemas.jsonld b/data/protparam/protparambioschemas.jsonld index d8766874a5917..5bd3258525bf7 100644 --- a/data/protparam/protparambioschemas.jsonld +++ b/data/protparam/protparambioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI (isoelectric point), amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).", "sc:name": "ProtParam", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://web.expasy.org/protparam" diff --git a/data/protphylo/protphylobioschemas.jsonld b/data/protphylo/protphylobioschemas.jsonld index 681d52e78fb8e..371b2fe462bb9 100644 --- a/data/protphylo/protphylobioschemas.jsonld +++ b/data/protphylo/protphylobioschemas.jsonld @@ -9,16 +9,12 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKV455", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/protphylo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Yiming Cheng", - "Dr. Fabiana Perocchi" + "Dr. Fabiana Perocchi", + "Dr. Yiming Cheng" ], "sc:additionalType": "Web application", "sc:citation": [ @@ -35,10 +31,14 @@ "sc:name": "ProtPhylo", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.protphylo.org/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKV455", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/protpy/protpybioschemas.jsonld b/data/protpy/protpybioschemas.jsonld index ec93e9e56398a..9e918492f91cc 100644 --- a/data/protpy/protpybioschemas.jsonld +++ b/data/protpy/protpybioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Software for calculating the widely used structural and physicochemical features of proteins and peptides from amino acid sequence.", "sc:name": "protpy", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://code.google.com/p/protpy/", "sc:version": "1.0" diff --git a/data/protsav/protsavbioschemas.jsonld b/data/protsav/protsavbioschemas.jsonld index 4d8234616504c..1151992ae1bc5 100644 --- a/data/protsav/protsavbioschemas.jsonld +++ b/data/protsav/protsavbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Meta-server, which has a collection of model quality assessment programs that evaluate the quality of a protein and correctness of the structural model.", "sc:name": "ProTSAV", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp" } \ No newline at end of file diff --git a/data/protscale/protscalebioschemas.jsonld b/data/protscale/protscalebioschemas.jsonld index f4547ca0103e6..4158024d5c945 100644 --- a/data/protscale/protscalebioschemas.jsonld +++ b/data/protscale/protscalebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Compute and represent the profile produced by any amino acid scale on a selected protein sequence. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but ProtScale provides more than 50 predefined scales entered from the literature.", "sc:name": "ProtScale", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://web.expasy.org/protscale/" } \ No newline at end of file diff --git a/data/protsweep/protsweepbioschemas.jsonld b/data/protsweep/protsweepbioschemas.jsonld index 132f89c9435f4..23ed53b189886 100644 --- a/data/protsweep/protsweepbioschemas.jsonld +++ b/data/protsweep/protsweepbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Protsweep can be used for analysis and possible identification of newly obtained protein sequences.", "sc:name": "ProtSweep", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.welcome#protsweep" diff --git a/data/protter/protterbioschemas.jsonld b/data/protter/protterbioschemas.jsonld index 8fa32f5e99ad3..61bafac92250b 100644 --- a/data/protter/protterbioschemas.jsonld +++ b/data/protter/protterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Interactive protein feature visualization and integration with experimental proteomic data.", "sc:name": "Protter", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://wlab.ethz.ch/protter/" } \ No newline at end of file diff --git a/data/prottest/prottestbioschemas.jsonld b/data/prottest/prottestbioschemas.jsonld index 56a45c01b996c..a09c24b80c921 100644 --- a/data/prottest/prottestbioschemas.jsonld +++ b/data/prottest/prottestbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/prottest", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "F. Abascal", - "D. Posada" + "D. Posada", + "F. Abascal" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:15647292", @@ -20,8 +20,8 @@ "sc:name": "ProtTest", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://darwin.uvigo.es/software/prottest_server.html?" } \ No newline at end of file diff --git a/data/prottrace/prottracebioschemas.jsonld b/data/prottrace/prottracebioschemas.jsonld index a3b625f198c2a..1162ecc86c98f 100644 --- a/data/prottrace/prottracebioschemas.jsonld +++ b/data/prottrace/prottracebioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Ingo Ebersberger", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6394115", { "@id": "https://doi.org/10.1093/gbe/evz008" }, - "pmcid:PMC6394115", "pubmed:30649284" ], "sc:description": "Simulation based framework to estimate the evolutionary traceability of protein.", diff --git a/data/provean/proveanbioschemas.jsonld b/data/provean/proveanbioschemas.jsonld index 04cda3c816a3d..dd0fcd6be5950 100644 --- a/data/provean/proveanbioschemas.jsonld +++ b/data/provean/proveanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "PROVEAN", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://provean.jcvi.org/index.php" } \ No newline at end of file diff --git a/data/proxl/proxlbioschemas.jsonld b/data/proxl/proxlbioschemas.jsonld index e54a3df9f92cf..d3dffec51effb 100644 --- a/data/proxl/proxlbioschemas.jsonld +++ b/data/proxl/proxlbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1021/acs.jproteome.6b00274", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/proxl", "@type": "sc:SoftwareApplication", @@ -33,40 +37,36 @@ } ], "sc:citation": [ + "pubmed:27302480", { "@id": "https://doi.org/10.1021/acs.jproteome.6b00274" }, - "pmcid:PMC4977572", - "pubmed:27302480" + "pmcid:PMC4977572" ], "sc:description": "Platform for the analysis, visualization and sharing of protein cross-linking mass spectrometry data", "sc:featureList": [ - { - "@id": "edam:operation_2406" - }, { "@id": "edam:operation_0564" }, { "@id": "edam:operation_0570" + }, + { + "@id": "edam:operation_2406" } ], "sc:isAccessibleForFree": true, "sc:license": "Apache-2.0", "sc:name": "ProXL", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:softwareHelp": { "@id": "https://proxl-web-app.readthedocs.io/en/latest/" }, "sc:url": "https://github.com/yeastrc/proxl-web-app" - }, - { - "@id": "https://doi.org/10.1021/acs.jproteome.6b00274", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/prs/prsbioschemas.jsonld b/data/prs/prsbioschemas.jsonld index 645855735e468..2db1330afa0e8 100644 --- a/data/prs/prsbioschemas.jsonld +++ b/data/prs/prsbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-7918-2040", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1101/467910", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/PRS", "@type": "sc:SoftwareApplication", @@ -25,32 +17,40 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6400585", { "@id": "https://doi.org/10.1101/467910" }, - "pubmed:30835202" + "pubmed:30835202", + "pmcid:PMC6400585" ], "sc:description": "Atlas of polygenic burden associations across the human phenome.", "sc:featureList": [ - { - "@id": "edam:operation_3196" - }, { "@id": "edam:operation_3435" }, { "@id": "edam:operation_0484" + }, + { + "@id": "edam:operation_3196" } ], "sc:license": "Unlicense", "sc:name": "PRS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://mrcieu.mrsoftware.org/PRS_atlas" + }, + { + "@id": "https://doi.org/10.1101/467910", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-7918-2040", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/prsice/prsicebioschemas.jsonld b/data/prsice/prsicebioschemas.jsonld index bf36c624039aa..88922877aa7b7 100644 --- a/data/prsice/prsicebioschemas.jsonld +++ b/data/prsice/prsicebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software package for calculating, applying, evaluating and plotting the results of polygenic risk scores.", "sc:name": "PRSice", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://prsice.info/" diff --git a/data/ps-plant/ps-plantbioschemas.jsonld b/data/ps-plant/ps-plantbioschemas.jsonld index 1f6b66356abde..689098db395c6 100644 --- a/data/ps-plant/ps-plantbioschemas.jsonld +++ b/data/ps-plant/ps-plantbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ056", - "@type": "sc:CreativeWork" + "@id": "https://orcid.org/0000-0002-7255-872X", + "@type": "schema:Person" }, { "@id": "https://bio.tools/PS-Plant", @@ -21,11 +21,11 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC6534809", + "pubmed:31127811", { "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ056" }, - "pubmed:31127811" + "pmcid:PMC6534809" ], "sc:description": "Photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth.", "sc:license": "GPL-3.0", @@ -38,8 +38,8 @@ "sc:url": "https://github.com/g2-bernotas/PS-Plant-Framework" }, { - "@id": "https://orcid.org/0000-0002-7255-872X", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ056", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ps2-v3/ps2-v3bioschemas.jsonld b/data/ps2-v3/ps2-v3bioschemas.jsonld index 169bdaec880ba..c9c468f8c8a66 100644 --- a/data/ps2-v3/ps2-v3bioschemas.jsonld +++ b/data/ps2-v3/ps2-v3bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Automated homology modeling server. The method uses an effective consensus strategy by combining PSI-BLAST, IMPALA, and T-Coffee in both template selection and target-template alignment. The final three dimensional structure is built using the modeling package MODELLER.", "sc:name": "(PS)2 - v3", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://ps2v3.life.nctu.edu.tw/", "sc:version": "3.0" diff --git a/data/psa/psabioschemas.jsonld b/data/psa/psabioschemas.jsonld index 60e2de2c7b696..6ef87b639e93f 100644 --- a/data/psa/psabioschemas.jsonld +++ b/data/psa/psabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Prediction of probable secondary structures and fold-class; good for visualizing amphipathic helices, where present.", "sc:name": "PSA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bmerc-www.bu.edu/psa/request.htm" } \ No newline at end of file diff --git a/data/psafe/psafebioschemas.jsonld b/data/psafe/psafebioschemas.jsonld index 4fe3afe2faf3a..2d1aa177e6437 100644 --- a/data/psafe/psafebioschemas.jsonld +++ b/data/psafe/psafebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Pipeline to adjust the biases and errors of sequencing data to gain more accurate allele frequency estimation.", "sc:name": "Psafe", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://zhaocenter.org/software/#Genomic_Protein_Sequence_Analysis" } \ No newline at end of file diff --git a/data/psamm/psammbioschemas.jsonld b/data/psamm/psammbioschemas.jsonld index 7f1395437392a..7ccddb4bbc735 100644 --- a/data/psamm/psammbioschemas.jsonld +++ b/data/psamm/psammbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Open source software that is designed for the curation and analysis of metabolic models. It supports model version tracking, model annotation, data integration, data parsing and formatting, consistency checking, automatic gap filling, and model simulations.", "sc:name": "PSAMM", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://zhanglab.github.io/psamm/" } \ No newline at end of file diff --git a/data/psaweb/psawebbioschemas.jsonld b/data/psaweb/psawebbioschemas.jsonld index d073ba97ee08b..7758febe67715 100644 --- a/data/psaweb/psawebbioschemas.jsonld +++ b/data/psaweb/psawebbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "PSAweb is a web server, developed to analyze the amino acid sequence and multiple sequence alignment of proteins. This is a comprehensive on-line Internet tool that allows the rapid visualization of an analysis, by output in GIF format. It assists the user in analyzing and presenting the primary structure of proteins and mutiple alignment of protein sequences", "sc:name": "PSAweb", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/psa/" } \ No newline at end of file diff --git a/data/psbvb/psbvbbioschemas.jsonld b/data/psbvb/psbvbbioschemas.jsonld index 34316605fcc6a..6c83947c7fa3a 100644 --- a/data/psbvb/psbvbbioschemas.jsonld +++ b/data/psbvb/psbvbbioschemas.jsonld @@ -17,16 +17,16 @@ "@id": "https://bio.tools/pSBVB", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Laura Zingaretti", - "M Pérez-Enciso" + "M Pérez-Enciso", + "Laura Zingaretti" ], "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:30573468", - "pmcid:PMC6385978", { "@id": "https://doi.org/10.1534/g3.118.200942" - } + }, + "pmcid:PMC6385978" ], "sc:description": "polyploid Sequence Based Virtual Breeding (pSBVB) - versatile simulation tool to evaluate genomic selection in polyploid species.", "sc:featureList": [ @@ -34,10 +34,10 @@ "@id": "edam:operation_3196" }, { - "@id": "edam:operation_0484" + "@id": "edam:operation_0487" }, { - "@id": "edam:operation_0487" + "@id": "edam:operation_0484" } ], "sc:name": "pSBVB", diff --git a/data/pscan/pscanbioschemas.jsonld b/data/pscan/pscanbioschemas.jsonld index 6fcc4b145e63c..4928c99094a0d 100644 --- a/data/pscan/pscanbioschemas.jsonld +++ b/data/pscan/pscanbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "EMBOSS Contributors", "UK MRC", + "EMBOSS Contributors", + "Wellcome Trust", "UK BBSRC" ], "sc:description": "Scan protein sequence(s) with fingerprints from the PRINTS database.", "sc:funder": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "pscan", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/pscanchip/pscanchipbioschemas.jsonld b/data/pscanchip/pscanchipbioschemas.jsonld index f09fd1f44165d..81aa52293df20 100644 --- a/data/pscanchip/pscanchipbioschemas.jsonld +++ b/data/pscanchip/pscanchipbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/pscanchip", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Giulio Pavesi", - "Federico Zambelli" + "Federico Zambelli", + "Giulio Pavesi" ], "sc:additionalType": [ "Command-line tool", @@ -22,9 +22,9 @@ "sc:license": "GPL-3.0", "sc:name": "PscanChIP", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-MILANO", "sc:url": "http://www.beaconlab.it/pscan_chip_dev", diff --git a/data/pscp/pscpbioschemas.jsonld b/data/pscp/pscpbioschemas.jsonld index 459d371b72977..46e6f84a0a865 100644 --- a/data/pscp/pscpbioschemas.jsonld +++ b/data/pscp/pscpbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PSCP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://brl.uiu.ac.bd/PL/" } \ No newline at end of file diff --git a/data/pse-analysis/pse-analysisbioschemas.jsonld b/data/pse-analysis/pse-analysisbioschemas.jsonld index ded07bfb3e385..290a724be481d 100644 --- a/data/pse-analysis/pse-analysisbioschemas.jsonld +++ b/data/pse-analysis/pse-analysisbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Bin Liu", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:28076851", { "@id": "https://doi.org/10.18632/ONCOTARGET.14524" }, - "pubmed:28076851", "pmcid:PMC5355101" ], "sc:description": "A python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods.", @@ -27,8 +27,8 @@ }, "sc:name": "Pse-Analysis", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioinformatics.hitsz.edu.cn/Pse-Analysis/" diff --git a/data/pse-in-one/pse-in-onebioschemas.jsonld b/data/pse-in-one/pse-in-onebioschemas.jsonld index c9feb4397b1ac..dc199619481a7 100644 --- a/data/pse-in-one/pse-in-onebioschemas.jsonld +++ b/data/pse-in-one/pse-in-onebioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKV458", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pse-in-one", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bin Liu", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC4489303", { "@id": "https://doi.org/10.1093/NAR/GKV458" }, - "pubmed:25958395", - "pmcid:PMC4489303" + "pubmed:25958395" ], "sc:description": "Web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "Pse-in-One", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinformatics.hitsz.edu.cn/Pse-in-One/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKV458", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pseaac/pseaacbioschemas.jsonld b/data/pseaac/pseaacbioschemas.jsonld index 263d4f190cf1d..08c6de04aea58 100644 --- a/data/pseaac/pseaacbioschemas.jsonld +++ b/data/pseaac/pseaacbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PseAAC", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/PseAAC/" } \ No newline at end of file diff --git a/data/pseknc/psekncbioschemas.jsonld b/data/pseknc/psekncbioschemas.jsonld index a58eac7987e42..46bcc16dcba7a 100644 --- a/data/pseknc/psekncbioschemas.jsonld +++ b/data/pseknc/psekncbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides.", "sc:name": "PseKNC", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://lin.uestc.edu.cn/pseknc/default.aspx" } \ No newline at end of file diff --git a/data/pseudo-nitzschia_multistriata_genome_portal/pseudo-nitzschia_multistriata_genome_portalbioschemas.jsonld b/data/pseudo-nitzschia_multistriata_genome_portal/pseudo-nitzschia_multistriata_genome_portalbioschemas.jsonld index 4f636e7ee2ba3..b19fc64ee4fb5 100644 --- a/data/pseudo-nitzschia_multistriata_genome_portal/pseudo-nitzschia_multistriata_genome_portalbioschemas.jsonld +++ b/data/pseudo-nitzschia_multistriata_genome_portal/pseudo-nitzschia_multistriata_genome_portalbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/Pseudo-nitzschia_multistriata_genome_portal", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:description": "Web portal dedicated to the diatom Pseudo-nitzschia multistriata. A genome browser, a BLAST service and a download section are available.", "sc:license": "Unlicense", "sc:name": "Pseudo-nitzschia multistriata genome portal", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo.szn.it/pmultistriata/" } \ No newline at end of file diff --git a/data/pseudocap/pseudocapbioschemas.jsonld b/data/pseudocap/pseudocapbioschemas.jsonld index bda4d9b484063..d43a9d2a84194 100644 --- a/data/pseudocap/pseudocapbioschemas.jsonld +++ b/data/pseudocap/pseudocapbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkq869", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0001-6848-1638", "@type": "schema:Person" @@ -32,8 +36,8 @@ "@id": "edam:topic_0621" }, "sc:citation": [ - "pmcid:PMC3013766", "pubmed:20929876", + "pmcid:PMC3013766", { "@id": "https://doi.org/10.1093/nar/gkq869" } @@ -48,14 +52,10 @@ "sc:name": "PseudoCAP pseudomonas genome database", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.pseudomonas.com/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkq869", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pseudomap/pseudomapbioschemas.jsonld b/data/pseudomap/pseudomapbioschemas.jsonld index 98264dba28b0d..3a3927450e2ca 100644 --- a/data/pseudomap/pseudomapbioschemas.jsonld +++ b/data/pseudomap/pseudomapbioschemas.jsonld @@ -31,9 +31,9 @@ }, "sc:name": "pseudoMap", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://pseudomap.mbc.nctu.edu.tw/php/index.php" } diff --git a/data/pseudomonas_genome_project/pseudomonas_genome_projectbioschemas.jsonld b/data/pseudomonas_genome_project/pseudomonas_genome_projectbioschemas.jsonld index ce1fe55e3eba5..21c52501947f5 100644 --- a/data/pseudomonas_genome_project/pseudomonas_genome_projectbioschemas.jsonld +++ b/data/pseudomonas_genome_project/pseudomonas_genome_projectbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Pseudomonas Genome Database", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://pseudomonas.com/" } \ No newline at end of file diff --git a/data/pseudoviewer/pseudoviewerbioschemas.jsonld b/data/pseudoviewer/pseudoviewerbioschemas.jsonld index c55fddc9bc744..6f33136463c2f 100644 --- a/data/pseudoviewer/pseudoviewerbioschemas.jsonld +++ b/data/pseudoviewer/pseudoviewerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.", "sc:name": "PSEUDOVIEWER", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://pseudoviewer.inha.ac.kr/" } \ No newline at end of file diff --git a/data/psi-blast/psi-blastbioschemas.jsonld b/data/psi-blast/psi-blastbioschemas.jsonld index 10efbf4252664..4b72c99aafc5c 100644 --- a/data/psi-blast/psi-blastbioschemas.jsonld +++ b/data/psi-blast/psi-blastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Iterative protein sequence similarity search based on BLAST: search with a custom, position-specific, scoring matrix which can help find distant evolutionary relationships.", "sc:name": "PSI-BLAST (EBI)", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": [ "NCBI", diff --git a/data/psi-blast_rest/psi-blast_restbioschemas.jsonld b/data/psi-blast_rest/psi-blast_restbioschemas.jsonld index e392bad874204..bd60da4d5b9e5 100644 --- a/data/psi-blast_rest/psi-blast_restbioschemas.jsonld +++ b/data/psi-blast_rest/psi-blast_restbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Position Specific Iterative BLAST (PSI-BLAST) refers to a feature of NCBI BLAST 2.0 in which a position-specific scoring matrix (PSSM) profile is constructed from set of BLAST alignments.", "sc:name": "PSI-BLAST API (EBI)", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/psiblast_rest", "sc:version": "1" diff --git a/data/psi-mi_validator/psi-mi_validatorbioschemas.jsonld b/data/psi-mi_validator/psi-mi_validatorbioschemas.jsonld index 3b769d1b2b9b4..9cd727867937a 100644 --- a/data/psi-mi_validator/psi-mi_validatorbioschemas.jsonld +++ b/data/psi-mi_validator/psi-mi_validatorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Validate files in PSI-MI XML 2.5 and PSI-PAR format, and generate a table with error messages.", "sc:name": "PSI-MI Validator", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/intact/validator/start.xhtml", diff --git a/data/psi-search/psi-searchbioschemas.jsonld b/data/psi-search/psi-searchbioschemas.jsonld index f070c6f862bff..f6d07ff3b152c 100644 --- a/data/psi-search/psi-searchbioschemas.jsonld +++ b/data/psi-search/psi-searchbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Iterative protein sequence similarity search based on Smith & Waterman algorithm with PSI-BLAST profile construction : find distantly related protein sequences.", "sc:name": "PSI-Search (EBI)", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "EMBL-EBI", diff --git a/data/psi-search_rest/psi-search_restbioschemas.jsonld b/data/psi-search_rest/psi-search_restbioschemas.jsonld index 289d952e9c32e..91fa50864ef90 100644 --- a/data/psi-search_rest/psi-search_restbioschemas.jsonld +++ b/data/psi-search_rest/psi-search_restbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This tool uses SSEARCH to perform a rigorous Smith & Waterman search of a protein database.", "sc:name": "PSI-Search API (EBI)", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/sss/psisearch_rest", "sc:version": "1" diff --git a/data/psi-sigma/psi-sigmabioschemas.jsonld b/data/psi-sigma/psi-sigmabioschemas.jsonld index 7004cdb6fba40..1913a716191df 100644 --- a/data/psi-sigma/psi-sigmabioschemas.jsonld +++ b/data/psi-sigma/psi-sigmabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Other", "sc:name": "PSI-Sigma", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/wososa/PSI-Sigma" } \ No newline at end of file diff --git a/data/psi/psibioschemas.jsonld b/data/psi/psibioschemas.jsonld index 78af9cd5a9ee2..dafc67d513975 100644 --- a/data/psi/psibioschemas.jsonld +++ b/data/psi/psibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server which performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach.", "sc:name": "PSI", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://tcoffee.crg.cat/apps/tcoffee/do:tmcoffee" } \ No newline at end of file diff --git a/data/psichomics/psichomicsbioschemas.jsonld b/data/psichomics/psichomicsbioschemas.jsonld index ca96f6bb6b950..8ddf334915be4 100644 --- a/data/psichomics/psichomicsbioschemas.jsonld +++ b/data/psichomics/psichomicsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nuno Agostinho", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:author": "Nuno Daniel Saraiva Agostinho", "sc:contributor": "Nuno Luís Barbosa Morais", @@ -21,9 +21,9 @@ "sc:license": "MIT", "sc:name": "psichomics", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://bioconductor.org/packages/psichomics/", "sc:version": "1.0.8" diff --git a/data/psicquic/bioconda_psicquic.yaml b/data/psicquic/bioconda_psicquic.yaml index 8c5e11a1edd58..5c4d2112a2c10 100644 --- a/data/psicquic/bioconda_psicquic.yaml +++ b/data/psicquic/bioconda_psicquic.yaml @@ -4,7 +4,6 @@ description: PSICQUIC is a project within the HUPO Proteomics Standard Initiativ home: https://bioconductor.org/packages/3.10/bioc/html/PSICQUIC.html identifiers: - biotools:psicquic -- doi:10.1038/nmeth.3252 license: Apache License 2.0 name: bioconductor-psicquic summary: Proteomics Standard Initiative Common QUery InterfaCe diff --git a/data/psicquic/psicquicbioschemas.jsonld b/data/psicquic/psicquicbioschemas.jsonld index d0520fd938f79..1dc05e50994d8 100644 --- a/data/psicquic/psicquicbioschemas.jsonld +++ b/data/psicquic/psicquicbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Paul Shannon", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Project within the HUPO Proteomics Standard Initiative (HUPO-PSI) that standardises programmatic access to molecular interaction databases.", "sc:license": "Apache-2.0", diff --git a/data/psicquic_view/psicquic_viewbioschemas.jsonld b/data/psicquic_view/psicquic_viewbioschemas.jsonld index dd1ad3ec8d015..1369420ae87cf 100644 --- a/data/psicquic_view/psicquic_viewbioschemas.jsonld +++ b/data/psicquic_view/psicquic_viewbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Standardises programmatic access to molecular interaction databases.", "sc:name": "PSICQUIC view", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/psicquic/view/home.xhtml" } \ No newline at end of file diff --git a/data/psionplus/psionplusbioschemas.jsonld b/data/psionplus/psionplusbioschemas.jsonld index 43bc20901f022..8aaf29af10b79 100644 --- a/data/psionplus/psionplusbioschemas.jsonld +++ b/data/psionplus/psionplusbioschemas.jsonld @@ -27,9 +27,9 @@ }, "sc:name": "PSIONplus", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://sourceforge.net/projects/psion/" }, diff --git a/data/psiphi/psiphibioschemas.jsonld b/data/psiphi/psiphibioschemas.jsonld index 83fa034c24d39..dee06a9328e3b 100644 --- a/data/psiphi/psiphibioschemas.jsonld +++ b/data/psiphi/psiphibioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK MRC", + "EMBOSS Contributors", "UK BBSRC", "Wellcome Trust" ], @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "psiphi", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/psiphi.html", "sc:version": "r6" diff --git a/data/psipred/psipredbioschemas.jsonld b/data/psipred/psipredbioschemas.jsonld index 7ff7540f84c68..e898c6f15dab6 100644 --- a/data/psipred/psipredbioschemas.jsonld +++ b/data/psipred/psipredbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PSIPRED", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinf.cs.ucl.ac.uk/psipred/" } \ No newline at end of file diff --git a/data/psiquic_dip/psiquic_dipbioschemas.jsonld b/data/psiquic_dip/psiquic_dipbioschemas.jsonld index 415420189ca83..3be8bb2eeb2fe 100644 --- a/data/psiquic_dip/psiquic_dipbioschemas.jsonld +++ b/data/psiquic_dip/psiquic_dipbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Database which catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. Search the database using a protein id.", "sc:name": "PSIQUIC (DIP)", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://dip.doe-mbi.ucla.edu/dip/Main.cgi", "sc:version": "1" diff --git a/data/pslpred/pslpredbioschemas.jsonld b/data/pslpred/pslpredbioschemas.jsonld index 07554e75b5e72..dcaa1e7d25451 100644 --- a/data/pslpred/pslpredbioschemas.jsonld +++ b/data/pslpred/pslpredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Method for subcellular localization proteins belongs to prokaryotic genomes.", "sc:name": "PSLpred", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.imtech.res.in/raghava/pslpred/" } \ No newline at end of file diff --git a/data/psoda/psodabioschemas.jsonld b/data/psoda/psodabioschemas.jsonld index 4a6a961a0a1c9..cd6f7e8a6c58c 100644 --- a/data/psoda/psodabioschemas.jsonld +++ b/data/psoda/psodabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PSODA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://dna.cs.byu.edu/psoda/", "sc:version": "0.96" diff --git a/data/psortb/psortbbioschemas.jsonld b/data/psortb/psortbbioschemas.jsonld index 483755e902a9a..62a7b6fb0bc2e 100644 --- a/data/psortb/psortbbioschemas.jsonld +++ b/data/psortb/psortbbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "It is a high-precision localization prediction method for bacterial proteins. It has remained the most precise bacterial protein subcellular localization (SCL) predictor.  PSORTb version improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies.", "sc:name": "PSORTb", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.psort.org/psortb/", "sc:version": "3.0.3" diff --git a/data/psortdb/psortdbbioschemas.jsonld b/data/psortdb/psortdbbioschemas.jsonld index 12ea7a54d340e..e141d19eac497 100644 --- a/data/psortdb/psortdbbioschemas.jsonld +++ b/data/psortdb/psortdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PSORTdb (part of the PSORT family) is a database of protein subcellular localizations for bacteria and archaea that contains both information determined through laboratory experimentation (ePSORTdb dataset) and computational predictions (cPSORTdb dataset).", "sc:name": "PSORTdb", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://db.psort.org" } \ No newline at end of file diff --git a/data/psrn/psrnbioschemas.jsonld b/data/psrn/psrnbioschemas.jsonld index b03eb16f0e3bb..5e7bfb7322d4d 100644 --- a/data/psrn/psrnbioschemas.jsonld +++ b/data/psrn/psrnbioschemas.jsonld @@ -14,23 +14,23 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Systems Biology Lab, National Chung Hsing University", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ - "pubmed:30587128", + "pmcid:PMC6307140", { "@id": "https://doi.org/10.1186/s12864-018-5367-5" }, - "pmcid:PMC6307140" + "pubmed:30587128" ], "sc:description": "Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells.", "sc:featureList": [ { - "@id": "edam:operation_3223" + "@id": "edam:operation_3800" }, { - "@id": "edam:operation_3800" + "@id": "edam:operation_3223" }, { "@id": "edam:operation_3680" @@ -39,9 +39,9 @@ "sc:license": "Unlicense", "sc:name": "PSRN", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://syslab5.nchu.edu.tw/" }, diff --git a/data/psrnatarget/psrnatargetbioschemas.jsonld b/data/psrnatarget/psrnatargetbioschemas.jsonld index 60bc3a2ade84d..58e5c630ee015 100644 --- a/data/psrnatarget/psrnatargetbioschemas.jsonld +++ b/data/psrnatarget/psrnatargetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "psRNATarget", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://plantgrn.noble.org/psRNATarget/." } \ No newline at end of file diff --git a/data/psrrr/psrrrbioschemas.jsonld b/data/psrrr/psrrrbioschemas.jsonld index d77777b45c2d6..83378fb670a4d 100644 --- a/data/psrrr/psrrrbioschemas.jsonld +++ b/data/psrrr/psrrrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PsRRR", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www2.imperial.ac.uk/~gmontana/psrrr.htm" } \ No newline at end of file diff --git a/data/pssa/pssabioschemas.jsonld b/data/pssa/pssabioschemas.jsonld index 4dade77f466f2..82cf20e5e21e5 100644 --- a/data/pssa/pssabioschemas.jsonld +++ b/data/pssa/pssabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "PSSA", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://pssa.itiud.org" diff --git a/data/pssalib/pssalibbioschemas.jsonld b/data/pssalib/pssalibbioschemas.jsonld index 80a609569c461..a802e11bb4790 100644 --- a/data/pssalib/pssalibbioschemas.jsonld +++ b/data/pssalib/pssalibbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "LGPL-3.0", "sc:name": "pSSAlib", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mosaic.mpi-cbg.de/?q=downloads/stochastic_chemical_net" } \ No newline at end of file diff --git a/data/pssmhcpan/pssmhcpanbioschemas.jsonld b/data/pssmhcpan/pssmhcpanbioschemas.jsonld index 15db8773e3f69..456cbd2bc41ef 100644 --- a/data/pssmhcpan/pssmhcpanbioschemas.jsonld +++ b/data/pssmhcpan/pssmhcpanbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/pssmhcpan", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dongli Li", - "Geng Liu" + "Geng Liu", + "Dongli Li" ], "sc:additionalType": "Command-line tool", "sc:description": "A novel PSSM based software for predicting class I peptide-HLA binding affinity.", "sc:license": "MIT", "sc:name": "PSSMHCpan", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/BGI2016/PSSMHCpan" } \ No newline at end of file diff --git a/data/pssrdb/pssrdbbioschemas.jsonld b/data/pssrdb/pssrdbbioschemas.jsonld index 8eb25ec2fdd2b..7f0f0db53891f 100644 --- a/data/pssrdb/pssrdbbioschemas.jsonld +++ b/data/pssrdb/pssrdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Relational database of polymorphic simple sequence repeats (PSSRs) extracted from different species of prokaryotes. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc.", "sc:name": "PSSRdb", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cdfd.org.in/PSSRdb/" } \ No newline at end of file diff --git a/data/pssrnaminer/pssrnaminerbioschemas.jsonld b/data/pssrnaminer/pssrnaminerbioschemas.jsonld index 2a93d9aad4935..11395c24cd2e9 100644 --- a/data/pssrnaminer/pssrnaminerbioschemas.jsonld +++ b/data/pssrnaminer/pssrnaminerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "pssRNAMiner", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo3.noble.org/pssRNAMiner/" } \ No newline at end of file diff --git a/data/pstdistancer/pstdistancerbioschemas.jsonld b/data/pstdistancer/pstdistancerbioschemas.jsonld index fb70028172b83..284efe0a8a652 100644 --- a/data/pstdistancer/pstdistancerbioschemas.jsonld +++ b/data/pstdistancer/pstdistancerbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "pSTDistanceR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/radamsRHA/pSTDistanceR/" } \ No newline at end of file diff --git a/data/pstr_finder/pstr_finderbioschemas.jsonld b/data/pstr_finder/pstr_finderbioschemas.jsonld index 8c89286f0d6c9..07d3ee7c3ee5f 100644 --- a/data/pstr_finder/pstr_finderbioschemas.jsonld +++ b/data/pstr_finder/pstr_finderbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web tool to efficiently analyse multiple genome sequence samples for the presence of STR loci using Tandem Repeats Finder (TRF) and generates identical, polymorphic, and different STR loci for each comparison between two samples.", "sc:name": "pSTR Finder", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://forensic.mc.ntu.edu.tw:9000/PSTRWeb/Default.aspx" } \ No newline at end of file diff --git a/data/psuc-lys/psuc-lysbioschemas.jsonld b/data/psuc-lys/psuc-lysbioschemas.jsonld index b00b93dac01e3..dc1eb50220a88 100644 --- a/data/psuc-lys/psuc-lysbioschemas.jsonld +++ b/data/psuc-lys/psuc-lysbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This web-server is used to predict the lysine succinylation in protein.", "sc:name": "pSuc-Lys", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.jci-bioinfo.cn/pSuc-Lys" } \ No newline at end of file diff --git a/data/psumo-cd/psumo-cdbioschemas.jsonld b/data/psumo-cd/psumo-cdbioschemas.jsonld index a7da7e927b14a..ab5ef3395faa7 100644 --- a/data/psumo-cd/psumo-cdbioschemas.jsonld +++ b/data/psumo-cd/psumo-cdbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "pSumo-CD", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.jci-bioinfo.cn/pSumo-CD" } \ No newline at end of file diff --git a/data/psvs/psvsbioschemas.jsonld b/data/psvs/psvsbioschemas.jsonld index 08f66b23540c1..68e0add79a642 100644 --- a/data/psvs/psvsbioschemas.jsonld +++ b/data/psvs/psvsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "It evaluates the quality of protein structures. It integrates analyses from several widely-used structure quality evaluation tools. It provides standard constraint analyses, statistics on the PDB validation goodness-of-fit between structures and experimental data, and knowledge-based structure quality scores in standardized format suitable for database integration. Global quality measures are reported as Z scores, based on calibration with a set of high-resolution X-ray crystal structures.", "sc:name": "PSVS", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://psvs-1_5-dev.nesg.org/" } \ No newline at end of file diff --git a/data/psychoprot/psychoprotbioschemas.jsonld b/data/psychoprot/psychoprotbioschemas.jsonld index 34af2224387f5..7c7faa958f846 100644 --- a/data/psychoprot/psychoprotbioschemas.jsonld +++ b/data/psychoprot/psychoprotbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0118684", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/psychoprot", "@type": "sc:SoftwareApplication", @@ -54,8 +50,8 @@ } ], "sc:citation": [ - "pubmed:25706742", "pmcid:PMC4338278", + "pubmed:25706742", { "@id": "https://doi.org/10.1371/journal.pone.0118684" } @@ -63,13 +59,13 @@ "sc:description": "Finds which amino acid descriptors explain the amino acid variability observed throughout an alignment or upon deep-sequencing of mutational libraries.", "sc:featureList": [ { - "@id": "edam:operation_3465" + "@id": "edam:operation_0292" }, { - "@id": "edam:operation_2480" + "@id": "edam:operation_3465" }, { - "@id": "edam:operation_0292" + "@id": "edam:operation_2480" }, { "@id": "edam:operation_2403" @@ -78,6 +74,10 @@ "sc:name": "PsychoProt", "sc:url": "http://psychoprot.epfl.ch", "sc:version": "1" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0118684", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/psygenet2r/psygenet2rbioschemas.jsonld b/data/psygenet2r/psygenet2rbioschemas.jsonld index 3aafc85fad038..f54a4934733df 100644 --- a/data/psygenet2r/psygenet2rbioschemas.jsonld +++ b/data/psygenet2r/psygenet2rbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alba Gutierrez-Sacristan", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Package to retrieve data from PsyGeNET database and to perform comorbidity studies with PsyGeNET's and user's data.", "sc:license": "MIT", diff --git a/data/pteros/pterosbioschemas.jsonld b/data/pteros/pterosbioschemas.jsonld index 3d6b74d9bd905..aa9571de4e05e 100644 --- a/data/pteros/pterosbioschemas.jsonld +++ b/data/pteros/pterosbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Fast parallel molecular analysis library.", "sc:name": "Pteros", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/yesint/pteros", "sc:version": "2.0" diff --git a/data/ptgl/ptglbioschemas.jsonld b/data/ptgl/ptglbioschemas.jsonld index f9ffcea96d99a..27d99f7aee477 100644 --- a/data/ptgl/ptglbioschemas.jsonld +++ b/data/ptgl/ptglbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/ptgl", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ina Koch", - "Tim Schaefer" + "Tim Schaefer", + "Ina Koch" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:19906706", diff --git a/data/pthgrn/pthgrnbioschemas.jsonld b/data/pthgrn/pthgrnbioschemas.jsonld index 293973c62083b..2afe5941c1a61 100644 --- a/data/pthgrn/pthgrnbioschemas.jsonld +++ b/data/pthgrn/pthgrnbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Web server for unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data.", "sc:name": "PTHGRN", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.byanbioinfo.org/pthgrn" } \ No newline at end of file diff --git a/data/ptmclust/ptmclustbioschemas.jsonld b/data/ptmclust/ptmclustbioschemas.jsonld index aefb2c6569681..e0201c28c7682 100644 --- a/data/ptmclust/ptmclustbioschemas.jsonld +++ b/data/ptmclust/ptmclustbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software that can be applied to the output of blind PTM (Post-translational Modification) search methods to improve prediction quality, by suppressing noise in the data and clustering peptides with the same underlying modification to form PTM groups. We showed that our technique outperforms two standard clustering algorithms on a simulated dataset.", "sc:name": "PTMClust", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://genes.toronto.edu/PTMClust/" } \ No newline at end of file diff --git a/data/ptmphinder/ptmphinderbioschemas.jsonld b/data/ptmphinder/ptmphinderbioschemas.jsonld index e23c939fada08..7295ab84bb0ab 100644 --- a/data/ptmphinder/ptmphinderbioschemas.jsonld +++ b/data/ptmphinder/ptmphinderbioschemas.jsonld @@ -15,30 +15,30 @@ "biotools:primaryContact": "Jacob M. Wozniak", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:31198645", { "@id": "https://doi.org/10.7717/peerj.7046" }, - "pmcid:PMC6555389" + "pmcid:PMC6555389", + "pubmed:31198645" ], "sc:description": "R package for PTM site localization and motif extraction from proteomic datasets.", "sc:featureList": [ { - "@id": "edam:operation_0417" + "@id": "edam:operation_0335" }, { - "@id": "edam:operation_3755" + "@id": "edam:operation_0417" }, { - "@id": "edam:operation_0335" + "@id": "edam:operation_3755" } ], "sc:license": "GPL-3.0", "sc:name": "PTMphinder", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/jmwozniak/PTMphinder", "sc:version": "0.1.0" diff --git a/data/ptmprophet/ptmprophetbioschemas.jsonld b/data/ptmprophet/ptmprophetbioschemas.jsonld index a869cd4bbe89b..d81543afb64ce 100644 --- a/data/ptmprophet/ptmprophetbioschemas.jsonld +++ b/data/ptmprophet/ptmprophetbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Tool to model the confidence with which mass modifications are correctly localized for each peptide. PTMProphet considers all of the possible configurations for localization, and applies a statistical model to predict which modification sites are most probable based on the spectrum evidence.", "sc:name": "PTMProphet", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP", diff --git a/data/ptrcombiner/ptrcombinerbioschemas.jsonld b/data/ptrcombiner/ptrcombinerbioschemas.jsonld index 717b9de989850..7d6b3f5134460 100644 --- a/data/ptrcombiner/ptrcombinerbioschemas.jsonld +++ b/data/ptrcombiner/ptrcombinerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for the study of the combinatorial nature of post-transcriptional trans-factors. It allows the identification of clusters of trans-factors (RBPs and miRNAs) from interaction maps and it performs the biological characterization of identified clusters giving information about the overlap among the target genes, the GO enrichments and similarity among GO terms.", "sc:name": "PTRcombiner", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://disi.unitn.it/~passerini/software/PTRcombiner/" } \ No newline at end of file diff --git a/data/ptrimmer/ptrimmerbioschemas.jsonld b/data/ptrimmer/ptrimmerbioschemas.jsonld index 188749924b07a..8ac776fdc7ab2 100644 --- a/data/ptrimmer/ptrimmerbioschemas.jsonld +++ b/data/ptrimmer/ptrimmerbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-019-2854-X", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pTrimmer", "@type": "sc:SoftwareApplication", @@ -18,35 +22,31 @@ ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6511130", - "pubmed:31077131", { "@id": "https://doi.org/10.1186/S12859-019-2854-X" - } + }, + "pmcid:PMC6511130", + "pubmed:31077131" ], "sc:description": "Tool to trim primers of multiplex deep sequencing data.", "sc:featureList": [ { - "@id": "edam:operation_0308" + "@id": "edam:operation_3237" }, { - "@id": "edam:operation_3192" + "@id": "edam:operation_0308" }, { - "@id": "edam:operation_3237" + "@id": "edam:operation_3192" } ], "sc:license": "GPL-3.0", "sc:name": "pTrimmer", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/DMU-lilab/pTrimmer" - }, - { - "@id": "https://doi.org/10.1186/S12859-019-2854-X", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ptrstalker/ptrstalkerbioschemas.jsonld b/data/ptrstalker/ptrstalkerbioschemas.jsonld index 137a12c65aec0..3ef3d4be16e1f 100644 --- a/data/ptrstalker/ptrstalkerbioschemas.jsonld +++ b/data/ptrstalker/ptrstalkerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PTRStalker", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioalgo.iit.cnr.it/index.php?pg=ptrs" } \ No newline at end of file diff --git a/data/pubchem/pubchembioschemas.jsonld b/data/pubchem/pubchembioschemas.jsonld index 4b9aea0f68223..97a428d85b496 100644 --- a/data/pubchem/pubchembioschemas.jsonld +++ b/data/pubchem/pubchembioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The PubChem BioAssay database is a public repository for biological activities of small molecules and small interfering RNAs (siRNAs). It archives experimental descriptions of assays and biological test results. A PubChem BioAssay data entry includes an assay description, a summary and detailed test results. Each assay record is linked to the molecular target, whenever possible, and is cross-referenced to other NCBI database records.", "sc:name": "PubChem", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://pubchem.ncbi.nlm.nih.gov/" } \ No newline at end of file diff --git a/data/pubgene/pubgenebioschemas.jsonld b/data/pubgene/pubgenebioschemas.jsonld index 7c6c5ceef547c..91bf118ce09b7 100644 --- a/data/pubgene/pubgenebioschemas.jsonld +++ b/data/pubgene/pubgenebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "PubGene", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.pubgene.org/" } \ No newline at end of file diff --git a/data/pubmed/pubmedbioschemas.jsonld b/data/pubmed/pubmedbioschemas.jsonld index 89d2adb5dbe3a..15576d251ae80 100644 --- a/data/pubmed/pubmedbioschemas.jsonld +++ b/data/pubmed/pubmedbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "PubMed", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "Instruct", "sc:url": "http://www.ncbi.nlm.nih.gov/pubmed" diff --git a/data/pubmed2ensembl/pubmed2ensemblbioschemas.jsonld b/data/pubmed2ensembl/pubmed2ensemblbioschemas.jsonld index 5997902b7a310..93090954cb76f 100644 --- a/data/pubmed2ensembl/pubmed2ensemblbioschemas.jsonld +++ b/data/pubmed2ensembl/pubmed2ensemblbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species.", "sc:name": "pubmed2ensembl", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.pubmed2ensembl.org/" } \ No newline at end of file diff --git a/data/pubmed_central/pubmed_centralbioschemas.jsonld b/data/pubmed_central/pubmed_centralbioschemas.jsonld index 53867f4d2ae44..c8d008541817c 100644 --- a/data/pubmed_central/pubmed_centralbioschemas.jsonld +++ b/data/pubmed_central/pubmed_centralbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.", "sc:name": "PubMed Central", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.ncbi.nlm.nih.gov/pmc/" } \ No newline at end of file diff --git a/data/pubmeth/pubmethbioschemas.jsonld b/data/pubmeth/pubmethbioschemas.jsonld index 4874af32ef337..1dbb630b0aa67 100644 --- a/data/pubmeth/pubmethbioschemas.jsonld +++ b/data/pubmeth/pubmethbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An annotated and reviewed database of methylation in cancer. It is based on automated textmining of literature and is afterwards manually curated and annotated.", "sc:name": "PubMeth reviewed methylation database in cancer", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.pubmeth.org" } \ No newline at end of file diff --git a/data/pubrunner/pubrunnerbioschemas.jsonld b/data/pubrunner/pubrunnerbioschemas.jsonld index 95e6baed70a9f..7759682a3db9f 100644 --- a/data/pubrunner/pubrunnerbioschemas.jsonld +++ b/data/pubrunner/pubrunnerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/pubrunner", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Framework which runs on a user defined schedule allowing you to download latest PubMed abstracts, run them through your favorite text mining tool and then uploads the results to public FTP", "sc:license": "MIT", diff --git a/data/pubserver/pubserverbioschemas.jsonld b/data/pubserver/pubserverbioschemas.jsonld index 51f0fbf90a178..ecdbe608aaa78 100644 --- a/data/pubserver/pubserverbioschemas.jsonld +++ b/data/pubserver/pubserverbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/pubserver", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lukasz Jaroszewski", - "Adam Godzik" + "Adam Godzik", + "Lukasz Jaroszewski" ], "sc:additionalType": "Web application", "sc:description": "PubServer collects homologous sequences from NR database and retrieves and filters associated publications.", diff --git a/data/pubtator/pubtatorbioschemas.jsonld b/data/pubtator/pubtatorbioschemas.jsonld index 5e631fc7d0357..3ed2204300f82 100644 --- a/data/pubtator/pubtatorbioschemas.jsonld +++ b/data/pubtator/pubtatorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for text based mining to assist biocuration.", "sc:name": "PubTator", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/" } \ No newline at end of file diff --git a/data/pubtator_central/pubtator_centralbioschemas.jsonld b/data/pubtator_central/pubtator_centralbioschemas.jsonld index 8e411c5d18cf4..d322e04e63931 100644 --- a/data/pubtator_central/pubtator_centralbioschemas.jsonld +++ b/data/pubtator_central/pubtator_centralbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKZ389", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0002-8301-9553", "@type": "schema:Person" @@ -25,11 +21,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6602571", { "@id": "https://doi.org/10.1093/NAR/GKZ389" }, - "pubmed:31114887" + "pubmed:31114887", + "pmcid:PMC6602571" ], "sc:description": "Web-based application that provides computer-annotated biomedical concepts, such as genes and mutations, in PubMed citations and PMC full-text articles.", "sc:featureList": [ @@ -47,10 +43,14 @@ "sc:name": "PubTator Central", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.ncbi.nlm.nih.gov/research/pubtator/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ389", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pubterm/pubtermbioschemas.jsonld b/data/pubterm/pubtermbioschemas.jsonld index cef52b6a3523f..540c4bcd693a7 100644 --- a/data/pubterm/pubtermbioschemas.jsonld +++ b/data/pubterm/pubtermbioschemas.jsonld @@ -19,19 +19,19 @@ "biotools:primaryContact": "Victor Trevino", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6323318", { "@id": "https://doi.org/10.1093/database/bay137" }, + "pmcid:PMC6323318", "pubmed:30624653" ], "sc:description": "Web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_3501" } ], "sc:name": "PubTerm", diff --git a/data/pudge/pudgebioschemas.jsonld b/data/pudge/pudgebioschemas.jsonld index fc38c73b6fd87..0e3e9c71f4118 100644 --- a/data/pudge/pudgebioschemas.jsonld +++ b/data/pudge/pudgebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "PUDGE is a protein structure prediction server. Modeling is divided into 5 stages: template selection, alignment, model building, model refinement and model evaluation.", "sc:name": "PUDGE", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PUDGE" } \ No newline at end of file diff --git a/data/pug/pugbioschemas.jsonld b/data/pug/pugbioschemas.jsonld index 0f2016e4857a0..9c143d7d84eeb 100644 --- a/data/pug/pugbioschemas.jsonld +++ b/data/pug/pugbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Interface to PubChem.", "sc:name": "PUG", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap_help.html", "sc:version": "1" diff --git a/data/pulse-phage/pulse-phagebioschemas.jsonld b/data/pulse-phage/pulse-phagebioschemas.jsonld index b9fcbf243f7aa..c081b1bbe42dd 100644 --- a/data/pulse-phage/pulse-phagebioschemas.jsonld +++ b/data/pulse-phage/pulse-phagebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/pulse-phage", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Manfred Auer", - "Steven Shave" + "Steven Shave", + "Manfred Auer" ], "sc:additionalType": "Command-line tool", "sc:description": "Tool to analyse protein sequence coverage of phage display libraries.", diff --git a/data/pulser/pulserbioschemas.jsonld b/data/pulser/pulserbioschemas.jsonld index cd655e239a939..38bcec85fdd5c 100644 --- a/data/pulser/pulserbioschemas.jsonld +++ b/data/pulser/pulserbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/pulser", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "A. Uvarovskii", - "C. Dieterich" + "C. Dieterich", + "A. Uvarovskii" ], "sc:additionalType": "Command-line tool", "sc:description": "Flexible interface and readily accommodates numerous different experimental designs.", "sc:license": "GPL-3.0", "sc:name": "pulseR", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/dieterich-lab/pulseR" } \ No newline at end of file diff --git a/data/puma/pumabioschemas.jsonld b/data/puma/pumabioschemas.jsonld index 37ad845c9af43..84e8629237628 100644 --- a/data/puma/pumabioschemas.jsonld +++ b/data/puma/pumabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-14-39", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/puma", "@type": "sc:SoftwareApplication", @@ -24,42 +20,46 @@ "@id": "edam:data_2884" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3320" + "@id": "edam:topic_0203" }, { - "@id": "edam:topic_0203" + "@id": "edam:topic_3320" } ], "sc:citation": [ "pubmed:23379655", + "pmcid:PMC3626802", { "@id": "https://doi.org/10.1186/1471-2105-14-39" - }, - "pmcid:PMC3626802" + } ], "sc:description": "This package calculates gene expression from Affymetrix 3' arrays and provides methods to process exon arrays, producing gene and isoform expression for alternative splicing study. It also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_3432" }, { - "@id": "edam:operation_3432" + "@id": "edam:operation_2495" } ], "sc:license": "GPL-3.0", "sc:name": "puma", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/puma.html", "sc:version": "3.16.0" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-39", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pure/purebioschemas.jsonld b/data/pure/purebioschemas.jsonld index 6ebd878dd5e26..3d4ba30a76394 100644 --- a/data/pure/purebioschemas.jsonld +++ b/data/pure/purebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PURE", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.bic.kyoto-u.ac.jp/pathway/PURE/" } \ No newline at end of file diff --git a/data/purecn/purecnbioschemas.jsonld b/data/purecn/purecnbioschemas.jsonld index 662cfbf6bb73b..a332871697b45 100644 --- a/data/purecn/purecnbioschemas.jsonld +++ b/data/purecn/purecnbioschemas.jsonld @@ -16,42 +16,42 @@ "@id": "http://orcid.org/0000-0002-4759-8332" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC5157099", + "pubmed:27999612", { "@id": "https://doi.org/10.1186/s13029-016-0060-z" - }, - "pubmed:27999612", - "pmcid:PMC5157099" + } ], "sc:description": "This package estimates tumor purity, copy number, loss of heterozygosity (LOH), and status of single nucleotide variants (SNVs). It is designed for targeted short read sequencing data, integrating well with standard somatic variant detection pipelines and supporting for tumor samples without matching normal samples.", "sc:featureList": [ { - "@id": "edam:operation_2995" + "@id": "edam:operation_3233" }, { - "@id": "edam:operation_3233" + "@id": "edam:operation_2995" } ], "sc:license": "Artistic-2.0", "sc:name": "PureCN", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PureCN.html", "sc:version": "1.2.3" }, - { - "@id": "https://doi.org/10.1186/s13029-016-0060-z", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-4759-8332", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/s13029-016-0060-z", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/putracer/putracerbioschemas.jsonld b/data/putracer/putracerbioschemas.jsonld index 989bb3a9b7f7f..6357388f89f90 100644 --- a/data/putracer/putracerbioschemas.jsonld +++ b/data/putracer/putracerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Reliable method to detect automatically structural domains as protein units. This server provides number of domains and domain boundary for a chain with continues-domains.", "sc:name": "Putracer", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioinf.modares.ac.ir/software/PUTracer/" } \ No newline at end of file diff --git a/data/pvac/pvacbioschemas.jsonld b/data/pvac/pvacbioschemas.jsonld index 2085850cb89b8..109456db98599 100644 --- a/data/pvac/pvacbioschemas.jsonld +++ b/data/pvac/pvacbioschemas.jsonld @@ -15,16 +15,16 @@ "Pierre R. Bushel" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package contains a function for filtering genes by the Proportion of Variation ACcounted for by the first principal component.", "sc:license": "GPL-2.0", "sc:name": "pvac", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pvac.html", "sc:version": "1.22.0" diff --git a/data/pvca/pvcabioschemas.jsonld b/data/pvca/pvcabioschemas.jsonld index 577fde8f3e4a0..ee3e238036190 100644 --- a/data/pvca/pvcabioschemas.jsonld +++ b/data/pvca/pvcabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jianying LI", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package contains the function to assess the batch sourcs by fitting all \"sources\" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix.", "sc:license": "GPL-2.0", "sc:name": "pvca", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pvca.html", "sc:version": "1.14.0" diff --git a/data/pview/pviewbioschemas.jsonld b/data/pview/pviewbioschemas.jsonld index 3f184334dd8dc..70a40b5facec9 100644 --- a/data/pview/pviewbioschemas.jsonld +++ b/data/pview/pviewbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software tool for the analysis and visualization of high resolution LC-MS/MS Data", "sc:name": "PVIEW", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://compbio.cs.princeton.edu/pview/" diff --git a/data/pviz-visual/pviz-visualbioschemas.jsonld b/data/pviz-visual/pviz-visualbioschemas.jsonld index 8b962ddc35617..6f68815208b22 100644 --- a/data/pviz-visual/pviz-visualbioschemas.jsonld +++ b/data/pviz-visual/pviz-visualbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/pviz-visual", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alexandre Masselot", - "Kiran Mukhyala" + "Kiran Mukhyala", + "Alexandre Masselot" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:25147360", "sc:description": "Visualization library for displaying protein sequence features in a web browser", "sc:name": "pviz", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://research-pub.gene.com/pviz/examples/" diff --git a/data/pviz/pvizbioschemas.jsonld b/data/pviz/pvizbioschemas.jsonld index 3e50187e2e03c..996d05233794a 100644 --- a/data/pviz/pvizbioschemas.jsonld +++ b/data/pviz/pvizbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "Pviz", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Pviz.html", "sc:version": "1.8.0" diff --git a/data/pvs/pvsbioschemas.jsonld b/data/pvs/pvsbioschemas.jsonld index 807960c6e4f2a..f4068d6146af9 100644 --- a/data/pvs/pvsbioschemas.jsonld +++ b/data/pvs/pvsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Protein Sequence Variability (PVS) is a web server for the prediction of conserved T-cell epitopes. Several variability metrics are used to compute the absolute site variability in multiple protein sequence alignments.", "sc:name": "PVS", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://imed.med.ucm.es/PVS/" } \ No newline at end of file diff --git a/data/pwmenrich/bioconda_pwmenrich.yaml b/data/pwmenrich/bioconda_pwmenrich.yaml index 3d323788407ae..a2b7d53df2373 100644 --- a/data/pwmenrich/bioconda_pwmenrich.yaml +++ b/data/pwmenrich/bioconda_pwmenrich.yaml @@ -8,7 +8,6 @@ description: A toolkit of high-level functions for DNA motif scanning and enrich home: https://bioconductor.org/packages/3.10/bioc/html/PWMEnrich.html identifiers: - biotools:pwmenrich -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-pwmenrich diff --git a/data/pwmenrich/pwmenrichbioschemas.jsonld b/data/pwmenrich/pwmenrichbioschemas.jsonld index 3b52fddee0491..b3928aff8b549 100644 --- a/data/pwmenrich/pwmenrichbioschemas.jsonld +++ b/data/pwmenrich/pwmenrichbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "PWMEnrich", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/PWMEnrich.html", "sc:version": "4.10.0" diff --git a/data/pwmscan/pwmscanbioschemas.jsonld b/data/pwmscan/pwmscanbioschemas.jsonld index 67a6c1c819c1a..5ae97f5a01662 100644 --- a/data/pwmscan/pwmscanbioschemas.jsonld +++ b/data/pwmscan/pwmscanbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Fast tool for scanning entire genomes with a position-specific weight matrix.", "sc:name": "PWMScan", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://ccg.vital-it.ch/pwmscan/" } \ No newline at end of file diff --git a/data/pwomics/pwomicsbioschemas.jsonld b/data/pwomics/pwomicsbioschemas.jsonld index 662095495fc30..451ac745a78a6 100644 --- a/data/pwomics/pwomicsbioschemas.jsonld +++ b/data/pwomics/pwomicsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "pwOmics", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/pwOmics.html", "sc:version": "1.6.0" diff --git a/data/pwrewas/pwrewasbioschemas.jsonld b/data/pwrewas/pwrewasbioschemas.jsonld index ca917567ff8fd..42772b6151969 100644 --- a/data/pwrewas/pwrewasbioschemas.jsonld +++ b/data/pwrewas/pwrewasbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Artistic-2.0", "sc:name": "pwrEWAS", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://biostats-shinyr.kumc.edu/pwrEWAS/" } \ No newline at end of file diff --git a/data/pximage/pximagebioschemas.jsonld b/data/pximage/pximagebioschemas.jsonld index bb2369bd517c0..84740e66f26b9 100644 --- a/data/pximage/pximagebioschemas.jsonld +++ b/data/pximage/pximagebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "PXImage", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "Instruct", "sc:url": "http://www.ccp4.ac.uk/jwc/Xhtml/PXImage/PXImage.html", diff --git a/data/pxsim/pxsimbioschemas.jsonld b/data/pxsim/pxsimbioschemas.jsonld index 3a2e497606228..3e992f1a7872f 100644 --- a/data/pxsim/pxsimbioschemas.jsonld +++ b/data/pxsim/pxsimbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A program for carrying out simulations of Protein Crystallographic diffraction images and analysing the unique data coverage for one or more crystal settings and series of diffraction images. It is itended primarly as a teaching tool.", "sc:name": "PXSim", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "Instruct", diff --git a/data/py-em/py-embioschemas.jsonld b/data/py-em/py-embioschemas.jsonld index fa26b276aa8ef..994146a7ff7d9 100644 --- a/data/py-em/py-embioschemas.jsonld +++ b/data/py-em/py-embioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Py-EM", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://git.embl.de/schorb/pyem" } \ No newline at end of file diff --git a/data/pyampli/pyamplibioschemas.jsonld b/data/pyampli/pyamplibioschemas.jsonld index 12a27eb63dab0..c9380d46b7111 100644 --- a/data/pyampli/pyamplibioschemas.jsonld +++ b/data/pyampli/pyamplibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "pyAmpli", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://mbeyens.github.io/pyAmpli/" } \ No newline at end of file diff --git a/data/pybedtools/pybedtoolsbioschemas.jsonld b/data/pybedtools/pybedtoolsbioschemas.jsonld index d0c95256ce2b0..6114107483879 100644 --- a/data/pybedtools/pybedtoolsbioschemas.jsonld +++ b/data/pybedtools/pybedtoolsbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-2.0", "sc:name": "Pybedtools", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://pypi.python.org/pypi/pybedtools" } \ No newline at end of file diff --git a/data/pybel/pybelbioschemas.jsonld b/data/pybel/pybelbioschemas.jsonld index 82a33146c6d8d..350758cfe75c8 100644 --- a/data/pybel/pybelbioschemas.jsonld +++ b/data/pybel/pybelbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "PyBEL", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/pybel/pybel" diff --git a/data/pybiomed/pybiomedbioschemas.jsonld b/data/pybiomed/pybiomedbioschemas.jsonld index 396db99e3c9fb..ec37d3d0e1e3d 100644 --- a/data/pybiomed/pybiomedbioschemas.jsonld +++ b/data/pybiomed/pybiomedbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "PyBioMed", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/gadsbyfly/PyBioMed" } \ No newline at end of file diff --git a/data/pybsaseq/pybsaseqbioschemas.jsonld b/data/pybsaseq/pybsaseqbioschemas.jsonld index 45d01f3351384..3ec03071e6763 100644 --- a/data/pybsaseq/pybsaseqbioschemas.jsonld +++ b/data/pybsaseq/pybsaseqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "PyBSASeq", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/dblhlx/PyBSASeq" } \ No newline at end of file diff --git a/data/pycellbase/pycellbasebioschemas.jsonld b/data/pycellbase/pycellbasebioschemas.jsonld index 886af54e0fb4b..c51cfa2dcefa2 100644 --- a/data/pycellbase/pycellbasebioschemas.jsonld +++ b/data/pycellbase/pycellbasebioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2726-4", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/PyCellBase", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Daniel Perez-Gil", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:30922213", { "@id": "https://doi.org/10.1186/s12859-019-2726-4" }, - "pubmed:30922213", "pmcid:PMC6438028" ], "sc:description": "Python package for easy retrieval of biological data from heterogeneous sources.", @@ -29,15 +33,11 @@ "sc:name": "PyCellBase", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://pypi.org/project/pycellbase/", "sc:version": "4.7.1" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2726-4", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pycogent/pycogentbioschemas.jsonld b/data/pycogent/pycogentbioschemas.jsonld index 1da099b2ec941..e8ffbe2eb086d 100644 --- a/data/pycogent/pycogentbioschemas.jsonld +++ b/data/pycogent/pycogentbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.", "sc:name": "PyCogent", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "unimelb.edu.au", "sc:url": "http://pycogent.org/", diff --git a/data/pydna/pydnabioschemas.jsonld b/data/pydna/pydnabioschemas.jsonld index e9dc3b7e426f8..6f279a81093dd 100644 --- a/data/pydna/pydnabioschemas.jsonld +++ b/data/pydna/pydnabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "An extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and homologous recombination.", "sc:name": "Pydna", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://pypi.python.org/pypi/pydna", "sc:version": "1.0.1" diff --git a/data/pydocksaxs/pydocksaxsbioschemas.jsonld b/data/pydocksaxs/pydocksaxsbioschemas.jsonld index 01dbb15907bf5..4ac9520effbda 100644 --- a/data/pydocksaxs/pydocksaxsbioschemas.jsonld +++ b/data/pydocksaxs/pydocksaxsbioschemas.jsonld @@ -9,15 +9,23 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkv368", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-7786-2109", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/pydocksaxs", "@type": "sc:SoftwareApplication", "edam:has_input": [ { - "@id": "edam:data_0937" + "@id": "edam:data_2877" }, { - "@id": "edam:data_2877" + "@id": "edam:data_0937" } ], "edam:has_output": { @@ -31,11 +39,11 @@ "@id": "http://orcid.org/0000-0001-7786-2109" }, "sc:citation": [ + "pubmed:25897115", + "pmcid:PMC4489248", { "@id": "https://doi.org/10.1093/nar/gkv368" - }, - "pmcid:PMC4489248", - "pubmed:25897115" + } ], "sc:description": "Web server for rigid-body protein-protein docking that combines computational and experimental information.", "sc:featureList": { @@ -44,9 +52,9 @@ "sc:isAccessibleForFree": true, "sc:name": "pyDockSAXS", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ "Barcelona Supercomputing Center", @@ -54,10 +62,10 @@ ], "sc:softwareHelp": [ { - "@id": "https://life.bsc.es/pid/pydocksaxs/info/faq_and_help" + "@id": "https://life.bsc.es/pid/pydocksaxs/info/faq_and_help#reference" }, { - "@id": "https://life.bsc.es/pid/pydocksaxs/info/faq_and_help#reference" + "@id": "https://life.bsc.es/pid/pydocksaxs/info/faq_and_help" } ], "sc:termsOfService": { @@ -65,14 +73,6 @@ }, "sc:url": "https://life.bsc.es/pid/pydocksaxs", "sc:version": "1" - }, - { - "@id": "https://doi.org/10.1093/nar/gkv368", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-7786-2109", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pydockweb/pydockwebbioschemas.jsonld b/data/pydockweb/pydockwebbioschemas.jsonld index 03b1209b8e4cf..f1229178ed6d1 100644 --- a/data/pydockweb/pydockwebbioschemas.jsonld +++ b/data/pydockweb/pydockwebbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7786-2109", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/pydockweb", "@type": "sc:SoftwareApplication", @@ -30,10 +34,6 @@ ], "sc:url": "https://life.bsc.es/servlet/pydock/", "sc:version": "1" - }, - { - "@id": "http://orcid.org/0000-0001-7786-2109", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/pydstool/pydstoolbioschemas.jsonld b/data/pydstool/pydstoolbioschemas.jsonld index c66926d26707f..f417b319a3b48 100644 --- a/data/pydstool/pydstoolbioschemas.jsonld +++ b/data/pydstool/pydstoolbioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1002628", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pydstool", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC3415397", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1002628" }, + "pmcid:PMC3415397", "pubmed:22912566" ], "sc:description": "Integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems).", "sc:featureList": [ { - "@id": "edam:operation_2426" + "@id": "edam:operation_3216" }, { - "@id": "edam:operation_3216" + "@id": "edam:operation_2426" } ], "sc:name": "PyDSTool", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://web.archive.org/web/20171201062820/http://www.ni.gsu.edu:80/~rclewley/PyDSTool/FrontPage.html", "sc:version": "0.90.2" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1002628", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pyfaidx/pyfaidxbioschemas.jsonld b/data/pyfaidx/pyfaidxbioschemas.jsonld index 9145f38bc1999..917bc8ab29326 100644 --- a/data/pyfaidx/pyfaidxbioschemas.jsonld +++ b/data/pyfaidx/pyfaidxbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "Not licensed", "sc:name": "pyfaidx", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://pythonhosted.org/pyfaidx/" } \ No newline at end of file diff --git a/data/pyfasta/pyfastabioschemas.jsonld b/data/pyfasta/pyfastabioschemas.jsonld index d44e2bca3aac2..f7d70d2e961d4 100644 --- a/data/pyfasta/pyfastabioschemas.jsonld +++ b/data/pyfasta/pyfastabioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/pyfasta", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Pythonic (and command-line) access to fasta sequence files.", "sc:license": "MIT", "sc:name": "pyfasta", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/brentp/pyfasta/" } \ No newline at end of file diff --git a/data/pyfolding/pyfoldingbioschemas.jsonld b/data/pyfolding/pyfoldingbioschemas.jsonld index c649d50cf1669..89c34e1a7d1b1 100644 --- a/data/pyfolding/pyfoldingbioschemas.jsonld +++ b/data/pyfolding/pyfoldingbioschemas.jsonld @@ -21,10 +21,10 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:29414697", { "@id": "https://doi.org/10.1016/j.bpj.2017.11.3779" }, + "pubmed:29414697", "pmcid:PMC5985001" ], "sc:description": "A Python framework for graphing, analysis, and simulation of the biophysical properties of proteins.", @@ -34,8 +34,8 @@ "sc:license": "MIT", "sc:name": "PyFolding", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/quantumjot/PyFolding" }, diff --git a/data/pyfrap/pyfrapbioschemas.jsonld b/data/pyfrap/pyfrapbioschemas.jsonld index 51146a3c7dcf7..be2ce4c66e88a 100644 --- a/data/pyfrap/pyfrapbioschemas.jsonld +++ b/data/pyfrap/pyfrapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A Python based FRAP analysis tool box.", "sc:name": "PyFRAP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/alexblaessle/PyFRAP" } \ No newline at end of file diff --git a/data/pygold/pygoldbioschemas.jsonld b/data/pygold/pygoldbioschemas.jsonld index ecfdb9e7308ad..a17cff25393a0 100644 --- a/data/pygold/pygoldbioschemas.jsonld +++ b/data/pygold/pygoldbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "API for docking based virtual screening workflow generation.", "sc:name": "PyGOLD", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ccb.tu-dortmund.de/ag-koch/pygold/" } \ No newline at end of file diff --git a/data/pyhla/pyhlabioschemas.jsonld b/data/pyhla/pyhlabioschemas.jsonld index 7e12a7bf33510..3c54370f8cd09 100644 --- a/data/pyhla/pyhlabioschemas.jsonld +++ b/data/pyhla/pyhlabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-017-1496-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/pyhla", "@type": "sc:SoftwareApplication", @@ -28,15 +32,11 @@ "sc:license": "GPL-2.0", "sc:name": "PyHLA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/felixfan/PyHLA" - }, - { - "@id": "https://doi.org/10.1186/s12859-017-1496-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pylda/pyldabioschemas.jsonld b/data/pylda/pyldabioschemas.jsonld index fefd384775f3f..3c9a47a73349f 100644 --- a/data/pylda/pyldabioschemas.jsonld +++ b/data/pylda/pyldabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Package that allowed the user to experiment with a number of different options and methods in order to produce the best lifetime density maps (LDMs) given their dataset.", "sc:name": "pylda", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/gadorlhiac/PyLDM" } \ No newline at end of file diff --git a/data/pyldm/pyldmbioschemas.jsonld b/data/pyldm/pyldmbioschemas.jsonld index b4c80c3e85c3c..27469ddbd8371 100644 --- a/data/pyldm/pyldmbioschemas.jsonld +++ b/data/pyldm/pyldmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "PyLDM", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/gadorlhiac/PyLDM" } \ No newline at end of file diff --git a/data/pyloh/pylohbioschemas.jsonld b/data/pyloh/pylohbioschemas.jsonld index 36a7b47a7fac3..03222ffd53457 100644 --- a/data/pyloh/pylohbioschemas.jsonld +++ b/data/pyloh/pylohbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool for discovering copy number variations in cancer genomes.", "sc:name": "PyLOH", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://cbcl.ics.uci.edu//doku.php/software#pyloh" diff --git a/data/pymbar/pymbarbioschemas.jsonld b/data/pymbar/pymbarbioschemas.jsonld index 818f9dae97b5b..9333025ef0d5b 100644 --- a/data/pymbar/pymbarbioschemas.jsonld +++ b/data/pymbar/pymbarbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/pymbar", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kyle A. Beauchamp", - "Michael R. Shirts", "John D. Chodera", - "Levi N. Naden" + "Levi N. Naden", + "Michael R. Shirts", + "Kyle A. Beauchamp" ], "sc:additionalType": "Library", "sc:description": "Python implementation of the multistate Bennett acceptance ratio (MBAR) method for estimating expectations and free energy differences from equilibrium samples from multiple probability densities.", "sc:license": "MIT", "sc:name": "pymbar", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/choderalab/pymbar" } \ No newline at end of file diff --git a/data/pymdsetup/pymdsetupbioschemas.jsonld b/data/pymdsetup/pymdsetupbioschemas.jsonld index a44b292d1f708..4a72caba8169d 100644 --- a/data/pymdsetup/pymdsetupbioschemas.jsonld +++ b/data/pymdsetup/pymdsetupbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Pau Andrio", "sc:additionalType": [ - "Suite", "Library", + "Command-line tool", "Workflow", - "Command-line tool" + "Suite" ], "sc:description": "Python package to setup and run molecular dynamics simulations.", "sc:name": "PyMDSetup", diff --git a/data/pymod/pymodbioschemas.jsonld b/data/pymod/pymodbioschemas.jsonld index 23af3458f6014..6f35ed493cc5f 100644 --- a/data/pymod/pymodbioschemas.jsonld +++ b/data/pymod/pymodbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "PyMod", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://schubert.bio.uniroma1.it/pymod/index.html" } \ No newline at end of file diff --git a/data/pymol/pymolbioschemas.jsonld b/data/pymol/pymolbioschemas.jsonld index 7a0b9473868ad..472b1b9ebb469 100644 --- a/data/pymol/pymolbioschemas.jsonld +++ b/data/pymol/pymolbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures.", "sc:name": "PyMOL", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.pymol.org/pymol" diff --git a/data/pyms/pymsbioschemas.jsonld b/data/pyms/pymsbioschemas.jsonld index 411b6f94d8e66..811419d61d147 100644 --- a/data/pyms/pymsbioschemas.jsonld +++ b/data/pyms/pymsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tools for reading LC-MS data in the ANDI-MS and JCAMP-DX formats.", "sc:name": "PyMS", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://code.google.com/p/pyms/" } \ No newline at end of file diff --git a/data/pymsxml/pymsxmlbioschemas.jsonld b/data/pymsxml/pymsxmlbioschemas.jsonld index a6e8a7a633205..0244689f5ce50 100644 --- a/data/pymsxml/pymsxmlbioschemas.jsonld +++ b/data/pymsxml/pymsxmlbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Convert vendor specific mass spectrometry data files for Applied Biosystems’ Q-Star, 4700, 4800, Mariner, and Voyager mass spectrometers from their raw binary form, to either of the emerging XML file formats for mass spectra: mzXML and mzData.", "sc:name": "PyMsXML", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://edwardslab.bmcb.georgetown.edu/software/PyMsXML.html", "sc:version": "0.5.4" diff --git a/data/pymut/pymutbioschemas.jsonld b/data/pymut/pymutbioschemas.jsonld index 450961aa84957..c4a88d4a27a38 100644 --- a/data/pymut/pymutbioschemas.jsonld +++ b/data/pymut/pymutbioschemas.jsonld @@ -37,22 +37,22 @@ "@id": "edam:topic_0080" }, "sc:citation": [ - "pubmed:28453649", "pmcid:PMC5793831", { "@id": "https://doi.org/10.1093/nar/gkx313" - } + }, + "pubmed:28453649" ], "sc:description": "PyMut is a Python3 module that fills the gap between machine learning and bioinformatics, providing methods that help in the prediction of pathology in protein mutations.", "sc:featureList": [ { - "@id": "edam:operation_3225" + "@id": "edam:operation_3092" }, { - "@id": "edam:operation_3661" + "@id": "edam:operation_3225" }, { - "@id": "edam:operation_3092" + "@id": "edam:operation_3661" } ], "sc:isAccessibleForFree": true, diff --git a/data/pymzml/pymzmlbioschemas.jsonld b/data/pymzml/pymzmlbioschemas.jsonld index aa574e2272062..2db0fedc68fa8 100644 --- a/data/pymzml/pymzmlbioschemas.jsonld +++ b/data/pymzml/pymzmlbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "pymzML", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://pymzml.github.com", "sc:version": "2.4.1" diff --git a/data/pypanda/pypandabioschemas.jsonld b/data/pypanda/pypandabioschemas.jsonld index c24f346ab0d04..a7f7e158cf243 100644 --- a/data/pypanda/pypandabioschemas.jsonld +++ b/data/pypanda/pypandabioschemas.jsonld @@ -22,11 +22,11 @@ ], "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5079480", "pubmed:27402905", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTW422" - }, - "pmcid:PMC5079480" + } ], "sc:description": "A Python package for gene regulatory network reconstruction.", "sc:featureList": { diff --git a/data/pypdb/pypdbbioschemas.jsonld b/data/pypdb/pypdbbioschemas.jsonld index 2260a481a49cc..fb1294eb762ae 100644 --- a/data/pypdb/pypdbbioschemas.jsonld +++ b/data/pypdb/pypdbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Python 3 toolkit for performing searches with the RCSB Protein Data Bank (PDB) using its XML-based API.", "sc:name": "PyPDB", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/williamgilpin/pypdb" diff --git a/data/pyplif/pyplifbioschemas.jsonld b/data/pyplif/pyplifbioschemas.jsonld index 5dd72859640e7..ad8f1e78dacca 100644 --- a/data/pyplif/pyplifbioschemas.jsonld +++ b/data/pyplif/pyplifbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Program/script written in Python to analyze protein-ligand interaction from the molecular docking result.", "sc:name": "PyPLIF", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://code.google.com/p/pyplif/", "sc:version": "0.1.1" diff --git a/data/pyqms/pyqmsbioschemas.jsonld b/data/pyqms/pyqmsbioschemas.jsonld index ada50c00714ab..af2b491617f1e 100644 --- a/data/pyqms/pyqmsbioschemas.jsonld +++ b/data/pyqms/pyqmsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "pyQms", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/pyQms/pyqms" } \ No newline at end of file diff --git a/data/pyrad/pyradbioschemas.jsonld b/data/pyrad/pyradbioschemas.jsonld index e1517fd5e8ddf..cfa62db1ddffd 100644 --- a/data/pyrad/pyradbioschemas.jsonld +++ b/data/pyrad/pyradbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets.", "sc:name": "PyRAD", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://dereneaton.com/software/pyrad/" } \ No newline at end of file diff --git a/data/pyrosetta/pyrosettabioschemas.jsonld b/data/pyrosetta/pyrosettabioschemas.jsonld index 91625496af5de..639c97cbbb6e1 100644 --- a/data/pyrosetta/pyrosettabioschemas.jsonld +++ b/data/pyrosetta/pyrosettabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables a user to create custom molecular modeling algorithms with Rosetta sampling and scoring functions using Python scripting.", "sc:name": "PyRosetta", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.pyrosetta.org/", diff --git a/data/pyrotrimmer/pyrotrimmerbioschemas.jsonld b/data/pyrotrimmer/pyrotrimmerbioschemas.jsonld index 83bf7f7df02e5..6c751c8ab1ed7 100644 --- a/data/pyrotrimmer/pyrotrimmerbioschemas.jsonld +++ b/data/pyrotrimmer/pyrotrimmerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Program that trims barcodes, linkers, primers, and sequence region with low quality scores from 454 sequence reads.", "sc:name": "PyroTrimmer", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://pyrotrimmer.kopri.re.kr/" diff --git a/data/pysam/pysambioschemas.jsonld b/data/pysam/pysambioschemas.jsonld index d8806e8a29a98..45c5df9e4f885 100644 --- a/data/pysam/pysambioschemas.jsonld +++ b/data/pysam/pysambioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "pysam", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/pysam-developers/pysam" diff --git a/data/pysamstats/pysamstatsbioschemas.jsonld b/data/pysamstats/pysamstatsbioschemas.jsonld index 77ec812e6a32e..995c3fe2cf555 100644 --- a/data/pysamstats/pysamstatsbioschemas.jsonld +++ b/data/pysamstats/pysamstatsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Not licensed", "sc:name": "pysamstats", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/alimanfoo/pysamstats" } \ No newline at end of file diff --git a/data/pyscestoolbox/pyscestoolboxbioschemas.jsonld b/data/pyscestoolbox/pyscestoolboxbioschemas.jsonld index 8cf97c79467ed..58122cfdcb8fa 100644 --- a/data/pyscestoolbox/pyscestoolboxbioschemas.jsonld +++ b/data/pyscestoolbox/pyscestoolboxbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "PySCeSToolbox", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/PySCeS/PyscesToolbox" } \ No newline at end of file diff --git a/data/pyseer/pyseerbioschemas.jsonld b/data/pyseer/pyseerbioschemas.jsonld index baf506d06581f..8ef8f6a71cca4 100644 --- a/data/pyseer/pyseerbioschemas.jsonld +++ b/data/pyseer/pyseerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/pyseer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Marco Galardini", - "John A. Lees" + "John A. Lees", + "Marco Galardini" ], "sc:additionalType": "Command-line tool", "sc:description": "Comprehensive tool for microbial pangenome-wide association studies.", diff --git a/data/pysradb/pysradbbioschemas.jsonld b/data/pysradb/pysradbbioschemas.jsonld index 08f1a70d7f122..365cb54112972 100644 --- a/data/pysradb/pysradbbioschemas.jsonld +++ b/data/pysradb/pysradbbioschemas.jsonld @@ -9,39 +9,39 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.12688/f1000research.18676.1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/pysradb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Saket Choudhary", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:31114675", + "pmcid:PMC6505635", { "@id": "https://doi.org/10.12688/f1000research.18676.1" - }, - "pmcid:PMC6505635", - "pubmed:31114675" + } ], "sc:description": "Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.", "sc:featureList": [ { - "@id": "edam:operation_2422" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_2422" } ], "sc:license": "BSD-3-Clause", "sc:name": "pysradb", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/saketkc/pysradb" + }, + { + "@id": "https://doi.org/10.12688/f1000research.18676.1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/pytarg/pytargbioschemas.jsonld b/data/pytarg/pytargbioschemas.jsonld index 5925dd840deed..e9beee3d600c2 100644 --- a/data/pytarg/pytargbioschemas.jsonld +++ b/data/pytarg/pytargbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "pyTARG", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/SergioBordel/pyTARG" } \ No newline at end of file diff --git a/data/pyteomics/pyteomicsbioschemas.jsonld b/data/pyteomics/pyteomicsbioschemas.jsonld index 22d909bf83596..2188b273543a5 100644 --- a/data/pyteomics/pyteomicsbioschemas.jsonld +++ b/data/pyteomics/pyteomicsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Apache-2.0", "sc:name": "Pyteomics", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://packages.python.org/pyteomics/", diff --git a/data/pytfa/pytfabioschemas.jsonld b/data/pytfa/pytfabioschemas.jsonld index 6ba749c7e00e0..3265c250cebc9 100644 --- a/data/pytfa/pytfabioschemas.jsonld +++ b/data/pytfa/pytfabioschemas.jsonld @@ -29,8 +29,8 @@ "sc:license": "Apache-2.0", "sc:name": "pyTFA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/EPFL-LCSB/pytfa" diff --git a/data/python_video_annotator/python_video_annotatorbioschemas.jsonld b/data/python_video_annotator/python_video_annotatorbioschemas.jsonld index d301ec6e49e8c..82c2e64b9a89b 100644 --- a/data/python_video_annotator/python_video_annotatorbioschemas.jsonld +++ b/data/python_video_annotator/python_video_annotatorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "Python Video Annotator", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://pythonvideoannotator.readthedocs.io", "sc:version": "3.306" diff --git a/data/pyviko/pyvikobioschemas.jsonld b/data/pyviko/pyvikobioschemas.jsonld index 6d7b524128f9a..287f21c6db0bc 100644 --- a/data/pyviko/pyvikobioschemas.jsonld +++ b/data/pyviko/pyvikobioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Louis J. Taylor", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5219722", "pubmed:28061810", { "@id": "https://doi.org/10.1186/s12866-016-0920-3" - } + }, + "pmcid:PMC5219722" ], "sc:description": "Design gene knockouts in complex viruses with overlapping genes automatically.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:license": "MIT", "sc:name": "Pyviko", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/louiejtaylor/pyViKO" } diff --git a/data/pyvolve/pyvolvebioschemas.jsonld b/data/pyvolve/pyvolvebioschemas.jsonld index 7163c2d44174f..195fb8fcc6369 100644 --- a/data/pyvolve/pyvolvebioschemas.jsonld +++ b/data/pyvolve/pyvolvebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution.", "sc:name": "Pyvolve", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/sjspielman/pyvolve" } \ No newline at end of file diff --git a/data/pywater/pywaterbioschemas.jsonld b/data/pywater/pywaterbioschemas.jsonld index 0e1d9f69cea57..d09fee0001446 100644 --- a/data/pywater/pywaterbioschemas.jsonld +++ b/data/pywater/pywaterbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/pywater", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": "pubmed:24990608", "sc:description": "PyMOL plugin to find conserved water molecules in X-ray protein structure.", "sc:name": "PyWATER", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/hiteshpatel379/PyWATER" } \ No newline at end of file diff --git a/data/q-hiu/q-hiubioschemas.jsonld b/data/q-hiu/q-hiubioschemas.jsonld index 569db6a9c3ae6..81ff351f48f35 100644 --- a/data/q-hiu/q-hiubioschemas.jsonld +++ b/data/q-hiu/q-hiubioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Q-HIU", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/LobanovaEG-LobanovSV/Q-HIU" } \ No newline at end of file diff --git a/data/q-nexus/q-nexusbioschemas.jsonld b/data/q-nexus/q-nexusbioschemas.jsonld index 322fa13bdf9c5..b78a9e03181c6 100644 --- a/data/q-nexus/q-nexusbioschemas.jsonld +++ b/data/q-nexus/q-nexusbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Peter Hansen", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27814676", "pmcid:PMC5097360", { "@id": "https://doi.org/10.1186/s12864-016-3164-6" - }, - "pubmed:27814676" + } ], "sc:description": "Q-nexus is a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control.", "sc:featureList": { diff --git a/data/q2_itsxpress/q2_itsxpressbioschemas.jsonld b/data/q2_itsxpress/q2_itsxpressbioschemas.jsonld index 8c3a36db8c42d..21cda0f941734 100644 --- a/data/q2_itsxpress/q2_itsxpressbioschemas.jsonld +++ b/data/q2_itsxpress/q2_itsxpressbioschemas.jsonld @@ -13,8 +13,8 @@ "biotools:primaryContact": "Adam Rivers", "sc:additionalType": "Command-line tool", "sc:author": [ - "Adam Rivers", - "Kyle Weber" + "Kyle Weber", + "Adam Rivers" ], "sc:description": "q2_ITSxpress: a Qiime2 plugin for ITSxpress, software to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files", "sc:license": "CC0-1.0", diff --git a/data/q2lm/q2lmbioschemas.jsonld b/data/q2lm/q2lmbioschemas.jsonld index fa0efa008421a..cdd4b1fa81dc3 100644 --- a/data/q2lm/q2lmbioschemas.jsonld +++ b/data/q2lm/q2lmbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/q2lm", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:22125256", "sc:description": "MATLAB library that uses constrained fuzzy logic models based on prior knowledge networks to address two questions about a biological system: 1) What perturbation results in a specified downstream effect? and 2) In what environments do those perturbations produce that effect?", "sc:name": "Q2LM", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ebi.ac.uk/saezrodriguez/cno/matlab/" } \ No newline at end of file diff --git a/data/q4srm/q4srmbioschemas.jsonld b/data/q4srm/q4srmbioschemas.jsonld index 2b7fd183dbd35..9820a51a1d504 100644 --- a/data/q4srm/q4srmbioschemas.jsonld +++ b/data/q4srm/q4srmbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/q4srm", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "A software tool that rapidly checks the signal from all heavy labeled peptides and flags those that fail quality control metrics in targeted proteomics experiments.", "sc:license": "Other", "sc:name": "Q4SRM", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/PNNL-Comp-Mass-Spec/Q4SRM" } \ No newline at end of file diff --git a/data/qa-recombineit/qa-recombineitbioschemas.jsonld b/data/qa-recombineit/qa-recombineitbioschemas.jsonld index 5c2341637f3dd..cba8ae66c4c20 100644 --- a/data/qa-recombineit/qa-recombineitbioschemas.jsonld +++ b/data/qa-recombineit/qa-recombineitbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "QA-RecombineIt is a web server for quality assessment and recombination of 3D protein models.", "sc:name": "QA-RecombineIt", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://iimcb.genesilico.pl/qarecombineit/" } \ No newline at end of file diff --git a/data/qalma/qalmabioschemas.jsonld b/data/qalma/qalmabioschemas.jsonld index f2ba661f9f3c0..77b9e905cc024 100644 --- a/data/qalma/qalmabioschemas.jsonld +++ b/data/qalma/qalmabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "QALMA", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00089", "sc:version": "V1" diff --git a/data/qarip/qaripbioschemas.jsonld b/data/qarip/qaripbioschemas.jsonld index 21df97fb82eff..fbfdde9e918f5 100644 --- a/data/qarip/qaripbioschemas.jsonld +++ b/data/qarip/qaripbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "QARIP", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://webclu.bio.wzw.tum.de/qarip/" } \ No newline at end of file diff --git a/data/qbic-pred/qbic-predbioschemas.jsonld b/data/qbic-pred/qbic-predbioschemas.jsonld index 8c116472a4af0..3387d88b57081 100644 --- a/data/qbic-pred/qbic-predbioschemas.jsonld +++ b/data/qbic-pred/qbic-predbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKZ363", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/QBiC-Pred", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Raluca Gordân", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6602471", + "pubmed:31114870", { "@id": "https://doi.org/10.1093/NAR/GKZ363" }, - "pubmed:31114870" + "pmcid:PMC6602471" ], "sc:description": "Quantitative predictions of transcription factor binding changes due to sequence variants.", "sc:featureList": [ @@ -27,24 +31,20 @@ "@id": "edam:operation_0445" }, { - "@id": "edam:operation_3799" + "@id": "edam:operation_0331" }, { - "@id": "edam:operation_0331" + "@id": "edam:operation_3799" } ], "sc:license": "MIT", "sc:name": "QBiC-Pred", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://qbic.genome.duke.edu" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ363", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/qbioimages/qbioimagesbioschemas.jsonld b/data/qbioimages/qbioimagesbioschemas.jsonld index 80b67379a7c45..b503931cd8901 100644 --- a/data/qbioimages/qbioimagesbioschemas.jsonld +++ b/data/qbioimages/qbioimagesbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/qbioimages", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Tytus Bernas", - "Błażej Ruszczycki" + "Błażej Ruszczycki", + "Tytus Bernas" ], "sc:additionalType": "Script", "sc:description": "Quality of biological images, reconstructed using localization microscopy data.", "sc:name": "qbioimages", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/blazi13/qbioimages/blob/master/storm_simulation_movie.py" } \ No newline at end of file diff --git a/data/qcewas/qcewasbioschemas.jsonld b/data/qcewas/qcewasbioschemas.jsonld index ca5d19c7bdc74..09d88120ca5b3 100644 --- a/data/qcewas/qcewasbioschemas.jsonld +++ b/data/qcewas/qcewasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "QCEWAS", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/QCEWAS/" } \ No newline at end of file diff --git a/data/qcmap/qcmapbioschemas.jsonld b/data/qcmap/qcmapbioschemas.jsonld index ad1200e1f7d0d..be335d37a8410 100644 --- a/data/qcmap/qcmapbioschemas.jsonld +++ b/data/qcmap/qcmapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "QCMAP", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://shiny.maths.usyd.edu.au/QCMAP/" diff --git a/data/qcmetrics/bioconda_qcmetrics.yaml b/data/qcmetrics/bioconda_qcmetrics.yaml index 444c2165c3711..9ec61baca262f 100644 --- a/data/qcmetrics/bioconda_qcmetrics.yaml +++ b/data/qcmetrics/bioconda_qcmetrics.yaml @@ -5,7 +5,6 @@ description: The package provides a framework for generic quality control of dat home: https://bioconductor.org/packages/3.10/bioc/html/qcmetrics.html identifiers: - biotools:qcmetrics -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-qcmetrics diff --git a/data/qcmetrics/qcmetricsbioschemas.jsonld b/data/qcmetrics/qcmetricsbioschemas.jsonld index 135688b25d242..a23ee736c4584 100644 --- a/data/qcmetrics/qcmetricsbioschemas.jsonld +++ b/data/qcmetrics/qcmetricsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "qcmetrics", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/qcmetrics.html", diff --git a/data/qcut/qcutbioschemas.jsonld b/data/qcut/qcutbioschemas.jsonld index a612b387242bf..eb129eb4c9cfa 100644 --- a/data/qcut/qcutbioschemas.jsonld +++ b/data/qcut/qcutbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Detect communities at a much finer scale or with a higher accuracy than other existing algorithms.", "sc:name": "Qcut", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://cs.utsa.edu/~jruan/Software.html" } \ No newline at end of file diff --git a/data/qdnaseq/qdnaseqbioschemas.jsonld b/data/qdnaseq/qdnaseqbioschemas.jsonld index 4d6cf36abe68d..c02bb4e835d3f 100644 --- a/data/qdnaseq/qdnaseqbioschemas.jsonld +++ b/data/qdnaseq/qdnaseqbioschemas.jsonld @@ -20,11 +20,11 @@ "Library" ], "sc:citation": [ - "pmcid:PMC4248318", - "pubmed:25236618", { "@id": "https://doi.org/10.1101/gr.175141.114" - } + }, + "pubmed:25236618", + "pmcid:PMC4248318" ], "sc:description": "Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.", "sc:featureList": { @@ -33,20 +33,20 @@ "sc:license": "GPL-3.0", "sc:name": "QDNAseq", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/QDNAseq.html", "sc:version": "1.10.0" }, - { - "@id": "http://orcid.org/0000-0001-6762-2582", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1101/gr.175141.114", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-6762-2582", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/qfam/qfambioschemas.jsonld b/data/qfam/qfambioschemas.jsonld index d6951330f413d..4b13f6d6c25fe 100644 --- a/data/qfam/qfambioschemas.jsonld +++ b/data/qfam/qfambioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "QFAM", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://www.cog-genomics.org/plink/1.9/fam_assoc" diff --git a/data/qgene/qgenebioschemas.jsonld b/data/qgene/qgenebioschemas.jsonld index 60f1b721e403d..d0d278b1c92c7 100644 --- a/data/qgene/qgenebioschemas.jsonld +++ b/data/qgene/qgenebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "QGene", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.qgene.org/", "sc:version": "4.3.10" diff --git a/data/qgrid/qgridbioschemas.jsonld b/data/qgrid/qgridbioschemas.jsonld index d151fe9cf6a38..9c8e51baba1ef 100644 --- a/data/qgrid/qgridbioschemas.jsonld +++ b/data/qgrid/qgridbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins.", "sc:name": "Qgrid", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://qgrid.readthedocs.io/en/latest/" } \ No newline at end of file diff --git a/data/qgrs-h_predictor/qgrs-h_predictorbioschemas.jsonld b/data/qgrs-h_predictor/qgrs-h_predictorbioschemas.jsonld index 4a70c2d2ea3c8..9e10621e2a724 100644 --- a/data/qgrs-h_predictor/qgrs-h_predictorbioschemas.jsonld +++ b/data/qgrs-h_predictor/qgrs-h_predictorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "QGRS-H Predictor is a webserver that maps and analyzes phylogenetically conserved putative Quadruplex forming ??G??-Rich Sequences (QGRS) in the mRNAs, ncRNAs and other nucleotide sequences. QGRS-H Predictor generates information on composition and distribution of putative homologous G-quadruplexes in semi-globally aligned nucleotide sequences based on published algorithms.", "sc:name": "QGRS-H Predictor", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://quadruplex.ramapo.edu/qgrs/app/start" } \ No newline at end of file diff --git a/data/qgrs_mapper/qgrs_mapperbioschemas.jsonld b/data/qgrs_mapper/qgrs_mapperbioschemas.jsonld index 37df2053cf214..7a7881ccffcac 100644 --- a/data/qgrs_mapper/qgrs_mapperbioschemas.jsonld +++ b/data/qgrs_mapper/qgrs_mapperbioschemas.jsonld @@ -11,10 +11,10 @@ "@id": "https://bio.tools/qgrs_mapper", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lawrence D'Antonio", - "Oleg Kikin", "Paramjeet Bagga", - "Manuel Viotti" + "Manuel Viotti", + "Lawrence D'Antonio", + "Oleg Kikin" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:16845096", diff --git a/data/qhot/qhotbioschemas.jsonld b/data/qhot/qhotbioschemas.jsonld index f5a390c8147df..e8098e976281f 100644 --- a/data/qhot/qhotbioschemas.jsonld +++ b/data/qhot/qhotbioschemas.jsonld @@ -19,19 +19,19 @@ "biotools:primaryContact": "Chen-Hung Kao", "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC6385979", + "pubmed:30541929", { "@id": "https://doi.org/10.1534/g3.118.200922" }, - "pubmed:30541929" + "pmcid:PMC6385979" ], "sc:description": "Statistical procedure for genome-wide detection of QTL hotspots using public databases.", "sc:featureList": [ { - "@id": "edam:operation_3232" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3232" }, { "@id": "edam:operation_0282" @@ -39,9 +39,9 @@ ], "sc:name": "QHOT", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.stat.sinica.edu.tw/chkao/RQTL/download.htm" } diff --git a/data/qmrlfs-finder/qmrlfs-finderbioschemas.jsonld b/data/qmrlfs-finder/qmrlfs-finderbioschemas.jsonld index 2eea9ec21386b..c50e391424aee 100644 --- a/data/qmrlfs-finder/qmrlfs-finderbioschemas.jsonld +++ b/data/qmrlfs-finder/qmrlfs-finderbioschemas.jsonld @@ -17,32 +17,32 @@ "@id": "https://bio.tools/qmrlfs-finder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Thidathip Wongsurawat", "Piroon Jenjaroenpun", - "Vladimir Kuznetsov", - "Thidathip Wongsurawat" + "Vladimir Kuznetsov" ], "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4489302", - "pubmed:25883153", { "@id": "https://doi.org/10.1093/NAR/GKV344" - } + }, + "pubmed:25883153", + "pmcid:PMC4489302" ], "sc:description": "Model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences.", "sc:featureList": [ { - "@id": "edam:operation_0278" + "@id": "edam:operation_2481" }, { - "@id": "edam:operation_2481" + "@id": "edam:operation_0278" } ], "sc:name": "QmRLFS-finder", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder" } diff --git a/data/qmsat/qmsatbioschemas.jsonld b/data/qmsat/qmsatbioschemas.jsonld index d99fee76cf795..6ca65feb17b3f 100644 --- a/data/qmsat/qmsatbioschemas.jsonld +++ b/data/qmsat/qmsatbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC3340416", { "@id": "https://doi.org/10.1093/nar/gks024" }, - "pubmed:22262732" + "pubmed:22262732", + "pmcid:PMC3340416" ], "sc:description": "A powerful test that directly incorporates sequencing qualities in association tests with multiple rare variants. It allows for the adjustment of additional covariates and is robust towards the inclusion of noncausal variants and variants having effects with different magnitudes and directions. Furthermore, it can coherently account for missing genotypes and conjoin in a principled way individuals or variants sequenced at varying coverage depths.", "sc:featureList": { diff --git a/data/qnet/qnetbioschemas.jsonld b/data/qnet/qnetbioschemas.jsonld index 3fe69618c258b..3083ffcd4f4bd 100644 --- a/data/qnet/qnetbioschemas.jsonld +++ b/data/qnet/qnetbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software package written in Java for generating phylogenetic networks from quartet data.", "sc:name": "QNet", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.uea.ac.uk/computing/qnet" } \ No newline at end of file diff --git a/data/qnr/qnrbioschemas.jsonld b/data/qnr/qnrbioschemas.jsonld index 81ec5096a063d..67e9f69877c75 100644 --- a/data/qnr/qnrbioschemas.jsonld +++ b/data/qnr/qnrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "qnr", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioinformatics.math.chalmers.se/qnr/" } \ No newline at end of file diff --git a/data/qoma/qomabioschemas.jsonld b/data/qoma/qomabioschemas.jsonld index e97cc8a79e6f3..5dc30f0b3af36 100644 --- a/data/qoma/qomabioschemas.jsonld +++ b/data/qoma/qomabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Aligner for three or more sequences. Used for phylogenetic analysis and identification of conserved motifs.", "sc:name": "QOMA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.cise.ufl.edu/~tamer/other_files/msa.html", "sc:version": "2.0" diff --git a/data/qpcrnorm/qpcrnormbioschemas.jsonld b/data/qpcrnorm/qpcrnormbioschemas.jsonld index 52c5b56deb107..2e6d283e35a58 100644 --- a/data/qpcrnorm/qpcrnormbioschemas.jsonld +++ b/data/qpcrnorm/qpcrnormbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "qpcrNorm", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/qpcrNorm.html", "sc:version": "1.32.0" diff --git a/data/qpgraph/qpgraphbioschemas.jsonld b/data/qpgraph/qpgraphbioschemas.jsonld index 742e03858cba0..386891d8da1ef 100644 --- a/data/qpgraph/qpgraphbioschemas.jsonld +++ b/data/qpgraph/qpgraphbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1534/genetics.114.169573", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/qpgraph", "@type": "sc:SoftwareApplication", @@ -20,13 +24,13 @@ }, "edam:has_output": [ { - "@id": "edam:data_2884" + "@id": "edam:data_1772" }, { - "@id": "edam:data_1669" + "@id": "edam:data_2884" }, { - "@id": "edam:data_1772" + "@id": "edam:data_1669" } ], "sc:additionalType": [ @@ -37,28 +41,28 @@ { "@id": "edam:topic_3518" }, - { - "@id": "edam:topic_3308" - }, { "@id": "edam:topic_0203" }, { - "@id": "edam:topic_0622" + "@id": "edam:topic_3308" }, { "@id": "edam:topic_2885" }, + { + "@id": "edam:topic_0622" + }, { "@id": "edam:topic_3053" } ], "sc:citation": [ + "pmcid:PMC4256758", + "pubmed:25271303", { "@id": "https://doi.org/10.1534/genetics.114.169573" - }, - "pmcid:PMC4256758", - "pubmed:25271303" + } ], "sc:description": "Estimate gene and eQTL networks from high-throughput expression and genotyping assays.", "sc:featureList": { @@ -67,17 +71,13 @@ "sc:license": "GPL-2.0", "sc:name": "qpgraph", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/qpgraph.html", "sc:version": "2.8.2" }, - { - "@id": "https://doi.org/10.1534/genetics.114.169573", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-2229-4508", "@type": "schema:Person" diff --git a/data/qq-snv/qq-snvbioschemas.jsonld b/data/qq-snv/qq-snvbioschemas.jsonld index 402e6b77c7b4b..e11a00d06dcef 100644 --- a/data/qq-snv/qq-snvbioschemas.jsonld +++ b/data/qq-snv/qq-snvbioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.1186/S12859-015-0812-9" }, - "pmcid:PMC4641353", - "pubmed:26554718" + "pubmed:26554718", + "pmcid:PMC4641353" ], "sc:description": "Single nucleotide variant detection at low frequency by comparing the quality quantiles.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "QQ-SNV", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/qqsnv/" } diff --git a/data/qrcme/qrcmebioschemas.jsonld b/data/qrcme/qrcmebioschemas.jsonld index a63ad70cd39f8..a994f4ce1e732 100644 --- a/data/qrcme/qrcmebioschemas.jsonld +++ b/data/qrcme/qrcmebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Yun Li", - "Jie Huang", - "Yun Li Statistical Genetics Group" + "Yun Li Statistical Genetics Group", + "Jie Huang" ], "sc:additionalType": "Web application", "sc:description": "Simple and reliable way to ensure that multiple DNA sequence data files represent the same individual person. This tool will identify any swaps that may have been made during wet lab processing or data file handling by ensuring that that two different DNA sequence data files represent the same person.", "sc:name": "QR Concordance (QRC)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://qrcme.tech/" } \ No newline at end of file diff --git a/data/qresearch/qresearchbioschemas.jsonld b/data/qresearch/qresearchbioschemas.jsonld index 6c14343ee055d..84ee12b0a1f14 100644 --- a/data/qresearch/qresearchbioschemas.jsonld +++ b/data/qresearch/qresearchbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "CC-BY-NC-SA-4.0", "sc:name": "QResearch", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.qresearch.org" } \ No newline at end of file diff --git a/data/qridge/qridgebioschemas.jsonld b/data/qridge/qridgebioschemas.jsonld index 61bebd2bc3b6e..1031c91bf46d5 100644 --- a/data/qridge/qridgebioschemas.jsonld +++ b/data/qridge/qridgebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Given a set of RNA-Seq data, this tool assembles the short reads into long full-length transcripts.", "sc:name": "QRidge", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://zhangroup.aporc.org/QRidgeWalker" } \ No newline at end of file diff --git a/data/qrqc/bioconda_qrqc.yaml b/data/qrqc/bioconda_qrqc.yaml index 153da8cc51fd8..cab91f24cd816 100644 --- a/data/qrqc/bioconda_qrqc.yaml +++ b/data/qrqc/bioconda_qrqc.yaml @@ -7,7 +7,6 @@ description: Quickly scans reads and gathers statistics on base and quality freq home: https://bioconductor.org/packages/3.10/bioc/html/qrqc.html identifiers: - biotools:qrqc -- doi:10.1038/nmeth.3252 license: GPL (>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-qrqc diff --git a/data/qrqc/qrqcbioschemas.jsonld b/data/qrqc/qrqcbioschemas.jsonld index f5ef273eecde5..04a311cd51ca1 100644 --- a/data/qrqc/qrqcbioschemas.jsonld +++ b/data/qrqc/qrqcbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "qrqc", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/qrqc.html", "sc:version": "1.28.0" diff --git a/data/qrtdesigner/qrtdesignerbioschemas.jsonld b/data/qrtdesigner/qrtdesignerbioschemas.jsonld index f8ae3520058f0..ad0175923bdd2 100644 --- a/data/qrtdesigner/qrtdesignerbioschemas.jsonld +++ b/data/qrtdesigner/qrtdesignerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Program for designing primers for real-time quantitative PCR assays.", "sc:name": "qRTDesigner", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioinfo.ut.ee/gwRTqPCR/", "sc:version": "1.2" diff --git a/data/qsar-co/qsar-cobioschemas.jsonld b/data/qsar-co/qsar-cobioschemas.jsonld index 598db273aa1f4..b89cb6655589e 100644 --- a/data/qsar-co/qsar-cobioschemas.jsonld +++ b/data/qsar-co/qsar-cobioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "QSAR-Co", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://sites.google.com/view/qsar-co" } \ No newline at end of file diff --git a/data/qsbio/qsbiobioschemas.jsonld b/data/qsbio/qsbiobioschemas.jsonld index d1601596305a0..521b70071e0fd 100644 --- a/data/qsbio/qsbiobioschemas.jsonld +++ b/data/qsbio/qsbiobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A dataset of conserved quaternary structure (QS) across Protein Data Ban (PDB).", "sc:name": "QSbio", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.QSbio.org" } \ No newline at end of file diff --git a/data/qscop_blast/qscop_blastbioschemas.jsonld b/data/qscop_blast/qscop_blastbioschemas.jsonld index d7181d9b4f736..82f649ee83747 100644 --- a/data/qscop_blast/qscop_blastbioschemas.jsonld +++ b/data/qscop_blast/qscop_blastbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).", "sc:name": "QSCOP BLAST", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://archive.is/9B7DA" diff --git a/data/qsea/qseabioschemas.jsonld b/data/qsea/qseabioschemas.jsonld index 180d75fe8a47c..0bc6fd850d8d4 100644 --- a/data/qsea/qseabioschemas.jsonld +++ b/data/qsea/qseabioschemas.jsonld @@ -18,10 +18,10 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:27913729", { "@id": "https://doi.org/10.1093/nar/gkw1193" }, - "pubmed:27913729", "pmcid:PMC5389680" ], "sc:description": "Tool developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, it provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.", @@ -32,8 +32,8 @@ "sc:name": "qsea", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/qsea.html", "sc:version": "1.0.3" diff --git a/data/qsurface/qsurfacebioschemas.jsonld b/data/qsurface/qsurfacebioschemas.jsonld index 729dd1b767bea..fc6569263bb2d 100644 --- a/data/qsurface/qsurfacebioschemas.jsonld +++ b/data/qsurface/qsurfacebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Analyze lineage- and mutation-specific cell surface transcriptome marker from patient cancer samples. It is a fast and efficient tool to find novel tumor-specific cell surface markers for advanced cancer therapies.", "sc:name": "QSurface", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://compbio.sookmyung.ac.kr/~qsurface/" } \ No newline at end of file diff --git a/data/qtl-all/qtl-allbioschemas.jsonld b/data/qtl-all/qtl-allbioschemas.jsonld index 8c3ec599e523d..7cf09a4b5a647 100644 --- a/data/qtl-all/qtl-allbioschemas.jsonld +++ b/data/qtl-all/qtl-allbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "QTL linkage analysis program. It calculates a wide variety of QTL linkage statistics for nuclear families. Score statistics are emphasized, as are statistics appropriate for ascertained (nonpopulation) samples such as concordant and discordant sibling pairs. Currently, only sib-pair and sibship data are supported, but we plan to extend the capability to arbitrary pedigrees soon.", "sc:name": "QTL-ALL", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://watson.hgen.pitt.edu/register/" } \ No newline at end of file diff --git a/data/qtl2pleio/qtl2pleiobioschemas.jsonld b/data/qtl2pleio/qtl2pleiobioschemas.jsonld index f93dfa43560bb..c962e106de844 100644 --- a/data/qtl2pleio/qtl2pleiobioschemas.jsonld +++ b/data/qtl2pleio/qtl2pleiobioschemas.jsonld @@ -17,30 +17,30 @@ }, "sc:additionalType": "Library", "sc:citation": [ + "pubmed:31092608", + "pmcid:PMC6643884", { "@id": "https://doi.org/10.1534/G3.119.400098" - }, - "pmcid:PMC6643884", - "pubmed:31092608" + } ], "sc:description": "Testing Pleiotropy vs. Separate QTL in Multiparental Populations.", "sc:featureList": [ { - "@id": "edam:operation_0282" + "@id": "edam:operation_3232" }, { - "@id": "edam:operation_2238" + "@id": "edam:operation_0282" }, { - "@id": "edam:operation_3232" + "@id": "edam:operation_2238" } ], "sc:license": "MIT", "sc:name": "qtl2pleio", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/fboehm/qtl2pleio" }, diff --git a/data/qtlnetwork/qtlnetworkbioschemas.jsonld b/data/qtlnetwork/qtlnetworkbioschemas.jsonld index 7b6f1519b303e..7ff70a4120b3b 100644 --- a/data/qtlnetwork/qtlnetworkbioschemas.jsonld +++ b/data/qtlnetwork/qtlnetworkbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "QTLNetwork is a software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines.", "sc:name": "QTLNETWORK", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://ibi.zju.edu.cn/software/qtlnetwork/", "sc:version": "2.1" diff --git a/data/qtlpoly/qtlpolybioschemas.jsonld b/data/qtlpoly/qtlpolybioschemas.jsonld index 6172ade12a0d6..9a79dd6712d4d 100644 --- a/data/qtlpoly/qtlpolybioschemas.jsonld +++ b/data/qtlpoly/qtlpolybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "QTLpoly", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/guilherme-pereira/qtlpoly" diff --git a/data/qtorch/qtorchbioschemas.jsonld b/data/qtorch/qtorchbioschemas.jsonld index b0628f861f3fc..5849d98966fe7 100644 --- a/data/qtorch/qtorchbioschemas.jsonld +++ b/data/qtorch/qtorchbioschemas.jsonld @@ -17,16 +17,16 @@ "@id": "https://bio.tools/qTorch", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "N. Sawaya", - "S. Fried" + "S. Fried", + "N. Sawaya" ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6287880", { "@id": "https://doi.org/10.1371/journal.pone.0208510" }, - "pubmed:30532242", - "pmcid:PMC6287880" + "pubmed:30532242" ], "sc:description": "The quantum tensor contraction handler.", "sc:featureList": { @@ -35,9 +35,9 @@ "sc:license": "Apache-2.0", "sc:name": "qTorch", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/aspuru-guzik-group/qtorch" } diff --git a/data/quacrs/quacrsbioschemas.jsonld b/data/quacrs/quacrsbioschemas.jsonld index a7db6471dd8c8..30f7d6326b18b 100644 --- a/data/quacrs/quacrsbioschemas.jsonld +++ b/data/quacrs/quacrsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/quacrs", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:25368506", "sc:description": "Integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies.", diff --git a/data/quadfinder/quadfinderbioschemas.jsonld b/data/quadfinder/quadfinderbioschemas.jsonld index de06748733b6e..4b6906ee0224e 100644 --- a/data/quadfinder/quadfinderbioschemas.jsonld +++ b/data/quadfinder/quadfinderbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "QuadFinder", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/xiuchengquek/QuadFinder" } \ No newline at end of file diff --git a/data/quadgt/quadgtbioschemas.jsonld b/data/quadgt/quadgtbioschemas.jsonld index 8416b6f246383..86aaa9b78b76c 100644 --- a/data/quadgt/quadgtbioschemas.jsonld +++ b/data/quadgt/quadgtbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "BSD-4-Clause", "sc:name": "QuadGT", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.iro.umontreal.ca/%7Ecsuros/quadgt/" diff --git a/data/quadruplex/quadruplexbioschemas.jsonld b/data/quadruplex/quadruplexbioschemas.jsonld index b61b1034c8fb6..6e93ef92bde5e 100644 --- a/data/quadruplex/quadruplexbioschemas.jsonld +++ b/data/quadruplex/quadruplexbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A website to serve the quadruplex community. Contains conference information, forums, database and parsers.", "sc:name": "Quadruplex", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.quadruplex.org" } \ No newline at end of file diff --git a/data/qualifier/qualifierbioschemas.jsonld b/data/qualifier/qualifierbioschemas.jsonld index 48f9c25eed205..d6c772b049ace 100644 --- a/data/qualifier/qualifierbioschemas.jsonld +++ b/data/qualifier/qualifierbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "QUALIFIER", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/QUALIFIER.html", "sc:version": "1.18.0" diff --git a/data/qualimap/qualimapbioschemas.jsonld b/data/qualimap/qualimapbioschemas.jsonld index df0f6679d0798..d062e4b3515e2 100644 --- a/data/qualimap/qualimapbioschemas.jsonld +++ b/data/qualimap/qualimapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.", "sc:name": "QualiMap", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://qualimap.bioinfo.cipf.es/" } \ No newline at end of file diff --git a/data/quality/qualitybioschemas.jsonld b/data/quality/qualitybioschemas.jsonld index 8c8e0a138e96f..d96be273f6a90 100644 --- a/data/quality/qualitybioschemas.jsonld +++ b/data/quality/qualitybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Variant of the minimum Chi-squared (MC) method for limiting dilution assays, and for which he has demonstrated by simulation desirable properties of minimum variance (i.e., high precision) and minimum bias. Our method modifies the MC method to allow the user to specify the probabilities of a false negative and false positive PCR.", "sc:name": "QUALITY", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://indra.mullins.microbiol.washington.edu/quality/" diff --git a/data/quality_assessment/quality_assessmentbioschemas.jsonld b/data/quality_assessment/quality_assessmentbioschemas.jsonld index b88932847d183..e36a534f96f47 100644 --- a/data/quality_assessment/quality_assessmentbioschemas.jsonld +++ b/data/quality_assessment/quality_assessmentbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Apply quality filter over NGS data. You can see quality distribution graphs and one graph for each base.", "sc:name": "Quality Assessment", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://sourceforge.net/projects/qualevaluato/" diff --git a/data/qualitysnpng/qualitysnpngbioschemas.jsonld b/data/qualitysnpng/qualitysnpngbioschemas.jsonld index 7bcf2b732830f..ed93bfe7f7b99 100644 --- a/data/qualitysnpng/qualitysnpngbioschemas.jsonld +++ b/data/qualitysnpng/qualitysnpngbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "QualitySNPng is a web tool for the detection and interactive visualization of single nucleotide polymorphisms. It does not require a sequenced reference genome.", "sc:name": "QualitySNPng", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.bioinformatics.nl/QualitySNPng" } \ No newline at end of file diff --git a/data/qualtofastq/qualtofastqbioschemas.jsonld b/data/qualtofastq/qualtofastqbioschemas.jsonld index 1b70137ced8e4..8c6622b757fd5 100644 --- a/data/qualtofastq/qualtofastqbioschemas.jsonld +++ b/data/qualtofastq/qualtofastqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Convert a file in FASTA/Qual format to FastQ format.", "sc:name": "qualtofastq", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/quantgenius/quantgeniusbioschemas.jsonld b/data/quantgenius/quantgeniusbioschemas.jsonld index 670e75bd3170c..7a3a0d3518bed 100644 --- a/data/quantgenius/quantgeniusbioschemas.jsonld +++ b/data/quantgenius/quantgeniusbioschemas.jsonld @@ -11,28 +11,28 @@ "@id": "https://bio.tools/quantgenius", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kristina Gruden", "Špela Baebler", + "Kristina Gruden", "Miha Svalina" ], "sc:additionalType": "Web application", "sc:author": "Miha Svalina", "sc:contributor": [ "Maruša Pompe-Novak", + "Marko Petek", "Katja Stare", - "Ana Rotter", - "Marko Petek" + "Ana Rotter" ], "sc:description": "Web-based tool for the quantification of qPCR data using standard curve approach and QC-based decision support system in a high-throughput setting. It deals with all the issues of qPCR related calculations from data consistency, pipetting errors, standard curve parameters, individual sample efficiencies/inhibition, range of quantification and normalization to one or several reference genes. In this way it enables robust quality controlled quantification of nucleic acids.", "sc:name": "quantGenius", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "ELIXIR-SI-hackathon", - "National Institute of Biology, Department of Biotechnology and Systems Biology" + "National Institute of Biology, Department of Biotechnology and Systems Biology", + "ELIXIR-SI-hackathon" ], "sc:url": "http://quantgenius.nib.si/", "sc:version": "1" diff --git a/data/quantifly/quantiflybioschemas.jsonld b/data/quantifly/quantiflybioschemas.jsonld index 023fe216582fe..574965e07412c 100644 --- a/data/quantifly/quantiflybioschemas.jsonld +++ b/data/quantifly/quantiflybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software package for automating egg counting in Drosophila genetics research.", "sc:name": "QuantiFly", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/dwaithe/quantifly" } \ No newline at end of file diff --git a/data/quantilebootstrap/quantilebootstrapbioschemas.jsonld b/data/quantilebootstrap/quantilebootstrapbioschemas.jsonld index 292daf7183fcd..1bbbc0cc7efa8 100644 --- a/data/quantilebootstrap/quantilebootstrapbioschemas.jsonld +++ b/data/quantilebootstrap/quantilebootstrapbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Unlicense", "sc:name": "QuantileBootstrap", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/owatson/QuantileBootstrap" diff --git a/data/quantiprot/quantiprotbioschemas.jsonld b/data/quantiprot/quantiprotbioschemas.jsonld index de2a75dc7b962..2622ee24f5aac 100644 --- a/data/quantiprot/quantiprotbioschemas.jsonld +++ b/data/quantiprot/quantiprotbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Witold Dyrka", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:28716000", { "@id": "https://doi.org/10.1186/s12859-017-1751-4" }, + "pubmed:28716000", "pmcid:PMC5512976" ], "sc:description": "Provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids.", @@ -28,8 +28,8 @@ "sc:license": "MIT", "sc:name": "quantiprot", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://git.e-science.pl/wdyrka/quantiprot" }, diff --git a/data/quantisnp/quantisnpbioschemas.jsonld b/data/quantisnp/quantisnpbioschemas.jsonld index 61c630b3aec5a..78b5901a358b6 100644 --- a/data/quantisnp/quantisnpbioschemas.jsonld +++ b/data/quantisnp/quantisnpbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Analytical tool for the analysis of copy number variation using whole genome SNP genotyping data. In its first implementation it was developed for data arising from Illumina® platforms.", "sc:name": "QuantiSNP", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sites.google.com/site/quantisnp/home" } \ No newline at end of file diff --git a/data/quantro/quantrobioschemas.jsonld b/data/quantro/quantrobioschemas.jsonld index a4b552fc5cd33..d4e1d36e799ee 100644 --- a/data/quantro/quantrobioschemas.jsonld +++ b/data/quantro/quantrobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-7858-0231", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s13059-015-0679-0", "@type": "sc:CreativeWork" @@ -24,15 +20,15 @@ "@id": "http://orcid.org/0000-0002-7858-0231" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:26040460", { "@id": "https://doi.org/10.1186/s13059-015-0679-0" }, - "pmcid:PMC4495646" + "pmcid:PMC4495646", + "pubmed:26040460" ], "sc:description": "A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.", "sc:featureList": { @@ -41,12 +37,16 @@ "sc:license": "GPL-3.0", "sc:name": "quantro", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/quantro.html", "sc:version": "1.8.0" + }, + { + "@id": "http://orcid.org/0000-0002-7858-0231", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/quantsmooth/bioconda_quantsmooth.yaml b/data/quantsmooth/bioconda_quantsmooth.yaml index b110a354dd53c..64486efc0e899 100644 --- a/data/quantsmooth/bioconda_quantsmooth.yaml +++ b/data/quantsmooth/bioconda_quantsmooth.yaml @@ -4,7 +4,6 @@ description: 'Implements quantile smoothing as introduced in: Quantile smoothing home: https://bioconductor.org/packages/3.10/bioc/html/quantsmooth.html identifiers: - biotools:quantsmooth -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-quantsmooth diff --git a/data/quantsmooth/quantsmoothbioschemas.jsonld b/data/quantsmooth/quantsmoothbioschemas.jsonld index 06ab843e7e7a4..b756ba785b4c3 100644 --- a/data/quantsmooth/quantsmoothbioschemas.jsonld +++ b/data/quantsmooth/quantsmoothbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "quantsmooth", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/quantsmooth.html", "sc:version": "1.40.0" diff --git a/data/quantum/quantumbioschemas.jsonld b/data/quantum/quantumbioschemas.jsonld index e8b5cac2c25af..163333cfebd38 100644 --- a/data/quantum/quantumbioschemas.jsonld +++ b/data/quantum/quantumbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "Quantum++", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/vsoftco/qpp" } \ No newline at end of file diff --git a/data/quantworm/quantwormbioschemas.jsonld b/data/quantworm/quantwormbioschemas.jsonld index 44a6409007349..cd9f7f18b1634 100644 --- a/data/quantworm/quantwormbioschemas.jsonld +++ b/data/quantworm/quantwormbioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0084830" }, - "pmcid:PMC3885606", - "pubmed:24416295" + "pubmed:24416295", + "pmcid:PMC3885606" ], "sc:description": "Comprehensive Software Package for Caenorhabditis elegans Phenotypic Assays.", "sc:featureList": [ @@ -38,8 +38,8 @@ "sc:name": "QuantWorm", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.quantworm.org/" } diff --git a/data/quark/quarkbioschemas.jsonld b/data/quark/quarkbioschemas.jsonld index 61a2cd01034f6..3d65db601eef4 100644 --- a/data/quark/quarkbioschemas.jsonld +++ b/data/quark/quarkbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "QUARK", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://zhanglab.ccmb.med.umich.edu/QUARK/" } \ No newline at end of file diff --git a/data/quartpac/quartpacbioschemas.jsonld b/data/quartpac/quartpacbioschemas.jsonld index 9bb9b333ca2bb..87168f5c2e893 100644 --- a/data/quartpac/quartpacbioschemas.jsonld +++ b/data/quartpac/quartpacbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Gregory Ryslik", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Identifies clustering of somatic mutations in proteins over the entire quaternary structure.", "sc:license": "GPL-2.0", "sc:name": "QuartPAC", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/QuartPAC.html", "sc:version": "1.6.0" diff --git a/data/quasimotifinder/quasimotifinderbioschemas.jsonld b/data/quasimotifinder/quasimotifinderbioschemas.jsonld index 137cf916c0f5d..b5fa739a3cc0f 100644 --- a/data/quasimotifinder/quasimotifinderbioschemas.jsonld +++ b/data/quasimotifinder/quasimotifinderbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "QuasiMotiFinder uses physicochemical similarity to PROSITE motifs and evolutionary conservation to predict sequence locations with possible function (pseudo-motifs).", "sc:name": "QuasiMotiFinder", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://quasimotifinder.tau.ac.il/" } \ No newline at end of file diff --git a/data/quasr/quasrbioschemas.jsonld b/data/quasr/quasrbioschemas.jsonld index 75e05d4587471..d394c842be26c 100644 --- a/data/quasr/quasrbioschemas.jsonld +++ b/data/quasr/quasrbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkq211", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/quasr", "@type": "sc:SoftwareApplication", @@ -22,10 +18,10 @@ }, "edam:has_output": [ { - "@id": "edam:data_1383" + "@id": "edam:data_2012" }, { - "@id": "edam:data_2012" + "@id": "edam:data_1383" } ], "sc:additionalType": [ @@ -34,52 +30,56 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3518" + "@id": "edam:topic_3169" }, { - "@id": "edam:topic_3168" + "@id": "edam:topic_3053" }, { - "@id": "edam:topic_3169" + "@id": "edam:topic_3170" }, { - "@id": "edam:topic_3170" + "@id": "edam:topic_3518" }, { "@id": "edam:topic_0769" }, { - "@id": "edam:topic_3053" + "@id": "edam:topic_3168" } ], "sc:citation": [ "pubmed:20371516", - "pmcid:PMC2919714", { "@id": "https://doi.org/10.1093/nar/gkq211" - } + }, + "pmcid:PMC2919714" ], "sc:description": "This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.", "sc:featureList": [ { - "@id": "edam:operation_3198" + "@id": "edam:operation_2238" }, { "@id": "edam:operation_3219" }, { - "@id": "edam:operation_2238" + "@id": "edam:operation_3198" } ], "sc:license": "GPL-2.0", "sc:name": "QuasR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/QuasR.html", "sc:version": "1.14.0" + }, + { + "@id": "https://doi.org/10.1093/nar/gkq211", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/quassi/quassibioschemas.jsonld b/data/quassi/quassibioschemas.jsonld index b4a60d725d3df..cadfe96900edf 100644 --- a/data/quassi/quassibioschemas.jsonld +++ b/data/quassi/quassibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A linear programming based approach to find significance residue positions as well as quantifying their significance in MHC II DR molecules.", "sc:name": "QUASSI", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://code.google.com/p/quassi/" } \ No newline at end of file diff --git a/data/quast/quastbioschemas.jsonld b/data/quast/quastbioschemas.jsonld index 4f5b2d9a298d3..e4cda81e67be9 100644 --- a/data/quast/quastbioschemas.jsonld +++ b/data/quast/quastbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-2.0", "sc:name": "QUAST", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://quast.sourceforge.net/quast" } \ No newline at end of file diff --git a/data/quaternaryprod/quaternaryprodbioschemas.jsonld b/data/quaternaryprod/quaternaryprodbioschemas.jsonld index 924f34d350991..f386c52f09312 100644 --- a/data/quaternaryprod/quaternaryprodbioschemas.jsonld +++ b/data/quaternaryprod/quaternaryprodbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Carl Tony Fakhry", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pubmed:23203871", { "@id": "https://doi.org/10.1093/nar/gks1094" }, - "pmcid:PMC3531103", - "pubmed:23203871" + "pmcid:PMC3531103" ], "sc:description": "R package that performs causal reasoning on biological networks, including publicly available networks such as String-db. It is a free alternative to commercial products such as Quiagen and Inginuity pathway analysis. For a given a set of differentially expressed genes, it computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic, Ternary Dot product Scoring Statistic and Fisher's exact test.", "sc:featureList": { @@ -36,8 +36,8 @@ "sc:name": "QuaternaryProd", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/QuaternaryProd.html", "sc:version": "1.2.0" diff --git a/data/qubic/qubicbioschemas.jsonld b/data/qubic/qubicbioschemas.jsonld index b4f2dd801216a..67a0d0222373b 100644 --- a/data/qubic/qubicbioschemas.jsonld +++ b/data/qubic/qubicbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "CC-BY-NC-ND-4.0", "sc:name": "QUBIC", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/QUBIC.html", "sc:version": "1.2.1" diff --git a/data/qubils-mas/qubils-masbioschemas.jsonld b/data/qubils-mas/qubils-masbioschemas.jsonld index 239927a0ee86c..8f4f77f5a6c01 100644 --- a/data/qubils-mas/qubils-masbioschemas.jsonld +++ b/data/qubils-mas/qubils-masbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13321-017-0211-5", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/qubils-mas", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pmcid:PMC5462671", - "pubmed:29086120", { "@id": "https://doi.org/10.1186/s13321-017-0211-5" - } + }, + "pubmed:29086120" ], "sc:description": "Calculation of 2D molecular descriptors based on the bilinear, quadratic and linear algebraic forms. Compute these kinds of indices, applying matrix transformations (simple-stochastic, double-stochastic and mutual probability), cut-offs, local calculations and aggregation operators.", "sc:featureList": { @@ -32,10 +36,6 @@ "Windows" ], "sc:url": "http://tomocomd.com/qubils-mas" - }, - { - "@id": "https://doi.org/10.1186/s13321-017-0211-5", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/queryor/queryorbioschemas.jsonld b/data/queryor/queryorbioschemas.jsonld index 649a40ac27a8f..2dab366fa0588 100644 --- a/data/queryor/queryorbioschemas.jsonld +++ b/data/queryor/queryorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A web-based platform to manage and retrieve data from human exome sequencing projects.", "sc:name": "QueryOr", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", diff --git a/data/quetal/quetalbioschemas.jsonld b/data/quetal/quetalbioschemas.jsonld index 168cece9a57b8..525391200f928 100644 --- a/data/quetal/quetalbioschemas.jsonld +++ b/data/quetal/quetalbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "QueTAL", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi" } \ No newline at end of file diff --git a/data/quetzal/quetzalbioschemas.jsonld b/data/quetzal/quetzalbioschemas.jsonld index 741d3be6b1b2e..85b9e7849258c 100644 --- a/data/quetzal/quetzalbioschemas.jsonld +++ b/data/quetzal/quetzalbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Quetzal", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://becheler.github.io/pages/quetzal.html" diff --git a/data/quickgo/quickgobioschemas.jsonld b/data/quickgo/quickgobioschemas.jsonld index 153165fd0f4f7..da57c63be4f7b 100644 --- a/data/quickgo/quickgobioschemas.jsonld +++ b/data/quickgo/quickgobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A fast browser for Gene Ontology terms and annotations.", "sc:name": "QuickGO", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ebi.ac.uk/QuickGO/" } \ No newline at end of file diff --git a/data/quicknii/quickniibioschemas.jsonld b/data/quicknii/quickniibioschemas.jsonld index 4d17483e3fa41..65593e6fa7d40 100644 --- a/data/quicknii/quickniibioschemas.jsonld +++ b/data/quicknii/quickniibioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216796", - "@type": "sc:CreativeWork" - }, { "@id": "https://orcid.org/0000-0001-7899-906X", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216796", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/QuickNII", "@type": "sc:SoftwareApplication", @@ -25,11 +25,11 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:31141518", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216796" }, - "pmcid:PMC6541252", - "pubmed:31141518" + "pmcid:PMC6541252" ], "sc:description": "Tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.", "sc:featureList": { @@ -38,8 +38,8 @@ "sc:license": "CC-BY-NC-SA-4.0", "sc:name": "QuickNII", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://www.nitrc.org/projects/quicknii" diff --git a/data/quin/quinbioschemas.jsonld b/data/quin/quinbioschemas.jsonld index d5b0a3c4ff875..e5938f101eb18 100644 --- a/data/quin/quinbioschemas.jsonld +++ b/data/quin/quinbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1004809", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/quin", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "DUYGU UCAR", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC4919057", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1004809" }, - "pmcid:PMC4919057", "pubmed:27336171" ], "sc:description": "Tool for visualizing, annotating, and querying chromatin interactions derived from technologies such as ChIA-PET or HiC.", @@ -32,10 +36,6 @@ "Mac" ], "sc:url": "https://quin.jax.org/" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1004809", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/quip/quipbioschemas.jsonld b/data/quip/quipbioschemas.jsonld index c92699fa27b18..5f414e22fa42c 100644 --- a/data/quip/quipbioschemas.jsonld +++ b/data/quip/quipbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "Quip", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://homes.cs.washington.edu/%7Edcjones/quip/" } \ No newline at end of file diff --git a/data/quokka/quokkabioschemas.jsonld b/data/quokka/quokkabioschemas.jsonld index b216d782ab321..923280091cb22 100644 --- a/data/quokka/quokkabioschemas.jsonld +++ b/data/quokka/quokkabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Fuyi Li", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:description": "Tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.", "sc:license": "Unlicense", "sc:name": "Quokka", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://quokka.erc.monash.edu/" } \ No newline at end of file diff --git a/data/qupath/qupathbioschemas.jsonld b/data/qupath/qupathbioschemas.jsonld index 66404d2e797e5..e3f496b0fc3b6 100644 --- a/data/qupath/qupathbioschemas.jsonld +++ b/data/qupath/qupathbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "QuPath", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://qupath.github.io/", "sc:version": "0.1.2" diff --git a/data/qupe/qupebioschemas.jsonld b/data/qupe/qupebioschemas.jsonld index 077a05cc8651e..d4149c058d9a6 100644 --- a/data/qupe/qupebioschemas.jsonld +++ b/data/qupe/qupebioschemas.jsonld @@ -15,14 +15,14 @@ "sc:license": "GPL-2.0", "sc:name": "QuPE", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": [ "CeBiTec", - "bigi", - "Bielefeld University" + "Bielefeld University", + "bigi" ], "sc:url": "https://qupe.cebitec.uni-bielefeld.de", "sc:version": "1.0" diff --git a/data/qusage/qusagebioschemas.jsonld b/data/qusage/qusagebioschemas.jsonld index 383cd65eeb8ba..44ed21cf7607a 100644 --- a/data/qusage/qusagebioschemas.jsonld +++ b/data/qusage/qusagebioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkt660", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0001-9311-9884", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1093/nar/gkt660", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/qusage", "@type": "sc:SoftwareApplication", @@ -37,22 +37,22 @@ "Command-line tool" ], "sc:applicationSubCategory": [ - { - "@id": "edam:topic_3518" - }, { "@id": "edam:topic_0203" }, { "@id": "edam:topic_3170" + }, + { + "@id": "edam:topic_3518" } ], "sc:citation": [ - "pubmed:23921631", "pmcid:PMC3794608", { "@id": "https://doi.org/10.1093/nar/gkt660" - } + }, + "pubmed:23921631" ], "sc:contributor": { "@id": "http://orcid.org/0000-0001-9311-9884" diff --git a/data/qvalue/qvaluebioschemas.jsonld b/data/qvalue/qvaluebioschemas.jsonld index 1ba2cfe298a96..3c513fa07ce96 100644 --- a/data/qvalue/qvaluebioschemas.jsonld +++ b/data/qvalue/qvaluebioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/qvalue", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "John D. Storey", - "Andrew J. Bass" + "Andrew J. Bass", + "John D. Storey" ], "sc:additionalType": "Library", "sc:description": "This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant.", "sc:license": "LGPL-2.0", "sc:name": "qvalue", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/qvalue.html", "sc:version": "2.12.0" diff --git a/data/qvz/qvzbioschemas.jsonld b/data/qvz/qvzbioschemas.jsonld index a5de10cfcc7df..a8777a6f9d8f9 100644 --- a/data/qvz/qvzbioschemas.jsonld +++ b/data/qvz/qvzbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "QVZ", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/mikelhernaez/qvz" } \ No newline at end of file diff --git a/data/r-cloud_workbench/r-cloud_workbenchbioschemas.jsonld b/data/r-cloud_workbench/r-cloud_workbenchbioschemas.jsonld index 354db2a6d29b3..6e279c0b812a2 100644 --- a/data/r-cloud_workbench/r-cloud_workbenchbioschemas.jsonld +++ b/data/r-cloud_workbench/r-cloud_workbenchbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software to remote access to R/Bioconductor on EBI’s 64-bit Linux Cluster. Start the workbench by downloading the package for your operating system or via Java Web Start, and you will get access to an instance of R running on one of EBI’s powerful machines. You can install additional packages, upload your own data, work with graphics and collaborate with colleagues, all as if you are running R locally, but unlimited by your machine’s memory, processor or data storage capacity.", "sc:name": "R-Cloud Workbench", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ebi.ac.uk/Tools/rcloud/" } \ No newline at end of file diff --git a/data/r-coffee/r-coffeebioschemas.jsonld b/data/r-coffee/r-coffeebioschemas.jsonld index 260e969ff624f..09fd72b027611 100644 --- a/data/r-coffee/r-coffeebioschemas.jsonld +++ b/data/r-coffee/r-coffeebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The R-Coffee web server uses pairwise or multiple sequence alignment methods to produce multiple alignments of non-coding RNA sequences, incorporating predicted or known secondary structures.", "sc:name": "R-Coffee", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://tcoffee.crg.cat/apps/tcoffee/do:rcoffee" } \ No newline at end of file diff --git a/data/r-qtl/r-qtlbioschemas.jsonld b/data/r-qtl/r-qtlbioschemas.jsonld index 8cda06da7047a..ae1c6c9b90416 100644 --- a/data/r-qtl/r-qtlbioschemas.jsonld +++ b/data/r-qtl/r-qtlbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-4914-6671", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/r-qtl", "@type": "sc:SoftwareApplication", @@ -25,11 +21,15 @@ "sc:license": "GPL-3.0", "sc:name": "R-QTL", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.rqtl.org/" + }, + { + "@id": "http://orcid.org/0000-0002-4914-6671", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/r/rbioschemas.jsonld b/data/r/rbioschemas.jsonld index c2381cf931405..e968df8f2b35d 100644 --- a/data/r/rbioschemas.jsonld +++ b/data/r/rbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/r", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Workbench" + "Workbench", + "Command-line tool" ], "sc:description": "Free software environment for statistical computing and graphics.", "sc:name": "R", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.r-project.org/" } \ No newline at end of file diff --git a/data/r2_platform/r2_platformbioschemas.jsonld b/data/r2_platform/r2_platformbioschemas.jsonld index 85680dad5a5d7..4d244d61cdd35 100644 --- a/data/r2_platform/r2_platformbioschemas.jsonld +++ b/data/r2_platform/r2_platformbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The R2 platform is an online genomics analysis tool which can analyze a large collection of public data, but also allows shielded analysis of your own microarray dataset. freely accessible and intended to be used by biologists, even those with little or no bioinformatics training.", "sc:name": "R2 platform", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://r2.amc.nl" diff --git a/data/r2dgc/r2dgcbioschemas.jsonld b/data/r2dgc/r2dgcbioschemas.jsonld index baab16bb0783c..f2e8d29b0808a 100644 --- a/data/r2dgc/r2dgcbioschemas.jsonld +++ b/data/r2dgc/r2dgcbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Sara Cooper", - "Ryne Ramaker", - "Emily Gordon" + "Emily Gordon", + "Ryne Ramaker" ], "sc:additionalType": "Library", "sc:description": "Provides functions for aligning 2D gas chromatography mass spectrometry derived metabolite peaks obtained from primary processing and generates an alignment table that allows for a comparison of common peaks across samples and metabolite identification.", diff --git a/data/r3cpet/r3cpetbioschemas.jsonld b/data/r3cpet/r3cpetbioschemas.jsonld index c5e46ba72792c..6270ba4c8807b 100644 --- a/data/r3cpet/r3cpetbioschemas.jsonld +++ b/data/r3cpet/r3cpetbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13059-015-0851-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/r3cpet", "@type": "sc:SoftwareApplication", @@ -31,22 +27,22 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0097" + "@id": "edam:topic_0203" }, { - "@id": "edam:topic_0128" + "@id": "edam:topic_3169" }, { - "@id": "edam:topic_0203" + "@id": "edam:topic_0128" }, { "@id": "edam:topic_2275" }, { - "@id": "edam:topic_3169" + "@id": "edam:topic_3511" }, { - "@id": "edam:topic_3511" + "@id": "edam:topic_0097" } ], "sc:citation": [ @@ -59,28 +55,32 @@ "sc:description": "The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.", "sc:featureList": [ { - "@id": "edam:operation_3658" + "@id": "edam:operation_2464" }, { - "@id": "edam:operation_3083" + "@id": "edam:operation_3439" }, { - "@id": "edam:operation_3439" + "@id": "edam:operation_3083" }, { - "@id": "edam:operation_2464" + "@id": "edam:operation_3658" } ], "sc:license": "GPL-2.0", "sc:name": "R3CPET", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/R3CPET.html", "sc:version": "1.6.0" }, + { + "@id": "https://doi.org/10.1186/s13059-015-0851-6", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0001-5361-1858", "@type": "schema:Person" diff --git a/data/r3d-2-msa/r3d-2-msabioschemas.jsonld b/data/r3d-2-msa/r3d-2-msabioschemas.jsonld index 67cded4342a30..3d2562406b9b7 100644 --- a/data/r3d-2-msa/r3d-2-msabioschemas.jsonld +++ b/data/r3d-2-msa/r3d-2-msabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Select nucleotides from representative RNA 3D structures and seamlessly access sequence variants from large and diverse sequence alignments.", "sc:name": "R3D-2-MSA", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://rna.bgsu.edu/r3d-2-msa" } \ No newline at end of file diff --git a/data/r3d-blast/r3d-blastbioschemas.jsonld b/data/r3d-blast/r3d-blastbioschemas.jsonld index 3c878ac6825a3..878946d98acee 100644 --- a/data/r3d-blast/r3d-blastbioschemas.jsonld +++ b/data/r3d-blast/r3d-blastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "BLAST-like search tool that allows users to quickly search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. Input is an RNA 3D structure in PDB format, output includes a graphical display showing structural superposition.", "sc:name": "R3D-BLAST", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://genome.cs.nthu.edu.tw/R3D-BLAST/" } \ No newline at end of file diff --git a/data/r3d-blast2/r3d-blast2bioschemas.jsonld b/data/r3d-blast2/r3d-blast2bioschemas.jsonld index 02b2bee054ee4..9e577b3a106bc 100644 --- a/data/r3d-blast2/r3d-blast2bioschemas.jsonld +++ b/data/r3d-blast2/r3d-blast2bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Search tool for similar RNA 3D substructures.", "sc:name": "R3D-BLAST2", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://140.114.85.168/R3D-BLAST2/" } \ No newline at end of file diff --git a/data/r453plus1toolbox/r453plus1toolboxbioschemas.jsonld b/data/r453plus1toolbox/r453plus1toolboxbioschemas.jsonld index 6b42255c581dd..435f94d35d455 100644 --- a/data/r453plus1toolbox/r453plus1toolboxbioschemas.jsonld +++ b/data/r453plus1toolbox/r453plus1toolboxbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6382-9428", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/r453plus1toolbox", "@type": "sc:SoftwareApplication", @@ -24,16 +28,12 @@ "sc:license": "GPL-3.0", "sc:name": "R453Plus1Toolbox", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/R453Plus1Toolbox.html", "sc:version": "1.24.0" - }, - { - "@id": "http://orcid.org/0000-0002-6382-9428", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/r4rna/r4rnabioschemas.jsonld b/data/r4rna/r4rnabioschemas.jsonld index f1304dfb7fc10..5b7f9fb704486 100644 --- a/data/r4rna/r4rnabioschemas.jsonld +++ b/data/r4rna/r4rnabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-9203-6323", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/r4rna", "@type": "sc:SoftwareApplication", @@ -20,27 +24,27 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC3384350", - "pubmed:22434875", { "@id": "https://doi.org/10.1093/nar/gks241" - } + }, + "pubmed:22434875", + "pmcid:PMC3384350" ], "sc:description": "A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.", "sc:featureList": [ { - "@id": "edam:operation_3800" + "@id": "edam:operation_0564" }, { - "@id": "edam:operation_0564" + "@id": "edam:operation_3800" } ], "sc:license": "GPL-3.0", "sc:name": "R4RNA", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/R4RNA.html", "sc:version": "1.2.0" @@ -48,10 +52,6 @@ { "@id": "https://doi.org/10.1093/nar/gks241", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-9203-6323", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/r_cloud_workbench/r_cloud_workbenchbioschemas.jsonld b/data/r_cloud_workbench/r_cloud_workbenchbioschemas.jsonld index b4596f53d9bc2..e1b259b9d5630 100644 --- a/data/r_cloud_workbench/r_cloud_workbenchbioschemas.jsonld +++ b/data/r_cloud_workbench/r_cloud_workbenchbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "R Cloud Workbench", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/rcloud/", diff --git a/data/r_for_cdna/r_for_cdnabioschemas.jsonld b/data/r_for_cdna/r_for_cdnabioschemas.jsonld index 0651523fd3afb..a9bd31c814f0c 100644 --- a/data/r_for_cdna/r_for_cdnabioschemas.jsonld +++ b/data/r_for_cdna/r_for_cdnabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Set of R functions for filtering, normalization, Bayesian hierarchical modelling and MCMC procedures in cDNA microarray analysis.", "sc:name": "R functions for cDNA array analysis", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://tsenglab.biostat.pitt.edu/software.htm#cDNA" } \ No newline at end of file diff --git a/data/r_qtl2/r_qtl2bioschemas.jsonld b/data/r_qtl2/r_qtl2bioschemas.jsonld index 0553e716d199c..043941f9f2418 100644 --- a/data/r_qtl2/r_qtl2bioschemas.jsonld +++ b/data/r_qtl2/r_qtl2bioschemas.jsonld @@ -18,27 +18,27 @@ { "@id": "https://doi.org/10.1534/genetics.118.301595" }, - "pmcid:PMC6366910", - "pubmed:30591514" + "pubmed:30591514", + "pmcid:PMC6366910" ], "sc:description": "Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations.", "sc:featureList": [ { - "@id": "edam:operation_3232" + "@id": "edam:operation_0282" }, { "@id": "edam:operation_3196" }, { - "@id": "edam:operation_0282" + "@id": "edam:operation_3232" } ], "sc:license": "GPL-3.0", "sc:name": "Rqtl2", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://kbroman.org/qtl2/" }, diff --git a/data/r_spider/r_spiderbioschemas.jsonld b/data/r_spider/r_spiderbioschemas.jsonld index d0c1d866a1898..e8a469adb4d66 100644 --- a/data/r_spider/r_spiderbioschemas.jsonld +++ b/data/r_spider/r_spiderbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "R spider is a web tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions from KEGG and Reactome.", "sc:name": "R spider", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mips.helmholtz-muenchen.de/proj/rspider" } \ No newline at end of file diff --git a/data/rabhit/rabhitbioschemas.jsonld b/data/rabhit/rabhitbioschemas.jsonld index d9bf0f5ba1fa6..a176ae5b8ff48 100644 --- a/data/rabhit/rabhitbioschemas.jsonld +++ b/data/rabhit/rabhitbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-SA-4.0", "sc:name": "RAbHIT", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://yaarilab.bitbucket.io/RAbHIT/", "sc:version": "0.1.1" diff --git a/data/rabit/rabitbioschemas.jsonld b/data/rabit/rabitbioschemas.jsonld index 64aef9adaaee5..0095a449311c8 100644 --- a/data/rabit/rabitbioschemas.jsonld +++ b/data/rabit/rabitbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Very efficient feature selection algorithm. It was applied to find tumor associated regulators in diverse cancer types.", "sc:name": "RABIT", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://rabit.dfci.harvard.edu/" } \ No newline at end of file diff --git a/data/rac/racbioschemas.jsonld b/data/rac/racbioschemas.jsonld index 6f89761a28545..3bfd6e182eaaf 100644 --- a/data/rac/racbioschemas.jsonld +++ b/data/rac/racbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Library which solves the individual bioenergetic balance for different aquaculture sea fish and shellfish. It also allows for spatialized model runs and population simulations.", "sc:name": "RAC", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/RAC/index.html" diff --git a/data/racipe/racipebioschemas.jsonld b/data/racipe/racipebioschemas.jsonld index 09565602fd583..6e9260a0b52ee 100644 --- a/data/racipe/racipebioschemas.jsonld +++ b/data/racipe/racipebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12918-018-0594-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/racipe", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC6006707", + "pubmed:29914482", { "@id": "https://doi.org/10.1186/s12918-018-0594-6" - }, - "pubmed:29914482" + } ], "sc:description": "Computational tool for modeling gene regulatory circuits using randomization.", "sc:featureList": { @@ -38,6 +34,10 @@ ], "sc:url": "https://github.com/simonhb1990/RACIPE-1.0", "sc:version": "1.0" + }, + { + "@id": "https://doi.org/10.1186/s12918-018-0594-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/radaa/radaabioschemas.jsonld b/data/radaa/radaabioschemas.jsonld index fed503cdbeb62..70300c2f0f9f6 100644 --- a/data/radaa/radaabioschemas.jsonld +++ b/data/radaa/radaabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "RadAA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/sciseim/RadAA" } \ No newline at end of file diff --git a/data/radar/radarbioschemas.jsonld b/data/radar/radarbioschemas.jsonld index e5f673c9b214b..4e479db511267 100644 --- a/data/radar/radarbioschemas.jsonld +++ b/data/radar/radarbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Identify gapped approximate repeats and complex repeat architectures involving many different types of repeats.", "sc:name": "RADAR", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/pfa/radar/", diff --git a/data/raedb/raedbbioschemas.jsonld b/data/raedb/raedbbioschemas.jsonld index 9184a76eab4d5..eca515646e5d7 100644 --- a/data/raedb/raedbbioschemas.jsonld +++ b/data/raedb/raedbbioschemas.jsonld @@ -19,29 +19,29 @@ "biotools:primaryContact": "Dr. Yousong Peng", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC6323319", { "@id": "https://doi.org/10.1093/database/bay140" }, - "pmcid:PMC6323319", "pubmed:30624654" ], "sc:description": "Database of enhancers identified by high-throughput reporter assays.", "sc:featureList": [ - { - "@id": "edam:operation_0224" - }, { "@id": "edam:operation_0438" }, { "@id": "edam:operation_3501" + }, + { + "@id": "edam:operation_0224" } ], "sc:name": "RAEdb", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.computationalbiology.cn/RAEdb/index.php" } diff --git a/data/rafsil/rafsilbioschemas.jsonld b/data/rafsil/rafsilbioschemas.jsonld index fef37c9f62baa..5b5691c290170 100644 --- a/data/rafsil/rafsilbioschemas.jsonld +++ b/data/rafsil/rafsilbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/bty260", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/rafsil", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dennis Kostka", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:29950006", "pmcid:PMC6022547", { "@id": "https://doi.org/10.1093/bioinformatics/bty260" - } + }, + "pubmed:29950006" ], "sc:description": "Random forest based similarity learning for single cell RNA sequencing data.", "sc:featureList": { @@ -28,14 +32,10 @@ "sc:name": "RAFSIL", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.kostkalab.net/software.html" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/bty260", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ragout/ragoutbioschemas.jsonld b/data/ragout/ragoutbioschemas.jsonld index 3ef45d614e566..96aae5076f287 100644 --- a/data/ragout/ragoutbioschemas.jsonld +++ b/data/ragout/ragoutbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for assisted assembly using multiple references. It takes a short read assembly (a set of contigs), a set of related references and a corresponding phylogenetic tree and then assembles the contigs into scaffolds.", "sc:name": "Ragout", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://fenderglass.github.io/Ragout/" } \ No newline at end of file diff --git a/data/raid/raidbioschemas.jsonld b/data/raid/raidbioschemas.jsonld index 96d3332cceb73..2d554444b4c22 100644 --- a/data/raid/raidbioschemas.jsonld +++ b/data/raid/raidbioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13104-018-3289-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/raid", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Brendan Joyce", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:citation": [ "pubmed:29544540", @@ -35,6 +31,10 @@ "sc:name": "RAId", "sc:operatingSystem": "Linux", "sc:url": "https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html" + }, + { + "@id": "https://doi.org/10.1186/s13104-018-3289-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/raida/raidabioschemas.jsonld b/data/raida/raidabioschemas.jsonld index 809ee490c989c..9eb810540d446 100644 --- a/data/raida/raidabioschemas.jsonld +++ b/data/raida/raidabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Robust approach for identifying differentially abundant features in metagenomic samples across different conditions. It utilizes the ratio between features in a modified zero-inflated lognormal model.", "sc:name": "RAIDA", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://cals.arizona.edu/~anling/sbg/software.htm" } \ No newline at end of file diff --git a/data/rain/rainbioschemas.jsonld b/data/rain/rainbioschemas.jsonld index f265d3787c997..6a2f8862ebac4 100644 --- a/data/rain/rainbioschemas.jsonld +++ b/data/rain/rainbioschemas.jsonld @@ -22,15 +22,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Paul F. Thaben", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4266694", - "pubmed:25326247", { "@id": "https://doi.org/10.1177/0748730414553029" - } + }, + "pubmed:25326247", + "pmcid:PMC4266694" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-6637-2566" @@ -43,8 +43,8 @@ "sc:name": "rain", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rain.html", "sc:version": "1.8.0" diff --git a/data/rainbio/rainbiobioschemas.jsonld b/data/rainbio/rainbiobioschemas.jsonld index dad563a791de2..2ca03d62630fd 100644 --- a/data/rainbio/rainbiobioschemas.jsonld +++ b/data/rainbio/rainbiobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-5477-180X", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/RainBio", "@type": "sc:SoftwareApplication", @@ -24,11 +20,15 @@ "sc:license": "LGPL-3.0", "sc:name": "RainBio", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.lesfleursdunormal.fr/static/appliweb/rainbio/index.html" + }, + { + "@id": "https://orcid.org/0000-0002-5477-180X", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/rama/ramabioschemas.jsonld b/data/rama/ramabioschemas.jsonld index 73537b4ac4785..ed1b36e319101 100644 --- a/data/rama/ramabioschemas.jsonld +++ b/data/rama/ramabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Raphael Gottardo", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Robust estimation of cDNA microarray intensities with replicates. The package uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance.", "sc:license": "GPL-2.0", "sc:name": "rama", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rama.html", "sc:version": "1.48.0" diff --git a/data/rambo-k/rambo-kbioschemas.jsonld b/data/rambo-k/rambo-kbioschemas.jsonld index 1477aa4bcfa7a..a329cfab859e8 100644 --- a/data/rambo-k/rambo-kbioschemas.jsonld +++ b/data/rambo-k/rambo-kbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Reference-based tool for rapid and sensitive extraction of one organisms reads from a mixed dataset.", "sc:name": "RAMBO-K", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://gitlab.com/SimonHTausch/RAMBO-K" } \ No newline at end of file diff --git a/data/ramedis/ramedisbioschemas.jsonld b/data/ramedis/ramedisbioschemas.jsonld index 209faf25ef034..0f019f517529d 100644 --- a/data/ramedis/ramedisbioschemas.jsonld +++ b/data/ramedis/ramedisbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thoralf Töpel", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": "pubmed:12542423", "sc:description": "Rare Metabolic Diseases Database: platform independent, web-based information system for rare metabolic diseases based on filed case reports.", "sc:name": "Ramedis", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://ramedis.de" diff --git a/data/ramigo/ramigobioschemas.jsonld b/data/ramigo/ramigobioschemas.jsonld index 85c979bda4999..4f1afc972c100 100644 --- a/data/ramigo/ramigobioschemas.jsonld +++ b/data/ramigo/ramigobioschemas.jsonld @@ -18,10 +18,10 @@ "Library" ], "sc:citation": [ - "pubmed:23297033", { "@id": "https://doi.org/10.1093/bioinformatics/bts708" }, + "pubmed:23297033", "pmcid:PMC3582261" ], "sc:description": "R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.", @@ -31,8 +31,8 @@ "sc:license": "Artistic-2.0", "sc:name": "RamiGO", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RamiGO.html", diff --git a/data/ramona/ramonabioschemas.jsonld b/data/ramona/ramonabioschemas.jsonld index 7cd5485193b10..a0d1b9c234297 100644 --- a/data/ramona/ramonabioschemas.jsonld +++ b/data/ramona/ramonabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RAMONA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mips.helmholtz-muenchen.de/mona/" } \ No newline at end of file diff --git a/data/ramp/rampbioschemas.jsonld b/data/ramp/rampbioschemas.jsonld index d6d6da1aacf52..bd42c5fb8d3b2 100644 --- a/data/ramp/rampbioschemas.jsonld +++ b/data/ramp/rampbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3390/metabo8010016", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ramp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ewy A. Mathé", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC5876005", "pubmed:29470400", { "@id": "https://doi.org/10.3390/metabo8010016" - } + }, + "pmcid:PMC5876005" ], "sc:description": "A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.", "sc:featureList": { @@ -27,14 +31,10 @@ }, "sc:name": "RaMP", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/Mathelab/RaMP-DB" - }, - { - "@id": "https://doi.org/10.3390/metabo8010016", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ranacapa/ranacapabioschemas.jsonld b/data/ranacapa/ranacapabioschemas.jsonld index e0f8105d66e30..e3f0f5d2de492 100644 --- a/data/ranacapa/ranacapabioschemas.jsonld +++ b/data/ranacapa/ranacapabioschemas.jsonld @@ -20,30 +20,30 @@ ], "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6305237", - "pubmed:30613396", { "@id": "https://doi.org/10.12688/f1000research.16680.1" - } + }, + "pmcid:PMC6305237", + "pubmed:30613396" ], "sc:description": "R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.", "sc:featureList": [ - { - "@id": "edam:operation_3797" - }, { "@id": "edam:operation_3501" }, { "@id": "edam:operation_3359" + }, + { + "@id": "edam:operation_3797" } ], "sc:license": "GPL-3.0", "sc:name": "ranacapa", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/gauravsk/ranacapa" }, diff --git a/data/randfold/randfoldbioschemas.jsonld b/data/randfold/randfoldbioschemas.jsonld index ebb0ed97e095a..6e182a5a891a2 100644 --- a/data/randfold/randfoldbioschemas.jsonld +++ b/data/randfold/randfoldbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Secondary structure calculation of non-coding RNA sequences.", "sc:name": "Randfold", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/Randfold", diff --git a/data/randomwalkrestartmh/randomwalkrestartmhbioschemas.jsonld b/data/randomwalkrestartmh/randomwalkrestartmhbioschemas.jsonld index 25b2aaabfddc8..095234bd76b2e 100644 --- a/data/randomwalkrestartmh/randomwalkrestartmhbioschemas.jsonld +++ b/data/randomwalkrestartmh/randomwalkrestartmhbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "RandomWalkRestartMH", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RandomWalkRestartMH.html", "sc:version": "1.0.0" diff --git a/data/randpack/bioconda_randpack.yaml b/data/randpack/bioconda_randpack.yaml index c75a31ac67905..9b1ff6cd894fd 100644 --- a/data/randpack/bioconda_randpack.yaml +++ b/data/randpack/bioconda_randpack.yaml @@ -4,7 +4,6 @@ description: A suite of classes and functions for randomizing patients in clinic home: https://bioconductor.org/packages/3.10/bioc/html/randPack.html identifiers: - biotools:randpack -- doi:10.1038/nmeth.3252 license: Artistic 2.0 name: bioconductor-randpack summary: Randomization routines for Clinical Trials diff --git a/data/randpack/randpackbioschemas.jsonld b/data/randpack/randpackbioschemas.jsonld index 54e4ff3a64800..d222ccfc4a66d 100644 --- a/data/randpack/randpackbioschemas.jsonld +++ b/data/randpack/randpackbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Robert Gentleman", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A suite of classes and functions for randomizing patients in clinical trials.", "sc:license": "Artistic-2.0", "sc:name": "randPack", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/randPack.html", "sc:version": "1.20.0" diff --git a/data/rankoptimizer/rankoptimizerbioschemas.jsonld b/data/rankoptimizer/rankoptimizerbioschemas.jsonld index b340b79fe1d75..a76b59921ca10 100644 --- a/data/rankoptimizer/rankoptimizerbioschemas.jsonld +++ b/data/rankoptimizer/rankoptimizerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Report taxonomic abundance, based on BLAST hits.", "sc:name": "rankoptimizer", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/taxonomy_analysis/rankoptimizer/0.0.5", diff --git a/data/rankpep/rankpepbioschemas.jsonld b/data/rankpep/rankpepbioschemas.jsonld index 09f59c4e5dfc3..2684ed8219425 100644 --- a/data/rankpep/rankpepbioschemas.jsonld +++ b/data/rankpep/rankpepbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This server predicts peptide binders to MHCI and MHCII molecules from protein sequence/s or sequence alignments using Position Specific Scoring Matrices (PSSMs). In addition, it predicts those MHCI ligands whose C-terminal end is likely to be the result of proteasomal cleavage. A detailed explanation of the method can be found here.", "sc:name": "Rankpep", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://imed.med.ucm.es/Tools/rankpep.html" } \ No newline at end of file diff --git a/data/rankprod/rankprodbioschemas.jsonld b/data/rankprod/rankprodbioschemas.jsonld index 2c47d17e98b66..e2641eab62bb0 100644 --- a/data/rankprod/rankprodbioschemas.jsonld +++ b/data/rankprod/rankprodbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Francesco Del Carratore", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification.", "sc:name": "RankProd", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RankProd.html", "sc:version": "3.0.0" diff --git a/data/ranks/ranksbioschemas.jsonld b/data/ranks/ranksbioschemas.jsonld index 3d3775e54662f..7b51a54c2d5fb 100644 --- a/data/ranks/ranksbioschemas.jsonld +++ b/data/ranks/ranksbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "RANKS", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://cran.r-project.org/package=RANKS" } \ No newline at end of file diff --git a/data/rap/rapbioschemas.jsonld b/data/rap/rapbioschemas.jsonld index 6748eeaf85da9..a8af92036da94 100644 --- a/data/rap/rapbioschemas.jsonld +++ b/data/rap/rapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "It is a web tool that performs a quite complete and customizable RNA-Seq pipeline and provides an easy and intuitive access through a web interface to intermediate and final results. The main aim of RAP is to provide to users information about gene and transcript expression, differential expression, alternative splicing, polyA signals, fusion transcripts, etc.", "sc:name": "RAP", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-CINECA", "sc:url": "https://bioinformatics.cineca.it/rap", diff --git a/data/raphael/raphaelbioschemas.jsonld b/data/raphael/raphaelbioschemas.jsonld index cc06bef176a1a..3f9032571c562 100644 --- a/data/raphael/raphaelbioschemas.jsonld +++ b/data/raphael/raphaelbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Protein Repeats. This server allows the analysis of one protein structure of interested to determine periodicity in protein structures.", "sc:name": "Raphael", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/raphael/", diff --git a/data/rapid/rapidbioschemas.jsonld b/data/rapid/rapidbioschemas.jsonld index 4c42af5c026e3..5e3eca51f4ca9 100644 --- a/data/rapid/rapidbioschemas.jsonld +++ b/data/rapid/rapidbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Server providing fast and accurate sequence based prediction of protein disorder content.", "sc:name": "RAPID", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://biomine.cs.vcu.edu/servers/RAPID/" } \ No newline at end of file diff --git a/data/rapidgsea/rapidgseabioschemas.jsonld b/data/rapidgsea/rapidgseabioschemas.jsonld index eb943080b13b7..ea4e3c1e02bd2 100644 --- a/data/rapidgsea/rapidgseabioschemas.jsonld +++ b/data/rapidgsea/rapidgseabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-7995-1858", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/rapidgsea", "@type": "sc:SoftwareApplication", @@ -17,11 +21,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5035472", { "@id": "https://doi.org/10.1186/s12859-016-1244-x" }, - "pubmed:27663265", - "pmcid:PMC5035472" + "pubmed:27663265" ], "sc:description": "We present rapidGSEA – a software suite consisting of two tools for facilitating permutation-based gene set enrichment analysis(GSEA): cudaGSEA and ompGSEA. cudaGSEA is a CUDA-accelerated tool using fine-grained parallelization schemes on massively parallel architectures while ompGSEA is a coarse-grained multi-threaded tool for multi-core CPUs.", "sc:featureList": { @@ -30,19 +34,15 @@ "sc:license": "Unlicense", "sc:name": "rapidGSEA", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/gravitino/cudaGSEA" }, { "@id": "https://doi.org/10.1186/s12859-016-1244-x", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-7995-1858", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/rapidnj/rapidnjbioschemas.jsonld b/data/rapidnj/rapidnjbioschemas.jsonld index 22c2f150f3762..1bf8cb93ae2de 100644 --- a/data/rapidnj/rapidnjbioschemas.jsonld +++ b/data/rapidnj/rapidnjbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool for fast canonical neighbor-joining tree construction.", "sc:name": "RapidNJ", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "birc.au.dk", "sc:url": "http://birc.au.dk/software/rapidnj/", diff --git a/data/rapido/rapidobioschemas.jsonld b/data/rapido/rapidobioschemas.jsonld index adc826296dde2..e1266a97c0a9e 100644 --- a/data/rapido/rapidobioschemas.jsonld +++ b/data/rapido/rapidobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "RAPIDO", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://webapps.embl-hamburg.de/rapido" } \ No newline at end of file diff --git a/data/rapidrmsd/rapidrmsdbioschemas.jsonld b/data/rapidrmsd/rapidrmsdbioschemas.jsonld index 651b4225e9ef9..3000dab59a782 100644 --- a/data/rapidrmsd/rapidrmsdbioschemas.jsonld +++ b/data/rapidrmsd/rapidrmsdbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-2-Clause", "sc:name": "RapidRMSD", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://team.inria.fr/nano-d/software/RapidRMSD/", "sc:version": "0.1" diff --git a/data/rapier/rapierbioschemas.jsonld b/data/rapier/rapierbioschemas.jsonld index c806ef4511591..317dfd4d17309 100644 --- a/data/rapier/rapierbioschemas.jsonld +++ b/data/rapier/rapierbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Run t test on pairs of array experiments.", "sc:name": "rapier", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.hpcf.upr.edu/~humberto/cmb/microarray/spatial/index.html" } \ No newline at end of file diff --git a/data/rapmap/rapmapbioschemas.jsonld b/data/rapmap/rapmapbioschemas.jsonld index 21040a0b0b192..9f2f9af3dbb01 100644 --- a/data/rapmap/rapmapbioschemas.jsonld +++ b/data/rapmap/rapmapbioschemas.jsonld @@ -9,25 +9,25 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0001-9798-2079", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1093/bioinformatics/btw277", "@type": "sc:CreativeWork" }, + { + "@id": "http://orcid.org/0000-0001-9798-2079", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/rapmap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Rob Patro", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4908361", { "@id": "https://doi.org/10.1093/bioinformatics/btw277" }, - "pubmed:27307617" + "pubmed:27307617", + "pmcid:PMC4908361" ], "sc:contributor": { "@id": "http://orcid.org/0000-0001-9798-2079" diff --git a/data/rapsearch/rapsearchbioschemas.jsonld b/data/rapsearch/rapsearchbioschemas.jsonld index 231e911abd40f..3692dca985236 100644 --- a/data/rapsearch/rapsearchbioschemas.jsonld +++ b/data/rapsearch/rapsearchbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "GPL-3.0", "sc:name": "RAPSearch", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://omics.informatics.indiana.edu/mg/RAPSearch2/" } \ No newline at end of file diff --git a/data/raptr-sv/raptr-svbioschemas.jsonld b/data/raptr-sv/raptr-svbioschemas.jsonld index 949a8fef01e1f..095232f1c2b5e 100644 --- a/data/raptr-sv/raptr-svbioschemas.jsonld +++ b/data/raptr-sv/raptr-svbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Read Pair and Split Read methods are used to identify structural variants in paired-end WGS data.", "sc:name": "RAPTR-SV", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/njdbickhart/RAPTR-SV" diff --git a/data/raremetal/raremetalbioschemas.jsonld b/data/raremetal/raremetalbioschemas.jsonld index dcfcd22da9a4f..7a8c99b06225a 100644 --- a/data/raremetal/raremetalbioschemas.jsonld +++ b/data/raremetal/raremetalbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.", "sc:name": "RAREMETAL", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://genome.sph.umich.edu/wiki/RAREMETAL" } \ No newline at end of file diff --git a/data/rarevariantvis/rarevariantvisbioschemas.jsonld b/data/rarevariantvis/rarevariantvisbioschemas.jsonld index 6b99d606dd42a..f29c8bb272ac3 100644 --- a/data/rarevariantvis/rarevariantvisbioschemas.jsonld +++ b/data/rarevariantvis/rarevariantvisbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "RareVariantVis", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RareVariantVis.html", "sc:version": "2.12.0" diff --git a/data/rariant/bioconda_rariant.yaml b/data/rariant/bioconda_rariant.yaml index fb88b8902a294..f83583d2fb9c3 100644 --- a/data/rariant/bioconda_rariant.yaml +++ b/data/rariant/bioconda_rariant.yaml @@ -5,7 +5,6 @@ description: The 'Rariant' package identifies single nucleotide variants from se home: https://bioconductor.org/packages/3.10/bioc/html/Rariant.html identifiers: - biotools:rariant -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rariant diff --git a/data/rariant/rariantbioschemas.jsonld b/data/rariant/rariantbioschemas.jsonld index aee7bddb624c3..6beb44cb264d7 100644 --- a/data/rariant/rariantbioschemas.jsonld +++ b/data/rariant/rariantbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "Rariant", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rariant.html", "sc:version": "1.10.0" diff --git a/data/rasmol/rasmolbioschemas.jsonld b/data/rasmol/rasmolbioschemas.jsonld index d422e77b640e5..39e95e2c28674 100644 --- a/data/rasmol/rasmolbioschemas.jsonld +++ b/data/rasmol/rasmolbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "3-D structure viewer, web browser helper application.", "sc:name": "RasMol", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bernstein-plus-sons.com/software/rasmol/" } \ No newline at end of file diff --git a/data/rasmot-3d_pro/rasmot-3d_probioschemas.jsonld b/data/rasmot-3d_pro/rasmot-3d_probioschemas.jsonld index 4d8db9c18f134..f64a2dbf6d8d6 100644 --- a/data/rasmot-3d_pro/rasmot-3d_probioschemas.jsonld +++ b/data/rasmot-3d_pro/rasmot-3d_probioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The RASMOT-3D PRO web server performs systematic searches in 3D protein structures for a set of residues exhibiting a particular topology. Input is a PDB file for the motif of interest; output is an interactive list of protein structures exhibiting resides of similar topology.", "sc:name": "RASMOT-3D PRO", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://biodev.extra.cea.fr/rasmot3d/" } \ No newline at end of file diff --git a/data/rasp/raspbioschemas.jsonld b/data/rasp/raspbioschemas.jsonld index 1b28a7e920af5..7356a00564ad5 100644 --- a/data/rasp/raspbioschemas.jsonld +++ b/data/rasp/raspbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for inferring ancestral state using S-DIVA (Statistical dispersal-vicariance analysis), Lagrange (DEC), Bayes-Lagrange (S-DEC), BayArea, BBM (Bayesian Binary MCMC), BayesTraits and ChromEvol.", "sc:name": "RASP", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mnh.scu.edu.cn/soft/blog/RASP/" } \ No newline at end of file diff --git a/data/rasqual/rasqualbioschemas.jsonld b/data/rasqual/rasqualbioschemas.jsonld index c00925778bad7..26b8e75dac40a 100644 --- a/data/rasqual/rasqualbioschemas.jsonld +++ b/data/rasqual/rasqualbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Map QTLs for sequenced based cellular traits by combining population and allele-specific signals.", "sc:name": "RASQUAL", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "sanger.ac.uk", "sc:url": "https://github.com/dg13/rasqual", diff --git a/data/rass/rassbioschemas.jsonld b/data/rass/rassbioschemas.jsonld index 47c5056a30198..e113b89247fe2 100644 --- a/data/rass/rassbioschemas.jsonld +++ b/data/rass/rassbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "RASS is a webserver for RNA alignment in the joint sequence-structure space.", "sc:name": "RASS", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://cloud.stat.fsu.edu/RASS/" } \ No newline at end of file diff --git a/data/rast/rastbioschemas.jsonld b/data/rast/rastbioschemas.jsonld index a8ef2b5d4de6f..a0b951de3c2d5 100644 --- a/data/rast/rastbioschemas.jsonld +++ b/data/rast/rastbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "\"RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating complete or nearly complete bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree.\"", "sc:name": "RAST", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://rast.nmpdr.org/" diff --git a/data/rasta-bacteria/rasta-bacteriabioschemas.jsonld b/data/rasta-bacteria/rasta-bacteriabioschemas.jsonld index cace101fbd3dd..b9795f6432e2b 100644 --- a/data/rasta-bacteria/rasta-bacteriabioschemas.jsonld +++ b/data/rasta-bacteria/rasta-bacteriabioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/rasta-bacteria", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Emeric Sevin", - "Frédérique Hubler" + "Frédérique Hubler", + "Emeric Sevin" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:17678530", "sc:description": "Automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not.", "sc:name": "RASTA-Bacteria", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://genoweb1.irisa.fr/duals/RASTA-Bacteria/" } \ No newline at end of file diff --git a/data/raster3d/raster3dbioschemas.jsonld b/data/raster3d/raster3dbioschemas.jsonld index a8da1135c6610..001776e52db58 100644 --- a/data/raster3d/raster3dbioschemas.jsonld +++ b/data/raster3d/raster3dbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Output is to pixel image files with 24 bits of color information per pixel.", "sc:name": "Raster3D", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://skuld.bmsc.washington.edu/raster3d/raster3d.html" } \ No newline at end of file diff --git a/data/ratcave/ratcavebioschemas.jsonld b/data/ratcave/ratcavebioschemas.jsonld index b4e6deea4ac6a..746b7e39b4c3f 100644 --- a/data/ratcave/ratcavebioschemas.jsonld +++ b/data/ratcave/ratcavebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "MIT", "sc:name": "Ratcave", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/ratcave/ratcave" diff --git a/data/ratrav/ratravbioschemas.jsonld b/data/ratrav/ratravbioschemas.jsonld index 7915fd87d9564..efec5cd1da89f 100644 --- a/data/ratrav/ratravbioschemas.jsonld +++ b/data/ratrav/ratravbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "RaTrav", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://sourceforge.net/projects/ratrav/" diff --git a/data/ravages/ravagesbioschemas.jsonld b/data/ravages/ravagesbioschemas.jsonld index 176cab7d0d533..e4f7922f5a260 100644 --- a/data/ravages/ravagesbioschemas.jsonld +++ b/data/ravages/ravagesbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Ravages", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/genostats/Ravages" } \ No newline at end of file diff --git a/data/raven_toolbox/raven_toolboxbioschemas.jsonld b/data/raven_toolbox/raven_toolboxbioschemas.jsonld index 8b940a7087c80..1a8ae63eecbdd 100644 --- a/data/raven_toolbox/raven_toolboxbioschemas.jsonld +++ b/data/raven_toolbox/raven_toolboxbioschemas.jsonld @@ -21,10 +21,10 @@ }, "edam:has_input": [ { - "@id": "edam:data_3112" + "@id": "edam:data_2600" }, { - "@id": "edam:data_2600" + "@id": "edam:data_3112" }, { "@id": "edam:data_2976" @@ -32,36 +32,36 @@ ], "edam:has_output": [ { - "@id": "edam:data_3722" + "@id": "edam:data_2600" }, { - "@id": "edam:data_2600" + "@id": "edam:data_3722" } ], "sc:additionalType": [ - "Script", - "Command-line tool" + "Command-line tool", + "Script" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0602" + "@id": "edam:topic_3398" }, { - "@id": "edam:topic_2259" + "@id": "edam:topic_3307" }, { - "@id": "edam:topic_3398" + "@id": "edam:topic_0602" }, { - "@id": "edam:topic_3307" + "@id": "edam:topic_2259" } ], "sc:citation": [ "pmcid:PMC6207324", - "pubmed:30335785", { "@id": "https://doi.org/10.1101/321067" - } + }, + "pubmed:30335785" ], "sc:description": "The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.", "sc:featureList": [ @@ -80,8 +80,8 @@ "sc:name": "RAVEN Toolbox", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:softwareHelp": { "@id": "https://github.com/SysBioChalmers/RAVEN/wiki" diff --git a/data/raw2mzdb/raw2mzdbbioschemas.jsonld b/data/raw2mzdb/raw2mzdbbioschemas.jsonld index c8b33e766a8e7..5aa16421096bd 100644 --- a/data/raw2mzdb/raw2mzdbbioschemas.jsonld +++ b/data/raw2mzdb/raw2mzdbbioschemas.jsonld @@ -13,12 +13,12 @@ "biotools:primaryContact": "Alexandre Burel", "sc:additionalType": "Command-line tool", "sc:author": [ - "David Bouyssié", - "Alexandre Burel" + "Alexandre Burel", + "David Bouyssié" ], "sc:citation": [ - "pmcid:PMC4349994", - "pubmed:25505153" + "pubmed:25505153", + "pmcid:PMC4349994" ], "sc:contributor": "ProFI", "sc:description": "An extension of the ProteoWizard framework enabling the support of the mzDB format. This tools is supported by the Proteomics French Infrastructure ProFI.", diff --git a/data/rawtools/rawtoolsbioschemas.jsonld b/data/rawtools/rawtoolsbioschemas.jsonld index ab93a04a6ea2d..6899183fd022c 100644 --- a/data/rawtools/rawtoolsbioschemas.jsonld +++ b/data/rawtools/rawtoolsbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/rawtools", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "A standalone tool for extracting data directly from raw files generated by Thermo Orbitrap family instruments.", "sc:license": "Apache-2.0", "sc:name": "RawTools", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/kevinkovalchik/RawTools", diff --git a/data/raxml-ng/raxml-ngbioschemas.jsonld b/data/raxml-ng/raxml-ngbioschemas.jsonld index a4464a3f22b56..e9a560e986732 100644 --- a/data/raxml-ng/raxml-ngbioschemas.jsonld +++ b/data/raxml-ng/raxml-ngbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Vital-IT helpdesk", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.", "sc:license": "GPL-3.0", "sc:name": "RAxML-NG", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://raxml-ng.vital-it.ch/", "sc:version": "0.8.0 beta" diff --git a/data/raxml/raxmlbioschemas.jsonld b/data/raxml/raxmlbioschemas.jsonld index 60c4cdf44f579..7fff19906c6f4 100644 --- a/data/raxml/raxmlbioschemas.jsonld +++ b/data/raxml/raxmlbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:description": "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.", "sc:name": "RAxML", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://sco.h-its.org/exelixis/web/software/raxml/" diff --git a/data/ray/raybioschemas.jsonld b/data/ray/raybioschemas.jsonld index 9e8dc810b2161..78fa5d0d6971e 100644 --- a/data/ray/raybioschemas.jsonld +++ b/data/ray/raybioschemas.jsonld @@ -14,27 +14,27 @@ "sc:additionalType": "Command-line tool", "sc:author": "Sébastien Boisvert", "sc:contributor": [ - "Jacques Corbeil", "Canadian Institutes of Health Research (CIHR), and other", - "François Laviolette", + "Frédéric Raymond", "Élénie Godzaridis", - "Frédéric Raymond" + "François Laviolette", + "Jacques Corbeil" ], "sc:description": "De novoassembly of single genomes and metagenomes. Also analyses microbe abundance and performs taxonomic profiling as well as making gene ontology profiling. It can also compare genomic content between samples.", "sc:funder": "Canadian Institutes of Health Research (CIHR), and other", "sc:license": "GPL-3.0", "sc:name": "Ray", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ "Faculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, Canada", "Infectious Diseases Research Center, CHUQ Research Center", - "Department of Molecular Medicine, Faculty of Medicine, Laval University", + "1065, av. de la Médecine, Québec (Québec), G1V 0A6, Canada", "NTNU", - "1065, av. de la Médecine, Québec (Québec), G1V 0A6, Canada" + "Department of Molecular Medicine, Faculty of Medicine, Laval University" ], "sc:url": "http://denovoassembler.sourceforge.net", "sc:version": "2.3.1" diff --git a/data/razers/razersbioschemas.jsonld b/data/razers/razersbioschemas.jsonld index ed40e87826d5e..98b344d5080da 100644 --- a/data/razers/razersbioschemas.jsonld +++ b/data/razers/razersbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/razers", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "David Weese", - "Anne-Katrin Emde" + "Anne-Katrin Emde", + "David Weese" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:19592482", diff --git a/data/rbamtools/rbamtoolsbioschemas.jsonld b/data/rbamtools/rbamtoolsbioschemas.jsonld index fac03007d0ac7..bb5c1879564d3 100644 --- a/data/rbamtools/rbamtoolsbioschemas.jsonld +++ b/data/rbamtools/rbamtoolsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool package provides a R-interface\nto the samtools C-library for BAM file processing.", "sc:name": "rbamtools", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://cran.r-project.org/web/packages/rbamtools/index.html" } \ No newline at end of file diff --git a/data/rbcbook1/bioconda_rbcbook1.yaml b/data/rbcbook1/bioconda_rbcbook1.yaml index 2d309956069cd..77154c0550ed5 100644 --- a/data/rbcbook1/bioconda_rbcbook1.yaml +++ b/data/rbcbook1/bioconda_rbcbook1.yaml @@ -3,7 +3,6 @@ description: tools for building book home: https://bioconductor.org/packages/3.10/bioc/html/RbcBook1.html identifiers: - biotools:rbcbook1 -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-rbcbook1 summary: Support for Springer monograph on Bioconductor diff --git a/data/rbcbook1/rbcbook1bioschemas.jsonld b/data/rbcbook1/rbcbook1bioschemas.jsonld index ef53aef1c7a96..6164d30ad75f1 100644 --- a/data/rbcbook1/rbcbook1bioschemas.jsonld +++ b/data/rbcbook1/rbcbook1bioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "RbcBook1", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RbcBook1.html", diff --git a/data/rbgl/rbglbioschemas.jsonld b/data/rbgl/rbglbioschemas.jsonld index 9b76ff90fd19f..a800f3b6befb6 100644 --- a/data/rbgl/rbglbioschemas.jsonld +++ b/data/rbgl/rbglbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "RBGL", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RBGL.html", diff --git a/data/rbioinf/bioconda_rbioinf.yaml b/data/rbioinf/bioconda_rbioinf.yaml index bc5824a9dd528..8490753ce1aa1 100644 --- a/data/rbioinf/bioconda_rbioinf.yaml +++ b/data/rbioinf/bioconda_rbioinf.yaml @@ -4,7 +4,6 @@ description: Functions and datasets and examples to accompany the monograph R Fo home: https://bioconductor.org/packages/3.10/bioc/html/RBioinf.html identifiers: - biotools:rbioinf -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-rbioinf summary: RBioinf diff --git a/data/rbioinf/rbioinfbioschemas.jsonld b/data/rbioinf/rbioinfbioschemas.jsonld index 054bdc2234e80..06beafd97ae9a 100644 --- a/data/rbioinf/rbioinfbioschemas.jsonld +++ b/data/rbioinf/rbioinfbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Robert Gentleman", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Functions and datasets and examples to accompany the monograph R For Bioinformatics.", "sc:license": "Artistic-2.0", "sc:name": "RBioinf", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RBioinf.html", "sc:version": "1.34.0" diff --git a/data/rbiomirgs/rbiomirgsbioschemas.jsonld b/data/rbiomirgs/rbiomirgsbioschemas.jsonld index 5aaa367b40569..2aa98682efc00 100644 --- a/data/rbiomirgs/rbiomirgsbioschemas.jsonld +++ b/data/rbiomirgs/rbiomirgsbioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.7717/peerj.4262" }, - "pubmed:29340253", - "pmcid:PMC5768164" + "pmcid:PMC5768164", + "pubmed:29340253" ], "sc:description": "Simple to use machine learning-based miRNA gene set analysis.", "sc:featureList": { diff --git a/data/rbiopaxparser/rbiopaxparserbioschemas.jsonld b/data/rbiopaxparser/rbiopaxparserbioschemas.jsonld index ad95d0b47da05..3ef110aaa73a7 100644 --- a/data/rbiopaxparser/rbiopaxparserbioschemas.jsonld +++ b/data/rbiopaxparser/rbiopaxparserbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Frank Kramer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:23274212", "sc:description": "Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.", @@ -21,8 +21,8 @@ "sc:name": "rBiopaxParser", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rBiopaxParser.html", "sc:version": "2.14.0" diff --git a/data/rbm/bioconda_rbm.yaml b/data/rbm/bioconda_rbm.yaml index fecf9bc15201b..63f77fed6db9a 100644 --- a/data/rbm/bioconda_rbm.yaml +++ b/data/rbm/bioconda_rbm.yaml @@ -4,7 +4,6 @@ description: Use A Resampling-Based Empirical Bayes Approach to Assess Different home: https://bioconductor.org/packages/3.10/bioc/html/RBM.html identifiers: - biotools:rbm -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rbm diff --git a/data/rbm/rbmbioschemas.jsonld b/data/rbm/rbmbioschemas.jsonld index c5718de342d75..bcfc38273eda1 100644 --- a/data/rbm/rbmbioschemas.jsonld +++ b/data/rbm/rbmbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "RBM", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RBM.html", "sc:version": "1.6.0" diff --git a/data/rbo_aleph/rbo_alephbioschemas.jsonld b/data/rbo_aleph/rbo_alephbioschemas.jsonld index 2006d6372a5c0..c92866ee4e7cb 100644 --- a/data/rbo_aleph/rbo_alephbioschemas.jsonld +++ b/data/rbo_aleph/rbo_alephbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Fully automated protein structure prediction. It implements template-based modeling, protein contact prediction, and ab initio structure prediction.", "sc:name": "RBO Aleph", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://compbio.robotics.tu-berlin.de/rbo_aleph/" diff --git a/data/rboanalyzer/rboanalyzerbioschemas.jsonld b/data/rboanalyzer/rboanalyzerbioschemas.jsonld index fd5d72c457e51..729a8532a5f21 100644 --- a/data/rboanalyzer/rboanalyzerbioschemas.jsonld +++ b/data/rboanalyzer/rboanalyzerbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-8886-7797", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/rboAnalyzer", "@type": "sc:SoftwareApplication", @@ -23,10 +27,6 @@ "sc:name": "rboAnalyzer", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/cas-bioinf/rboAnalyzer" - }, - { - "@id": "http://orcid.org/0000-0002-8886-7797", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/rbowtie/bioconda_rbowtie.yaml b/data/rbowtie/bioconda_rbowtie.yaml index d03afd11b7eff..c618fc32e33cf 100644 --- a/data/rbowtie/bioconda_rbowtie.yaml +++ b/data/rbowtie/bioconda_rbowtie.yaml @@ -6,7 +6,6 @@ description: This package provides an R wrapper around the popular bowtie short home: https://bioconductor.org/packages/3.10/bioc/html/Rbowtie.html identifiers: - biotools:rbowtie -- doi:10.1038/nmeth.3252 license: Artistic-2.0 | file LICENSE license_file: LICENSE name: bioconductor-rbowtie diff --git a/data/rbowtie/rbowtiebioschemas.jsonld b/data/rbowtie/rbowtiebioschemas.jsonld index ce6fabd51feb6..71554d9a7e248 100644 --- a/data/rbowtie/rbowtiebioschemas.jsonld +++ b/data/rbowtie/rbowtiebioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Stadler", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use QuasR instead of using this package directly.", "sc:license": "Artistic-1.0", diff --git a/data/rbowtie2/rbowtie2bioschemas.jsonld b/data/rbowtie2/rbowtie2bioschemas.jsonld index 1b8beadb83790..45f3ed91cff6a 100644 --- a/data/rbowtie2/rbowtie2bioschemas.jsonld +++ b/data/rbowtie2/rbowtie2bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Rbowtie2", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rbowtie2.html", "sc:version": "1.2.0" diff --git a/data/rbp-maps/rbp-mapsbioschemas.jsonld b/data/rbp-maps/rbp-mapsbioschemas.jsonld index 88d597b6b879f..81f7a000799b0 100644 --- a/data/rbp-maps/rbp-mapsbioschemas.jsonld +++ b/data/rbp-maps/rbp-mapsbioschemas.jsonld @@ -19,29 +19,29 @@ "biotools:primaryContact": "Yeo LAB", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:30413564", { "@id": "https://doi.org/10.1261/rna.069237.118" }, - "pmcid:PMC6348990", - "pubmed:30413564" + "pmcid:PMC6348990" ], "sc:description": "Enables robust generation of splicing regulatory maps and rapid query of regulatory patterns of RNA binding protein (RBP) of interest.", "sc:featureList": [ { - "@id": "edam:operation_0232" + "@id": "edam:operation_0433" }, { "@id": "edam:operation_0264" }, { - "@id": "edam:operation_0433" + "@id": "edam:operation_0232" } ], "sc:license": "Unlicense", "sc:name": "RBP-Maps", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/YeoLab/rbp-maps" } diff --git a/data/rbpdb/rbpdbbioschemas.jsonld b/data/rbpdb/rbpdbbioschemas.jsonld index 03f4a73050afc..2babd08a9e58a 100644 --- a/data/rbpdb/rbpdbbioschemas.jsonld +++ b/data/rbpdb/rbpdbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "RBPDB", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://rbpdb.ccbr.utoronto.ca/" } \ No newline at end of file diff --git a/data/rbrothers/rbrothersbioschemas.jsonld b/data/rbrothers/rbrothersbioschemas.jsonld index aad0a4b059f0a..abeb62f3d4529 100644 --- a/data/rbrothers/rbrothersbioschemas.jsonld +++ b/data/rbrothers/rbrothersbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "rbrothers", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://evolmod.r-forge.r-project.org/#rbrothers" } \ No newline at end of file diff --git a/data/rbscore/rbscorebioschemas.jsonld b/data/rbscore/rbscorebioschemas.jsonld index 025641be3fb56..cced00d7e55ec 100644 --- a/data/rbscore/rbscorebioschemas.jsonld +++ b/data/rbscore/rbscorebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RBscore", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://ahsoka.u-strasbg.fr/rbscore/" } \ No newline at end of file diff --git a/data/rbsurv/rbsurvbioschemas.jsonld b/data/rbsurv/rbsurvbioschemas.jsonld index 2d9984940d904..11fbb6bd5a095 100644 --- a/data/rbsurv/rbsurvbioschemas.jsonld +++ b/data/rbsurv/rbsurvbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "rbsurv", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rbsurv.html", "sc:version": "2.32.0" diff --git a/data/rca/rcabioschemas.jsonld b/data/rca/rcabioschemas.jsonld index 751a0889b77be..531b064036773 100644 --- a/data/rca/rcabioschemas.jsonld +++ b/data/rca/rcabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Relative codon adaptation is a novel index for measuring codon adaptation in genomic sequences. Similar to CAI, it can use a reference geneset to estimate gene expression, but it takes directly into account the background nucleotide distribution.", "sc:name": "RCA", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://erilllab.umbc.edu/research/software/201-2/" } \ No newline at end of file diff --git a/data/rcade-recognition/rcade-recognitionbioschemas.jsonld b/data/rcade-recognition/rcade-recognitionbioschemas.jsonld index d9f4d09546ef1..602984856d22d 100644 --- a/data/rcade-recognition/rcade-recognitionbioschemas.jsonld +++ b/data/rcade-recognition/rcade-recognitionbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Recognition Code-Assisted Discovery of regulatory Elements combines predictions from a DNA recognition code of C2H2-ZFs with ChIP-seq data to identify models that represent the genuine DNA binding prefer-ences of C2H2-ZF proteins.", "sc:name": "RCADE", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://rcade.ccbr.utoronto.ca/" } \ No newline at end of file diff --git a/data/rcade/rcadebioschemas.jsonld b/data/rcade/rcadebioschemas.jsonld index bcb453af9d9cd..a4308d01e5857 100644 --- a/data/rcade/rcadebioschemas.jsonld +++ b/data/rcade/rcadebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "Rcade", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rcade.html", diff --git a/data/rcare/rcarebioschemas.jsonld b/data/rcare/rcarebioschemas.jsonld index 2ae74a819dc52..bcc88f4232f3b 100644 --- a/data/rcare/rcarebioschemas.jsonld +++ b/data/rcare/rcarebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "RCARE searches, annotates and visualizes RNA editing sites using thousands of previously known editing sites.", "sc:name": "RCARE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.snubi.org/software/rcare/" } \ No newline at end of file diff --git a/data/rcas/rcasbioschemas.jsonld b/data/rcas/rcasbioschemas.jsonld index 55aae81c2e877..d2b0e61a26cfb 100644 --- a/data/rcas/rcasbioschemas.jsonld +++ b/data/rcas/rcasbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-3170-4890", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/rcas", "@type": "sc:SoftwareApplication", @@ -36,45 +32,49 @@ } ], "sc:additionalType": [ - "Workflow", "Library", - "Command-line tool" + "Command-line tool", + "Workflow" ], "sc:citation": [ + "pubmed:28334930", + "pmcid:PMC5449606", { "@id": "https://doi.org/10.1093/nar/gkx120" - }, - "pubmed:28334930", - "pmcid:PMC5449606" + } ], "sc:description": "Automated system that provides dynamic genome annotations for custom input files that contain transcriptomic regions, which can be peak regions detected by CLIP-Seq analysis (that detect protein-RNA interactions), RNA modifications (alias the epitranscriptome), CAGE-tag locations, or any other collection of target regions at the level of the transcriptome. It is designed as a reporting tool for the functional analysis of RNA-binding sites detected by high-throughput experiments.", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_3194" }, { "@id": "edam:operation_0531" }, { - "@id": "edam:operation_3194" + "@id": "edam:operation_0362" }, { "@id": "edam:operation_3501" }, { - "@id": "edam:operation_0362" + "@id": "edam:operation_0337" } ], "sc:license": "Artistic-2.0", "sc:name": "RCAS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RCAS.html", "sc:version": "1.4.2" }, + { + "@id": "http://orcid.org/0000-0002-3170-4890", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/nar/gkx120", "@type": "sc:CreativeWork" diff --git a/data/rcasc/rcascbioschemas.jsonld b/data/rcasc/rcascbioschemas.jsonld index 2b40428f8324d..c5adc2e845f74 100644 --- a/data/rcasc/rcascbioschemas.jsonld +++ b/data/rcasc/rcascbioschemas.jsonld @@ -28,8 +28,8 @@ "sc:license": "GPL-3.0", "sc:name": "rCASC", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/kendomaniac/rCASC", "sc:version": "2.0.1" diff --git a/data/rcaspar/bioconda_rcaspar.yaml b/data/rcaspar/bioconda_rcaspar.yaml index 0333b30198555..dde9adafb1525 100644 --- a/data/rcaspar/bioconda_rcaspar.yaml +++ b/data/rcaspar/bioconda_rcaspar.yaml @@ -10,7 +10,6 @@ description: 'The package is the R-version of the C-based software \bold{CASPAR} home: https://bioconductor.org/packages/3.10/bioc/html/RCASPAR.html identifiers: - biotools:rcaspar -- doi:10.1038/nmeth.3252 license: GPL (>=3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rcaspar diff --git a/data/rcaspar/rcasparbioschemas.jsonld b/data/rcaspar/rcasparbioschemas.jsonld index b2df23ee4676e..ec26983b15dff 100644 --- a/data/rcaspar/rcasparbioschemas.jsonld +++ b/data/rcaspar/rcasparbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/rcaspar", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lars Kaderali", - "Douaa Mugahid" + "Douaa Mugahid", + "Lars Kaderali" ], "sc:additionalType": [ "Command-line tool", @@ -22,9 +22,9 @@ "sc:license": "GPL-3.0", "sc:name": "RCASPAR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RCASPAR.html", "sc:version": "1.20.0" diff --git a/data/rcellminer/rcellminerbioschemas.jsonld b/data/rcellminer/rcellminerbioschemas.jsonld index 2a20a606dc2a4..a58ad23a00232 100644 --- a/data/rcellminer/rcellminerbioschemas.jsonld +++ b/data/rcellminer/rcellminerbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btv701", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rcellminer", "@type": "sc:SoftwareApplication", @@ -25,10 +21,10 @@ }, "edam:has_output": [ { - "@id": "edam:data_0993" + "@id": "edam:data_2899" }, { - "@id": "edam:data_2899" + "@id": "edam:data_0993" } ], "sc:additionalType": [ @@ -37,27 +33,27 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_2640" + "@id": "edam:topic_3366" }, { - "@id": "edam:topic_3365" + "@id": "edam:topic_0622" }, { - "@id": "edam:topic_3373" + "@id": "edam:topic_2640" }, { - "@id": "edam:topic_0622" + "@id": "edam:topic_3365" }, { - "@id": "edam:topic_3366" + "@id": "edam:topic_3373" } ], "sc:citation": [ + "pubmed:26635141", + "pmcid:PMC4907377", { "@id": "https://doi.org/10.1093/bioinformatics/btv701" - }, - "pubmed:26635141", - "pmcid:PMC4907377" + } ], "sc:description": "The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of this project has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.", "sc:featureList": { @@ -67,11 +63,15 @@ "sc:name": "rcellminer", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rcellminer.html", "sc:version": "1.6.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv701", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rcgh/rcghbioschemas.jsonld b/data/rcgh/rcghbioschemas.jsonld index 4e4f730b24f7f..b3f679e10504f 100644 --- a/data/rcgh/rcghbioschemas.jsonld +++ b/data/rcgh/rcghbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "rCGH", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rCGH.html", diff --git a/data/rchemcpp/rchemcppbioschemas.jsonld b/data/rchemcpp/rchemcppbioschemas.jsonld index cdbf69fafdad6..b862f20fd85e4 100644 --- a/data/rchemcpp/rchemcppbioschemas.jsonld +++ b/data/rchemcpp/rchemcppbioschemas.jsonld @@ -24,9 +24,9 @@ "sc:license": "GPL-2.0", "sc:name": "Rchemcpp", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rchemcpp.html", "sc:version": "2.12.0" diff --git a/data/rchyoptimyx/rchyoptimyxbioschemas.jsonld b/data/rchyoptimyx/rchyoptimyxbioschemas.jsonld index 6e269836652ae..c47c0a2dbc93f 100644 --- a/data/rchyoptimyx/rchyoptimyxbioschemas.jsonld +++ b/data/rchyoptimyx/rchyoptimyxbioschemas.jsonld @@ -15,16 +15,16 @@ "Adrin Jalali" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).", "sc:license": "Artistic-2.0", "sc:name": "RchyOptimyx", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RchyOptimyx.html", "sc:version": "2.14.0" diff --git a/data/rcistarget/rcistargetbioschemas.jsonld b/data/rcistarget/rcistargetbioschemas.jsonld index 5ff3d7a272e92..26156a4951a26 100644 --- a/data/rcistarget/rcistargetbioschemas.jsonld +++ b/data/rcistarget/rcistargetbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "RcisTarget", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RcisTarget.html", diff --git a/data/rclick/rclickbioschemas.jsonld b/data/rclick/rclickbioschemas.jsonld index 1d7fd93e77e6b..efd60f166f312 100644 --- a/data/rclick/rclickbioschemas.jsonld +++ b/data/rclick/rclickbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The application is capable of superimposing the RNA 3D structures by using the algorithm of clique matching and 3D least squares fitting.", "sc:name": "Rclick", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://mspc.bii.a-star.edu.sg/minhn/rclick.html" diff --git a/data/rcorrector/rcorrectorbioschemas.jsonld b/data/rcorrector/rcorrectorbioschemas.jsonld index bd004d887a9d6..1e3808a7454f9 100644 --- a/data/rcorrector/rcorrectorbioschemas.jsonld +++ b/data/rcorrector/rcorrectorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.", "sc:name": "Rcorrector", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/mourisl/Rcorrector/" } \ No newline at end of file diff --git a/data/rcount/rcountbioschemas.jsonld b/data/rcount/rcountbioschemas.jsonld index 5e074a5d572fb..c6a3931556519 100644 --- a/data/rcount/rcountbioschemas.jsonld +++ b/data/rcount/rcountbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software for simple and flexible RNA-Seq read counting. It allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA- coding genes) or to add flanking regions.", "sc:name": "Rcount", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.botinst.uzh.ch/research/development/grossnik/rcount.html" } \ No newline at end of file diff --git a/data/rcpi/rcpibioschemas.jsonld b/data/rcpi/rcpibioschemas.jsonld index 8618ff1c5c3b7..145fb393441b0 100644 --- a/data/rcpi/rcpibioschemas.jsonld +++ b/data/rcpi/rcpibioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-0250-5673", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/rcpi", "@type": "sc:SoftwareApplication", @@ -20,20 +16,24 @@ "@id": "http://orcid.org/0000-0002-0250-5673" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:25246429", "sc:description": "This molecular informatics toolkit offers a comprehensive integration of bioinformatics and chemoinformatics tools for drug discovery.", "sc:license": "Artistic-2.0", "sc:name": "Rcpi", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rcpi.html", "sc:version": "1.10.6" + }, + { + "@id": "http://orcid.org/0000-0002-0250-5673", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/rcy3/rcy3bioschemas.jsonld b/data/rcy3/rcy3bioschemas.jsonld index cb94f4fbae597..ce59c7d037a8b 100644 --- a/data/rcy3/rcy3bioschemas.jsonld +++ b/data/rcy3/rcy3bioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/rcy3", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Tanja Muetze", "Paul Shannon", - "Alexander Pico", - "Tanja Muetze" + "Alexander Pico" ], "sc:additionalType": "Library", "sc:description": "Vizualize, analyze and explore networks using Cytoscape via R.", "sc:license": "MIT", "sc:name": "RCy3", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RCy3.html", "sc:version": "2.0.84" diff --git a/data/rcyjs/rcyjsbioschemas.jsonld b/data/rcyjs/rcyjsbioschemas.jsonld index ad0f4a3785b0f..e64525933e43b 100644 --- a/data/rcyjs/rcyjsbioschemas.jsonld +++ b/data/rcyjs/rcyjsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "RCyjs", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RCyjs.html", diff --git a/data/rcytoscape/rcytoscapebioschemas.jsonld b/data/rcytoscape/rcytoscapebioschemas.jsonld index bef06e0e86944..cb424828938b9 100644 --- a/data/rcytoscape/rcytoscapebioschemas.jsonld +++ b/data/rcytoscape/rcytoscapebioschemas.jsonld @@ -9,23 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-14-217", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rcytoscape", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Paul Shannon", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pmcid:PMC3751905", { "@id": "https://doi.org/10.1186/1471-2105-14-217" }, + "pmcid:PMC3751905", "pubmed:23837656" ], "sc:description": "Interactvive viewing and exploration of graphs, connecting R to Cytoscape.", @@ -46,6 +42,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RCytoscape.html", "sc:version": "1.24.1" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-217", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rd-connect/rd-connectbioschemas.jsonld b/data/rd-connect/rd-connectbioschemas.jsonld index 163a2514d1a4d..b5f7aaab47cf8 100644 --- a/data/rd-connect/rd-connectbioschemas.jsonld +++ b/data/rd-connect/rd-connectbioschemas.jsonld @@ -14,23 +14,23 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Libby Wood", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ + "pubmed:25029978", { "@id": "https://doi.org/10.1007/s11606-014-2908-8" }, - "pubmed:25029978", "pmcid:PMC4124112" ], "sc:description": "Integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_3561" }, { - "@id": "edam:operation_3561" + "@id": "edam:operation_3431" }, { "@id": "edam:operation_3197" diff --git a/data/rd-connect_platform/rd-connect_platformbioschemas.jsonld b/data/rd-connect_platform/rd-connect_platformbioschemas.jsonld index c5cbad77da170..24a14b6dae786 100644 --- a/data/rd-connect_platform/rd-connect_platformbioschemas.jsonld +++ b/data/rd-connect_platform/rd-connect_platformbioschemas.jsonld @@ -14,29 +14,29 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:25029978", { "@id": "https://doi.org/10.1007/s11606-014-2908-8" }, - "pmcid:PMC4124112" + "pmcid:PMC4124112", + "pubmed:25029978" ], "sc:description": "An online tool for diagnosis and gene discovery in rare disease research. The platform features allow identifying disease-causing mutations in rare disease patients and linking them with detailed clinical information.", "sc:featureList": [ - { - "@id": "edam:operation_3197" - }, { "@id": "edam:operation_2403" }, { "@id": "edam:operation_2422" + }, + { + "@id": "edam:operation_3197" } ], "sc:name": "RD-Connect Genome-Phenome Analysis Platform", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://platform.rd-connect.eu/" }, diff --git a/data/rd-connect_sample_catalogue/rd-connect_sample_cataloguebioschemas.jsonld b/data/rd-connect_sample_catalogue/rd-connect_sample_cataloguebioschemas.jsonld index cd3ad76f2a73c..758ddef6ea69c 100644 --- a/data/rd-connect_sample_catalogue/rd-connect_sample_cataloguebioschemas.jsonld +++ b/data/rd-connect_sample_catalogue/rd-connect_sample_cataloguebioschemas.jsonld @@ -17,24 +17,24 @@ "@id": "https://bio.tools/rd-connect_sample_catalogue", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": [ - "pmcid:PMC3040526", "pubmed:17297480", { "@id": "https://doi.org/10.1186/1471-2105-11-S12-S12" }, - "pubmed:21210979" + "pubmed:21210979", + "pmcid:PMC3040526" ], "sc:description": "This catalogue is intended to facilitate the discovery of samples and samples data from Rare Diseases biobanks.\nIt also provides information about sample collections and studies done on the registered samples.", "sc:license": "Other", "sc:name": "RD-Connect Sample Catalogue", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://samples.rd-connect.eu/" } diff --git a/data/rdavidwebservice/rdavidwebservicebioschemas.jsonld b/data/rdavidwebservice/rdavidwebservicebioschemas.jsonld index d4e58b5e074c7..658f0192cc2ad 100644 --- a/data/rdavidwebservice/rdavidwebservicebioschemas.jsonld +++ b/data/rdavidwebservice/rdavidwebservicebioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "RDAVIDWebService", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RDAVIDWebService.html", "sc:version": "1.12.0" diff --git a/data/rdfio/rdfiobioschemas.jsonld b/data/rdfio/rdfiobioschemas.jsonld index 2b26443f4764c..e0592fe89331a 100644 --- a/data/rdfio/rdfiobioschemas.jsonld +++ b/data/rdfio/rdfiobioschemas.jsonld @@ -14,26 +14,26 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "SPARQL endpoint", "sc:citation": [ - "pubmed:28870259", + "pmcid:PMC5584330", { "@id": "https://doi.org/10.1186/s13326-017-0136-y" }, - "pmcid:PMC5584330" + "pubmed:28870259" ], "sc:description": "Extends the RDF import and export functionality in Semantic MediaWiki (SMW) to enable using SMW as a collaborative platform for editing semantic data.", "sc:featureList": [ { - "@id": "edam:operation_3096" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_3096" } ], "sc:name": "RDFIO", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://pharmb.io/project/rdfio/" }, diff --git a/data/rdfscape/rdfscapebioschemas.jsonld b/data/rdfscape/rdfscapebioschemas.jsonld index ed46f12b9ac26..97950d170c786 100644 --- a/data/rdfscape/rdfscapebioschemas.jsonld +++ b/data/rdfscape/rdfscapebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This is a project that brings Semantic Web “features” to the popular Systems Biology software Cytoscape. It allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape.", "sc:name": "RDFScape", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bioinformatics.org/rdfscape/wiki/" } \ No newline at end of file diff --git a/data/rdiff/rdiffbioschemas.jsonld b/data/rdiff/rdiffbioschemas.jsonld index dca90b738ea33..309287ef31688 100644 --- a/data/rdiff/rdiffbioschemas.jsonld +++ b/data/rdiff/rdiffbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "rDiff is an open source tool for accurate detection of differential RNA processing from RNA-Seq data. It implements two statistical tests to detect changes of the RNA processing between two samples. rDiff.parametric is a powerful test, which can be applied for well annotated organisms to detect changes in the relative abundance of isoforms. rDiff.nonparametric is an alternative when the annotation is incomplete or missing.", "sc:name": "RDiff", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioweb.me/rdiff" } \ No newline at end of file diff --git a/data/rdisop/rdisopbioschemas.jsonld b/data/rdisop/rdisopbioschemas.jsonld index 75dde95fbe66c..ad4fc2761dba6 100644 --- a/data/rdisop/rdisopbioschemas.jsonld +++ b/data/rdisop/rdisopbioschemas.jsonld @@ -14,12 +14,12 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Steffen Neumann", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:19015140", "pmcid:PMC2639009", + "pubmed:19015140", { "@id": "https://doi.org/10.1093/bioinformatics/btn603" } diff --git a/data/rdml/rdmlbioschemas.jsonld b/data/rdml/rdmlbioschemas.jsonld index 2d308d3a1272d..09041b0715d4c 100644 --- a/data/rdml/rdmlbioschemas.jsonld +++ b/data/rdml/rdmlbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "RDML", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/RDML/index.html" } \ No newline at end of file diff --git a/data/rdp/rdpbioschemas.jsonld b/data/rdp/rdpbioschemas.jsonld index ab17d64c635ad..c4e54c18cdc81 100644 --- a/data/rdp/rdpbioschemas.jsonld +++ b/data/rdp/rdpbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Ribosomal Database Project (RDP)", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://rdp.cme.msu.edu/" } \ No newline at end of file diff --git a/data/rdp_pyrosequencing_pipeline/rdp_pyrosequencing_pipelinebioschemas.jsonld b/data/rdp_pyrosequencing_pipeline/rdp_pyrosequencing_pipelinebioschemas.jsonld index cd38a0a077df7..e6f25ba6d7848 100644 --- a/data/rdp_pyrosequencing_pipeline/rdp_pyrosequencing_pipelinebioschemas.jsonld +++ b/data/rdp_pyrosequencing_pipeline/rdp_pyrosequencing_pipelinebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The Ribosomal Database Project's Pyrosequencing Pipeline aims to simplify the processing of large 16s rRNA sequence libraries obtained through pyrosequencing. This site processes and converts the data to formats suitable for common ecological and statistical packages such as SPADE, EstimateS, and R.", "sc:name": "RDP Pyrosequencing Pipeline", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://pyro.cme.msu.edu/index.jsp" } \ No newline at end of file diff --git a/data/rdrf/rdrfbioschemas.jsonld b/data/rdrf/rdrfbioschemas.jsonld index 27ae15bd7274f..ad885c001cb79 100644 --- a/data/rdrf/rdrfbioschemas.jsonld +++ b/data/rdrf/rdrfbioschemas.jsonld @@ -9,35 +9,31 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1751-0473-9-14", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rdrf", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "RDRF Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4075501", - "pubmed:24982690", { "@id": "https://doi.org/10.1186/1751-0473-9-14" - } + }, + "pmcid:PMC4075501", + "pubmed:24982690" ], "sc:description": "The Rare Disease Registry Framework (RDRF) is an open source tool for the creation of web-based patient registries. It enables to create and modify registries without changes to the programming code. It has many features which include its ability to create multiple registries within the same framework, patients are defined once, and the ability for curators to create data elements dynamically well after the registry has been defined.", "sc:featureList": [ { - "@id": "edam:operation_3436" + "@id": "edam:operation_3435" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3431" }, { - "@id": "edam:operation_3435" + "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_3196" } ], "sc:license": "GPL-3.0", @@ -47,6 +43,10 @@ "Linux" ], "sc:url": "https://muccg.github.io/rdrf/" + }, + { + "@id": "https://doi.org/10.1186/1751-0473-9-14", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rdrtoolbox/rdrtoolboxbioschemas.jsonld b/data/rdrtoolbox/rdrtoolboxbioschemas.jsonld index 133b9c3785167..d79cca2d598a1 100644 --- a/data/rdrtoolbox/rdrtoolboxbioschemas.jsonld +++ b/data/rdrtoolbox/rdrtoolboxbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christoph Bartenhagen", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset.", "sc:license": "GPL-2.0", diff --git a/data/rdt/rdtbioschemas.jsonld b/data/rdt/rdtbioschemas.jsonld index 1cceef62739de..b779ac5c85cc2 100644 --- a/data/rdt/rdtbioschemas.jsonld +++ b/data/rdt/rdtbioschemas.jsonld @@ -18,10 +18,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC4920114", + "pubmed:27153692", { "@id": "https://doi.org/10.1093/bioinformatics/btw096" - }, - "pubmed:27153692" + } ], "sc:description": "Reaction Detection Tool (RDT) extracts chemical features like Atom–Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions.", "sc:featureList": { @@ -30,8 +30,8 @@ "sc:license": "GPL-3.0", "sc:name": "RDT", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/asad/ReactionDecoder" diff --git a/data/rdxplorer/rdxplorerbioschemas.jsonld b/data/rdxplorer/rdxplorerbioschemas.jsonld index d8a625df9dfa3..c2aa1bad37f38 100644 --- a/data/rdxplorer/rdxplorerbioschemas.jsonld +++ b/data/rdxplorer/rdxplorerbioschemas.jsonld @@ -15,12 +15,12 @@ "biotools:primaryContact": "Makarov V.", "sc:additionalType": "Script", "sc:citation": [ - "pubmed:19657104", - "pubmed:31136576", - "pmcid:PMC6555534", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1007069" - } + }, + "pmcid:PMC6555534", + "pubmed:19657104", + "pubmed:31136576" ], "sc:description": "> LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'LUMPY', 'CNVnator RDXplorer', 'CNVnator' (bio.tools/cnvnator), 'CNV' | Comprehensively benchmarking applications for detecting copy number variation | The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group", "sc:license": "Other", diff --git a/data/re-music/re-musicbioschemas.jsonld b/data/re-music/re-musicbioschemas.jsonld index 39ef8b13ccc55..3492587209717 100644 --- a/data/re-music/re-musicbioschemas.jsonld +++ b/data/re-music/re-musicbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "RE-MuSiC", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://genome.cs.nthu.edu.tw/RE-MUSIC/" } \ No newline at end of file diff --git a/data/rea/reabioschemas.jsonld b/data/rea/reabioschemas.jsonld index a26315f25b0aa..5076447c3b3e5 100644 --- a/data/rea/reabioschemas.jsonld +++ b/data/rea/reabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Collection of methods for RIP-chip Enrichment Analysis. A table of normalized expression values from a RIP-chip experiment is read (e.g. as produced by the Affymetrix PowerTools) and two main steps are performed: Subtraction of the background of non target genes and secondary normalization for differing IP efficiencies.", "sc:name": "REA", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bio.ifi.lmu.de/REA", "sc:version": "1.1" diff --git a/data/reactionflow/reactionflowbioschemas.jsonld b/data/reactionflow/reactionflowbioschemas.jsonld index a2ee929e261c2..f71d43efa071f 100644 --- a/data/reactionflow/reactionflowbioschemas.jsonld +++ b/data/reactionflow/reactionflowbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This is a visual analytics application for pathway analysis that emphasizes the structural and causal relationships amongst proteins, complexes, and biochemical reactions within a given pathway.", "sc:name": "ReactionFlow", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/CreativeCodingLab/ReactionFlow" } \ No newline at end of file diff --git a/data/reactome_graph_database/reactome_graph_databasebioschemas.jsonld b/data/reactome_graph_database/reactome_graph_databasebioschemas.jsonld index 5ef33917e633f..103e9999cc1e9 100644 --- a/data/reactome_graph_database/reactome_graph_databasebioschemas.jsonld +++ b/data/reactome_graph_database/reactome_graph_databasebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Reactome Graph Database", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://reactome.org/dev/graph-database" } \ No newline at end of file diff --git a/data/reactome_small_molecule_search/reactome_small_molecule_searchbioschemas.jsonld b/data/reactome_small_molecule_search/reactome_small_molecule_searchbioschemas.jsonld index 7ec1ea77be338..df0f8c1b8f518 100644 --- a/data/reactome_small_molecule_search/reactome_small_molecule_searchbioschemas.jsonld +++ b/data/reactome_small_molecule_search/reactome_small_molecule_searchbioschemas.jsonld @@ -16,13 +16,13 @@ "sc:description": "Launch a search in the ChEBI database of small molecules (also used by RHEA).", "sc:name": "Reactome Small Molecule Search", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ - "EMBL-EBI", - "OICR" + "OICR", + "EMBL-EBI" ], "sc:url": "http://www.reactome.org/cgi-bin/small_molecule_search?DB=gk_current", "sc:version": "1" diff --git a/data/reactomefiviz/reactomefivizbioschemas.jsonld b/data/reactomefiviz/reactomefivizbioschemas.jsonld index 8dddb76bdd83d..990da5cc8f90b 100644 --- a/data/reactomefiviz/reactomefivizbioschemas.jsonld +++ b/data/reactomefiviz/reactomefivizbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-8196-1177", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/reactomefiviz", "@type": "sc:SoftwareApplication", @@ -17,41 +21,37 @@ }, "sc:additionalType": "Plug-in", "sc:citation": [ + "pubmed:25309732", { "@id": "https://doi.org/10.12688/F1000RESEARCH.4431.2" }, - "pubmed:25309732", "pmcid:PMC4184317" ], "sc:description": "Perform pathway- and network-based data analysis. It uses highly reliable gene functional interaction network combined with human curated pathways derived from Reactome and other pathway databases. BiIt allows to uncover network and pathway patterns, search for gene signatures from gene expression data sets, reveal pathways significantly enriched by genes in a list, and integrate multiple genomic data types into a pathway context using probabilistic graphical models.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_0277" }, { - "@id": "edam:operation_3083" + "@id": "edam:operation_3439" }, { - "@id": "edam:operation_0277" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3439" + "@id": "edam:operation_3083" } ], "sc:license": "CC-BY-4.0", "sc:name": "ReactomeFIViz", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin", "sc:version": "7.1.0" }, - { - "@id": "http://orcid.org/0000-0001-8196-1177", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.12688/F1000RESEARCH.4431.2", "@type": "sc:CreativeWork" diff --git a/data/reactomepa/reactomepabioschemas.jsonld b/data/reactomepa/reactomepabioschemas.jsonld index 5ec0163c45164..689394e8fa6db 100644 --- a/data/reactomepa/reactomepabioschemas.jsonld +++ b/data/reactomepa/reactomepabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-6485-8781", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/reactomepa", "@type": "sc:SoftwareApplication", @@ -25,15 +29,11 @@ "sc:name": "ReactomePA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ReactomePA.html", "sc:version": "1.18.1" - }, - { - "@id": "http://orcid.org/0000-0002-6485-8781", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/reactpred/reactpredbioschemas.jsonld b/data/reactpred/reactpredbioschemas.jsonld index 24c51262992c9..dcdaf56e31780 100644 --- a/data/reactpred/reactpredbioschemas.jsonld +++ b/data/reactpred/reactpredbioschemas.jsonld @@ -23,8 +23,8 @@ "sc:name": "ReactPRED", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sourceforge.net/projects/reactpred/" } \ No newline at end of file diff --git a/data/readat/readatbioschemas.jsonld b/data/readat/readatbioschemas.jsonld index 99d1dc68f8655..9b17d8554aea1 100644 --- a/data/readat/readatbioschemas.jsonld +++ b/data/readat/readatbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-3015-5850", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1186/s12859-016-1007-8", "@type": "sc:CreativeWork" @@ -18,15 +22,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Richard Cotton", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:27146037", { "@id": "https://doi.org/10.1186/s12859-016-1007-8" }, - "pmcid:PMC4857291" + "pmcid:PMC4857291", + "pubmed:27146037" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-3015-5850" @@ -44,15 +48,11 @@ "sc:name": "readat", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/readat.html", "sc:version": "1.0.0" - }, - { - "@id": "http://orcid.org/0000-0002-3015-5850", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/readdy/readdybioschemas.jsonld b/data/readdy/readdybioschemas.jsonld index aad8a9e79b7c8..4928d0d438696 100644 --- a/data/readdy/readdybioschemas.jsonld +++ b/data/readdy/readdybioschemas.jsonld @@ -20,21 +20,21 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:30818351", - "pmcid:PMC6413953", { "@id": "https://doi.org/10.1371/journal.pcbi.1006830" - } + }, + "pmcid:PMC6413953" ], "sc:description": "Reaction Diffusion Dynamics (ReaDDy) - software framework for interacting-particle reaction dynamics.", "sc:featureList": [ { - "@id": "edam:operation_2476" + "@id": "edam:operation_3457" }, { "@id": "edam:operation_0334" }, { - "@id": "edam:operation_3457" + "@id": "edam:operation_2476" } ], "sc:license": "GPL-3.0", diff --git a/data/reademption/reademptionbioschemas.jsonld b/data/reademption/reademptionbioschemas.jsonld index bd1d8e0d34d3e..056bb36d10444 100644 --- a/data/reademption/reademptionbioschemas.jsonld +++ b/data/reademption/reademptionbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "ISC", "sc:name": "READemption", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://pythonhosted.org/READemption/" } \ No newline at end of file diff --git a/data/readfastafile/readfastafilebioschemas.jsonld b/data/readfastafile/readfastafilebioschemas.jsonld index 7fbb8301c1684..963da927d524a 100644 --- a/data/readfastafile/readfastafilebioschemas.jsonld +++ b/data/readfastafile/readfastafilebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "readfastafile", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://bioweb.pasteur.fr/packages/pack@FastqProcessing@0.38.1", "sc:version": "0.38" diff --git a/data/readqpcr/readqpcrbioschemas.jsonld b/data/readqpcr/readqpcrbioschemas.jsonld index 16b37d7ada8e2..529726e790f9e 100644 --- a/data/readqpcr/readqpcrbioschemas.jsonld +++ b/data/readqpcr/readqpcrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2164-13-296", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/readqpcr", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ "Library" ], "sc:citation": [ - "pmcid:PMC3443438", - "pubmed:22748112", { "@id": "https://doi.org/10.1186/1471-2164-13-296" - } + }, + "pmcid:PMC3443438", + "pubmed:22748112" ], "sc:description": "The package provides functions to read raw RT-qPCR data of different platforms.", "sc:featureList": { @@ -31,16 +35,12 @@ "sc:license": "GPL-3.0", "sc:name": "ReadqPCR", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ReadqPCR.html", "sc:version": "1.20.0" - }, - { - "@id": "https://doi.org/10.1186/1471-2164-13-296", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/reads2type/reads2typebioschemas.jsonld b/data/reads2type/reads2typebioschemas.jsonld index 644d78a6b42e0..00202bc300cbf 100644 --- a/data/reads2type/reads2typebioschemas.jsonld +++ b/data/reads2type/reads2typebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Reads2Type", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.cbs.dtu.dk/~dhany/reads2type.html" } \ No newline at end of file diff --git a/data/readscan/readscanbioschemas.jsonld b/data/readscan/readscanbioschemas.jsonld index 9aa2ec8d6fe1e..da7c3747f7958 100644 --- a/data/readscan/readscanbioschemas.jsonld +++ b/data/readscan/readscanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets.", "sc:name": "Readscan", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cbrc.kaust.edu.sa/readscan/" } \ No newline at end of file diff --git a/data/readseq/readseqbioschemas.jsonld b/data/readseq/readseqbioschemas.jsonld index 4229974cc3052..c359cf231e1f6 100644 --- a/data/readseq/readseqbioschemas.jsonld +++ b/data/readseq/readseqbioschemas.jsonld @@ -13,19 +13,19 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "Don Gilbert", - "Web Production" + "Web Production", + "Don Gilbert" ], "sc:description": "Convert biosequences between a selection of common biological sequence formats.", "sc:name": "Readseq", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ - "Indiana University", - "EMBL-EBI" + "EMBL-EBI", + "Indiana University" ], "sc:url": "http://www.ebi.ac.uk/Tools/sfc/readseq/", "sc:version": "1" diff --git a/data/readtools/readtoolsbioschemas.jsonld b/data/readtools/readtoolsbioschemas.jsonld index 7b906272b3586..07191472410c4 100644 --- a/data/readtools/readtoolsbioschemas.jsonld +++ b/data/readtools/readtoolsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "ReadTools", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://magicdgs.github.io/ReadTools/" } \ No newline at end of file diff --git a/data/readxplorer/readxplorerbioschemas.jsonld b/data/readxplorer/readxplorerbioschemas.jsonld index 96dd796fbba59..c6d60c2091386 100644 --- a/data/readxplorer/readxplorerbioschemas.jsonld +++ b/data/readxplorer/readxplorerbioschemas.jsonld @@ -14,10 +14,10 @@ "@type": "sc:SoftwareApplication", "edam:has_input": [ { - "@id": "edam:data_0863" + "@id": "edam:data_2887" }, { - "@id": "edam:data_2887" + "@id": "edam:data_0863" } ], "sc:additionalType": "Desktop application", @@ -25,8 +25,8 @@ { "@id": "https://doi.org/10.1093/bioinformatics/btu205" }, - "pmcid:PMC4217279", - "pubmed:24790157" + "pubmed:24790157", + "pmcid:PMC4217279" ], "sc:description": "Freely available comprehensive exploration and evaluation tool for NGS data. It extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads. This classification is then taken into account for the different data views and all supported automatic analysis functions.", "sc:featureList": { @@ -35,8 +35,8 @@ "sc:license": "GPL-2.0", "sc:name": "ReadXplorer", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "bigi", diff --git a/data/realphy/realphybioschemas.jsonld b/data/realphy/realphybioschemas.jsonld index a7168e90b3d66..f48395bae12d3 100644 --- a/data/realphy/realphybioschemas.jsonld +++ b/data/realphy/realphybioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide genome sequences in FASTA, GenBank or FASTQ formats. From these sequences phylogenetic trees are inferred via PhyML. The alignments, tree files and information on SNPs and deleted sites will be available for download after the analysis is finished.", "sc:name": "REALPHY", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://realphy.unibas.ch/fcgi/realphy" } \ No newline at end of file diff --git a/data/reb/rebbioschemas.jsonld b/data/reb/rebbioschemas.jsonld index be4e7c382c4ca..7acbd63744ea6 100644 --- a/data/reb/rebbioschemas.jsonld +++ b/data/reb/rebbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Karl J. Dykema", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A set of functions to dentify regional expression biases.", "sc:license": "GPL-2.0", "sc:name": "reb", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/reb.html", "sc:version": "1.52.0" diff --git a/data/rebacca/rebaccabioschemas.jsonld b/data/rebacca/rebaccabioschemas.jsonld index f3ee4f15302dd..bbc33d9a462b1 100644 --- a/data/rebacca/rebaccabioschemas.jsonld +++ b/data/rebacca/rebaccabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This R code is based on a novel method to identify significant co-occurrence patterns by finding sparse solutions to a system with a deficient rank.", "sc:name": "REBACCA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://faculty.wcas.northwestern.edu/~hji403/REBACCA.htm" diff --git a/data/rebase/rebasebioschemas.jsonld b/data/rebase/rebasebioschemas.jsonld index b601bb034be55..e7019adb48b71 100644 --- a/data/rebase/rebasebioschemas.jsonld +++ b/data/rebase/rebasebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "REBASE", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://rebase.neb.com/rebase/rebase.html" } \ No newline at end of file diff --git a/data/rebaseextract/rebaseextractbioschemas.jsonld b/data/rebaseextract/rebaseextractbioschemas.jsonld index 24658ca496cfc..8c68a83e6f5df 100644 --- a/data/rebaseextract/rebaseextractbioschemas.jsonld +++ b/data/rebaseextract/rebaseextractbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "EMBOSS Contributors", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "UK MRC", + "EMBOSS Contributors" ], "sc:description": "Process the REBASE database for use by restriction enzyme applications.", "sc:funder": [ + "UK BBSRC", "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "rebaseextract", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/rebaseextract.html", "sc:version": "r6" diff --git a/data/recal2/recal2bioschemas.jsonld b/data/recal2/recal2bioschemas.jsonld index 2390006863037..98c15d8afb48c 100644 --- a/data/recal2/recal2bioschemas.jsonld +++ b/data/recal2/recal2bioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "recal2", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ms-utils.org/recal2.html" } \ No newline at end of file diff --git a/data/recentrifuge/recentrifugebioschemas.jsonld b/data/recentrifuge/recentrifugebioschemas.jsonld index a71c934587811..e44523f7598f3 100644 --- a/data/recentrifuge/recentrifugebioschemas.jsonld +++ b/data/recentrifuge/recentrifugebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pcbi.1006967", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Recentrifuge", "@type": "sc:SoftwareApplication", @@ -18,34 +22,30 @@ { "@id": "https://doi.org/10.1371/journal.pcbi.1006967" }, - "pmcid:PMC6472834", - "pubmed:30958827" + "pubmed:30958827", + "pmcid:PMC6472834" ], "sc:description": "Robust comparative analysis and contamination removal for metagenomics.", "sc:featureList": [ { - "@id": "edam:operation_3460" + "@id": "edam:operation_2495" }, { "@id": "edam:operation_3730" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3460" } ], "sc:license": "AGPL-3.0", "sc:name": "Recentrifuge", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://sites.google.com/view/recentrifuge", "sc:version": "0.28.10" - }, - { - "@id": "https://doi.org/10.1371/journal.pcbi.1006967", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/recirc/recircbioschemas.jsonld b/data/recirc/recircbioschemas.jsonld index 95a216b87a3f5..8fb8deef2bfc1 100644 --- a/data/recirc/recircbioschemas.jsonld +++ b/data/recirc/recircbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "ReCirc", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://licpathway.net:8080/ReCirc/" } \ No newline at end of file diff --git a/data/recode/recodebioschemas.jsonld b/data/recode/recodebioschemas.jsonld index 301b540eda0ce..f90e8e10d65fc 100644 --- a/data/recode/recodebioschemas.jsonld +++ b/data/recode/recodebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Recode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon redefinition. Recode-2 provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements.", "sc:name": "Recode", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://recode.ucc.ie" } \ No newline at end of file diff --git a/data/recoder/recoderbioschemas.jsonld b/data/recoder/recoderbioschemas.jsonld index 1eb022773b64a..02d78ce8f1867 100644 --- a/data/recoder/recoderbioschemas.jsonld +++ b/data/recoder/recoderbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", - "UK BBSRC", "Wellcome Trust", + "UK BBSRC", "UK MRC" ], "sc:description": "Find restriction sites to remove (mutate) with no translation change.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "recoder", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/recoittv/recoittvbioschemas.jsonld b/data/recoittv/recoittvbioschemas.jsonld index 7acaed0c8bb6b..c700967455eaa 100644 --- a/data/recoittv/recoittvbioschemas.jsonld +++ b/data/recoittv/recoittvbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RecoItTV", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/arcosuc3m/recoittv", "sc:version": "1.4.1" diff --git a/data/recon/reconbioschemas.jsonld b/data/recon/reconbioschemas.jsonld index 618ecd0c7b80b..4b7db4c398203 100644 --- a/data/recon/reconbioschemas.jsonld +++ b/data/recon/reconbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "RECON", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/" } \ No newline at end of file diff --git a/data/recount_bioconductor/recount_bioconductorbioschemas.jsonld b/data/recount_bioconductor/recount_bioconductorbioschemas.jsonld index efe12b706c937..76dfb2f27b62f 100644 --- a/data/recount_bioconductor/recount_bioconductorbioschemas.jsonld +++ b/data/recount_bioconductor/recount_bioconductorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-2-Clause", "sc:name": "recount_Bioconductor", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/recount.html", diff --git a/data/recoup/bioconda_recoup.yaml b/data/recoup/bioconda_recoup.yaml index ebef088f22b87..71aca8cbd3772 100644 --- a/data/recoup/bioconda_recoup.yaml +++ b/data/recoup/bioconda_recoup.yaml @@ -8,7 +8,6 @@ description: recoup calculates and plots signal profiles created from short sequ home: https://bioconductor.org/packages/3.10/bioc/html/recoup.html identifiers: - biotools:recoup -- doi:10.1038/nmeth.3252 license: GPL (>= 3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-recoup diff --git a/data/recoup/recoupbioschemas.jsonld b/data/recoup/recoupbioschemas.jsonld index f3f88cb05fa21..bb8cffe2c3997 100644 --- a/data/recoup/recoupbioschemas.jsonld +++ b/data/recoup/recoupbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "recoup", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/recoup.html", "sc:version": "1.2.0" diff --git a/data/recovery/recoverybioschemas.jsonld b/data/recovery/recoverybioschemas.jsonld index 12c960dda5d98..c98d2f02dcb0c 100644 --- a/data/recovery/recoverybioschemas.jsonld +++ b/data/recovery/recoverybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/recovery", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Paul Medvedev", - "Kateryna D Makova" + "Kateryna D Makova", + "Paul Medvedev" ], "sc:additionalType": "Command-line tool", "sc:description": "K-mer-based read classification for Y-chromosome-specific sequencing and assembly.", diff --git a/data/recphyloxml/recphyloxmlbioschemas.jsonld b/data/recphyloxml/recphyloxmlbioschemas.jsonld index a8a5d3c04c5d2..ab0f2d18c3557 100644 --- a/data/recphyloxml/recphyloxmlbioschemas.jsonld +++ b/data/recphyloxml/recphyloxmlbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Format for reconciled gene trees.", "sc:name": "RecPhyloXML", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://phylariane.univ-lyon1.fr/recphyloxml/" } \ No newline at end of file diff --git a/data/red-ml/red-mlbioschemas.jsonld b/data/red-ml/red-mlbioschemas.jsonld index d9ed10016b808..695a588823385 100644 --- a/data/red-ml/red-mlbioschemas.jsonld +++ b/data/red-ml/red-mlbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/red-ml", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Xun Xu", - "Leo J. Lee" + "Leo J. Lee", + "Xun Xu" ], "sc:additionalType": "Command-line tool", "sc:description": "RNA editing detection based on machine learning.", diff --git a/data/red/redbioschemas.jsonld b/data/red/redbioschemas.jsonld index 51ed0315b5be0..27af7a3046d3e 100644 --- a/data/red/redbioschemas.jsonld +++ b/data/red/redbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/red", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Di Wu", - "Xing Li" + "Xing Li", + "Di Wu" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:26930599", @@ -20,8 +20,8 @@ "sc:name": "RED", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/REDetector/RED" } \ No newline at end of file diff --git a/data/redata/redatabioschemas.jsonld b/data/redata/redatabioschemas.jsonld index ec9b1c4b08119..abda00aa12c03 100644 --- a/data/redata/redatabioschemas.jsonld +++ b/data/redata/redatabioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "EMBOSS Contributors", + "UK MRC", "Wellcome Trust", - "UK MRC" + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Retrieve information from REBASE restriction enzyme database.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", + "Wellcome Trust", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "redata", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/redata.html", "sc:version": "r6" diff --git a/data/redcap/redcapbioschemas.jsonld b/data/redcap/redcapbioschemas.jsonld index 7859a59d8a1ac..e3bf88d82066b 100644 --- a/data/redcap/redcapbioschemas.jsonld +++ b/data/redcap/redcapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "REDCap", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.project-redcap.org/" } \ No newline at end of file diff --git a/data/redemption/redemptionbioschemas.jsonld b/data/redemption/redemptionbioschemas.jsonld index 3809805cd1ad9..4b9d1bf8f78ad 100644 --- a/data/redemption/redemptionbioschemas.jsonld +++ b/data/redemption/redemptionbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This is a MATLAB toolbox for the identification of parameters and parameter ensembles of ODE models from time-series data. The toolbox is based on incremental parameter estimation (IPE) and integrated flux parameter estimation (IFPE) methods .", "sc:name": "REDEMPTION", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.cabsel.ethz.ch/tools/redemption" } \ No newline at end of file diff --git a/data/reder/rederbioschemas.jsonld b/data/reder/rederbioschemas.jsonld index b5ad0d8a819c3..f338bbcd581ba 100644 --- a/data/reder/rederbioschemas.jsonld +++ b/data/reder/rederbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-4942-8131", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/reder", "@type": "sc:SoftwareApplication", @@ -26,8 +22,8 @@ "@id": "edam:data_2600" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": { "@id": "edam:topic_0092" @@ -42,10 +38,10 @@ "sc:description": "R-based package combined with a stand-alone Java application for interactive visualization and manipulation of modular structures, nested networks and multiple levels of hierarchical associations.", "sc:featureList": [ { - "@id": "edam:operation_3083" + "@id": "edam:operation_2497" }, { - "@id": "edam:operation_2497" + "@id": "edam:operation_3083" } ], "sc:license": "GPL-2.0", @@ -58,6 +54,10 @@ "sc:url": "http://bioconductor.org/packages/release/bioc/html/RedeR.html", "sc:version": "1.22.0" }, + { + "@id": "http://orcid.org/0000-0003-4942-8131", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1186/gb-2012-13-4-r29", "@type": "sc:CreativeWork" diff --git a/data/redfly/redflybioschemas.jsonld b/data/redfly/redflybioschemas.jsonld index f76fac4bf209b..5988cc2e76155 100644 --- a/data/redfly/redflybioschemas.jsonld +++ b/data/redfly/redflybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The REDfly database of Drosophila transcriptional cis-regulatory elements provides experimentally validated cis-regulatory modules and transcription factor binding sites. The user interface is designed for access by both causal and power users and is intended as a tool for facilitating computational as well as experimental studies of transcriptional regulation.", "sc:name": "REDfly", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://redfly.ccr.buffalo.edu" } \ No newline at end of file diff --git a/data/redhom/redhombioschemas.jsonld b/data/redhom/redhombioschemas.jsonld index 06d80895a24f4..49e01833a2c99 100644 --- a/data/redhom/redhombioschemas.jsonld +++ b/data/redhom/redhombioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "RedHom", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/RedHom/", diff --git a/data/redhorse/redhorsebioschemas.jsonld b/data/redhorse/redhorsebioschemas.jsonld index 03c1b3a5b1f60..6d531ebf2998b 100644 --- a/data/redhorse/redhorsebioschemas.jsonld +++ b/data/redhorse/redhorsebioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12864-015-1309-7", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/redhorse", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4348101", + "pubmed:25766039", { "@id": "https://doi.org/10.1186/S12864-015-1309-7" - }, - "pubmed:25766039", - "pmcid:PMC4348101" + } ], "sc:description": "REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data.", "sc:featureList": { @@ -32,10 +28,14 @@ "sc:name": "REDHORSE", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://redhorse.sourceforge.net/" + }, + { + "@id": "https://doi.org/10.1186/S12864-015-1309-7", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/redidb/redidbbioschemas.jsonld b/data/redidb/redidbbioschemas.jsonld index 96d163df3981f..5d71c37cecbf3 100644 --- a/data/redidb/redidbbioschemas.jsonld +++ b/data/redidb/redidbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "RNA editing database in organelles.", "sc:name": "RNA editing database (REDIdb)", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ELIXIR-ITA-CNR", "sc:url": "http://srv00.recas.ba.infn.it/py_script/REDIdb/" diff --git a/data/rediportal/rediportalbioschemas.jsonld b/data/rediportal/rediportalbioschemas.jsonld index d4dad259b6f11..d8345c98186f5 100644 --- a/data/rediportal/rediportalbioschemas.jsonld +++ b/data/rediportal/rediportalbioschemas.jsonld @@ -9,46 +9,46 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkw767", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/rediportal", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:27587585", { "@id": "https://doi.org/10.1093/nar/gkw767" }, - "pubmed:27587585", "pmcid:PMC5210607" ], "sc:description": "Database of A-to-I (deamination of adenosines to inosines) events that enables to search RNA editing sites by genomic region, gene name and other relevant features as the tissue of origin.", "sc:featureList": [ { - "@id": "edam:operation_0224" - }, - { - "@id": "edam:operation_3080" + "@id": "edam:operation_3196" }, { "@id": "edam:operation_0314" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3080" }, { "@id": "edam:operation_3096" + }, + { + "@id": "edam:operation_0224" } ], "sc:name": "REDIportal", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://srv00.recas.ba.infn.it/atlas/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkw767", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/reditools/reditoolsbioschemas.jsonld b/data/reditools/reditoolsbioschemas.jsonld index d1a779fdbdaa7..c2668872d9e24 100644 --- a/data/reditools/reditoolsbioschemas.jsonld +++ b/data/reditools/reditoolsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "REDItools", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ELIXIR-ITA-CNR", "sc:url": "https://code.google.com/p/reditools/", diff --git a/data/redoxmech/redoxmechbioschemas.jsonld b/data/redoxmech/redoxmechbioschemas.jsonld index 9d11468cca718..04f1600acbdab 100644 --- a/data/redoxmech/redoxmechbioschemas.jsonld +++ b/data/redoxmech/redoxmechbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RedoxMech", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.igb.uci.edu/tools/sb/metabolic-modeling/81-redoxmech.html" } \ No newline at end of file diff --git a/data/refbool/refboolbioschemas.jsonld b/data/refbool/refboolbioschemas.jsonld index 957e2cfc06a5c..fb012b03d695b 100644 --- a/data/refbool/refboolbioschemas.jsonld +++ b/data/refbool/refboolbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Reference-based algorithm for discretizing gene expression data.", "sc:name": "RefBool", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/saschajung/RefBool" } \ No newline at end of file diff --git a/data/reference_panel_reconstruction/reference_panel_reconstructionbioschemas.jsonld b/data/reference_panel_reconstruction/reference_panel_reconstructionbioschemas.jsonld index 24d86b8700748..1391f2b2af073 100644 --- a/data/reference_panel_reconstruction/reference_panel_reconstructionbioschemas.jsonld +++ b/data/reference_panel_reconstruction/reference_panel_reconstructionbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "Reference Panel Reconstruction", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/Abyss-bai/reference-panel-reconstruction" diff --git a/data/refernment/refernmentbioschemas.jsonld b/data/refernment/refernmentbioschemas.jsonld index 9e35916076e49..11a46944187fa 100644 --- a/data/refernment/refernmentbioschemas.jsonld +++ b/data/refernment/refernmentbioschemas.jsonld @@ -19,8 +19,8 @@ "biotools:primaryContact": "Tanner Robison", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6384294", "pubmed:30828503", + "pmcid:PMC6384294", { "@id": "https://doi.org/10.1002/aps3.1216" } @@ -40,9 +40,9 @@ "sc:license": "GPL-3.0", "sc:name": "ReFernment", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/TARobison/ReFernment", "sc:version": "1.1.2" diff --git a/data/refinehmm/refinehmmbioschemas.jsonld b/data/refinehmm/refinehmmbioschemas.jsonld index 3b650059077a5..d12304c3de2a5 100644 --- a/data/refinehmm/refinehmmbioschemas.jsonld +++ b/data/refinehmm/refinehmmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool refines an original hidden Markov model (HMM) to find an optimal fit against the evolutionary group that the HMM models, and it does this using through iterative database searches and incremental subsequent adaptation of the seed set.", "sc:name": "RefineHMM", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://sourceforge.net/projects/refinehmm/" } \ No newline at end of file diff --git a/data/refnet/bioconda_refnet.yaml b/data/refnet/bioconda_refnet.yaml index 07bd2ff1454f9..8f7fc17b552d5 100644 --- a/data/refnet/bioconda_refnet.yaml +++ b/data/refnet/bioconda_refnet.yaml @@ -4,7 +4,6 @@ description: Obtain molecular interactions with metadata, some archived, some dy home: https://bioconductor.org/packages/3.10/bioc/html/RefNet.html identifiers: - biotools:refnet -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-refnet summary: A queryable collection of molecular interactions, from many sources diff --git a/data/refnet/refnetbioschemas.jsonld b/data/refnet/refnetbioschemas.jsonld index 0d881c4da88ec..ccc8680b54453 100644 --- a/data/refnet/refnetbioschemas.jsonld +++ b/data/refnet/refnetbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "RefNet", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RefNet.html", "sc:version": "1.10.1" diff --git a/data/refold/refoldbioschemas.jsonld b/data/refold/refoldbioschemas.jsonld index bfe66306da67e..6a54eb2715f88 100644 --- a/data/refold/refoldbioschemas.jsonld +++ b/data/refold/refoldbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKX249", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/refold", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr Liam J. McGuffin", "edam:has_input": [ { - "@id": "edam:data_0950" + "@id": "edam:data_2974" }, { - "@id": "edam:data_2974" + "@id": "edam:data_0950" } ], "edam:has_output": [ @@ -58,6 +54,10 @@ ], "sc:name": "reFOLD", "sc:url": "http://www.reading.ac.uk/bioinf/ReFOLD/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKX249", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/reformat_fastq/reformat_fastqbioschemas.jsonld b/data/reformat_fastq/reformat_fastqbioschemas.jsonld index f2d68fba3017e..9a86cecbb850b 100644 --- a/data/reformat_fastq/reformat_fastqbioschemas.jsonld +++ b/data/reformat_fastq/reformat_fastqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Reformats an input file generated by a MiSeq/HiSeq system, where reads are formatted in a scheme that includes a space-character, which might not correctly be used in downstream operations.", "sc:name": "reformat_fastq", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://bioweb.pasteur.fr/packages/pack@PGP_tools@0.0.1", diff --git a/data/reformat_snpeff_for_syntview/reformat_snpeff_for_syntviewbioschemas.jsonld b/data/reformat_snpeff_for_syntview/reformat_snpeff_for_syntviewbioschemas.jsonld index a113e2cd10f71..ee76f0994b477 100644 --- a/data/reformat_snpeff_for_syntview/reformat_snpeff_for_syntviewbioschemas.jsonld +++ b/data/reformat_snpeff_for_syntview/reformat_snpeff_for_syntviewbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Convert a tabular snpEff file into a SynTView .snp and .indel files.", "sc:name": "reformat_snpeff_for_syntview", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://bioweb.pasteur.fr/packages/pack@SynTViewTools@0.0.1", diff --git a/data/refplus/refplusbioschemas.jsonld b/data/refplus/refplusbioschemas.jsonld index 6cfee14ea0c98..ff13f37d6426f 100644 --- a/data/refplus/refplusbioschemas.jsonld +++ b/data/refplus/refplusbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "RefPlus", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RefPlus.html", "sc:version": "1.44.0" diff --git a/data/refseq/refseqbioschemas.jsonld b/data/refseq/refseqbioschemas.jsonld index 9f9dfeb884e69..73820b71ed364 100644 --- a/data/refseq/refseqbioschemas.jsonld +++ b/data/refseq/refseqbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. Provides a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.", "sc:name": "NCBI reference sequences", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/RefSeq/" } \ No newline at end of file diff --git a/data/refseqget/refseqgetbioschemas.jsonld b/data/refseqget/refseqgetbioschemas.jsonld index a428d8eb652f5..5848f1e709bfd 100644 --- a/data/refseqget/refseqgetbioschemas.jsonld +++ b/data/refseqget/refseqgetbioschemas.jsonld @@ -14,21 +14,21 @@ "sc:contributor": [ "EMBOSS Contributors", "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:description": "An Emboss tool that reads a reference sequence and returns the data in one of the EMBOSS reference sequence formats.", "sc:funder": [ - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "refseqget", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/regbenchmark/regbenchmarkbioschemas.jsonld b/data/regbenchmark/regbenchmarkbioschemas.jsonld index 23d99bc6e7689..b21c90638604f 100644 --- a/data/regbenchmark/regbenchmarkbioschemas.jsonld +++ b/data/regbenchmark/regbenchmarkbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Comparative analysis of tissue reconstruction algorithms for 3D histology.", "sc:name": "RegBenchmark", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/BioimageInformaticsTampere/RegBenchmark" } \ No newline at end of file diff --git a/data/regent/regentbioschemas.jsonld b/data/regent/regentbioschemas.jsonld index cab96f920fe4c..d80aa24dd77f7 100644 --- a/data/regent/regentbioschemas.jsonld +++ b/data/regent/regentbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "REGENT", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/clewis/software/regent/index.aspx" } \ No newline at end of file diff --git a/data/regeo/regeobioschemas.jsonld b/data/regeo/regeobioschemas.jsonld index f4ac9d5ad54ab..087aea6cac3fd 100644 --- a/data/regeo/regeobioschemas.jsonld +++ b/data/regeo/regeobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/database/bay145", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ReGEO", "@type": "sc:SoftwareApplication", @@ -27,26 +31,22 @@ "sc:description": "Restructured version of Gene Expression Omnibus (GEO) that provides a user friendly interface for curating GEO database", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_0306" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_0306" } ], "sc:name": "ReGEO", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.regeo.org/" - }, - { - "@id": "https://doi.org/10.1093/database/bay145", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/regionalhapmapextractor/regionalhapmapextractorbioschemas.jsonld b/data/regionalhapmapextractor/regionalhapmapextractorbioschemas.jsonld index 79f9174355505..f027d02a3a32c 100644 --- a/data/regionalhapmapextractor/regionalhapmapextractorbioschemas.jsonld +++ b/data/regionalhapmapextractor/regionalhapmapextractorbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Software to extract a region from hapMapII for MaCH imputation.", "sc:name": "RegionalHapMapExtractor", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://yunliweb.its.unc.edu/software.html" } \ No newline at end of file diff --git a/data/regionalp/regionalpbioschemas.jsonld b/data/regionalp/regionalpbioschemas.jsonld index a519ab80f6f1e..d1a051ccc492a 100644 --- a/data/regionalp/regionalpbioschemas.jsonld +++ b/data/regionalp/regionalpbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/regionalp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Yik Ying Teo", - "Wang Xu" + "Wang Xu", + "Dr. Yik Ying Teo" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:22126751", "sc:description": "The software works by quantifying the degree of over-representation of associated SNPs in a pre-defined genomic region, given a specific definition of statistical significance.", "sc:name": "RegionalP", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.statgen.nus.edu.sg/~software/regionalP.html" } \ No newline at end of file diff --git a/data/regioner/regionerbioschemas.jsonld b/data/regioner/regionerbioschemas.jsonld index bf0bca224c291..f066cc78190b6 100644 --- a/data/regioner/regionerbioschemas.jsonld +++ b/data/regioner/regionerbioschemas.jsonld @@ -22,10 +22,10 @@ "Library" ], "sc:citation": [ - "pubmed:26424858", { "@id": "https://doi.org/10.1093/bioinformatics/btv562" }, + "pubmed:26424858", "pmcid:PMC4708104" ], "sc:description": "Offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.", @@ -40,9 +40,9 @@ "sc:license": "Artistic-2.0", "sc:name": "regioneR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/regioneR.html", "sc:version": "1.6.0" diff --git a/data/regionreport/regionreportbioschemas.jsonld b/data/regionreport/regionreportbioschemas.jsonld index d6d1e352bd5f9..0f88bb3c796fd 100644 --- a/data/regionreport/regionreportbioschemas.jsonld +++ b/data/regionreport/regionreportbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkw852", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/regionreport", "@type": "sc:SoftwareApplication", @@ -20,8 +24,8 @@ "@id": "edam:data_2048" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": { "@id": "edam:topic_3170" @@ -46,10 +50,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/regionReport.html", "sc:version": "1.8.0" - }, - { - "@id": "https://doi.org/10.1093/nar/gkw852", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/regprecise/regprecisebioschemas.jsonld b/data/regprecise/regprecisebioschemas.jsonld index d83ed811f989e..b4fc7516668c3 100644 --- a/data/regprecise/regprecisebioschemas.jsonld +++ b/data/regprecise/regprecisebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "The database was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach.", "sc:name": "RegPrecise", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://regprecise.lbl.gov", "sc:version": "3.0" diff --git a/data/regresshaplo/regresshaplobioschemas.jsonld b/data/regresshaplo/regresshaplobioschemas.jsonld index 19394ce0db54d..4ccb213e5a66d 100644 --- a/data/regresshaplo/regresshaplobioschemas.jsonld +++ b/data/regresshaplo/regresshaplobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection.", "sc:name": "RegressHaplo", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/SLeviyang/RegressHaplo" } \ No newline at end of file diff --git a/data/regrna/regrnabioschemas.jsonld b/data/regrna/regrnabioschemas.jsonld index 153ebf6be72f8..e6fec408214e8 100644 --- a/data/regrna/regrnabioschemas.jsonld +++ b/data/regrna/regrnabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5'-UTR and 3'-UTR, motifs involved in mRNA splicing and transcriptional regulation, other motifs in mRNA such as riboswitches and splice donor/acceptor sites, RNA structural features, and miRNA target sites.", "sc:name": "RegRNA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://regrna.mbc.nctu.edu.tw/" } \ No newline at end of file diff --git a/data/regscan/regscanbioschemas.jsonld b/data/regscan/regscanbioschemas.jsonld index 5ef72d77cc068..f11c9cb2473b0 100644 --- a/data/regscan/regscanbioschemas.jsonld +++ b/data/regscan/regscanbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "T. Haller", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4293375", { "@id": "https://doi.org/10.1093/bib/bbt066" }, - "pubmed:24008273", - "pmcid:PMC4293375" + "pubmed:24008273" ], "sc:description": "Performance of fast association analysis between allele frequencies and continuous traits. Uses linear regression to estimate marker effects on continuous traits.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "Unlicense", "sc:name": "RegScan", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://www.geenivaramu.ee/en/tools/regscan", "sc:version": "0.5" diff --git a/data/regshape/regshapebioschemas.jsonld b/data/regshape/regshapebioschemas.jsonld index 0c7a54120160a..e6cbc3122306b 100644 --- a/data/regshape/regshapebioschemas.jsonld +++ b/data/regshape/regshapebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This R package  provides a classifier for predicting whether a given oligonucleotide sequence (of length l bp, where l would typically vary from six to as high as 25 bp) is, or is not, a transcription factor (TF) binding site.", "sc:name": "regshape", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/ramseylab/regshape/" } \ No newline at end of file diff --git a/data/regsplice/bioconda_regsplice.yaml b/data/regsplice/bioconda_regsplice.yaml index bf08c7af5f221..7e3f9c4cd3980 100644 --- a/data/regsplice/bioconda_regsplice.yaml +++ b/data/regsplice/bioconda_regsplice.yaml @@ -5,7 +5,6 @@ description: Statistical methods for detection of differential splicing (differe home: https://bioconductor.org/packages/3.10/bioc/html/regsplice.html identifiers: - biotools:regsplice -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-regsplice diff --git a/data/regsplice/regsplicebioschemas.jsonld b/data/regsplice/regsplicebioschemas.jsonld index a2e518ac8aec1..1c6690c79d36b 100644 --- a/data/regsplice/regsplicebioschemas.jsonld +++ b/data/regsplice/regsplicebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lukas M. Weber", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Statistical methods for detection of differential exon usage in RNA-seq and exon microarray data sets, using L1 regularization (lasso) to improve power.", "sc:license": "MIT", "sc:name": "regsplice", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/regsplice.html", "sc:version": "1.0.0" diff --git a/data/regulationspotter/regulationspotterbioschemas.jsonld b/data/regulationspotter/regulationspotterbioschemas.jsonld index 9384c69aaa1d0..423e22b05fe9f 100644 --- a/data/regulationspotter/regulationspotterbioschemas.jsonld +++ b/data/regulationspotter/regulationspotterbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of 'extratranscriptic' DNA variants. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region.\nPhenotypic data can be used to focus on likely disease genes.", "sc:name": "RegulationSpotter", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://www.regulationspotter.org/" } \ No newline at end of file diff --git a/data/regulondb/regulondbbioschemas.jsonld b/data/regulondb/regulondbbioschemas.jsonld index 72ce7c609d5bf..3c799c746c8ca 100644 --- a/data/regulondb/regulondbbioschemas.jsonld +++ b/data/regulondb/regulondbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "It is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. It has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry.", "sc:name": "RegulonDB", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://regulondb.ccg.unam.mx/" } \ No newline at end of file diff --git a/data/rehh/rehhbioschemas.jsonld b/data/rehh/rehhbioschemas.jsonld index 8292dbf657882..b08a8d11933e3 100644 --- a/data/rehh/rehhbioschemas.jsonld +++ b/data/rehh/rehhbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Rehh", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cran.r-project.org/web/packages/rehh/", "sc:version": "1.13" diff --git a/data/rehr/rehrbioschemas.jsonld b/data/rehr/rehrbioschemas.jsonld index d64cc16725ff4..bda5ea4841c43 100644 --- a/data/rehr/rehrbioschemas.jsonld +++ b/data/rehr/rehrbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Process and extract clinical information from Electronic Medical Records.", "sc:name": "rEHR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/rOpenHealth/rEHR" } \ No newline at end of file diff --git a/data/reinvent/reinventbioschemas.jsonld b/data/reinvent/reinventbioschemas.jsonld index 091de561bcef8..07e3daceef9d2 100644 --- a/data/reinvent/reinventbioschemas.jsonld +++ b/data/reinvent/reinventbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "REINVENT", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/MarcusOlivecrona/REINVENT" diff --git a/data/relate/relatebioschemas.jsonld b/data/relate/relatebioschemas.jsonld index a992b4c9aa1b5..2d2e2285c85e2 100644 --- a/data/relate/relatebioschemas.jsonld +++ b/data/relate/relatebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Search every one of 168,297 protein sequences from 8826 animals, plants and microorganisms and return the protein that contains the closest match to the letters of your sequence.", "sc:name": "reLATE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/cgi-bin/decode/relate.cgi", diff --git a/data/relateadmix/relateadmixbioschemas.jsonld b/data/relateadmix/relateadmixbioschemas.jsonld index 3a8f702163b13..eb3664eef4df6 100644 --- a/data/relateadmix/relateadmixbioschemas.jsonld +++ b/data/relateadmix/relateadmixbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RelateAdmix", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.popgen.dk/software/index.php/Relate" } \ No newline at end of file diff --git a/data/relna/relnabioschemas.jsonld b/data/relna/relnabioschemas.jsonld index 3870e52dd2716..687ea44d4ab3d 100644 --- a/data/relna/relnabioschemas.jsonld +++ b/data/relna/relnabioschemas.jsonld @@ -12,20 +12,20 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Juan Miguel Cejuela", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:author": [ - "Ashish Baghudana", - "Juan Miguel Cejuela" + "Juan Miguel Cejuela", + "Ashish Baghudana" ], "sc:description": "Text mining tool for relation extraction of Protein to DNA and to RNA interactions.", "sc:license": "MIT", "sc:name": "relna", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "RostLab", diff --git a/data/remap/remapbioschemas.jsonld b/data/remap/remapbioschemas.jsonld index b9975d3993dfd..3316a96b8dadf 100644 --- a/data/remap/remapbioschemas.jsonld +++ b/data/remap/remapbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "EMBOSS Contributors", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Display restriction enzyme binding sites in a nucleotide sequence.", "sc:funder": [ + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "remap", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/remap.html", "sc:version": "r6" diff --git a/data/removeexonlines/removeexonlinesbioschemas.jsonld b/data/removeexonlines/removeexonlinesbioschemas.jsonld index 0ffb21b6b6f23..e038ea718c654 100644 --- a/data/removeexonlines/removeexonlinesbioschemas.jsonld +++ b/data/removeexonlines/removeexonlinesbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "removeexonlines", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/remp/rempbioschemas.jsonld b/data/remp/rempbioschemas.jsonld index 9798bae0750d9..9aeb7ac2ed7c8 100644 --- a/data/remp/rempbioschemas.jsonld +++ b/data/remp/rempbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "REMP", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/REMP.html", "sc:version": "1.4.0" diff --git a/data/rems/remsbioschemas.jsonld b/data/rems/remsbioschemas.jsonld index 45d08500ae1f0..e4085b018a244 100644 --- a/data/rems/remsbioschemas.jsonld +++ b/data/rems/remsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "LGPL-3.0", "sc:name": "REMS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "CSC - IT Center for Science", diff --git a/data/renato/renatobioschemas.jsonld b/data/renato/renatobioschemas.jsonld index 776c4b91f8d41..f05b5eb9310c3 100644 --- a/data/renato/renatobioschemas.jsonld +++ b/data/renato/renatobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "RENATO", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://renato.bioinfo.cipf.es" } \ No newline at end of file diff --git a/data/rene/renebioschemas.jsonld b/data/rene/renebioschemas.jsonld index d6b4f4182a754..9aa7c987fd74a 100644 --- a/data/rene/renebioschemas.jsonld +++ b/data/rene/renebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A new Cytoscape 3.x plugin, which enables integration, merging, enhancement, visualization, and exporting of pathways from multiple repositories.", "sc:name": "ReNE", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.sysbio.polito.it/index.php/tools-and-downloads/item/220-rene" } \ No newline at end of file diff --git a/data/repairtoire/repairtoirebioschemas.jsonld b/data/repairtoire/repairtoirebioschemas.jsonld index f819eef23a52b..b94223e74d8b7 100644 --- a/data/repairtoire/repairtoirebioschemas.jsonld +++ b/data/repairtoire/repairtoirebioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/repairtoire", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "REPAIRtoire Support", - "Contact List" + "Contact List", + "REPAIRtoire Support" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:21051355", "sc:description": "REPAIRtoire is a database resource for systems biology of DNA damage and repair. The database collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins.", "sc:name": "REPAIRtoire", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://repairtoire.genesilico.pl/" } \ No newline at end of file diff --git a/data/repeat_explorer/repeat_explorerbioschemas.jsonld b/data/repeat_explorer/repeat_explorerbioschemas.jsonld index b7aba12fcfc9e..ac63340fe998b 100644 --- a/data/repeat_explorer/repeat_explorerbioschemas.jsonld +++ b/data/repeat_explorer/repeat_explorerbioschemas.jsonld @@ -15,9 +15,9 @@ "Web application" ], "sc:author": [ - "Petr Novak", "Jiri Macas", - "Pavel Neumann" + "Pavel Neumann", + "Petr Novak" ], "sc:description": "RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes. It employs graph-based clustering of sequence reads to identify repetitive elements and several additional programs that aid in their annotation and quantification.", "sc:license": "GPL-3.0", diff --git a/data/repeatanalyzer/repeatanalyzerbioschemas.jsonld b/data/repeatanalyzer/repeatanalyzerbioschemas.jsonld index 86ef44407604e..e24ad4b50a935 100644 --- a/data/repeatanalyzer/repeatanalyzerbioschemas.jsonld +++ b/data/repeatanalyzer/repeatanalyzerbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12864-016-2686-2", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/repeatanalyzer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Assefaw H. Gebremedhin", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4891823", { "@id": "https://doi.org/10.1186/s12864-016-2686-2" }, - "pubmed:27260942", - "pmcid:PMC4891823" + "pubmed:27260942" ], "sc:description": "RepeatAnalyzer is a software tool capable of tracking, managing, analysing and cataloguing short-sequence repeats and genotypes using Anaplasma marginale as a model species.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "GPL-3.0", "sc:name": "RepeatAnalyzer", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bitbucket.org/repeatgroup/repeatanalyzer/overview" - }, - { - "@id": "https://doi.org/10.1186/s12864-016-2686-2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/repeatedhighdim/repeatedhighdimbioschemas.jsonld b/data/repeatedhighdim/repeatedhighdimbioschemas.jsonld index 1d746812de367..3fe03fb194e59 100644 --- a/data/repeatedhighdim/repeatedhighdimbioschemas.jsonld +++ b/data/repeatedhighdim/repeatedhighdimbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An R package of global tests for expression data of high-dimensional sets of molecular features.", "sc:name": "RepeatedHighDim", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ams.med.uni-goettingen.de/software-en.shtml" diff --git a/data/repeatoire/repeatoirebioschemas.jsonld b/data/repeatoire/repeatoirebioschemas.jsonld index d15a6aa1c0f33..5c2f28e88c17f 100644 --- a/data/repeatoire/repeatoirebioschemas.jsonld +++ b/data/repeatoire/repeatoirebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A software on a hybrid data set of real genomic DNA with simulated interspersed repeats.", "sc:name": "Repeatoire", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://wwwabi.snv.jussieu.fr/public/Repeatoire/" } \ No newline at end of file diff --git a/data/repeatsdb/repeatsdbbioschemas.jsonld b/data/repeatsdb/repeatsdbbioschemas.jsonld index 3cdb6ec97e09f..8731024e44b2d 100644 --- a/data/repeatsdb/repeatsdbbioschemas.jsonld +++ b/data/repeatsdb/repeatsdbbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkw1268", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/repeatsdb", "@type": "sc:SoftwareApplication", @@ -21,13 +17,13 @@ }, "edam:has_input": [ { - "@id": "edam:data_1127" + "@id": "edam:data_3021" }, { "@id": "edam:data_2007" }, { - "@id": "edam:data_3021" + "@id": "edam:data_1127" } ], "edam:has_output": { @@ -35,22 +31,22 @@ }, "sc:additionalType": [ "Web application", - "Database portal", - "Web API" + "Web API", + "Database portal" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0157" + "@id": "edam:topic_2814" }, { - "@id": "edam:topic_2814" + "@id": "edam:topic_0157" } ], "sc:citation": [ + "pubmed:27928056", { "@id": "https://doi.org/10.1093/nar/gkw1268" }, - "pubmed:27928056", "pmcid:PMC5389603" ], "sc:description": "Database of annotated tandem repeat protein structures.", @@ -58,9 +54,6 @@ { "@id": "edam:operation_0224" }, - { - "@id": "edam:operation_0564" - }, { "@id": "edam:operation_2406" }, @@ -69,18 +62,25 @@ }, { "@id": "edam:operation_0570" + }, + { + "@id": "edam:operation_0564" } ], "sc:name": "RepeatsDB", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", "sc:url": "http://repeatsdb.bio.unipd.it", "sc:version": "2.0" }, + { + "@id": "https://doi.org/10.1093/nar/gkw1268", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0003-4525-7793", "@type": "schema:Person" diff --git a/data/repet/repetbioschemas.jsonld b/data/repet/repetbioschemas.jsonld index 704c2c745767f..09d0c8c14efce 100644 --- a/data/repet/repetbioschemas.jsonld +++ b/data/repet/repetbioschemas.jsonld @@ -10,11 +10,11 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1371/journal.pone.0016526", + "@id": "https://doi.org/10.1371/journal.pone.0091929", "@type": "sc:CreativeWork" }, { - "@id": "https://doi.org/10.1371/journal.pone.0091929", + "@id": "https://doi.org/10.1371/journal.pone.0016526", "@type": "sc:CreativeWork" }, { @@ -23,30 +23,30 @@ "sc:additionalType": "Command-line tool", "sc:author": "URGI", "sc:citation": [ - "pubmed:21304975", { - "@id": "https://doi.org/10.1371/journal.pcbi.0010022" + "@id": "https://doi.org/10.1371/journal.pone.0091929" }, - "pmcid:PMC1185648", - "pubmed:15008403", "pmcid:PMC3031573", + "pubmed:16110336", + "pubmed:21304975", + "pmcid:PMC4008368", + "pubmed:24786468", + "pmcid:PMC1185648", { - "@id": "https://doi.org/10.1371/journal.pone.0091929" + "@id": "https://doi.org/10.1371/journal.pcbi.0010022" }, - "pmcid:PMC4008368", + "pubmed:15008403", { "@id": "https://doi.org/10.1371/journal.pone.0016526" - }, - "pubmed:24786468", - "pubmed:16110336" + } ], "sc:contributor": "URGI", "sc:description": "The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)\n TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.", "sc:license": "CECILL-2.0", "sc:name": "REPET", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "URGI", "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", diff --git a/data/repetita/repetitabioschemas.jsonld b/data/repetita/repetitabioschemas.jsonld index 2afc676ce9fb8..94f5f8f4bc0f4 100644 --- a/data/repetita/repetitabioschemas.jsonld +++ b/data/repetita/repetitabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Protein solenoid repeat detection from sequence.", "sc:name": "Repetita", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/services", diff --git a/data/repex/repexbioschemas.jsonld b/data/repex/repexbioschemas.jsonld index 28755cce14967..41237c9a4619b 100644 --- a/data/repex/repexbioschemas.jsonld +++ b/data/repex/repexbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Professor K. Sekar", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": "pubmed:30598392", "sc:description": "Web server to extract sequence repeats from protein and DNA sequences.", "sc:name": "RepEx", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioserver2.physics.iisc.ac.in/RepEx/" } \ No newline at end of file diff --git a/data/repfdr/repfdrbioschemas.jsonld b/data/repfdr/repfdrbioschemas.jsonld index 53c07bfdb3744..f516a420bd926 100644 --- a/data/repfdr/repfdrbioschemas.jsonld +++ b/data/repfdr/repfdrbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool for replicability analysis for genome-wide association studies.", "sc:name": "repfdr", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://cran.r-project.org/web/packages/repfdr/index.html" diff --git a/data/repgenhmm/repgenhmmbioschemas.jsonld b/data/repgenhmm/repgenhmmbioschemas.jsonld index a68c83b624db0..e28c20f22911b 100644 --- a/data/repgenhmm/repgenhmmbioschemas.jsonld +++ b/data/repgenhmm/repgenhmmbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btw112", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/repgenhmm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yuval Elthanati", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4920122", { "@id": "https://doi.org/10.1093/bioinformatics/btw112" }, + "pmcid:PMC4920122", "pubmed:27153709" ], "sc:description": "repgenHMM is a dynamic programming tool to infer the rules of immune receptor generation from sequence data.", @@ -29,10 +33,6 @@ "sc:name": "repgenHMM", "sc:operatingSystem": "Windows", "sc:url": "https://bitbucket.org/yuvalel/repgenhmm/overview" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btw112", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/repitools/repitoolsbioschemas.jsonld b/data/repitools/repitoolsbioschemas.jsonld index 727e7f7735dab..fe8011c210dd7 100644 --- a/data/repitools/repitoolsbioschemas.jsonld +++ b/data/repitools/repitoolsbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "http://orcid.org/0000-0002-3048-5518", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1186/gb-2014-15-2-r35", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/repitools", "@type": "sc:SoftwareApplication", @@ -28,30 +24,34 @@ "Library" ], "sc:citation": [ - "pubmed:24517713", - "pmcid:PMC4053803", { "@id": "https://doi.org/10.1186/gb-2014-15-2-r35" - } + }, + "pmcid:PMC4053803", + "pubmed:24517713" ], "sc:description": "Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.", "sc:featureList": [ { - "@id": "edam:operation_3809" + "@id": "edam:operation_0438" }, { - "@id": "edam:operation_0438" + "@id": "edam:operation_3809" } ], "sc:license": "GPL-2.0", "sc:name": "Repitools", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Repitools.html", "sc:version": "1.20.0" + }, + { + "@id": "https://doi.org/10.1186/gb-2014-15-2-r35", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/repk/repkbioschemas.jsonld b/data/repk/repkbioschemas.jsonld index 9fa2b0f853ffd..17ad0ccb9b426 100644 --- a/data/repk/repkbioschemas.jsonld +++ b/data/repk/repkbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.", "sc:name": "REPK", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://rocaplab.ocean.washington.edu/tools/repk" } \ No newline at end of file diff --git a/data/replace_regex/replace_regexbioschemas.jsonld b/data/replace_regex/replace_regexbioschemas.jsonld index 4c3f72c2b59ea..f8ae38563f3a0 100644 --- a/data/replace_regex/replace_regexbioschemas.jsonld +++ b/data/replace_regex/replace_regexbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool replaces the string or regular expression given in \"pattern to search\" field by the string given in \"replacing string\" field.", "sc:name": "replace_regex", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/text_manipulation_utilities/replace_regex/0.0.1", "sc:version": "0.0.1" diff --git a/data/repliscan/repliscanbioschemas.jsonld b/data/repliscan/repliscanbioschemas.jsonld index 13658f933269b..d7ddd1e327fda 100644 --- a/data/repliscan/repliscanbioschemas.jsonld +++ b/data/repliscan/repliscanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool for classifying replication timing regions.", "sc:name": "Repliscan", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/zyndagj/repliscan" } \ No newline at end of file diff --git a/data/repo/repobioschemas.jsonld b/data/repo/repobioschemas.jsonld index a8814aa43d1fc..6a7c28b10d15f 100644 --- a/data/repo/repobioschemas.jsonld +++ b/data/repo/repobioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1510-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/repo", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:28209127", + "pmcid:PMC5314482", { "@id": "https://doi.org/10.1186/s12859-017-1510-6" - }, - "pmcid:PMC5314482" + } ], "sc:description": "A data manager meant to avoid manual storage/retrieval of data to/from the file system. It builds one (or more) centralized repository where R objects are stored with rich annotations, including corresponding code chunks, and easily searched and retrieved.", "sc:featureList": [ @@ -37,12 +33,16 @@ "sc:license": "GPL-3.0", "sc:name": "repo", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/repo/", "sc:version": "2.1.3" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1510-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/reporter/reporterbioschemas.jsonld b/data/reporter/reporterbioschemas.jsonld index 1b3d74a206a55..c5af9fd29b955 100644 --- a/data/reporter/reporterbioschemas.jsonld +++ b/data/reporter/reporterbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Protein quantification based on reporter ions.", "sc:name": "Reporter", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "ugent.be", diff --git a/data/reportingtools/reportingtoolsbioschemas.jsonld b/data/reportingtools/reportingtoolsbioschemas.jsonld index ccc030e1d4a26..6b9ac37848ea8 100644 --- a/data/reportingtools/reportingtoolsbioschemas.jsonld +++ b/data/reportingtools/reportingtoolsbioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btt551", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/reportingtools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jason A. Hackney", + "Jessica L. Larson", "Gabriel Becker", - "Jessica L. Larson" + "Jason A. Hackney" ], "edam:has_input": { "@id": "edam:data_2603" @@ -28,8 +24,8 @@ "@id": "edam:data_1270" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": { "@id": "edam:topic_3316" @@ -54,6 +50,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ReportingTools.html", "sc:version": "2.14.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btt551", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/repro/reprobioschemas.jsonld b/data/repro/reprobioschemas.jsonld index 8d8189ad3d201..536f5ce4ecd38 100644 --- a/data/repro/reprobioschemas.jsonld +++ b/data/repro/reprobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "REPRO", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ibi.vu.nl/programs/reprowww/" } \ No newline at end of file diff --git a/data/reprof/reprofbioschemas.jsonld b/data/reprof/reprofbioschemas.jsonld index 52bd6bd786488..05611fe108bf1 100644 --- a/data/reprof/reprofbioschemas.jsonld +++ b/data/reprof/reprofbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Protein secondary structure and accessibility predictor from the Rost Lab. Prediction is either done from protein sequence alone or from an alignment - the latter should be used for optimal performance. The language choosen was Perl.", "sc:name": "reprof", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "tum.de", "sc:url": "https://github.com/Rostlab/reprof", diff --git a/data/reprogenomics_viewer/reprogenomics_viewerbioschemas.jsonld b/data/reprogenomics_viewer/reprogenomics_viewerbioschemas.jsonld index 78587579dbd2f..1c8d25f19bbc7 100644 --- a/data/reprogenomics_viewer/reprogenomics_viewerbioschemas.jsonld +++ b/data/reprogenomics_viewer/reprogenomics_viewerbioschemas.jsonld @@ -16,13 +16,13 @@ "sc:description": "The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community.", "sc:name": "ReproGenomics Viewer", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "GenOuest", - "irisa.fr" + "irisa.fr", + "GenOuest" ], "sc:url": "http://rgv.genouest.org", "sc:version": "1" diff --git a/data/reputer/reputerbioschemas.jsonld b/data/reputer/reputerbioschemas.jsonld index 9fb13982037c5..66d633122e889 100644 --- a/data/reputer/reputerbioschemas.jsonld +++ b/data/reputer/reputerbioschemas.jsonld @@ -23,26 +23,26 @@ "@id": "edam:data_1276" }, "sc:additionalType": [ - "Web application", "Command-line tool", - "Web API" + "Web API", + "Web application" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0654" + "@id": "edam:topic_0622" }, { - "@id": "edam:topic_0157" + "@id": "edam:topic_0654" }, { - "@id": "edam:topic_0622" + "@id": "edam:topic_0157" } ], "sc:citation": [ + "pmcid:PMC92531", { "@id": "https://doi.org/10.1093/nar/29.22.4633" }, - "pmcid:PMC92531", "pubmed:11713313" ], "sc:description": "The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization.", @@ -57,8 +57,8 @@ "sc:isAccessibleForFree": true, "sc:name": "REPuter", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "BiBiServ", "sc:softwareHelp": { diff --git a/data/reqon/reqonbioschemas.jsonld b/data/reqon/reqonbioschemas.jsonld index 5e253376a4584..337401152998d 100644 --- a/data/reqon/reqonbioschemas.jsonld +++ b/data/reqon/reqonbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "ReQON", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ReQON.html", "sc:version": "1.20.0" diff --git a/data/rerconverge/rerconvergebioschemas.jsonld b/data/rerconverge/rerconvergebioschemas.jsonld index 89f6b7bb9c92a..d002d3fc4bb89 100644 --- a/data/rerconverge/rerconvergebioschemas.jsonld +++ b/data/rerconverge/rerconvergebioschemas.jsonld @@ -11,29 +11,29 @@ "@id": "https://bio.tools/RERconverge", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Raghavendran Partha", "Nathan Clark", - "Wynn Meyer", "Maria Chikina", "Weiguang (Wayne) Mao", - "Raghavendran Partha" + "Wynn Meyer" ], "sc:additionalType": "Library", "sc:author": [ - "Nathan Clark", + "Raghavendran Partha", "Wynn Meyer", - "Amanda Kowalczyk", "Weiguang (Wayne) Mao", "Maria Chikina", - "Raghavendran Partha" + "Nathan Clark", + "Amanda Kowalczyk" ], "sc:citation": "pubmed:31192356", "sc:description": "R package for associating evolutionary rates with convergent traits.", "sc:license": "GPL-3.0", "sc:name": "RERconverge", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/nclark-lab/RERconverge" } \ No newline at end of file diff --git a/data/rescue-ese/rescue-esebioschemas.jsonld b/data/rescue-ese/rescue-esebioschemas.jsonld index 11b5d360c917d..9de98920bb0f7 100644 --- a/data/rescue-ese/rescue-esebioschemas.jsonld +++ b/data/rescue-ese/rescue-esebioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/rescue-ese", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ru-Fang Yeh", "Gene Yeo", - "Will Fairbrother" + "Will Fairbrother", + "Ru-Fang Yeh" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:12114529", "sc:description": "Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.", "sc:name": "Rescue-ESE", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://genes.mit.edu/burgelab/rescue-ese/" } \ No newline at end of file diff --git a/data/rescuenet/rescuenetbioschemas.jsonld b/data/rescuenet/rescuenetbioschemas.jsonld index 73d622ccc17fb..1c298f411dad7 100644 --- a/data/rescuenet/rescuenetbioschemas.jsonld +++ b/data/rescuenet/rescuenetbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An application that uses the Self-Organizing Map neural network algorithm for codon usage anaysis and gene-prediction. In its gene prediction functionality, RescueNet can estimate multiple models of gene codon usage properties during training. This offers advantageous gene-finding performance in cases where a diverse number of codon usage patterns are displayed.", "sc:name": "RescueNet", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinf.nuigalway.ie/RescueNet/" } \ No newline at end of file diff --git a/data/resfinder/resfinderbioschemas.jsonld b/data/resfinder/resfinderbioschemas.jsonld index 41c6146eda6b2..f68c198d0d40b 100644 --- a/data/resfinder/resfinderbioschemas.jsonld +++ b/data/resfinder/resfinderbioschemas.jsonld @@ -28,11 +28,11 @@ "@id": "edam:topic_0804" }, "sc:citation": [ + "pmcid:PMC3468078", "pubmed:22782487", { "@id": "https://doi.org/10.1093/jac/dks261" - }, - "pmcid:PMC3468078" + } ], "sc:description": "Identification of acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.", "sc:featureList": { @@ -42,8 +42,8 @@ "sc:license": "Other", "sc:name": "ResFinder", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "CBS", diff --git a/data/resicon/resiconbioschemas.jsonld b/data/resicon/resiconbioschemas.jsonld index fc4ec3164dcc3..5e11f02117a42 100644 --- a/data/resicon/resiconbioschemas.jsonld +++ b/data/resicon/resiconbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A method for the identification of dynamic domains, hinges and interfacial regions in proteins", "sc:name": "ResiCon", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://dworkowa.imdik.pan.pl/EP/ResiCon/" } \ No newline at end of file diff --git a/data/resid/residbioschemas.jsonld b/data/resid/residbioschemas.jsonld index 68dd08c6ed7b4..1d0a7405dd47d 100644 --- a/data/resid/residbioschemas.jsonld +++ b/data/resid/residbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.", "sc:name": "RESID database of protein modifications", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://pir.georgetown.edu/resid/" } \ No newline at end of file diff --git a/data/resourcerer/resourcererbioschemas.jsonld b/data/resourcerer/resourcererbioschemas.jsonld index 13616642e219b..5fb73a0528ab8 100644 --- a/data/resourcerer/resourcererbioschemas.jsonld +++ b/data/resourcerer/resourcererbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for cross-referencing microarray data derived from different species and across different expression analysis platforms. Built using the analysis of ESTs, the TIGR Gene Index (TGI), and Eukaryotic Gene Orthologs (EGO) databases.", "sc:name": "Resourcerer", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://compbio.dfci.harvard.edu/tgi/cgi-bin/magic/r1.pl" diff --git a/data/responsenet/responsenetbioschemas.jsonld b/data/responsenet/responsenetbioschemas.jsonld index 9f58ca1645b0d..17a332014ed03 100644 --- a/data/responsenet/responsenetbioschemas.jsonld +++ b/data/responsenet/responsenetbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:license": "Unlicense", "sc:name": "ResponseNet", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://netbio.bgu.ac.il/respnet/" diff --git a/data/respre/resprebioschemas.jsonld b/data/respre/resprebioschemas.jsonld index be3dfcbd20825..a45432a84f818 100644 --- a/data/respre/resprebioschemas.jsonld +++ b/data/respre/resprebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Unlicense", "sc:name": "ResPRE", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://zhanglab.ccmb.med.umich.edu/ResPRE" diff --git a/data/resprox/resproxbioschemas.jsonld b/data/resprox/resproxbioschemas.jsonld index fcf1bdd0d1484..5d922fe83e9be 100644 --- a/data/resprox/resproxbioschemas.jsonld +++ b/data/resprox/resproxbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "ResProx (Resolution-by-proxy or Res(p)) is a web server that predicts the atomic resolution of NMR protein structures using only PDB coordinate data as input. More specfically, ResProx uses machine learning techniques to accurately estimate (with a correlation coefficient of 0.92 between observed and calculated) the atomic resolution of a protein structure from 25 measurable features that can be derived from its atomic coordinates.", "sc:name": "ResProx", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.resprox.ca/" diff --git a/data/restauro-g/restauro-gbioschemas.jsonld b/data/restauro-g/restauro-gbioschemas.jsonld index 822f447a544a8..8fde7bd905258 100644 --- a/data/restauro-g/restauro-gbioschemas.jsonld +++ b/data/restauro-g/restauro-gbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An open-source rapid genome re-annotation software system , specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLAST-Like Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases.", "sc:name": "Restauro-G", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://restauro-g.iab.keio.ac.jp/" } \ No newline at end of file diff --git a/data/restfulse/restfulsebioschemas.jsonld b/data/restfulse/restfulsebioschemas.jsonld index 6815baef4051c..12746727c590a 100644 --- a/data/restfulse/restfulsebioschemas.jsonld +++ b/data/restfulse/restfulsebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "restfulSE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/restfulSE.html", "sc:version": "1.2.0" diff --git a/data/restover/restoverbioschemas.jsonld b/data/restover/restoverbioschemas.jsonld index c822a2eec8f0e..3d872d1f5389d 100644 --- a/data/restover/restoverbioschemas.jsonld +++ b/data/restover/restoverbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "EMBOSS Contributors", "UK MRC", - "Wellcome Trust" + "EMBOSS Contributors", + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Find restriction enzymes producing a specific overhang.", "sc:funder": [ "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "restover", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/restrict/restrictbioschemas.jsonld b/data/restrict/restrictbioschemas.jsonld index 52e66ee92f432..e1e7072cae611 100644 --- a/data/restrict/restrictbioschemas.jsonld +++ b/data/restrict/restrictbioschemas.jsonld @@ -20,19 +20,19 @@ "sc:description": "Report restriction enzyme cleavage sites in a nucleotide sequence.", "sc:funder": [ "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "restrict", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/restrict.html", "sc:version": "r6" diff --git a/data/restrictfromsize/restrictfromsizebioschemas.jsonld b/data/restrictfromsize/restrictfromsizebioschemas.jsonld index d80a6bde360df..4936d29b7eac8 100644 --- a/data/restrictfromsize/restrictfromsizebioschemas.jsonld +++ b/data/restrictfromsize/restrictfromsizebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Select the elements of a list of sequences or transcripts with a given size.", "sc:name": "restrictfromsize", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/restrictsequencelist/restrictsequencelistbioschemas.jsonld b/data/restrictsequencelist/restrictsequencelistbioschemas.jsonld index 8a194e75e2b8f..b6a8cd171b64a 100644 --- a/data/restrictsequencelist/restrictsequencelistbioschemas.jsonld +++ b/data/restrictsequencelist/restrictsequencelistbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Keep the elements of a list of sequences whose name is mentionned in a given file.", "sc:name": "restrictsequencelist", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/restricttranscriptlist/restricttranscriptlistbioschemas.jsonld b/data/restricttranscriptlist/restricttranscriptlistbioschemas.jsonld index 0a7d91ad9ea7e..b0e5fbaa348cc 100644 --- a/data/restricttranscriptlist/restricttranscriptlistbioschemas.jsonld +++ b/data/restricttranscriptlist/restricttranscriptlistbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Keep the coordinates which are located in a given position.", "sc:name": "restricttranscriptlist", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/retentionprediction/retentionpredictionbioschemas.jsonld b/data/retentionprediction/retentionpredictionbioschemas.jsonld index 86a2feeb6a8e6..779d82878cdc9 100644 --- a/data/retentionprediction/retentionpredictionbioschemas.jsonld +++ b/data/retentionprediction/retentionpredictionbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A related web utility for projecting/predicting retention times.", "sc:name": "retentionprediction", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://retentionprediction.org/" diff --git a/data/retromap/retromapbioschemas.jsonld b/data/retromap/retromapbioschemas.jsonld index 52476fbec213f..d6425714fdf1d 100644 --- a/data/retromap/retromapbioschemas.jsonld +++ b/data/retromap/retromapbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An application designed to help characterize LTR retroelements on a genome scale in a visually interactive manner. This is NOT a particularly great for comprehensive identification of elements found in highly nested contexts. Only the most internal element of those which are nested is likely to be identified as a complete element. The other elements will be treated as solo LTRs and internal regions depending on how you have set up your element searches.", "sc:name": "RetroMap", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.burchsite.com/bioi/RetroMapHome.html" } \ No newline at end of file diff --git a/data/retrotector/retrotectorbioschemas.jsonld b/data/retrotector/retrotectorbioschemas.jsonld index a3515d97c3ab8..eb0490276d0b6 100644 --- a/data/retrotector/retrotectorbioschemas.jsonld +++ b/data/retrotector/retrotectorbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences.", "sc:name": "RetroTector", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "bils.se", diff --git a/data/reupred/reupredbioschemas.jsonld b/data/reupred/reupredbioschemas.jsonld index 101fb769107a5..58c0f44c4e4a6 100644 --- a/data/reupred/reupredbioschemas.jsonld +++ b/data/reupred/reupredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A novel method for the fast automatic prediction of repeat units and repeat classification using an extensive Structure Repeat Unit Library (SRUL) derived from RepeatsDB.", "sc:name": "ReUPRed", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://protein.bio.unipd.it/reupred/" } \ No newline at end of file diff --git a/data/revbayes/revbayesbioschemas.jsonld b/data/revbayes/revbayesbioschemas.jsonld index 2f5b8f70dca21..0e1d72e4fef00 100644 --- a/data/revbayes/revbayesbioschemas.jsonld +++ b/data/revbayes/revbayesbioschemas.jsonld @@ -9,25 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/sysbio/syw021", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-0776-4460", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/revbayes", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sebastian Höhna", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4911942", - "pubmed:27235697", { "@id": "https://doi.org/10.1093/sysbio/syw021" - } + }, + "pubmed:27235697", + "pmcid:PMC4911942" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-0776-4460" @@ -39,10 +31,18 @@ "sc:license": "GPL-3.0", "sc:name": "RevBayes", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://revbayes.github.io/" + }, + { + "@id": "http://orcid.org/0000-0003-0776-4460", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/sysbio/syw021", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/reveal/revealbioschemas.jsonld b/data/reveal/revealbioschemas.jsonld index 3314a161bca50..f24eabaee02b5 100644 --- a/data/reveal/revealbioschemas.jsonld +++ b/data/reveal/revealbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A viewer for automated active-site predictions for polypeptides.", "sc:name": "Reveal", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.bioinformatics.cm-uj.krakow.pl/reveal/" } \ No newline at end of file diff --git a/data/revecor/revecorbioschemas.jsonld b/data/revecor/revecorbioschemas.jsonld index 842547bd910bf..4c28e279bbefc 100644 --- a/data/revecor/revecorbioschemas.jsonld +++ b/data/revecor/revecorbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-016-1088-4", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/revecor", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yang Cao", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:27473172", + "pmcid:PMC4965897", { "@id": "https://doi.org/10.1186/s12859-016-1088-4" }, - "pmcid:PMC4965897" + "pubmed:27473172" ], "sc:description": "An implementation of the reverse ecology framework. Reverse ecology refers to the use of genomics to study ecology with no a priori assumptions about the organism(s) under consideration, linking organisms to their environment. It allows researchers to reconstruct the metabolic networks and study the ecology of poorly characterized microbial species from their genomic information, and has substantial potentials for microbial community ecological analysis.", "sc:featureList": { @@ -29,15 +33,11 @@ "sc:name": "RevEcoR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/RevEcoR/", "sc:version": "0.99.3" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1088-4", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/revseq/revseqbioschemas.jsonld b/data/revseq/revseqbioschemas.jsonld index 2a021ba8ecf17..95030c6c6a012 100644 --- a/data/revseq/revseqbioschemas.jsonld +++ b/data/revseq/revseqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "EMBOSS Contributors", "UK MRC", - "Wellcome Trust" + "UK BBSRC", + "Wellcome Trust", + "EMBOSS Contributors" ], "sc:description": "Reverse and complement a nucleotide sequence.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "revseq", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/revseq.html", "sc:version": "r6" diff --git a/data/revtrans/revtransbioschemas.jsonld b/data/revtrans/revtransbioschemas.jsonld index 7eb696d7b391e..c43c88d71e44d 100644 --- a/data/revtrans/revtransbioschemas.jsonld +++ b/data/revtrans/revtransbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/revtrans", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Technical problems: Rasmus Wernersson", - "Scientific problems: Anders Gorm Pedersen" + "Scientific problems: Anders Gorm Pedersen", + "Technical problems: Rasmus Wernersson" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:12824361", @@ -20,8 +20,8 @@ "sc:license": "Other", "sc:name": "RevTrans", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.cbs.dtu.dk/services/RevTrans/" diff --git a/data/rexposome/rexposomebioschemas.jsonld b/data/rexposome/rexposomebioschemas.jsonld index bcba3f69d46f6..9e893ab40ac22 100644 --- a/data/rexposome/rexposomebioschemas.jsonld +++ b/data/rexposome/rexposomebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "rexposome", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rexposome.html", diff --git a/data/rexprimer/rexprimerbioschemas.jsonld b/data/rexprimer/rexprimerbioschemas.jsonld index 45d31dce38327..f75ca2874383f 100644 --- a/data/rexprimer/rexprimerbioschemas.jsonld +++ b/data/rexprimer/rexprimerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web application that provides many functionalities for improved PCR primer design.", "sc:name": "RExPrimer", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www4a.biotec.or.th/rexprimer/" } \ No newline at end of file diff --git a/data/rf_qsar/rf_qsarbioschemas.jsonld b/data/rf_qsar/rf_qsarbioschemas.jsonld index ea1fe4eec5d3a..e37ab086bebe9 100644 --- a/data/rf_qsar/rf_qsarbioschemas.jsonld +++ b/data/rf_qsar/rf_qsarbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Ligand-based virtual screening model comprising 1121 target SAR models built using a random forest algorithm.", "sc:name": "RF QSAR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://rfqsar.kaist.ac.kr/home.php" } \ No newline at end of file diff --git a/data/rfam/rfambioschemas.jsonld b/data/rfam/rfambioschemas.jsonld index fbd6d12aaffc1..8aadc1261e141 100644 --- a/data/rfam/rfambioschemas.jsonld +++ b/data/rfam/rfambioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/rfam", "@type": "sc:SoftwareApplication", "sc:additionalType": [ + "Web application", "Database portal", - "Web API", - "Web application" + "Web API" ], "sc:description": "Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs)", "sc:name": "Rfam", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://rfam.org" } \ No newline at end of file diff --git a/data/rfam_search/rfam_searchbioschemas.jsonld b/data/rfam_search/rfam_searchbioschemas.jsonld index d3fbc0210d5e4..315f900a73203 100644 --- a/data/rfam_search/rfam_searchbioschemas.jsonld +++ b/data/rfam_search/rfam_searchbioschemas.jsonld @@ -13,8 +13,8 @@ "biotools:primaryContact": "Rfam group", "sc:additionalType": "Web application", "sc:author": [ - "Eric Nawrocki", - "Rfam group" + "Rfam group", + "Eric Nawrocki" ], "sc:description": "Search of Rfam's CM collection.", "sc:name": "Rfam search", @@ -24,9 +24,9 @@ "Linux" ], "sc:provider": [ - "EMBL-EBI", + "Sanger Institute", "HHMI", - "Sanger Institute" + "EMBL-EBI" ], "sc:url": "http://rfam.xfam.org/search", "sc:version": "1" diff --git a/data/rfcoil/rfcoilbioschemas.jsonld b/data/rfcoil/rfcoilbioschemas.jsonld index b26fc227590a4..493da078b84c0 100644 --- a/data/rfcoil/rfcoilbioschemas.jsonld +++ b/data/rfcoil/rfcoilbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A predictor that could distinguish parallel dimeric and trimeric coiled coils. It uses the most efficient and non-redundant amino acid indices combined with the state-of-the-art machine learning method Random Forest to make the prediction.", "sc:name": "RFCoil", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://protein.cau.edu.cn/RFCoil/" } \ No newline at end of file diff --git a/data/rfpred/rfpredbioschemas.jsonld b/data/rfpred/rfpredbioschemas.jsonld index 213aac83a837c..f5604b79a830d 100644 --- a/data/rfpred/rfpredbioschemas.jsonld +++ b/data/rfpred/rfpredbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "rfPred", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rfPred.html", "sc:version": "1.12.0" diff --git a/data/rgadem/rgadembioschemas.jsonld b/data/rgadem/rgadembioschemas.jsonld index b26d3a49d4f06..4b0e488a6a316 100644 --- a/data/rgadem/rgadembioschemas.jsonld +++ b/data/rgadem/rgadembioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Arnaud Droit", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.", "sc:license": "Artistic-2.0", "sc:name": "rGADEM", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rGADEM.html", "sc:version": "2.22.0" diff --git a/data/rgalaxy/bioconda_rgalaxy.yaml b/data/rgalaxy/bioconda_rgalaxy.yaml index df45c951d70a6..eab0512a3a7a5 100644 --- a/data/rgalaxy/bioconda_rgalaxy.yaml +++ b/data/rgalaxy/bioconda_rgalaxy.yaml @@ -4,7 +4,6 @@ description: Given an R function and its manual page, make the documented functi home: https://bioconductor.org/packages/3.10/bioc/html/RGalaxy.html identifiers: - biotools:rgalaxy -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-rgalaxy summary: Make an R function available in the Galaxy web platform diff --git a/data/rgalaxy/rgalaxybioschemas.jsonld b/data/rgalaxy/rgalaxybioschemas.jsonld index 4f5c49f1c56c0..bdc1b41923764 100644 --- a/data/rgalaxy/rgalaxybioschemas.jsonld +++ b/data/rgalaxy/rgalaxybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Given an R function and its manual page, make the documented function available in Galaxy.", "sc:license": "Artistic-2.0", "sc:name": "RGalaxy", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RGalaxy.html", "sc:version": "1.18.0" diff --git a/data/rgb/rgbbioschemas.jsonld b/data/rgb/rgbbioschemas.jsonld index d11806590d765..1ea78a46b44b9 100644 --- a/data/rgb/rgbbioschemas.jsonld +++ b/data/rgb/rgbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This package is dedicated to memory efficient genome browsing strategies (both in scripts and interactive sessions) using the R scripting language. It includes classes and functions to manipulate genomic tracks, and a higher level interactive genome browser.", "sc:name": "Rgb", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinformatics.ovsa.fr/72/Rgb_130" } \ No newline at end of file diff --git a/data/rgd/rgdbioschemas.jsonld b/data/rgd/rgdbioschemas.jsonld index ef5c2ebc3df9e..be558db90a9f2 100644 --- a/data/rgd/rgdbioschemas.jsonld +++ b/data/rgd/rgdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Rat Genome Database (RGD) is a repository of rat genetic and genomic data. As well as integrating this data with mapping, physiological and strain information, RGD also provides researchers with several tools that facilitate searching, data mining and data analysis.", "sc:name": "Rat Genome Database (RGD)", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://rgd.mcw.edu/" } \ No newline at end of file diff --git a/data/rgestlibcomp/rgestlibcompbioschemas.jsonld b/data/rgestlibcomp/rgestlibcompbioschemas.jsonld index aaba29ba0b24d..ca9eecca58672 100644 --- a/data/rgestlibcomp/rgestlibcompbioschemas.jsonld +++ b/data/rgestlibcomp/rgestlibcompbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Attempts to estimate library complexity from sequence alone. Does so by sorting all reads by the first N bases (5 by default) of each read and then comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default).", "sc:name": "rgestlibcomp", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://broadinstitute.github.io/picard/", diff --git a/data/rgmql/rgmqlbioschemas.jsonld b/data/rgmql/rgmqlbioschemas.jsonld index f44c59a244b3c..3cc6891d81e8e 100644 --- a/data/rgmql/rgmqlbioschemas.jsonld +++ b/data/rgmql/rgmqlbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "RGMQL", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RGMQL.html", "sc:version": "1.0.0" diff --git a/data/rgpicfixmate/rgpicfixmatebioschemas.jsonld b/data/rgpicfixmate/rgpicfixmatebioschemas.jsonld index 9ddb93d947b81..00ff7683f18f6 100644 --- a/data/rgpicfixmate/rgpicfixmatebioschemas.jsonld +++ b/data/rgpicfixmate/rgpicfixmatebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Ensure that all mate-pair information is in sync between each read and it's mate pair.", "sc:name": "rgpicfixmate", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://broadinstitute.github.io/picard/", "sc:version": "1.56.0" diff --git a/data/rgraph2js/bioconda_rgraph2js.yaml b/data/rgraph2js/bioconda_rgraph2js.yaml index a5ed022c3077d..f20f5a80fae84 100644 --- a/data/rgraph2js/bioconda_rgraph2js.yaml +++ b/data/rgraph2js/bioconda_rgraph2js.yaml @@ -4,7 +4,6 @@ description: Generator of web pages which display interactive network/graph visu home: https://bioconductor.org/packages/3.10/bioc/html/RGraph2js.html identifiers: - biotools:rgraph2js -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-rgraph2js diff --git a/data/rgraph2js/rgraph2jsbioschemas.jsonld b/data/rgraph2js/rgraph2jsbioschemas.jsonld index 59e2806f232f5..728e9c243e2b8 100644 --- a/data/rgraph2js/rgraph2jsbioschemas.jsonld +++ b/data/rgraph2js/rgraph2jsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Stephane Cano", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael.", "sc:license": "GPL-2.0", "sc:name": "RGraph2js", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RGraph2js.html", "sc:version": "1.2.0" diff --git a/data/rgraphviz/rgraphvizbioschemas.jsonld b/data/rgraphviz/rgraphvizbioschemas.jsonld index 37084abcb9464..f0f233d921011 100644 --- a/data/rgraphviz/rgraphvizbioschemas.jsonld +++ b/data/rgraphviz/rgraphvizbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Kasper Daniel Hansen", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.", "sc:license": "EPL-1.0", "sc:name": "Rgraphviz", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html", "sc:version": "2.18.0" diff --git a/data/rgreat/bioconda_rgreat.yaml b/data/rgreat/bioconda_rgreat.yaml index 6ed0f80fa294e..a8047113ef28e 100644 --- a/data/rgreat/bioconda_rgreat.yaml +++ b/data/rgreat/bioconda_rgreat.yaml @@ -5,7 +5,6 @@ description: This package makes GREAT (Genomic Regions Enrichment of Annotations home: https://bioconductor.org/packages/3.10/bioc/html/rGREAT.html identifiers: - biotools:rgreat -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-rgreat diff --git a/data/rgreat/rgreatbioschemas.jsonld b/data/rgreat/rgreatbioschemas.jsonld index 205899a72b22b..199d7278a51d6 100644 --- a/data/rgreat/rgreatbioschemas.jsonld +++ b/data/rgreat/rgreatbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Zuguang Gu", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:author": "Zuguang Gu", "sc:description": "This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server.", "sc:license": "GPL-2.0", "sc:name": "rGREAT", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rGREAT.html", diff --git a/data/rgsea/bioconda_rgsea.yaml b/data/rgsea/bioconda_rgsea.yaml index 8309e32e491a4..c67e0d178e53b 100644 --- a/data/rgsea/bioconda_rgsea.yaml +++ b/data/rgsea/bioconda_rgsea.yaml @@ -5,7 +5,6 @@ description: Combining bootstrap aggregating and Gene set enrichment analysis (G home: https://bioconductor.org/packages/3.10/bioc/html/RGSEA.html identifiers: - biotools:rgsea -- doi:10.1038/nmeth.3252 license: GPL(>=3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rgsea diff --git a/data/rgsea/rgseabioschemas.jsonld b/data/rgsea/rgseabioschemas.jsonld index 712c2a47d2fbc..7d3bda4e465fa 100644 --- a/data/rgsea/rgseabioschemas.jsonld +++ b/data/rgsea/rgseabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chengcheng Ma", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Combining bootstrap aggregating and Gene Set Enrichment Analysis, this software is a classfication algorithm with high robustness and no over-fitting problem. It performs especially well for the data generated from different exprements.", "sc:license": "GPL-3.0", "sc:name": "RGSEA", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RGSEA.html", "sc:version": "1.8.0" diff --git a/data/rgsepd/bioconda_rgsepd.yaml b/data/rgsepd/bioconda_rgsepd.yaml index 650219cefe4a7..84642eb82aa23 100644 --- a/data/rgsepd/bioconda_rgsepd.yaml +++ b/data/rgsepd/bioconda_rgsepd.yaml @@ -6,7 +6,6 @@ description: R/GSEPD is a bioinformatics package for R to help disambiguate tran home: https://bioconductor.org/packages/3.10/bioc/html/rgsepd.html identifiers: - biotools:rgsepd -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rgsepd diff --git a/data/rgsepd/rgsepdbioschemas.jsonld b/data/rgsepd/rgsepdbioschemas.jsonld index 3d508230d86d8..ded2ff4532d78 100644 --- a/data/rgsepd/rgsepdbioschemas.jsonld +++ b/data/rgsepd/rgsepdbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Karl Stamm", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.", "sc:license": "GPL-3.0", "sc:name": "rgsepd", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rgsepd.html", "sc:version": "1.6.0" diff --git a/data/rhdf5/rhdf5bioschemas.jsonld b/data/rhdf5/rhdf5bioschemas.jsonld index 83ba2a33e3d84..06f2c31be031b 100644 --- a/data/rhdf5/rhdf5bioschemas.jsonld +++ b/data/rhdf5/rhdf5bioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "Artistic-2.0", "sc:name": "rhdf5", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/rhdf5/", "sc:version": "2.26.0" diff --git a/data/rhdf5client/rhdf5clientbioschemas.jsonld b/data/rhdf5client/rhdf5clientbioschemas.jsonld index ce40708481f5d..e257a4c3dc50b 100644 --- a/data/rhdf5client/rhdf5clientbioschemas.jsonld +++ b/data/rhdf5client/rhdf5clientbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "rhdf5client", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rhdf5client.html", "sc:version": "1.2.2" diff --git a/data/rhdf5lib/rhdf5libbioschemas.jsonld b/data/rhdf5lib/rhdf5libbioschemas.jsonld index 066ae596d248b..fffec881ce64a 100644 --- a/data/rhdf5lib/rhdf5libbioschemas.jsonld +++ b/data/rhdf5lib/rhdf5libbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Rhdf5lib", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/Rhdf5lib/", "sc:version": "1.4.0" diff --git a/data/rhea/rheabioschemas.jsonld b/data/rhea/rheabioschemas.jsonld index bfdd81e75619c..c5fc82772d804 100644 --- a/data/rhea/rheabioschemas.jsonld +++ b/data/rhea/rheabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Manually annotated database of biochemical reactions created in collaboration with the Swiss Institute of Bioinformatics (SIB).", "sc:name": "Rhea", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.ebi.ac.uk/rhea/" diff --git a/data/rhtslib/bioconda_rhtslib.yaml b/data/rhtslib/bioconda_rhtslib.yaml index 3f3ed88d91844..34bbbe05bd780 100644 --- a/data/rhtslib/bioconda_rhtslib.yaml +++ b/data/rhtslib/bioconda_rhtslib.yaml @@ -6,7 +6,6 @@ description: This package provides version 1.7 of the 'HTSlib' C library for hig home: https://bioconductor.org/packages/3.10/bioc/html/Rhtslib.html identifiers: - biotools:rhtslib -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-rhtslib diff --git a/data/rhtslib/rhtslibbioschemas.jsonld b/data/rhtslib/rhtslibbioschemas.jsonld index 7fa0f8fd61fbe..6bbcb19bf72eb 100644 --- a/data/rhtslib/rhtslibbioschemas.jsonld +++ b/data/rhtslib/rhtslibbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides version 1.1 of the 'HTSlib' C library for high-throughput sequence analysis. It is primarily useful to developers of other R packages who wish to make use of HTSlib.", "sc:license": "GPL-2.0", "sc:name": "Rhtslib", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rhtslib.html", "sc:version": "1.6.0" diff --git a/data/rhvdm/rhvdmbioschemas.jsonld b/data/rhvdm/rhvdmbioschemas.jsonld index 2cdf692a90581..9c49b555cd467 100644 --- a/data/rhvdm/rhvdmbioschemas.jsonld +++ b/data/rhvdm/rhvdmbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "rHVDM", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rHVDM.html", "sc:version": "1.40.0" diff --git a/data/rhythm/rhythmbioschemas.jsonld b/data/rhythm/rhythmbioschemas.jsonld index 4b21d2794ecf2..c7a83313f7178 100644 --- a/data/rhythm/rhythmbioschemas.jsonld +++ b/data/rhythm/rhythmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "RHYTHM predicts buried vs. exposed residues of helical membrane proteins. Users input either primary, secondary or tertiary structure information. Output includes secondary structure and topology information, and the contact type and conservation of each residue.", "sc:name": "RHYTHM", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://proteinformatics.charite.de/rhythm/" } \ No newline at end of file diff --git a/data/ribex/ribexbioschemas.jsonld b/data/ribex/ribexbioschemas.jsonld index 4e14f0c474a1e..c675c33ac7003 100644 --- a/data/ribex/ribexbioschemas.jsonld +++ b/data/ribex/ribexbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Seach sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conserved.", "sc:name": "RibEx", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.ibt.unam.mx/biocomputo/RibEx.html" } \ No newline at end of file diff --git a/data/riblast/riblastbioschemas.jsonld b/data/riblast/riblastbioschemas.jsonld index d772abc9db1bf..930066b4b13a4 100644 --- a/data/riblast/riblastbioschemas.jsonld +++ b/data/riblast/riblastbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "MIT", "sc:name": "RIblast", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://funpopgen.github.io/veqtl-mapper/" } \ No newline at end of file diff --git a/data/ribocat/ribocatbioschemas.jsonld b/data/ribocat/ribocatbioschemas.jsonld index 9106742ceed8c..1929ab12b7b8f 100644 --- a/data/ribocat/ribocatbioschemas.jsonld +++ b/data/ribocat/ribocatbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1261/rna.058404.116", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ribocat", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC5238798", - "pubmed:27821510", { "@id": "https://doi.org/10.1261/rna.058404.116" - } + }, + "pubmed:27821510", + "pmcid:PMC5238798" ], "sc:description": "Capillary electrophoresis data analysis tool for nucleic acid probing.", "sc:featureList": { @@ -36,6 +32,10 @@ "Linux" ], "sc:url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5238798/" + }, + { + "@id": "https://doi.org/10.1261/rna.058404.116", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/riboframe/riboframebioschemas.jsonld b/data/riboframe/riboframebioschemas.jsonld index 0393cf33af8a1..bb216a9b7a125 100644 --- a/data/riboframe/riboframebioschemas.jsonld +++ b/data/riboframe/riboframebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "It is a novel method for microbial profiling based on the identification and classification of 16S rRNA sequences in non targeted metagenomics datasets. Reads overlapping the 16S rRNA genes are identified using Hidden Markov Models and a taxonomic assignment is obtained by naive Bayesian classification. All reads identified as ribosomal are coherently positioned in the 16S rRNA gene, allowing the use of the topology of the gene to instruct the abundance analysis.", "sc:name": "RiboFrame", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioserver2.sbsc.unifi.it/bioinfo/riboframe.html", "sc:version": "1.1" diff --git a/data/ribogalaxy/ribogalaxybioschemas.jsonld b/data/ribogalaxy/ribogalaxybioschemas.jsonld index 2b07fa3082d4a..e9e0e73ab20cd 100644 --- a/data/ribogalaxy/ribogalaxybioschemas.jsonld +++ b/data/ribogalaxy/ribogalaxybioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-3307-2938", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1080/15476286.2016.1141862", "@type": "sc:CreativeWork" @@ -28,10 +24,10 @@ "@id": "edam:data_2968" }, { - "@id": "edam:data_2969" + "@id": "edam:data_0863" }, { - "@id": "edam:data_0863" + "@id": "edam:data_2969" } ], "sc:additionalType": "Workbench", @@ -52,28 +48,28 @@ "sc:description": "Galaxy-based web server where researchers can pre-process, align, analyze and visualize their own ribosome profiling (ribo-seq) data. GUI-based tools are provided to determine the strength of the triplet periodicity signal in ribo-seq data, generate metagene and ribosome profiles and carry out differential translation expression analysis using the riboSeqR suite. The RUST suite of tools can be used to quickly characterize ribosome profiling datasets to assess their quality and more.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_2928" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_0314" }, { - "@id": "edam:operation_2928" + "@id": "edam:operation_0337" }, { - "@id": "edam:operation_0314" + "@id": "edam:operation_2495" } ], "sc:funder": "Science Foundation Ireland", "sc:isAccessibleForFree": true, "sc:name": "RiboGalaxy", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "School of Biochemistry & Cell Biology, University College Cork", - "ucc.ie" + "ucc.ie", + "School of Biochemistry & Cell Biology, University College Cork" ], "sc:softwareHelp": { "@id": "http://ribogalaxy.ucc.ie/" @@ -83,6 +79,10 @@ }, "sc:url": "http://ribogalaxy.ucc.ie", "sc:version": "1" + }, + { + "@id": "http://orcid.org/0000-0002-3307-2938", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/ribomaker/ribomakerbioschemas.jsonld b/data/ribomaker/ribomakerbioschemas.jsonld index 9bd5d3efd9a2e..d327fef5f2d22 100644 --- a/data/ribomaker/ribomakerbioschemas.jsonld +++ b/data/ribomaker/ribomakerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A webserver for the computational design of conformation-based riboregulation.", "sc:name": "Ribomaker", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/Ribomaker/" diff --git a/data/ribopeaks/ribopeaksbioschemas.jsonld b/data/ribopeaks/ribopeaksbioschemas.jsonld index dcc3149e6f8a7..d764a9801b973 100644 --- a/data/ribopeaks/ribopeaksbioschemas.jsonld +++ b/data/ribopeaks/ribopeaksbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Ribopeaks", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ribopeaks.com." } \ No newline at end of file diff --git a/data/ribopicker/ribopickerbioschemas.jsonld b/data/ribopicker/ribopickerbioschemas.jsonld index 48bfb41562e2f..a28595f734e0f 100644 --- a/data/ribopicker/ribopickerbioschemas.jsonld +++ b/data/ribopicker/ribopickerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic datasets. The tool was designed to process longer-read datasets (150+bp read length), but works on 100+bp reads too.", "sc:name": "riboPicker", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://ribopicker.sourceforge.net/" diff --git a/data/riboprofiling/riboprofilingbioschemas.jsonld b/data/riboprofiling/riboprofilingbioschemas.jsonld index b59173cfcc628..e9a9fa96b04d9 100644 --- a/data/riboprofiling/riboprofilingbioschemas.jsonld +++ b/data/riboprofiling/riboprofilingbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "A. Popa", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.", "sc:license": "GPL-3.0", "sc:name": "RiboProfiling", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RiboProfiling.html", "sc:version": "1.3.2" diff --git a/data/riborex/riborexbioschemas.jsonld b/data/riborex/riborexbioschemas.jsonld index 4bd6eb63eadac..cd9a70ecba51c 100644 --- a/data/riborex/riborexbioschemas.jsonld +++ b/data/riborex/riborexbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/riborex", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Weili Wang", "Wenzheng Li", + "Weili Wang", "Andrew D. Smith" ], "sc:additionalType": "Command-line tool", "sc:description": "Fast and flexible identification of differential translation from Ribo-seq data.", "sc:name": "Riborex", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/smithlabcode/riborex" } \ No newline at end of file diff --git a/data/riboseed/riboseedbioschemas.jsonld b/data/riboseed/riboseedbioschemas.jsonld index 03b4dd02904e6..9c2517ee3bb51 100644 --- a/data/riboseed/riboseedbioschemas.jsonld +++ b/data/riboseed/riboseedbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/riboSeed", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Workflow", - "Command-line tool" + "Command-line tool", + "Workflow" ], "sc:description": "Prokaryotic genome assembly polisher -- uses targeted subassembly to resolve gaps caused by repeated rDNA operons.", "sc:license": "MIT", diff --git a/data/riboseqr/riboseqrbioschemas.jsonld b/data/riboseqr/riboseqrbioschemas.jsonld index 991e3d5222d62..4c31ecdaa96cf 100644 --- a/data/riboseqr/riboseqrbioschemas.jsonld +++ b/data/riboseqr/riboseqrbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "riboSeqR", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/riboSeqR.html", "sc:version": "1.8.0" diff --git a/data/riboswitch_finder/riboswitch_finderbioschemas.jsonld b/data/riboswitch_finder/riboswitch_finderbioschemas.jsonld index 49824612687c9..1634b8ab68bd8 100644 --- a/data/riboswitch_finder/riboswitch_finderbioschemas.jsonld +++ b/data/riboswitch_finder/riboswitch_finderbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Riboswitch finder", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html" } \ No newline at end of file diff --git a/data/riboswitch_scanner/riboswitch_scannerbioschemas.jsonld b/data/riboswitch_scanner/riboswitch_scannerbioschemas.jsonld index 8f43deb1cccb7..545dd4500000d 100644 --- a/data/riboswitch_scanner/riboswitch_scannerbioschemas.jsonld +++ b/data/riboswitch_scanner/riboswitch_scannerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Riboswitch Scanner", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://service.iiserkol.ac.in/~riboscan/" } \ No newline at end of file diff --git a/data/ribovision/ribovisionbioschemas.jsonld b/data/ribovision/ribovisionbioschemas.jsonld index f20c20815f339..d8b5cae09bdc7 100644 --- a/data/ribovision/ribovisionbioschemas.jsonld +++ b/data/ribovision/ribovisionbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A visualization and analysis tool for the simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes.", "sc:name": "RiboVision", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://apollo.chemistry.gatech.edu/RiboVision/" } \ No newline at end of file diff --git a/data/rice_galaxy/rice_galaxybioschemas.jsonld b/data/rice_galaxy/rice_galaxybioschemas.jsonld index 20a519ff292d8..dfa662e3b2abf 100644 --- a/data/rice_galaxy/rice_galaxybioschemas.jsonld +++ b/data/rice_galaxy/rice_galaxybioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ028", "@type": "sc:CreativeWork" }, - { - "@id": "https://orcid.org/0000-0001-8512-144X", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/Rice_Galaxy", "@type": "sc:SoftwareApplication", @@ -26,18 +22,18 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:31107941", - "pmcid:PMC6527052", { "@id": "https://doi.org/10.1093/GIGASCIENCE/GIZ028" - } + }, + "pmcid:PMC6527052" ], "sc:description": "Open resource for plant science.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_0308" }, { - "@id": "edam:operation_0308" + "@id": "edam:operation_3196" }, { "@id": "edam:operation_3232" @@ -46,11 +42,15 @@ "sc:license": "AFL-3.0", "sc:name": "Rice Galaxy", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://13.250.174.27:8080/" + }, + { + "@id": "https://orcid.org/0000-0001-8512-144X", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/riddle/riddlebioschemas.jsonld b/data/riddle/riddlebioschemas.jsonld index 38b5736fe0b59..27276f1f58362 100644 --- a/data/riddle/riddlebioschemas.jsonld +++ b/data/riddle/riddlebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A network-based method for characterizing gene sets. It asks if an input query set is significantly “close” to a known pathway or disease set in the human functional network.", "sc:name": "RIDDLE", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.functionalnet.org/riddle/" } \ No newline at end of file diff --git a/data/rightfield/rightfieldbioschemas.jsonld b/data/rightfield/rightfieldbioschemas.jsonld index 4c53da0984ada..40da45749bb8a 100644 --- a/data/rightfield/rightfieldbioschemas.jsonld +++ b/data/rightfield/rightfieldbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "RightField", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ "manchester.ac.uk", diff --git a/data/riken/rikenbioschemas.jsonld b/data/riken/rikenbioschemas.jsonld index 965ca33dac6ba..b497a7dac94eb 100644 --- a/data/riken/rikenbioschemas.jsonld +++ b/data/riken/rikenbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "It integrates not only RIKEN’s original databases, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations.", "sc:name": "RIKEN integrated database of mammals", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://metadb.riken.jp/metadb/db/SciNetS_ria254i" } \ No newline at end of file diff --git a/data/ril-contour/ril-contourbioschemas.jsonld b/data/ril-contour/ril-contourbioschemas.jsonld index 92cdad107c8b4..f4279c043e401 100644 --- a/data/ril-contour/ril-contourbioschemas.jsonld +++ b/data/ril-contour/ril-contourbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RIL-Contour", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://gitlab.com/Philbrick/rilcontour" } \ No newline at end of file diff --git a/data/rilogo/rilogobioschemas.jsonld b/data/rilogo/rilogobioschemas.jsonld index 9042f11564152..80fba824974cf 100644 --- a/data/rilogo/rilogobioschemas.jsonld +++ b/data/rilogo/rilogobioschemas.jsonld @@ -25,9 +25,9 @@ "sc:license": "LGPL-2.1", "sc:name": "RILogo", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "binf.ku.dk", "sc:url": "http://rth.dk/resources/rilogo/", diff --git a/data/rimmport/rimmportbioschemas.jsonld b/data/rimmport/rimmportbioschemas.jsonld index c91faf5ce13ac..3b6254f7e9899 100644 --- a/data/rimmport/rimmportbioschemas.jsonld +++ b/data/rimmport/rimmportbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ravi Shankar", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.", "sc:license": "GPL-3.0", "sc:name": "RImmPort", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RImmPort.html", "sc:version": "1.2.0" diff --git a/data/ring/ringbioschemas.jsonld b/data/ring/ringbioschemas.jsonld index 3d47fec1a2ff9..2e569f5d8d53c 100644 --- a/data/ring/ringbioschemas.jsonld +++ b/data/ring/ringbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "RING", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", "sc:url": "http://protein.bio.unipd.it/ring", diff --git a/data/ringer/ringerbioschemas.jsonld b/data/ringer/ringerbioschemas.jsonld index fcb20f2d5a018..05b8bb9b78855 100644 --- a/data/ringer/ringerbioschemas.jsonld +++ b/data/ringer/ringerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The program detects molecular motions by automatic electron density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which part are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design.", "sc:name": "Ringer", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bl831.als.lbl.gov/ringer/" } \ No newline at end of file diff --git a/data/ringo/ringobioschemas.jsonld b/data/ringo/ringobioschemas.jsonld index 6a72e2c46022a..55b6ed3bf8600 100644 --- a/data/ringo/ringobioschemas.jsonld +++ b/data/ringo/ringobioschemas.jsonld @@ -16,15 +16,15 @@ "@id": "http://orcid.org/0000-0003-1471-1295" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pubmed:17594472", + "pmcid:PMC1906858", { "@id": "https://doi.org/10.1186/1471-2105-8-221" - }, - "pmcid:PMC1906858", - "pubmed:17594472" + } ], "sc:description": "The package facilitates primary analysis of ChIP-chip data. Its main functionalities are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. It has functions to deal with two-color nucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList or ExpressionSet. It employs functions from various other packages.", "sc:featureList": { @@ -33,9 +33,9 @@ "sc:license": "Artistic-2.0", "sc:name": "Ringo", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Ringo.html", "sc:version": "1.38.0" diff --git a/data/rinspector/rinspectorbioschemas.jsonld b/data/rinspector/rinspectorbioschemas.jsonld index 46eaf1f440ca7..5661e6a8401db 100644 --- a/data/rinspector/rinspectorbioschemas.jsonld +++ b/data/rinspector/rinspectorbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btx586", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/RINspector", "@type": "sc:SoftwareApplication", @@ -27,16 +31,12 @@ }, "sc:name": "RINspector", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://apps.cytoscape.org/apps/rinspector", "sc:version": "1.1.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btx586", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ripseeker/ripseekerbioschemas.jsonld b/data/ripseeker/ripseekerbioschemas.jsonld index 9ade704ed68c0..4f88458426fbb 100644 --- a/data/ripseeker/ripseekerbioschemas.jsonld +++ b/data/ripseeker/ripseekerbioschemas.jsonld @@ -18,11 +18,11 @@ "Library" ], "sc:citation": [ - "pubmed:23455476", - "pmcid:PMC3632129", { "@id": "https://doi.org/10.1093/nar/gkt142" - } + }, + "pubmed:23455476", + "pmcid:PMC3632129" ], "sc:description": "Infers and discriminates RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While this tool is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.", "sc:featureList": { @@ -31,9 +31,9 @@ "sc:license": "GPL-2.0", "sc:name": "RIPSeeker", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RIPSeeker.html", "sc:version": "1.14.0" diff --git a/data/riptide/riptidebioschemas.jsonld b/data/riptide/riptidebioschemas.jsonld index dfdc325a66dcf..9becd8d274093 100644 --- a/data/riptide/riptidebioschemas.jsonld +++ b/data/riptide/riptidebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "RIPTiDe", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/mjenior/riptide" diff --git a/data/risa/risabioschemas.jsonld b/data/risa/risabioschemas.jsonld index 2bb7849711e5d..f13ff115d74f3 100644 --- a/data/risa/risabioschemas.jsonld +++ b/data/risa/risabioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "http://orcid.org/0000-0003-3499-8262", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/1471-2105-15-S7-S11", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/risa", "@type": "sc:SoftwareApplication", @@ -26,18 +30,18 @@ "@id": "edam:data_1270" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": { "@id": "edam:topic_3361" }, "sc:citation": [ - "pubmed:24564732", "pmcid:PMC4015122", { "@id": "https://doi.org/10.1186/1471-2105-15-S7-S11" - } + }, + "pubmed:24564732" ], "sc:description": "This tool allows to access metadata/data in ISA-Tab (Investigation / Study / Assay tab-delimited) format and build BioConductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported. The package is extendable and efforts are undergoing to support metadata associated to proteomics assays.", "sc:featureList": { @@ -46,16 +50,12 @@ "sc:license": "GPL-3.0", "sc:name": "Risa", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Risa.html", "sc:version": "1.16.0" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-15-S7-S11", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/riscoper/riscoperbioschemas.jsonld b/data/riscoper/riscoperbioschemas.jsonld index c280158f3aaea..1b5b3fb7e1393 100644 --- a/data/riscoper/riscoperbioschemas.jsonld +++ b/data/riscoper/riscoperbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "RIscoper", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.rna-society.org/riscoper/" } \ No newline at end of file diff --git a/data/river/riverbioschemas.jsonld b/data/river/riverbioschemas.jsonld index c37890b3a6212..3d48be0c26eb3 100644 --- a/data/river/riverbioschemas.jsonld +++ b/data/river/riverbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "RIVER", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RIVER.html", "sc:version": "1.4.0" diff --git a/data/rjmcmcnucleosomes/rjmcmcnucleosomesbioschemas.jsonld b/data/rjmcmcnucleosomes/rjmcmcnucleosomesbioschemas.jsonld index b7e0ed3cd58c5..69b89bbb4b358 100644 --- a/data/rjmcmcnucleosomes/rjmcmcnucleosomesbioschemas.jsonld +++ b/data/rjmcmcnucleosomes/rjmcmcnucleosomesbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "RJMCMCNucleosomes", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RJMCMCNucleosomes.html", "sc:version": "1.4.0" diff --git a/data/rl-csa/rl-csabioschemas.jsonld b/data/rl-csa/rl-csabioschemas.jsonld index efb84d5d55064..6d6a9dc336aea 100644 --- a/data/rl-csa/rl-csabioschemas.jsonld +++ b/data/rl-csa/rl-csabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool for regular-language constrained pairwise global sequence alignment.", "sc:name": "RL-CSA", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.cs.bgu.ac.il/~negevcb/RL-CSA/" diff --git a/data/rlims-p/rlims-pbioschemas.jsonld b/data/rlims-p/rlims-pbioschemas.jsonld index de36ddbea8844..0c0daaf9845c2 100644 --- a/data/rlims-p/rlims-pbioschemas.jsonld +++ b/data/rlims-p/rlims-pbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Rule-based text-mining program specifically designed to extract protein phosphorylation information on protein kinase, substrate and phosphorylation sites from biomedical literature.", "sc:name": "RLIMS-P", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://research.bioinformatics.udel.edu/rlimsp/", diff --git a/data/rlmm/rlmmbioschemas.jsonld b/data/rlmm/rlmmbioschemas.jsonld index b43410daa308a..861d3df7d0db2 100644 --- a/data/rlmm/rlmmbioschemas.jsonld +++ b/data/rlmm/rlmmbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nusrat Rabbee", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, the algorithm will obtain more accurate classification results on new data. It is based on a linear model, uses the Mahalanobis distance for classification. Non-biological variation is removed through normalization. It captures similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification.", "sc:license": "GPL-2.0", "sc:name": "RLMM", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RLMM.html", "sc:version": "1.36.0" diff --git a/data/rloom/rloombioschemas.jsonld b/data/rloom/rloombioschemas.jsonld index 7f356a8af5c45..087de60fde504 100644 --- a/data/rloom/rloombioschemas.jsonld +++ b/data/rloom/rloombioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. It allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface.", "sc:name": "RLooM", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://rloom.mpimp-golm.mpg.de/" } \ No newline at end of file diff --git a/data/rmaexpress/rmaexpressbioschemas.jsonld b/data/rmaexpress/rmaexpressbioschemas.jsonld index f8103b5bbb0dd..1b26451df87b2 100644 --- a/data/rmaexpress/rmaexpressbioschemas.jsonld +++ b/data/rmaexpress/rmaexpressbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "RMAExpress", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://rmaexpress.bmbolstad.com/", "sc:version": "1.1.0" diff --git a/data/rmagpie/rmagpiebioschemas.jsonld b/data/rmagpie/rmagpiebioschemas.jsonld index 14ff86c909f47..6ed96d230055d 100644 --- a/data/rmagpie/rmagpiebioschemas.jsonld +++ b/data/rmagpie/rmagpiebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "Rmagpie", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rmagpie.html", "sc:version": "1.30.0" diff --git a/data/rmap/rmapbioschemas.jsonld b/data/rmap/rmapbioschemas.jsonld index 5aee23b4d0f91..0f474633252d5 100644 --- a/data/rmap/rmapbioschemas.jsonld +++ b/data/rmap/rmapbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-9-128", - "@type": "sc:CreativeWork" - }, { "@id": "https://doi.org/10.1186/1471-2105-14-184", "@type": "sc:CreativeWork" @@ -26,33 +22,37 @@ ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC3694458", - "pmcid:PMC2335322", - "pubmed:23758764", "pubmed:18307793", { - "@id": "https://doi.org/10.1186/1471-2105-9-128" + "@id": "https://doi.org/10.1186/1471-2105-14-184" }, + "pubmed:23758764", + "pmcid:PMC2335322", + "pmcid:PMC3694458", { - "@id": "https://doi.org/10.1186/1471-2105-14-184" + "@id": "https://doi.org/10.1186/1471-2105-9-128" } ], "sc:description": "Assembles 20 - 64 bp Solexa reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required.", "sc:featureList": [ { - "@id": "edam:operation_3198" + "@id": "edam:operation_3186" }, { - "@id": "edam:operation_3186" + "@id": "edam:operation_3198" } ], "sc:license": "GPL-3.0", "sc:name": "RMAP", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://rulai.cshl.edu/rmap" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-9-128", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rmassbank/rmassbankbioschemas.jsonld b/data/rmassbank/rmassbankbioschemas.jsonld index 07402c826004b..95afd9d17d3d9 100644 --- a/data/rmassbank/rmassbankbioschemas.jsonld +++ b/data/rmassbank/rmassbankbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "RMassBank at Eawag", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:23303751", "sc:description": "Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.", "sc:license": "Artistic-2.0", "sc:name": "RMassBank", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RMassBank.html", "sc:version": "2.2.1" diff --git a/data/rmat/rmatbioschemas.jsonld b/data/rmat/rmatbioschemas.jsonld index d7a95a1289d31..e05b0815dfa32 100644 --- a/data/rmat/rmatbioschemas.jsonld +++ b/data/rmat/rmatbioschemas.jsonld @@ -11,12 +11,12 @@ "@id": "https://bio.tools/rmat", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Raphael Gottardo", - "Arnaud Droit" + "Arnaud Droit", + "Raphael Gottardo" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and BioConductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments.", "sc:license": "Artistic-2.0", diff --git a/data/rmbase/rmbasebioschemas.jsonld b/data/rmbase/rmbasebioschemas.jsonld index a7c5ca291d246..4a14123787b25 100644 --- a/data/rmbase/rmbasebioschemas.jsonld +++ b/data/rmbase/rmbasebioschemas.jsonld @@ -18,24 +18,24 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jian-Hua Yang", "sc:additionalType": [ - "Web service", "Database portal", + "Web service", "Web application" ], "sc:citation": [ + "pubmed:29040692", "pmcid:PMC5753293", { "@id": "https://doi.org/10.1093/nar/gkx934" - }, - "pubmed:29040692" + } ], "sc:description": "Database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs, as well as their relationships with microRNA binding events, disease-related SNPs and RNA-binding proteins (RBP).", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_0417" }, { - "@id": "edam:operation_0417" + "@id": "edam:operation_2495" }, { "@id": "edam:operation_3196" @@ -44,9 +44,9 @@ "sc:license": "GPL-3.0", "sc:name": "RMBase", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://rna.sysu.edu.cn/rmbase/index.php", "sc:version": "2.0" diff --git a/data/rmir/bioconda_rmir.yaml b/data/rmir/bioconda_rmir.yaml index 9d048609608ca..82a8a64c5c5a2 100644 --- a/data/rmir/bioconda_rmir.yaml +++ b/data/rmir/bioconda_rmir.yaml @@ -4,7 +4,6 @@ description: Useful functions to merge microRNA and respective targets using dif home: https://bioconductor.org/packages/3.10/bioc/html/RmiR.html identifiers: - biotools:rmir -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-rmir summary: Package to work with miRNAs and miRNA targets with R diff --git a/data/rmir/rmirbioschemas.jsonld b/data/rmir/rmirbioschemas.jsonld index c63a2e25e6ec8..2851a33744710 100644 --- a/data/rmir/rmirbioschemas.jsonld +++ b/data/rmir/rmirbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "RmiR", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RmiR.html", "sc:version": "1.30.0" diff --git a/data/rmsi/rmsibioschemas.jsonld b/data/rmsi/rmsibioschemas.jsonld index 5c1b8ca21ebd3..de9f0ead91145 100644 --- a/data/rmsi/rmsibioschemas.jsonld +++ b/data/rmsi/rmsibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "rMSI", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/prafols/rMSI" } \ No newline at end of file diff --git a/data/rmut/rmutbioschemas.jsonld b/data/rmut/rmutbioschemas.jsonld index 4ca15d1892140..c39ba87c68467 100644 --- a/data/rmut/rmutbioschemas.jsonld +++ b/data/rmut/rmutbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Apache-2.0", "sc:name": "RMut", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/csclab/RMut" } \ No newline at end of file diff --git a/data/rmycoportal/rmycoportalbioschemas.jsonld b/data/rmycoportal/rmycoportalbioschemas.jsonld index e3699722f1358..1309363b7415f 100644 --- a/data/rmycoportal/rmycoportalbioschemas.jsonld +++ b/data/rmycoportal/rmycoportalbioschemas.jsonld @@ -15,27 +15,27 @@ "biotools:primaryContact": "Franz-Sebastian Krah", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6341041", { "@id": "https://doi.org/10.3897/BDJ.7.e31511" }, - "pubmed:30686929" + "pubmed:30686929", + "pmcid:PMC6341041" ], "sc:description": "R package to interface with the Mycology Collections Portal.", "sc:featureList": [ { - "@id": "edam:operation_3435" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_3435" } ], "sc:license": "GPL-3.0", "sc:name": "rMyCoPortal", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/FranzKrah/rMyCoPortal" }, diff --git a/data/rna-express/rna-expressbioschemas.jsonld b/data/rna-express/rna-expressbioschemas.jsonld index b677d7f3a8dc9..f3868cd53e82c 100644 --- a/data/rna-express/rna-expressbioschemas.jsonld +++ b/data/rna-express/rna-expressbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. This approach complements existing gene annotation databases by ensuring all transcripts present in the sample are considered for further analysis.", "sc:name": "RNA-eXpress", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.rnaexpress.org/" diff --git a/data/rna-molp/rna-molpbioschemas.jsonld b/data/rna-molp/rna-molpbioschemas.jsonld index ea7451f06455a..69e21888bbe0c 100644 --- a/data/rna-molp/rna-molpbioschemas.jsonld +++ b/data/rna-molp/rna-molpbioschemas.jsonld @@ -9,29 +9,25 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkx429", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rna-molp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jérôme Waldispühl", "edam:has_input": [ { - "@id": "edam:data_3496" + "@id": "edam:data_0850" }, { - "@id": "edam:data_0850" + "@id": "edam:data_3496" } ], "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5793723", { "@id": "https://doi.org/10.1093/nar/gkx429" }, - "pubmed:28525607" + "pubmed:28525607", + "pmcid:PMC5793723" ], "sc:description": "Predicting RNA hybrid 2D–3D structures from sequence data only. Optionally, it can be used for (i) local 3D motif prediction or (ii) the refinement of user-defined secondary structures. Importantly, our web server automatically generates a script for the MC-Sym software, which can be immediately used to quickly predict all-atom RNA 3D models.", "sc:featureList": [ @@ -39,14 +35,18 @@ "@id": "edam:operation_0278" }, { - "@id": "edam:operation_0267" + "@id": "edam:operation_0502" }, { - "@id": "edam:operation_0502" + "@id": "edam:operation_0267" } ], "sc:name": "RNA-MolP", "sc:url": "http://rnamoip.cs.mcgill.ca/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkx429", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rna-seqc/rna-seqcbioschemas.jsonld b/data/rna-seqc/rna-seqcbioschemas.jsonld index e30eb56593e98..a3d1dc04aef9b 100644 --- a/data/rna-seqc/rna-seqcbioschemas.jsonld +++ b/data/rna-seqc/rna-seqcbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Computes a series of quality control metrics for RNA-seq data.", "sc:name": "RNA-SeQC", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.broadinstitute.org/cancer/cga/rna-seqc", "sc:version": "1.1.8" diff --git a/data/rna2dmap/rna2dmapbioschemas.jsonld b/data/rna2dmap/rna2dmapbioschemas.jsonld index 0bb9240eb38ed..b5f26f40584ce 100644 --- a/data/rna2dmap/rna2dmapbioschemas.jsonld +++ b/data/rna2dmap/rna2dmapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A structural interface to comparative data. Currently, it presents three-dimensional RNA distances, tertiary interactions, conservation values, motifs, basepair groups, basepair conformations and coaxial stacks on interactive secondary structure models.", "sc:name": "RNA2DMap", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.rna.icmb.utexas.edu/SIM/4F/RNA2DMap/" diff --git a/data/rna_analyzer/rna_analyzerbioschemas.jsonld b/data/rna_analyzer/rna_analyzerbioschemas.jsonld index be2d994f0e98a..22fbde0ce55cb 100644 --- a/data/rna_analyzer/rna_analyzerbioschemas.jsonld +++ b/data/rna_analyzer/rna_analyzerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Searches for known structures and identifies RNA motifs in your input sequence.", "sc:name": "RNA Analyzer", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/" } \ No newline at end of file diff --git a/data/rna_compass/rna_compassbioschemas.jsonld b/data/rna_compass/rna_compassbioschemas.jsonld index 4080bcd005591..b10940a47a7c4 100644 --- a/data/rna_compass/rna_compassbioschemas.jsonld +++ b/data/rna_compass/rna_compassbioschemas.jsonld @@ -22,16 +22,16 @@ { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0089445" }, - "pubmed:24586784", - "pmcid:PMC3934900" + "pmcid:PMC3934900", + "pubmed:24586784" ], "sc:description": "A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets.", "sc:featureList": [ { - "@id": "edam:operation_3461" + "@id": "edam:operation_3680" }, { - "@id": "edam:operation_3680" + "@id": "edam:operation_3461" } ], "sc:name": "RNA CoMPASS", diff --git a/data/rna_cossmos/rna_cossmosbioschemas.jsonld b/data/rna_cossmos/rna_cossmosbioschemas.jsonld index 9b0b1b06e02b5..997916269e3c5 100644 --- a/data/rna_cossmos/rna_cossmosbioschemas.jsonld +++ b/data/rna_cossmos/rna_cossmosbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Characterization of Secondary Structure Motifs: a searchable database of secondary structure motifs in RNA three-dimensional structures.", "sc:name": "RNA CoSSMos", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://cossmos.slu.edu/" } \ No newline at end of file diff --git a/data/rna_frabase/rna_frabasebioschemas.jsonld b/data/rna_frabase/rna_frabasebioschemas.jsonld index 7e14983e66e0b..9cef55da1be45 100644 --- a/data/rna_frabase/rna_frabasebioschemas.jsonld +++ b/data/rna_frabase/rna_frabasebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "An engine with database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation.", "sc:name": "RNA FRABASE", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://rnafrabase.ibch.poznan.pl/", diff --git a/data/rna_helicase_database/rna_helicase_databasebioschemas.jsonld b/data/rna_helicase_database/rna_helicase_databasebioschemas.jsonld index 6e42178a31531..dbc579ad37c1f 100644 --- a/data/rna_helicase_database/rna_helicase_databasebioschemas.jsonld +++ b/data/rna_helicase_database/rna_helicase_databasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Integrates information on RNA helicases. The database allows retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mouse and human. The database is structured according to the most recent helicase classification into helicase superfamilies and families, emphasizes phyologenetic relations.", "sc:name": "RNA helicase database", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.rnahelicase.org" } \ No newline at end of file diff --git a/data/rna_movies/rna_moviesbioschemas.jsonld b/data/rna_movies/rna_moviesbioschemas.jsonld index bf8dc01366c26..4c7114dbb7930 100644 --- a/data/rna_movies/rna_moviesbioschemas.jsonld +++ b/data/rna_movies/rna_moviesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data.", "sc:name": "RNA Movies", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bibiserv.techfak.uni-bielefeld.de/rnamovies/" } \ No newline at end of file diff --git a/data/rnaalishapes/rnaalishapesbioschemas.jsonld b/data/rnaalishapes/rnaalishapesbioschemas.jsonld index 020d3272c95b2..0ca5ee72c05a7 100644 --- a/data/rnaalishapes/rnaalishapesbioschemas.jsonld +++ b/data/rnaalishapes/rnaalishapesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool for secondary structure prediction, using shape abstraction. Input is a multiple sequence alignment. Pseudoknots are not considered at all.", "sc:name": "RNAalishapes", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bibiserv2.cebitec.uni-bielefeld.de/rnaalishapes" } \ No newline at end of file diff --git a/data/rnabindr/rnabindrbioschemas.jsonld b/data/rnabindr/rnabindrbioschemas.jsonld index aead98294adf9..22323e78aa479 100644 --- a/data/rnabindr/rnabindrbioschemas.jsonld +++ b/data/rnabindr/rnabindrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A server for analyzing and predicting RNA binding sites in proteins.", "sc:name": "RNABindR", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://ailab1.ist.psu.edu/RNABindR/" } \ No newline at end of file diff --git a/data/rnabindrplus/rnabindrplusbioschemas.jsonld b/data/rnabindrplus/rnabindrplusbioschemas.jsonld index 84b83ab790d95..20c3b4ccc47b8 100644 --- a/data/rnabindrplus/rnabindrplusbioschemas.jsonld +++ b/data/rnabindrplus/rnabindrplusbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0097725", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/rnabindrplus", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4028231", + "pubmed:24846307", { "@id": "https://doi.org/10.1371/journal.pone.0097725" - }, - "pmcid:PMC4028231", - "pubmed:24846307" + } ], "sc:contributor": { "@id": "http://orcid.org/0000-0001-7088-5535" @@ -29,9 +33,9 @@ }, "sc:name": "RNABindRPlus", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ailab1.ist.psu.edu/RNABindRPlus/", "sc:version": "1.0" @@ -39,10 +43,6 @@ { "@id": "http://orcid.org/0000-0001-7088-5535", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0097725", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rnablueprint/rnablueprintbioschemas.jsonld b/data/rnablueprint/rnablueprintbioschemas.jsonld index 23c8462e76602..ddb18084b112b 100644 --- a/data/rnablueprint/rnablueprintbioschemas.jsonld +++ b/data/rnablueprint/rnablueprintbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/rnablueprint", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Stefan Hammer", "Sven Findeiß", - "Ivo L. Hofacker" + "Ivo L. Hofacker", + "Stefan Hammer" ], "sc:additionalType": "Command-line tool", "sc:description": "Flexible multiple target nucleic acid sequence design.", "sc:name": "RNAblueprint", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/ViennaRNA/RNAblueprint" } \ No newline at end of file diff --git a/data/rnabrowse/rnabrowsebioschemas.jsonld b/data/rnabrowse/rnabrowsebioschemas.jsonld index 4436e11de7c57..89c115a067e8b 100644 --- a/data/rnabrowse/rnabrowsebioschemas.jsonld +++ b/data/rnabrowse/rnabrowsebioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/rnabrowse", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:24823498", "sc:description": "The tool permits sequencing facilities and, even small, bioinformatic teams to give a user-friendly access to RNA-Seq de novo results, helping biologists to analyse and extract meaningful information from their data.", "sc:name": "RNAbrowse", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/ngspipelines/index.php/RNA-seq_denovo" } \ No newline at end of file diff --git a/data/rnacommender/rnacommenderbioschemas.jsonld b/data/rnacommender/rnacommenderbioschemas.jsonld index ff1dfb0e64298..999f400a413a1 100644 --- a/data/rnacommender/rnacommenderbioschemas.jsonld +++ b/data/rnacommender/rnacommenderbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/rnacommender", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Plug-in", - "Command-line tool" + "Command-line tool", + "Plug-in" ], "sc:citation": "pubmed:27503225", "sc:description": "A tool for genome-wide recommendation of RNA-protein interactions. It is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information, taking into account the protein domain composition and the RNA predicted secondary structure.", "sc:name": "RNAcommender", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://rnacommender.disi.unitn.it" } \ No newline at end of file diff --git a/data/rnacontext/rnacontextbioschemas.jsonld b/data/rnacontext/rnacontextbioschemas.jsonld index 211bedf2b8d3d..7308631836e53 100644 --- a/data/rnacontext/rnacontextbioschemas.jsonld +++ b/data/rnacontext/rnacontextbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "RNAcontext", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.cs.toronto.edu/~hilal/rnacontext/" } \ No newline at end of file diff --git a/data/rnact/rnactbioschemas.jsonld b/data/rnact/rnactbioschemas.jsonld index 6c1790514124d..7328204e96909 100644 --- a/data/rnact/rnactbioschemas.jsonld +++ b/data/rnact/rnactbioschemas.jsonld @@ -10,12 +10,12 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0001-6358-8380", + "@id": "https://orcid.org/0000-0003-0607-5663", "@type": "schema:Person" }, { - "@id": "https://doi.org/10.1093/nar/gky967", - "@type": "sc:CreativeWork" + "@id": "https://orcid.org/0000-0001-7524-6310", + "@type": "schema:Person" }, { "@id": "https://bio.tools/RNAct", @@ -27,14 +27,14 @@ { "@id": "edam:data_3021" }, - { - "@id": "edam:data_2725" - }, { "@id": "edam:data_1026" }, { "@id": "edam:data_1033" + }, + { + "@id": "edam:data_2725" } ], "edam:has_output": { @@ -43,10 +43,10 @@ "sc:additionalType": "Database portal", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0128" + "@id": "edam:topic_0099" }, { - "@id": "edam:topic_0099" + "@id": "edam:topic_0128" }, { "@id": "edam:topic_0602" @@ -56,11 +56,11 @@ "@id": "http://orcid.org/0000-0001-6358-8380" }, "sc:citation": [ + "pmcid:PMC6324028", "pubmed:30445601", { "@id": "https://doi.org/10.1093/nar/gky967" - }, - "pmcid:PMC6324028" + } ], "sc:contributor": { "@id": "https://orcid.org/0000-0003-0607-5663" @@ -78,11 +78,11 @@ "sc:url": "https://rnact.crg.eu" }, { - "@id": "https://orcid.org/0000-0003-0607-5663", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/nar/gky967", + "@type": "sc:CreativeWork" }, { - "@id": "https://orcid.org/0000-0001-7524-6310", + "@id": "http://orcid.org/0000-0001-6358-8380", "@type": "schema:Person" } ] diff --git a/data/rnadecay/rnadecaybioschemas.jsonld b/data/rnadecay/rnadecaybioschemas.jsonld index c59fa48e2d619..a2f665853674b 100644 --- a/data/rnadecay/rnadecaybioschemas.jsonld +++ b/data/rnadecay/rnadecaybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "RNAdecay", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RNAdecay.html", "sc:version": "1.0.2" diff --git a/data/rnaeditingatlas/rnaeditingatlasbioschemas.jsonld b/data/rnaeditingatlas/rnaeditingatlasbioschemas.jsonld index fbdebed23661b..2cbd8aa446f6e 100644 --- a/data/rnaeditingatlas/rnaeditingatlasbioschemas.jsonld +++ b/data/rnaeditingatlas/rnaeditingatlasbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An Atlas of RNA editing events in human tissues.", "sc:name": "RNAeditingAtlas", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ELIXIR-ITA-CNR", "sc:url": "http://srv00.recas.ba.infn.it/editing/" diff --git a/data/rnaex/rnaexbioschemas.jsonld b/data/rnaex/rnaexbioschemas.jsonld index 849ac3f556643..5cb4d6d6255b8 100644 --- a/data/rnaex/rnaexbioschemas.jsonld +++ b/data/rnaex/rnaexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RNAex", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://lulab.life.tsinghua.edu.cn/RNAex/" } \ No newline at end of file diff --git a/data/rnahybrid/rnahybridbioschemas.jsonld b/data/rnahybrid/rnahybridbioschemas.jsonld index 9e442fe804fc5..df9d9765e05e4 100644 --- a/data/rnahybrid/rnahybridbioschemas.jsonld +++ b/data/rnahybrid/rnahybridbioschemas.jsonld @@ -11,21 +11,21 @@ "@id": "https://bio.tools/rnahybrid", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", + "Web application", "Web API", - "Web application" + "Command-line tool" ], "sc:author": "Marc Rehmsmeier", "sc:description": "Tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.", "sc:name": "RNAhybrid", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": [ - "BiBiServ", - "Bielefeld university" + "Bielefeld university", + "BiBiServ" ], "sc:url": "http://bibiserv.cebitec.uni-bielefeld.de/rnahybrid", "sc:version": "2.2.1" diff --git a/data/rnainteract/rnainteractbioschemas.jsonld b/data/rnainteract/rnainteractbioschemas.jsonld index e1d2b6707afec..e6abb24747e63 100644 --- a/data/rnainteract/rnainteractbioschemas.jsonld +++ b/data/rnainteract/rnainteractbioschemas.jsonld @@ -16,17 +16,17 @@ "@id": "http://orcid.org/0000-0001-9437-2099" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:21378980", "sc:description": "This tool estimates genetic interactions from multi-dimensional read-outs like features extracted from images. The screen is assumed to be performed in multi-well plates or similar designs. Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis.", "sc:license": "Artistic-2.0", "sc:name": "RNAinteract", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RNAinteract.html", "sc:version": "1.22.0" diff --git a/data/rnaither/rnaitherbioschemas.jsonld b/data/rnaither/rnaitherbioschemas.jsonld index 014bee551207f..147a2ca248c20 100644 --- a/data/rnaither/rnaitherbioschemas.jsonld +++ b/data/rnaither/rnaitherbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lars Kaderali", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This tool analyzes cell-based RNAi screens, including quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes.", "sc:license": "Artistic-2.0", diff --git a/data/rnalien/rnalienbioschemas.jsonld b/data/rnalien/rnalienbioschemas.jsonld index e82dcd114708d..62add47916d97 100644 --- a/data/rnalien/rnalienbioschemas.jsonld +++ b/data/rnalien/rnalienbioschemas.jsonld @@ -23,19 +23,19 @@ "@id": "http://orcid.org/0000-0001-9564-7525" }, "sc:citation": [ - "pubmed:27330139", - "pmcid:PMC5041467", { "@id": "https://doi.org/10.1093/nar/gkw558" - } + }, + "pmcid:PMC5041467", + "pubmed:27330139" ], "sc:description": "RNAlien is a tool for automatic construction of RNA family models from a single sequence. Results include a covariance model, structural alignment and consensus secondary structure.", "sc:featureList": [ { - "@id": "edam:operation_0338" + "@id": "edam:operation_0504" }, { - "@id": "edam:operation_0504" + "@id": "edam:operation_0338" }, { "@id": "edam:operation_2441" diff --git a/data/rnaloss/rnalossbioschemas.jsonld b/data/rnaloss/rnalossbioschemas.jsonld index c995d24289ca5..7a6540d245d5d 100644 --- a/data/rnaloss/rnalossbioschemas.jsonld +++ b/data/rnaloss/rnalossbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "RNALOSS (RNA locally optimal secondary structure) is a tool for the computation of locally optimal secondary structures.", "sc:name": "RNALOSS", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioinformatics.bc.edu/clotelab/RNALOSS/" diff --git a/data/rnamdb/rnamdbbioschemas.jsonld b/data/rnamdb/rnamdbbioschemas.jsonld index 2f19fd1e3fbd4..de5325cb0c752 100644 --- a/data/rnamdb/rnamdbbioschemas.jsonld +++ b/data/rnamdb/rnamdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The RNA Modification Database contains information pertaining to naturally occurring RNA modifications. The database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. Each entry provides the chemical structure, common name and symbol, elemental composition and mass, CA registry numbers and index name, phylogenetic source, type of RNA species.", "sc:name": "The RNA Modification Database (RNAMDB)", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mods.rna.albany.edu/" } \ No newline at end of file diff --git a/data/rnammer/rnammerbioschemas.jsonld b/data/rnammer/rnammerbioschemas.jsonld index 0177c856aa879..702e16ec8c5b3 100644 --- a/data/rnammer/rnammerbioschemas.jsonld +++ b/data/rnammer/rnammerbioschemas.jsonld @@ -13,8 +13,8 @@ "biotools:primaryContact": "Hans-Henrik Staerfeldt", "sc:additionalType": [ "Web service", - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Prediction of 5S/8S, 16S/18S, and 23S/28S ribosomal RNA in full genome sequences.", "sc:license": "Other", diff --git a/data/rnamutants/rnamutantsbioschemas.jsonld b/data/rnamutants/rnamutantsbioschemas.jsonld index a27e5d0911781..5c923dd6d655f 100644 --- a/data/rnamutants/rnamutantsbioschemas.jsonld +++ b/data/rnamutants/rnamutantsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "A web server to explore the effect of mutations on the RNA secondary structures.", "sc:name": "RNAmutants", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioinformatics.bc.edu/clotelab/RNAmutants/" } \ No newline at end of file diff --git a/data/rnapagenumber/rnapagenumberbioschemas.jsonld b/data/rnapagenumber/rnapagenumberbioschemas.jsonld index d7c9d679a3c9f..f128b17fe5b60 100644 --- a/data/rnapagenumber/rnapagenumberbioschemas.jsonld +++ b/data/rnapagenumber/rnapagenumberbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "rnapagenumber", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioinformatics.bc.edu/clotelab/RNApagenumber/index.spy" } \ No newline at end of file diff --git a/data/rnaparametric/rnaparametricbioschemas.jsonld b/data/rnaparametric/rnaparametricbioschemas.jsonld index 994318d6eb3b7..81794d1ec4c3b 100644 --- a/data/rnaparametric/rnaparametricbioschemas.jsonld +++ b/data/rnaparametric/rnaparametricbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A RNA parametric structure webserver that can compute the minimum free energy structure, the partition function Z(k) over all secondary structures having exactly k hairpins, minimum free energy structure and partition function Z(k) over all secondary structures having exactly k multiloops.", "sc:name": "RNAparametric", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioinformatics.bc.edu/clotelab/RNAparametric/index.spy" } \ No newline at end of file diff --git a/data/rnapasta/rnapastabioschemas.jsonld b/data/rnapasta/rnapastabioschemas.jsonld index 55ca657a25bac..1e9c3f7ffd8c3 100644 --- a/data/rnapasta/rnapastabioschemas.jsonld +++ b/data/rnapasta/rnapastabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A utility for collecting statistics from aligned and structurally annotated RNA sequences. It is a java utility intended to work with RNA structural alignments, including the motifs of stem-loops and pseudoknots. It can perform a variety of statistical analyses, and has editing capabilities intended to be useful with alignments that contain variable data such as the presence or absence of stem-loops or pseudoknots across sequences.", "sc:name": "RNApasta", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://rna-informatics.uga.edu/malmberg/rlmlab/index.php?s=1&n=5&r=0" } \ No newline at end of file diff --git a/data/rnapdbee/rnapdbeebioschemas.jsonld b/data/rnapdbee/rnapdbeebioschemas.jsonld index 879f69ef474a0..252dbccaa448d 100644 --- a/data/rnapdbee/rnapdbeebioschemas.jsonld +++ b/data/rnapdbee/rnapdbeebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RNApdbee", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://rnapdbee.cs.put.poznan.pl/" } \ No newline at end of file diff --git a/data/rnaplex/rnaplexbioschemas.jsonld b/data/rnaplex/rnaplexbioschemas.jsonld index 41a0963d033e2..ccfafc6cf13e6 100644 --- a/data/rnaplex/rnaplexbioschemas.jsonld +++ b/data/rnaplex/rnaplexbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Rapidly search for short interactions between two long RNAs.", "sc:name": "RNAplex", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bioinf.uni-leipzig.de/Software/RNAplex/", "sc:version": "0.2" diff --git a/data/rnapred/rnapredbioschemas.jsonld b/data/rnapred/rnapredbioschemas.jsonld index 072c6dd9fd447..cf85f7c0581b5 100644 --- a/data/rnapred/rnapredbioschemas.jsonld +++ b/data/rnapred/rnapredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RNApred", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.imtech.res.in/raghava/rnapred/" } \ No newline at end of file diff --git a/data/rnapredator/rnapredatorbioschemas.jsonld b/data/rnapredator/rnapredatorbioschemas.jsonld index 105c29211e7f6..147a6a3ca18aa 100644 --- a/data/rnapredator/rnapredatorbioschemas.jsonld +++ b/data/rnapredator/rnapredatorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "RNApredator is a web server for the prediction of bacterial sRNA targets. The user can choose from a large selection of genomes. Accessibility of the target to the sRNA is considered.", "sc:name": "RNApredator", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://rna.tbi.univie.ac.at/RNApredator" } \ No newline at end of file diff --git a/data/rnaprobr/rnaprobrbioschemas.jsonld b/data/rnaprobr/rnaprobrbioschemas.jsonld index 93dda0249c366..c422253d79f15 100644 --- a/data/rnaprobr/rnaprobrbioschemas.jsonld +++ b/data/rnaprobr/rnaprobrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-1854-1193", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/rnaprobr", "@type": "sc:SoftwareApplication", @@ -16,8 +20,8 @@ "@id": "http://orcid.org/0000-0002-1854-1193" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:26068741", "sc:description": "This package facilitates analysis of Next Generation Sequencing data for which positional information with a single nucleotide resolution is a key. It allows for applying different types of relevant normalizations, data visualization and export in a table or UCSC compatible bedgraph file.", @@ -25,15 +29,11 @@ "sc:name": "RNAprobR", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RNAprobR.html", "sc:version": "1.6.0" - }, - { - "@id": "http://orcid.org/0000-0002-1854-1193", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/rnaquast/rnaquastbioschemas.jsonld b/data/rnaquast/rnaquastbioschemas.jsonld index fa398c8cf8dcd..8b354ce004ac9 100644 --- a/data/rnaquast/rnaquastbioschemas.jsonld +++ b/data/rnaquast/rnaquastbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "rnaQUAST", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cab.spbu.ru/software/rnaquast/" } \ No newline at end of file diff --git a/data/rnaredprint/rnaredprintbioschemas.jsonld b/data/rnaredprint/rnaredprintbioschemas.jsonld index d73b7602e5335..c06e025a1a47b 100644 --- a/data/rnaredprint/rnaredprintbioschemas.jsonld +++ b/data/rnaredprint/rnaredprintbioschemas.jsonld @@ -19,10 +19,10 @@ "biotools:primaryContact": "Yann Ponty", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6482512", { "@id": "https://doi.org/10.1186/s12859-019-2784-7" }, - "pmcid:PMC6482512", "pubmed:31023239" ], "sc:description": "Fixed-parameter tractable sampling for RNA design with multiple target structures.", diff --git a/data/rnasamba/rnasambabioschemas.jsonld b/data/rnasamba/rnasambabioschemas.jsonld index dc0f1e98f0802..825273b411d65 100644 --- a/data/rnasamba/rnasambabioschemas.jsonld +++ b/data/rnasamba/rnasambabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "RNAsamba", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://rnasamba.lge.ibi.unicamp.br/", "sc:version": "0.2.4" diff --git a/data/rnascclust/rnascclustbioschemas.jsonld b/data/rnascclust/rnascclustbioschemas.jsonld index fa8427d686ced..e47b9df211607 100644 --- a/data/rnascclust/rnascclustbioschemas.jsonld +++ b/data/rnascclust/rnascclustbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/rnascclust", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rolf Backofen", - "Jan Gorodkin" + "Jan Gorodkin", + "Rolf Backofen" ], "sc:additionalType": "Command-line tool", "sc:description": "Clustering RNA sequences using structure conservation and graph based motifs.", "sc:license": "GPL-3.0", "sc:name": "RNAscClust", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bioinf.uni-freiburg.de/Software/RNAscClust/" } \ No newline at end of file diff --git a/data/rnaseqbrowser/rnaseqbrowserbioschemas.jsonld b/data/rnaseqbrowser/rnaseqbrowserbioschemas.jsonld index 73ee198272fed..45fb0f868b105 100644 --- a/data/rnaseqbrowser/rnaseqbrowserbioschemas.jsonld +++ b/data/rnaseqbrowser/rnaseqbrowserbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-4927-5123", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/rnaseqbrowser", "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:25766521", "pmcid:PMC4355470", { "@id": "https://doi.org/10.1186/s12864-015-1346-2" - } + }, + "pubmed:25766521" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-4927-5123" @@ -29,9 +33,9 @@ }, "sc:name": "RNASeqBrowser", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.australianprostatecentre.org/research/software/rnaseqbrowser", "sc:version": "V2" @@ -39,10 +43,6 @@ { "@id": "https://doi.org/10.1186/s12864-015-1346-2", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-4927-5123", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/rnaseqcomp/rnaseqcompbioschemas.jsonld b/data/rnaseqcomp/rnaseqcompbioschemas.jsonld index 08e60999db20e..2746d96e6c11b 100644 --- a/data/rnaseqcomp/rnaseqcompbioschemas.jsonld +++ b/data/rnaseqcomp/rnaseqcompbioschemas.jsonld @@ -18,10 +18,10 @@ "Library" ], "sc:citation": [ + "pmcid:PMC5045616", { "@id": "https://doi.org/10.1186/s13059-016-1060-7" }, - "pmcid:PMC5045616", "pubmed:27716375" ], "sc:description": "Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with necessary meta information should be organized into numeric matrices in order to proceed the evaluation.", @@ -32,8 +32,8 @@ "sc:name": "rnaseqcomp", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rnaseqcomp.html", "sc:version": "1.4.0" diff --git a/data/rnaseqgui/rnaseqguibioschemas.jsonld b/data/rnaseqgui/rnaseqguibioschemas.jsonld index 64047e0ba189b..54a0e2b40225c 100644 --- a/data/rnaseqgui/rnaseqguibioschemas.jsonld +++ b/data/rnaseqgui/rnaseqguibioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "A graphical user interface for the identification of differentially expressed genes from RNA-Seq experiments.", "sc:name": "RNASeqGUI", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioinfo.na.iac.cnr.it/RNASeqGUI/" diff --git a/data/rnaseqmap/rnaseqmapbioschemas.jsonld b/data/rnaseqmap/rnaseqmapbioschemas.jsonld index e40ffb471648b..b7e47ff2c9980 100644 --- a/data/rnaseqmap/rnaseqmapbioschemas.jsonld +++ b/data/rnaseqmap/rnaseqmapbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "rnaSeqMap", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rnaSeqMap.html", diff --git a/data/rnaseqmut/rnaseqmutbioschemas.jsonld b/data/rnaseqmut/rnaseqmutbioschemas.jsonld index 175b6888830b0..ce70dfc7b7f61 100644 --- a/data/rnaseqmut/rnaseqmutbioschemas.jsonld +++ b/data/rnaseqmut/rnaseqmutbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "RNASeqMut is an easy-to-use program to detection variants in RNA-Seq read alignments. rnaseqmut is a light-weight C++ program to detect variants (or mutations, including SNPs, indels, RNA editing events) from a single or multiple RNA-Seq BAM files.", "sc:name": "RNASeqMut", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://allaboutbioinfo.blogspot.ca/2013/09/detecting-mutations-from-rna-seq.html", "sc:version": "0.7" diff --git a/data/rnaseqpower/rnaseqpowerbioschemas.jsonld b/data/rnaseqpower/rnaseqpowerbioschemas.jsonld index 9481d83117117..81a7b137e0877 100644 --- a/data/rnaseqpower/rnaseqpowerbioschemas.jsonld +++ b/data/rnaseqpower/rnaseqpowerbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Terry M Therneau", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Sample size and power computation for RNA-seq studies.", "sc:license": "GPL-2.0", "sc:name": "RNASeqPower", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RNASeqPower.html", "sc:version": "1.14.0" diff --git a/data/rnaseqpowercalculator/rnaseqpowercalculatorbioschemas.jsonld b/data/rnaseqpowercalculator/rnaseqpowercalculatorbioschemas.jsonld index fc4388b2a54ec..8bc8d8bc8beda 100644 --- a/data/rnaseqpowercalculator/rnaseqpowercalculatorbioschemas.jsonld +++ b/data/rnaseqpowercalculator/rnaseqpowercalculatorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool captures the dispersion in the data and can serve as a practical reference under the budget constraint of RNA-Seq experiments.", "sc:name": "RNASeqPowerCalculator", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www2.hawaii.edu/~lgarmire/RNASeqPowerCalculator.htm" } \ No newline at end of file diff --git a/data/rnaseqsamplesize/rnaseqsamplesizebioschemas.jsonld b/data/rnaseqsamplesize/rnaseqsamplesizebioschemas.jsonld index 3e1cc81b24e62..c702cb0667e61 100644 --- a/data/rnaseqsamplesize/rnaseqsamplesizebioschemas.jsonld +++ b/data/rnaseqsamplesize/rnaseqsamplesizebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Shilin Zhao", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data.", "sc:license": "GPL-2.0", "sc:name": "RnaSeqSampleSize", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RnaSeqSampleSize.html", "sc:version": "1.6.0" diff --git a/data/rnasnoop/rnasnoopbioschemas.jsonld b/data/rnasnoop/rnasnoopbioschemas.jsonld index 9bce7783b70bc..fb7c64db6f55d 100644 --- a/data/rnasnoop/rnasnoopbioschemas.jsonld +++ b/data/rnasnoop/rnasnoopbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool especially designed to search for putative interactions between a H/ACA snoRNA stem and a list of target sequence. It implements a dynamic programming algorithm that computes thermodynamically optimal H/ACA-RNA interactions in an efficient scanning variant.", "sc:name": "RNAsnoop", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.bioinf.uni-leipzig.de/~htafer/RNAsnoop/RNAsnoop.html" } \ No newline at end of file diff --git a/data/rnasnp/rnasnpbioschemas.jsonld b/data/rnasnp/rnasnpbioschemas.jsonld index fd28a39bec46f..390a0690b3912 100644 --- a/data/rnasnp/rnasnpbioschemas.jsonld +++ b/data/rnasnp/rnasnpbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "RNAsnp", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://rth.dk/resources/rnasnp" } \ No newline at end of file diff --git a/data/rnasoft/rnasoftbioschemas.jsonld b/data/rnasoft/rnasoftbioschemas.jsonld index a3e11f87a962f..7d2f4f332c7a3 100644 --- a/data/rnasoft/rnasoftbioschemas.jsonld +++ b/data/rnasoft/rnasoftbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Software for RNA/DNA secondary structure prediction and design.", "sc:name": "RNAsoft", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.rnasoft.ca/" } \ No newline at end of file diff --git a/data/rnaspades/rnaspadesbioschemas.jsonld b/data/rnaspades/rnaspadesbioschemas.jsonld index 08ebd608ad9ff..331d8d0abdeb0 100644 --- a/data/rnaspades/rnaspadesbioschemas.jsonld +++ b/data/rnaspades/rnaspadesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Pipeline for de novo transcriptome assembly from RNA-Seq.", "sc:name": "rnaspades", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://cab.spbu.ru/software/spades/", "sc:version": "3.9.0" diff --git a/data/rnassess/rnassessbioschemas.jsonld b/data/rnassess/rnassessbioschemas.jsonld index 85bd01c460b65..ab7f740b4e4cf 100644 --- a/data/rnassess/rnassessbioschemas.jsonld +++ b/data/rnassess/rnassessbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKV557", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/rnassess", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact form", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4489242", - "pubmed:26068469", { "@id": "https://doi.org/10.1093/NAR/GKV557" - } + }, + "pmcid:PMC4489242", + "pubmed:26068469" ], "sc:description": "A web server for quality assessment of RNA 3D structure.", "sc:featureList": [ @@ -32,15 +36,11 @@ ], "sc:name": "RNAssess", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://rnassess.cs.put.poznan.pl/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKV557", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rnastrand/rnastrandbioschemas.jsonld b/data/rnastrand/rnastrandbioschemas.jsonld index b3b371ca296e4..775cf459d8b42 100644 --- a/data/rnastrand/rnastrandbioschemas.jsonld +++ b/data/rnastrand/rnastrandbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "RNAstrand predicts the reading direction of a structured RNA in a multiple sequence alignment by employing a support vector machine (SVM)", "sc:name": "RNAstrand", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.bioinf.uni-leipzig.de/Software/RNAstrand/", "sc:version": "2.0" diff --git a/data/rnastructure/rnastructurebioschemas.jsonld b/data/rnastructure/rnastructurebioschemas.jsonld index 7aaef9b322a0a..21b854a28bca6 100644 --- a/data/rnastructure/rnastructurebioschemas.jsonld +++ b/data/rnastructure/rnastructurebioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "RNAstructure", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://rna.urmc.rochester.edu/RNAstructure.html" } \ No newline at end of file diff --git a/data/rnathermsw/rnathermswbioschemas.jsonld b/data/rnathermsw/rnathermswbioschemas.jsonld index 0dd04a363a17f..4a1f56bcfef39 100644 --- a/data/rnathermsw/rnathermswbioschemas.jsonld +++ b/data/rnathermsw/rnathermswbioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PONE.0094340", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rnathermsw", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC3981793", "pubmed:24718440", + "pmcid:PMC3981793", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0094340" } @@ -32,10 +28,14 @@ "sc:name": "RNAthermsw", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.cs.bgu.ac.il/~rnathemsw/RNAthemsw/" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PONE.0094340", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rnatips/rnatipsbioschemas.jsonld b/data/rnatips/rnatipsbioschemas.jsonld index 46e7ef3fc9d54..02ab30882f4b2 100644 --- a/data/rnatips/rnatipsbioschemas.jsonld +++ b/data/rnatips/rnatipsbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Unlicense", "sc:name": "RNAtips", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://webclu.bio.wzw.tum.de/cgi-bin/RNAtips/start.cgi" diff --git a/data/rnavirusdb/rnavirusdbbioschemas.jsonld b/data/rnavirusdb/rnavirusdbbioschemas.jsonld index 652e4116f6376..db3dcde0baf21 100644 --- a/data/rnavirusdb/rnavirusdbbioschemas.jsonld +++ b/data/rnavirusdb/rnavirusdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "RNA virus genome database.", "sc:name": "RNA virus genome database (RNAVirusDB)", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioafrica.mrc.ac.za/rnavirusdb/" } \ No newline at end of file diff --git a/data/rnaz/rnazbioschemas.jsonld b/data/rnaz/rnazbioschemas.jsonld index befdce46e1ab0..831b9fa2f7659 100644 --- a/data/rnaz/rnazbioschemas.jsonld +++ b/data/rnaz/rnazbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "RNAz", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://rna.tbi.univie.ac.at/cgi-bin/RNAz/RNAz.cgi" } \ No newline at end of file diff --git a/data/rnits/bioconda_rnits.yaml b/data/rnits/bioconda_rnits.yaml index c491aab9a91df..9c376fe82ca52 100644 --- a/data/rnits/bioconda_rnits.yaml +++ b/data/rnits/bioconda_rnits.yaml @@ -4,7 +4,6 @@ description: R/Bioconductor package for normalization, curve registration and in home: https://bioconductor.org/packages/3.10/bioc/html/Rnits.html identifiers: - biotools:rnits -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rnits diff --git a/data/rnits/rnitsbioschemas.jsonld b/data/rnits/rnitsbioschemas.jsonld index 90786b76eec82..da7953fb5c8e6 100644 --- a/data/rnits/rnitsbioschemas.jsonld +++ b/data/rnits/rnitsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "Rnits", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rnits.html", "sc:version": "1.8.0" diff --git a/data/rnmr/rnmrbioschemas.jsonld b/data/rnmr/rnmrbioschemas.jsonld index 88fbeb7a5c29d..92d06111af848 100644 --- a/data/rnmr/rnmrbioschemas.jsonld +++ b/data/rnmr/rnmrbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Open source software package for visualizing and interpreting one and two dimensional NMR data.", "sc:name": "rNMR", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://rnmr.nmrfam.wisc.edu/" } \ No newline at end of file diff --git a/data/rnnotator/rnnotatorbioschemas.jsonld b/data/rnnotator/rnnotatorbioschemas.jsonld index e873b04768988..850c97ba10de3 100644 --- a/data/rnnotator/rnnotatorbioschemas.jsonld +++ b/data/rnnotator/rnnotatorbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/rnnotator", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jeff Martin", "David Gilbert", "Xiandong Meng", + "Jeff Martin", "Zhong Wang" ], "sc:additionalType": "Workflow", diff --git a/data/rnsc/rnscbioschemas.jsonld b/data/rnsc/rnscbioschemas.jsonld index 73153172cd613..5ab98f2da5fcf 100644 --- a/data/rnsc/rnscbioschemas.jsonld +++ b/data/rnsc/rnscbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This tool efficiently partitions networks into clusters using a cost function. Used to detect known and predict still undiscovered protein complexes within the cell's protein-protein interaction (PPI) network. The increasing amount of available PPI data necessitates an accurate and scalable approach to protein complex identification.", "sc:name": "RNSC", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.cs.utoronto.ca/~juris/data/rnsc/" } \ No newline at end of file diff --git a/data/roadmap_epigenomics/roadmap_epigenomicsbioschemas.jsonld b/data/roadmap_epigenomics/roadmap_epigenomicsbioschemas.jsonld index c6d1687c71fc1..9a4936a0bdfbd 100644 --- a/data/roadmap_epigenomics/roadmap_epigenomicsbioschemas.jsonld +++ b/data/roadmap_epigenomics/roadmap_epigenomicsbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Jin Wook Lee", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:25693563", + "pmcid:PMC4530010", { "@id": "https://doi.org/10.1038/nature14248" - }, - "pmcid:PMC4530010", - "pubmed:25693563" + } ], "sc:description": "Data repository of NIH Roadmap Epigenomics Mapping Consortium containing genome-wide maps of histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human cell types and tissues.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "Unlicense", "sc:name": "ROADMAP epigenomics", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://egg2.wustl.edu/roadmap/web_portal/index.html" }, diff --git a/data/roar/bioconda_roar.yaml b/data/roar/bioconda_roar.yaml index 1f1c48c472193..59c9c8d5c29d1 100644 --- a/data/roar/bioconda_roar.yaml +++ b/data/roar/bioconda_roar.yaml @@ -5,7 +5,6 @@ description: Identify preferential usage of APA sites, comparing two biological home: https://bioconductor.org/packages/3.10/bioc/html/roar.html identifiers: - biotools:roar -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-roar diff --git a/data/roar/roarbioschemas.jsonld b/data/roar/roarbioschemas.jsonld index 492f0a610e14e..bc81d955c79ad 100644 --- a/data/roar/roarbioschemas.jsonld +++ b/data/roar/roarbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "roar", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/roar.html", "sc:version": "1.10.0" diff --git a/data/robetta/robettabioschemas.jsonld b/data/robetta/robettabioschemas.jsonld index b2737e1b2f71c..db3ce6a9a54c6 100644 --- a/data/robetta/robettabioschemas.jsonld +++ b/data/robetta/robettabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations.", "sc:name": "Robetta", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://robetta.bakerlab.org/" diff --git a/data/robina/robinabioschemas.jsonld b/data/robina/robinabioschemas.jsonld index 4ef854746033f..37bb1b9d24a9e 100644 --- a/data/robina/robinabioschemas.jsonld +++ b/data/robina/robinabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "RobiNA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mapman.gabipd.org/web/guest/robin" } \ No newline at end of file diff --git a/data/robpower/robpowerbioschemas.jsonld b/data/robpower/robpowerbioschemas.jsonld index dd8f3666d6d81..d570a3a4ea1c4 100644 --- a/data/robpower/robpowerbioschemas.jsonld +++ b/data/robpower/robpowerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "R Program to compute algebric formulas in references to the article “Inuence of population structure on power and robustness of current association mapping tests”.", "sc:name": "RobPower", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://qgsp.jouy.inra.fr/index.php?option=com_content&view=article&id=54&Itemid=59" } \ No newline at end of file diff --git a/data/robustrankaggregation/robustrankaggregationbioschemas.jsonld b/data/robustrankaggregation/robustrankaggregationbioschemas.jsonld index 220141e43f98a..faf7ea355f74f 100644 --- a/data/robustrankaggregation/robustrankaggregationbioschemas.jsonld +++ b/data/robustrankaggregation/robustrankaggregationbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Methods for aggregating ranked lists, especially lists of genes. It implements the Robust Rank Aggregation (RRA) and some other simple algorithms for the task. RRA method uses a probabilistic model for aggregation that isrobust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.", "sc:name": "RobustRankAggregation", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "ELIXIR-EE", "sc:url": "http://cran.r-project.org/web/packages/RobustRankAggreg/", diff --git a/data/roc/bioconda_roc.yaml b/data/roc/bioconda_roc.yaml index 9f14685d37d66..04e668e750d4c 100644 --- a/data/roc/bioconda_roc.yaml +++ b/data/roc/bioconda_roc.yaml @@ -3,7 +3,6 @@ description: Provide utilities for ROC, with microarray focus. home: https://bioconductor.org/packages/3.10/bioc/html/ROC.html identifiers: - biotools:roc -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-roc summary: utilities for ROC, with microarray focus diff --git a/data/roc/rocbioschemas.jsonld b/data/roc/rocbioschemas.jsonld index 3917329f31d5d..40c9a2b3e1f1d 100644 --- a/data/roc/rocbioschemas.jsonld +++ b/data/roc/rocbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Vince Carey", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Various functionals of receiver operating characteristic curves.", "sc:license": "Artistic-2.0", "sc:name": "ROC", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ROC.html", "sc:version": "1.50.0" diff --git a/data/roci/rocibioschemas.jsonld b/data/roci/rocibioschemas.jsonld index 3fd2a722219bf..f6da2d00cd90f 100644 --- a/data/roci/rocibioschemas.jsonld +++ b/data/roci/rocibioschemas.jsonld @@ -19,13 +19,13 @@ "sc:name": "Roci", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ + "CeBiTec", "BiBiServ", - "Bielefeld University", - "CeBiTec" + "Bielefeld University" ], "sc:url": "https://bibiserv.cebitec.uni-bielefeld.de/roci", "sc:version": "1" diff --git a/data/rocketship/rocketshipbioschemas.jsonld b/data/rocketship/rocketshipbioschemas.jsonld index a60c5e5072b21..8d342c26628b6 100644 --- a/data/rocketship/rocketshipbioschemas.jsonld +++ b/data/rocketship/rocketshipbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12880-015-0062-3", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-1065-8442", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/rocketship", "@type": "sc:SoftwareApplication", @@ -17,11 +25,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4466867", "pubmed:26076957", { "@id": "https://doi.org/10.1186/s12880-015-0062-3" - } + }, + "pmcid:PMC4466867" ], "sc:description": "ROCKETSHIP, an open-source software for dynamic contrast-enhanced magnetic resonance imaging analysis.", "sc:featureList": { @@ -30,19 +38,11 @@ "sc:license": "GPL-2.0", "sc:name": "ROCKETSHIP", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/petmri/ROCKETSHIP" - }, - { - "@id": "http://orcid.org/0000-0002-1065-8442", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/s12880-015-0062-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/roddy/roddybioschemas.jsonld b/data/roddy/roddybioschemas.jsonld index 7049054d63d9f..82b247a4d05e5 100644 --- a/data/roddy/roddybioschemas.jsonld +++ b/data/roddy/roddybioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "German Cancer Research Center (DKFZ)", "sc:additionalType": [ - "Command-line tool", - "Workbench" + "Workbench", + "Command-line tool" ], "sc:author": "Philip R. Kensche", "sc:description": "Roddy is a workflow management system for large scale NGS processing pipelines on Petabyte scale. It is used for Pan-Cancer Analysis of Whole Genomes (PCAWG) project and has a focus on high-throughput computing infrastructures.", diff --git a/data/roi_feature_projection/roi_feature_projectionbioschemas.jsonld b/data/roi_feature_projection/roi_feature_projectionbioschemas.jsonld index 1d1c30eab2e27..a7ffb7293aff1 100644 --- a/data/roi_feature_projection/roi_feature_projectionbioschemas.jsonld +++ b/data/roi_feature_projection/roi_feature_projectionbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "roi_feature_projection", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_feature_projection/0.2.2.1", "sc:version": "0.2.2.1" diff --git a/data/roi_filter/roi_filterbioschemas.jsonld b/data/roi_filter/roi_filterbioschemas.jsonld index 541987e248949..3df0aa3248119 100644 --- a/data/roi_filter/roi_filterbioschemas.jsonld +++ b/data/roi_filter/roi_filterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Filter ROI files.", "sc:name": "roi_filter", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_filter/0.2.2", diff --git a/data/roi_metrics/roi_metricsbioschemas.jsonld b/data/roi_metrics/roi_metricsbioschemas.jsonld index b936e870d8a52..5faec36764224 100644 --- a/data/roi_metrics/roi_metricsbioschemas.jsonld +++ b/data/roi_metrics/roi_metricsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Compute metrics for records in an ROI file.", "sc:name": "roi_metrics", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_metrics/0.2.2", "sc:version": "0.2.2" diff --git a/data/roi_pca/roi_pcabioschemas.jsonld b/data/roi_pca/roi_pcabioschemas.jsonld index 3684e37f26039..c4951f11e6c8d 100644 --- a/data/roi_pca/roi_pcabioschemas.jsonld +++ b/data/roi_pca/roi_pcabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "roi_pca", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_pca/0.2.2", "sc:version": "0.2.2" diff --git a/data/roi_sort/roi_sortbioschemas.jsonld b/data/roi_sort/roi_sortbioschemas.jsonld index 75cbbb11ded3c..f567585c6c9df 100644 --- a/data/roi_sort/roi_sortbioschemas.jsonld +++ b/data/roi_sort/roi_sortbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Sort ROI file.", "sc:name": "roi_sort", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_sort/0.2.2", "sc:version": "0.2.2" diff --git a/data/roi_table/roi_tablebioschemas.jsonld b/data/roi_table/roi_tablebioschemas.jsonld index 834c444da090e..c058e52a59ec8 100644 --- a/data/roi_table/roi_tablebioschemas.jsonld +++ b/data/roi_table/roi_tablebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "ROI Overview Report.", "sc:name": "roi_table", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_table/0.2.2", diff --git a/data/roimcr/roimcrbioschemas.jsonld b/data/roimcr/roimcrbioschemas.jsonld index 4b393907eb6b0..ff42c8dd17878 100644 --- a/data/roimcr/roimcrbioschemas.jsonld +++ b/data/roimcr/roimcrbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Romà Tauler", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6525397", - "pubmed:31101001", { "@id": "https://doi.org/10.1186/s12859-019-2848-8" - } + }, + "pmcid:PMC6525397", + "pubmed:31101001" ], "sc:description": "Powerful analysis strategy for LC-MS metabolomic datasets.", "sc:featureList": [ diff --git a/data/roleswitch/roleswitchbioschemas.jsonld b/data/roleswitch/roleswitchbioschemas.jsonld index 97619914e37da..281c04fa72342 100644 --- a/data/roleswitch/roleswitchbioschemas.jsonld +++ b/data/roleswitch/roleswitchbioschemas.jsonld @@ -9,17 +9,13 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gku182", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/roleswitch", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yue Li", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC4027195", @@ -35,12 +31,16 @@ "sc:license": "GPL-2.0", "sc:name": "Roleswitch", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Roleswitch.html", "sc:version": "1.12.0" + }, + { + "@id": "https://doi.org/10.1093/nar/gku182", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rolexa/rolexabioschemas.jsonld b/data/rolexa/rolexabioschemas.jsonld index 8ea495d33f46e..6df3132eea2e1 100644 --- a/data/rolexa/rolexabioschemas.jsonld +++ b/data/rolexa/rolexabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.", "sc:name": "Rolexa", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://master.bioconductor.org/packages//2.10/bioc/html/Rolexa.html" } \ No newline at end of file diff --git a/data/rols/bioconda_rols.yaml b/data/rols/bioconda_rols.yaml index f4a449a95b005..6541e843fa85c 100644 --- a/data/rols/bioconda_rols.yaml +++ b/data/rols/bioconda_rols.yaml @@ -4,7 +4,6 @@ description: The rols package is an interface to the Ontology Lookup Service (OL home: https://bioconductor.org/packages/3.10/bioc/html/rols.html identifiers: - biotools:rols -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-rols diff --git a/data/rols/rolsbioschemas.jsonld b/data/rols/rolsbioschemas.jsonld index 7c8b0793ba672..8b1c5894d12da 100644 --- a/data/rols/rolsbioschemas.jsonld +++ b/data/rols/rolsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laurent Gatto", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.", "sc:license": "GPL-2.0", "sc:name": "rols", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rols.html", "sc:version": "2.2.2" diff --git a/data/roma/romabioschemas.jsonld b/data/roma/romabioschemas.jsonld index 2694059dcda75..fcb1e7449d4d4 100644 --- a/data/roma/romabioschemas.jsonld +++ b/data/roma/romabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "roma", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/roma.html", diff --git a/data/romprev/romprevbioschemas.jsonld b/data/romprev/romprevbioschemas.jsonld index b84ba67e2127c..dff2e19d40d8c 100644 --- a/data/romprev/romprevbioschemas.jsonld +++ b/data/romprev/romprevbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ROMPrev 0.2.1 beta", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://research.nhgri.nih.gov/ROMPrev/" } \ No newline at end of file diff --git a/data/ronn/ronnbioschemas.jsonld b/data/ronn/ronnbioschemas.jsonld index 0ef256443acc9..1ab615d0dea7f 100644 --- a/data/ronn/ronnbioschemas.jsonld +++ b/data/ronn/ronnbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Predictor of regions of disorder in proteins.", "sc:name": "RONN", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "Instruct", "sc:url": "http://www.strubi.ox.ac.uk/RONN", diff --git a/data/rontotools/rontotoolsbioschemas.jsonld b/data/rontotools/rontotoolsbioschemas.jsonld index e931d26477256..937f42509a189 100644 --- a/data/rontotools/rontotoolsbioschemas.jsonld +++ b/data/rontotools/rontotoolsbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Calin Voichita", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Suite of tools for functional analysis.", "sc:license": "CC-BY-NC-ND-4.0", "sc:name": "ROntoTools", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ROntoTools.html", diff --git a/data/rootarray/rootarraybioschemas.jsonld b/data/rootarray/rootarraybioschemas.jsonld index 0d33a674abb16..40a4f84fc39f7 100644 --- a/data/rootarray/rootarraybioschemas.jsonld +++ b/data/rootarray/rootarraybioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Imaging pipeline that includes automated tracking of growing roots, automated image acquisition and gene expression quantification.", "sc:name": "RootArray", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://ohlerlab.mdc-berlin.de/software/Imaging_pipeline_106/" diff --git a/data/ropls/roplsbioschemas.jsonld b/data/ropls/roplsbioschemas.jsonld index 5685360209509..f12f0a8f0e088 100644 --- a/data/ropls/roplsbioschemas.jsonld +++ b/data/ropls/roplsbioschemas.jsonld @@ -16,17 +16,17 @@ "@id": "http://orcid.org/0000-0003-1019-4577" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:26088811", "sc:description": "The package includes methods for variable modeling as PCA or PLS, that can be useful for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) also enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation.", "sc:license": "CECILL-2.1", "sc:name": "ropls", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ropls.html", "sc:version": "1.6.2" diff --git a/data/rosetta_flexpepdock/rosetta_flexpepdockbioschemas.jsonld b/data/rosetta_flexpepdock/rosetta_flexpepdockbioschemas.jsonld index 4b80d19475099..bd59062c2df60 100644 --- a/data/rosetta_flexpepdock/rosetta_flexpepdockbioschemas.jsonld +++ b/data/rosetta_flexpepdock/rosetta_flexpepdockbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Rosetta FlexPepDock web server is a high resolution peptide docking protocol for modeling of peptide-protein complexes.", "sc:name": "Rosetta FlexPepDock", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://flexpepdock.furmanlab.cs.huji.ac.il/" } \ No newline at end of file diff --git a/data/rosettaantibody/rosettaantibodybioschemas.jsonld b/data/rosettaantibody/rosettaantibodybioschemas.jsonld index 4054f7038375e..a83ad97e4bd2b 100644 --- a/data/rosettaantibody/rosettaantibodybioschemas.jsonld +++ b/data/rosettaantibody/rosettaantibodybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The RosettaAntibody server predicts the structure of an antibody variable region given the amino acid sequences of the light and heavy chains. 2000 independent structures are generated and scored, with the top 10 models being returned in high resolution and detailed format.", "sc:name": "RosettaAntibody", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://antibody.graylab.jhu.edu" } \ No newline at end of file diff --git a/data/rosettadesign/rosettadesignbioschemas.jsonld b/data/rosettadesign/rosettadesignbioschemas.jsonld index 72753e3177753..2b38edf15d2e7 100644 --- a/data/rosettadesign/rosettadesignbioschemas.jsonld +++ b/data/rosettadesign/rosettadesignbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.", "sc:name": "RosettaDesign", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://rosettadesign.med.unc.edu" diff --git a/data/rosettadock_server/rosettadock_serverbioschemas.jsonld b/data/rosettadock_server/rosettadock_serverbioschemas.jsonld index a7dbd1b35cd7d..a2b85537038a0 100644 --- a/data/rosettadock_server/rosettadock_serverbioschemas.jsonld +++ b/data/rosettadock_server/rosettadock_serverbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Structure prediction program that searches the rigid body and side chain conformational space of two interacting proteins to find a minimum free-energy complex for the protein-protein interaction structure.", "sc:name": "RosettaDock Server", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://rosie.graylab.jhu.edu/" } \ No newline at end of file diff --git a/data/rosettr/rosettrbioschemas.jsonld b/data/rosettr/rosettrbioschemas.jsonld index 1661fec1468c3..1c1a4a20c80e5 100644 --- a/data/rosettr/rosettrbioschemas.jsonld +++ b/data/rosettr/rosettrbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13007-017-0163-9", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rosettr", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC5353781", + "pubmed:28331535", { "@id": "https://doi.org/10.1186/s13007-017-0163-9" - }, - "pubmed:28331535" + } ], "sc:description": "A high-throughput affordable in vitro growth assay for Arabidopsis.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "GPL-3.0", "sc:name": "rosettR", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://hredestig.github.io/rosettR/" + }, + { + "@id": "https://doi.org/10.1186/s13007-017-0163-9", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rouge/rougebioschemas.jsonld b/data/rouge/rougebioschemas.jsonld index c35a88c1f5b2a..9d8baa4dd6a15 100644 --- a/data/rouge/rougebioschemas.jsonld +++ b/data/rouge/rougebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Rouge", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.kazusa.or.jp/rouge/" } \ No newline at end of file diff --git a/data/rpa/rpabioschemas.jsonld b/data/rpa/rpabioschemas.jsonld index 31c625f9023a4..5fb21a72a6895 100644 --- a/data/rpa/rpabioschemas.jsonld +++ b/data/rpa/rpabioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Leo Lahti", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:21071809", "sc:description": "Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays. Lahti et al. \"Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays\", TCBB/IEEE, 2011.", "sc:license": "BSD-4-Clause", "sc:name": "RPA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RPA.html", "sc:version": "1.30.0" diff --git a/data/rpf/rpfbioschemas.jsonld b/data/rpf/rpfbioschemas.jsonld index e8b9a85f642bd..bf4cabc4aa28f 100644 --- a/data/rpf/rpfbioschemas.jsonld +++ b/data/rpf/rpfbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "RPF webserver uses RECALL, PRECISION, and F-MEASURE (RPF) for calculating global NMR structure quality scores, or how well a query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data.", "sc:name": "RPF", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://nmr.cabm.rutgers.edu/rpf" } \ No newline at end of file diff --git a/data/rpicoo/rpicoobioschemas.jsonld b/data/rpicoo/rpicoobioschemas.jsonld index ccb44b738ab75..9ccd2cb88c0d8 100644 --- a/data/rpicoo/rpicoobioschemas.jsonld +++ b/data/rpicoo/rpicoobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "In Silico RNA-protein interaction detection using random forest.", "sc:name": "rpiCOO", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://biocool.ir/softs/rpicool.html" } \ No newline at end of file diff --git a/data/rpiter/rpiterbioschemas.jsonld b/data/rpiter/rpiterbioschemas.jsonld index 8e894a350beaa..74cf19545131b 100644 --- a/data/rpiter/rpiterbioschemas.jsonld +++ b/data/rpiter/rpiterbioschemas.jsonld @@ -9,25 +9,29 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3390/ijms20051070", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/RPITER", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "C. Peng", "sc:additionalType": "Script", "sc:citation": [ + "pubmed:30832218", + "pmcid:PMC6429152", { "@id": "https://doi.org/10.3390/ijms20051070" - }, - "pmcid:PMC6429152", - "pubmed:30832218" + } ], "sc:description": "Hierarchical deep learning model for predicting ncRNA-protein interaction.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_0267" }, { - "@id": "edam:operation_0267" + "@id": "edam:operation_2495" }, { "@id": "edam:operation_0278" @@ -36,14 +40,10 @@ "sc:license": "MIT", "sc:name": "RPITER", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/Pengeace/RPITER" - }, - { - "@id": "https://doi.org/10.3390/ijms20051070", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rpoly/rpolybioschemas.jsonld b/data/rpoly/rpolybioschemas.jsonld index a939589a923ec..a8373dc5f4eb3 100644 --- a/data/rpoly/rpolybioschemas.jsonld +++ b/data/rpoly/rpolybioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Infer haplotypes from genotype data (by pseudo-Boolean optimization) using the pure parsimony criterion.", "sc:name": "RPOLY", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sat.inesc-id.pt/software/rpoly/", "sc:version": "1.2.1" diff --git a/data/rppapipe/rppapipebioschemas.jsonld b/data/rppapipe/rppapipebioschemas.jsonld index 68ef8469b0b04..fb772ad11917a 100644 --- a/data/rppapipe/rppapipebioschemas.jsonld +++ b/data/rppapipe/rppapipebioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-3.0", "sc:name": "RPPApipe", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ra.cs.uni-tuebingen.de/software/RPPApipe/" } \ No newline at end of file diff --git a/data/rpredictor/rpredictorbioschemas.jsonld b/data/rpredictor/rpredictorbioschemas.jsonld index 013fe9bb72e31..3d527ec0acaaf 100644 --- a/data/rpredictor/rpredictorbioschemas.jsonld +++ b/data/rpredictor/rpredictorbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A web database for prediction, analysis and storage of secondary structures of RNAs.", "sc:name": "rPredictor", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-CZ", "sc:url": "http://rpredictordb.elixir-czech.cz", diff --git a/data/rproteomics/rproteomicsbioschemas.jsonld b/data/rproteomics/rproteomicsbioschemas.jsonld index 3aae77fdc7bc8..c6a39689b5eaf 100644 --- a/data/rproteomics/rproteomicsbioschemas.jsonld +++ b/data/rproteomics/rproteomicsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Set of routines for analyzing proteomics data, an XML database to store the results and a user interface.", "sc:name": "Rproteomics", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/NCIP/cagrid-general/tree/master/demos/06annual/workflow/JRProteomicsGridSkeletonValue-1.0/src/org/globus/cagrid/RProteomics" } \ No newline at end of file diff --git a/data/rprotobuflib/rprotobuflibbioschemas.jsonld b/data/rprotobuflib/rprotobuflibbioschemas.jsonld index 03a25febdd22d..bc2d2b6fe459b 100644 --- a/data/rprotobuflib/rprotobuflibbioschemas.jsonld +++ b/data/rprotobuflib/rprotobuflibbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "RProtoBufLib", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RProtoBufLib.html", "sc:version": "1.2.0" diff --git a/data/rpsixml/rpsixmlbioschemas.jsonld b/data/rpsixml/rpsixmlbioschemas.jsonld index 018b30ffa351e..25e67680de8e7 100644 --- a/data/rpsixml/rpsixmlbioschemas.jsonld +++ b/data/rpsixml/rpsixmlbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "RpsiXML", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RpsiXML.html", "sc:version": "2.16.0" diff --git a/data/rpx/rpxbioschemas.jsonld b/data/rpx/rpxbioschemas.jsonld index df86ad7555e66..445b2eecff9f4 100644 --- a/data/rpx/rpxbioschemas.jsonld +++ b/data/rpx/rpxbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "rpx", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rpx.html", "sc:version": "1.10.0" diff --git a/data/rqc/rqcbioschemas.jsonld b/data/rqc/rqcbioschemas.jsonld index 5466c422005d2..d7fe8193880ab 100644 --- a/data/rqc/rqcbioschemas.jsonld +++ b/data/rqc/rqcbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "Rqc", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rqc.html", "sc:version": "1.8.0" diff --git a/data/rqt/rqtbioschemas.jsonld b/data/rqt/rqtbioschemas.jsonld index 5eae720f36c83..842c6f8428443 100644 --- a/data/rqt/rqtbioschemas.jsonld +++ b/data/rqt/rqtbioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/btx395", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rqt", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ilya Zhbannikov", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pubmed:28633423", "pmcid:PMC5860520", { "@id": "https://doi.org/10.1093/bioinformatics/btx395" - }, - "pubmed:28633423" + } ], "sc:description": "Gene-level GWAS meta-analysis. The package can be easily included into bioinformatics pipeline or used stand-alone.", "sc:featureList": { @@ -35,12 +31,16 @@ "sc:license": "GPL-1.0", "sc:name": "rqt", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/izhbannikov/rqt", "sc:version": "1.6.0" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btx395", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rqubic/rqubicbioschemas.jsonld b/data/rqubic/rqubicbioschemas.jsonld index 7784db8cd6bde..ae256a12b5fe7 100644 --- a/data/rqubic/rqubicbioschemas.jsonld +++ b/data/rqubic/rqubicbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkp491", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/rqubic", "@type": "sc:SoftwareApplication", @@ -19,10 +23,10 @@ ], "sc:citation": [ "pubmed:19509312", + "pmcid:PMC2731891", { "@id": "https://doi.org/10.1093/nar/gkp491" - }, - "pmcid:PMC2731891" + } ], "sc:description": "This package implements the QUBIC algorithm for the qualitative biclustering with gene expression data.", "sc:featureList": { @@ -37,10 +41,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rqubic.html", "sc:version": "1.20.0" - }, - { - "@id": "https://doi.org/10.1093/nar/gkp491", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rrdb/rrdbbioschemas.jsonld b/data/rrdb/rrdbbioschemas.jsonld index 59045bb29d781..c53f21f0f1bed 100644 --- a/data/rrdb/rrdbbioschemas.jsonld +++ b/data/rrdb/rrdbbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Comprehensive and non-redundant benchmark for RNA–RNA docking and scoring.", "sc:name": "RRDB", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://huanglab.phys.hust.edu.cn/RRDbenchmark/" diff --git a/data/rrdistmaps/rrdistmapsbioschemas.jsonld b/data/rrdistmaps/rrdistmapsbioschemas.jsonld index 2079e726a07bd..9539f48820eda 100644 --- a/data/rrdistmaps/rrdistmapsbioschemas.jsonld +++ b/data/rrdistmaps/rrdistmapsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "RRDistMaps", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html" diff --git a/data/rrdp/bioconda_rrdp.yaml b/data/rrdp/bioconda_rrdp.yaml index 04cb8d1a838e7..256b653fcc4a2 100644 --- a/data/rrdp/bioconda_rrdp.yaml +++ b/data/rrdp/bioconda_rrdp.yaml @@ -3,7 +3,6 @@ description: Seamlessly interfaces RDP classifier (version 2.9). home: https://bioconductor.org/packages/3.10/bioc/html/rRDP.html identifiers: - biotools:rrdp -- doi:10.1038/nmeth.3252 license: GPL-2 | file LICENSE license_file: LICENSE name: bioconductor-rrdp diff --git a/data/rrdp/rrdpbioschemas.jsonld b/data/rrdp/rrdpbioschemas.jsonld index f432c0f269f59..00e9bd890ac78 100644 --- a/data/rrdp/rrdpbioschemas.jsonld +++ b/data/rrdp/rrdpbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Hahsler", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Seamlessly interfaces RDP classifier.", "sc:license": "GPL-2.0", "sc:name": "rRDP", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rRDP.html", diff --git a/data/rre/rrebioschemas.jsonld b/data/rre/rrebioschemas.jsonld index 018d2969ee7e4..13ed15ec2dd95 100644 --- a/data/rre/rrebioschemas.jsonld +++ b/data/rre/rrebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Extract non-coding regions associated to annotated genes.", "sc:name": "RRE", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.bioinformatica.unito.it/bioinformatics/rre/rre.html", "sc:version": "20040401" diff --git a/data/rregrs/rregrsbioschemas.jsonld b/data/rregrs/rregrsbioschemas.jsonld index 4b2a7c9d04522..0d6472b8f1ab5 100644 --- a/data/rregrs/rregrsbioschemas.jsonld +++ b/data/rregrs/rregrsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7209-3670", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/rregrs", "@type": "sc:SoftwareApplication", @@ -17,11 +21,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:26379782", + "pmcid:PMC4570700", { "@id": "https://doi.org/10.1186/s13321-015-0094-2" - }, - "pmcid:PMC4570700", - "pubmed:26379782" + } ], "sc:description": "RRegrs is an integrated framework for creating multiple regression models.", "sc:featureList": { @@ -30,16 +34,12 @@ "sc:license": "BSD-2-Clause", "sc:name": "RRegrs", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/enanomapper/RRegrs", "sc:version": "0.0.5" }, - { - "@id": "http://orcid.org/0000-0001-7209-3670", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s13321-015-0094-2", "@type": "sc:CreativeWork" diff --git a/data/rrest/rrestbioschemas.jsonld b/data/rrest/rrestbioschemas.jsonld index e758d147f57ed..3fca58b7491c1 100644 --- a/data/rrest/rrestbioschemas.jsonld +++ b/data/rrest/rrestbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1007/S10548-019-00707-X", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/rREST", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dezhong Yao", - "Pedro A. Valdés Sosa" + "Pedro A. Valdés Sosa", + "Dezhong Yao" ], "sc:additionalType": "Script", "sc:citation": [ { "@id": "https://doi.org/10.1007/S10548-019-00707-X" }, - "pmcid:PMC6592976", - "pubmed:31037477" + "pubmed:31037477", + "pmcid:PMC6592976" ], "sc:description": "Regularized reference electrode standardization technique.", "sc:featureList": { @@ -36,10 +40,6 @@ "Windows" ], "sc:url": "https://github.com/ShiangHu/Unified-EEG-reference-rREST" - }, - { - "@id": "https://doi.org/10.1007/S10548-019-00707-X", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rrho/bioconda_rrho.yaml b/data/rrho/bioconda_rrho.yaml index 1cd76fdf1de8c..3c5098c267c60 100644 --- a/data/rrho/bioconda_rrho.yaml +++ b/data/rrho/bioconda_rrho.yaml @@ -4,7 +4,6 @@ description: The package is aimed at inference on the amount of agreement in two home: https://bioconductor.org/packages/3.10/bioc/html/RRHO.html identifiers: - biotools:rrho -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-rrho diff --git a/data/rrho/rrhobioschemas.jsonld b/data/rrho/rrhobioschemas.jsonld index 5035c4ab01323..524e85a60ebcd 100644 --- a/data/rrho/rrhobioschemas.jsonld +++ b/data/rrho/rrhobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jonathan Rosenblatt", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.", "sc:license": "GPL-2.0", diff --git a/data/rrmdb/rrmdbbioschemas.jsonld b/data/rrmdb/rrmdbbioschemas.jsonld index b30a2a75cf14b..12cc6c918f864 100644 --- a/data/rrmdb/rrmdbbioschemas.jsonld +++ b/data/rrmdb/rrmdbbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/database/bay148", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/RRMdb", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ "Web application" ], "sc:citation": [ - "pmcid:PMC6334006", - "pubmed:30649297", { "@id": "https://doi.org/10.1093/database/bay148" - } + }, + "pubmed:30649297", + "pmcid:PMC6334006" ], "sc:description": "Evolutionary-oriented database of RNA recognition motif sequences.", "sc:featureList": [ @@ -30,23 +34,19 @@ "@id": "edam:operation_0239" }, { - "@id": "edam:operation_0303" + "@id": "edam:operation_0246" }, { - "@id": "edam:operation_0246" + "@id": "edam:operation_0303" } ], "sc:name": "RRMdb", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://iimcb.genesilico.pl/rrm/" - }, - { - "@id": "https://doi.org/10.1093/database/bay148", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rs-expnet-crnmf/rs-expnet-crnmfbioschemas.jsonld b/data/rs-expnet-crnmf/rs-expnet-crnmfbioschemas.jsonld index a20ffab65c94f..c47321cb3dca6 100644 --- a/data/rs-expnet-crnmf/rs-expnet-crnmfbioschemas.jsonld +++ b/data/rs-expnet-crnmf/rs-expnet-crnmfbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "RS-ExpNet-CRNMF", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/USTC-HIlab/RS-ExpNet-CRNMF" } \ No newline at end of file diff --git a/data/rs-webpredictor/rs-webpredictorbioschemas.jsonld b/data/rs-webpredictor/rs-webpredictorbioschemas.jsonld index 58fd252e3673a..39196904a2daf 100644 --- a/data/rs-webpredictor/rs-webpredictorbioschemas.jsonld +++ b/data/rs-webpredictor/rs-webpredictorbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTS705", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rs-webpredictor", "@type": "sc:SoftwareApplication", @@ -22,25 +18,29 @@ { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTS705" }, - "pubmed:23242264", - "pmcid:PMC3570214" + "pmcid:PMC3570214", + "pubmed:23242264" ], "sc:description": "Server for predicting CYP-mediated sites of metabolism on drug-like molecules.", "sc:featureList": [ { - "@id": "edam:operation_3092" + "@id": "edam:operation_3660" }, { - "@id": "edam:operation_3660" + "@id": "edam:operation_3092" } ], "sc:name": "RS-WebPredictor", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://reccr.chem.rpi.edu/Software/RS-WebPredictor/" + }, + { + "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTS705", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rsalvador/rsalvadorbioschemas.jsonld b/data/rsalvador/rsalvadorbioschemas.jsonld index 4fca2fa1beb89..c81e100030f62 100644 --- a/data/rsalvador/rsalvadorbioschemas.jsonld +++ b/data/rsalvador/rsalvadorbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Qi Zheng", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:29084818", "pmcid:PMC5714482", { "@id": "https://doi.org/10.1534/g3.117.300120" - }, - "pubmed:29084818" + } ], "sc:description": "An R Tool for the Luria-Delbruck Fluctuation Assay.", "sc:featureList": { @@ -27,8 +27,8 @@ }, "sc:name": "rSalvador", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://eeeeeric.com/rSalvador/", "sc:version": "1.7" diff --git a/data/rsamtools/bioconda_rsamtools.yaml b/data/rsamtools/bioconda_rsamtools.yaml index a49e39fb5007a..411c491120b17 100644 --- a/data/rsamtools/bioconda_rsamtools.yaml +++ b/data/rsamtools/bioconda_rsamtools.yaml @@ -5,7 +5,6 @@ description: This package provides an interface to the 'samtools', 'bcftools', a home: https://bioconductor.org/packages/3.10/bioc/html/Rsamtools.html identifiers: - biotools:rsamtools -- doi:10.1038/nmeth.3252 license: Artistic-2.0 | file LICENSE license_file: LICENSE name: bioconductor-rsamtools diff --git a/data/rsamtools/rsamtoolsbioschemas.jsonld b/data/rsamtools/rsamtoolsbioschemas.jsonld index 97223a731de13..f8dd08b51ce7c 100644 --- a/data/rsamtools/rsamtoolsbioschemas.jsonld +++ b/data/rsamtools/rsamtoolsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.", "sc:license": "Artistic-2.0", "sc:name": "Rsamtools", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html", "sc:version": "1.26.1" diff --git a/data/rsat/rsatbioschemas.jsonld b/data/rsat/rsatbioschemas.jsonld index 26a3cbd42dccf..9fe77cc6b0f19 100644 --- a/data/rsat/rsatbioschemas.jsonld +++ b/data/rsat/rsatbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "Other", "sc:name": "RSAT suite", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://rsat.eu" } \ No newline at end of file diff --git a/data/rsat_-_retrieve_sequence/rsat_-_retrieve_sequencebioschemas.jsonld b/data/rsat_-_retrieve_sequence/rsat_-_retrieve_sequencebioschemas.jsonld index f9b97b4fd2e9b..bd8a4fd3e3852 100644 --- a/data/rsat_-_retrieve_sequence/rsat_-_retrieve_sequencebioschemas.jsonld +++ b/data/rsat_-_retrieve_sequence/rsat_-_retrieve_sequencebioschemas.jsonld @@ -20,9 +20,9 @@ "@id": "https://orcid.org/0000-0002-8799-8584" }, "sc:additionalType": [ - "Command-line tool", - "Web application", "Web API", + "Web application", + "Command-line tool", "Web service" ], "sc:author": { diff --git a/data/rsat_var-tools/rsat_var-toolsbioschemas.jsonld b/data/rsat_var-tools/rsat_var-toolsbioschemas.jsonld index 13b2f4c184f55..45c98cd88fedc 100644 --- a/data/rsat_var-tools/rsat_var-toolsbioschemas.jsonld +++ b/data/rsat_var-tools/rsat_var-toolsbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/RSAT_Var-tools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alejandra Medina-Rivera", - "Jacques van Helden" + "Jacques van Helden", + "Alejandra Medina-Rivera" ], "sc:additionalType": [ - "Web application", - "Suite" + "Suite", + "Web application" ], "sc:description": "Accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.", "sc:license": "Unlicense", "sc:name": "RSAT Var-tools", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://rsat.eu" } \ No newline at end of file diff --git a/data/rsbml/rsbmlbioschemas.jsonld b/data/rsbml/rsbmlbioschemas.jsonld index 969b921b9f8da..633b9b4d1d57e 100644 --- a/data/rsbml/rsbmlbioschemas.jsonld +++ b/data/rsbml/rsbmlbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Lawrence", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.", "sc:license": "Artistic-2.0", "sc:name": "rsbml", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rsbml.html", diff --git a/data/rscripts_for_data_analysis/rscripts_for_data_analysisbioschemas.jsonld b/data/rscripts_for_data_analysis/rscripts_for_data_analysisbioschemas.jsonld index bc3138e561572..860d8975c0aa9 100644 --- a/data/rscripts_for_data_analysis/rscripts_for_data_analysisbioschemas.jsonld +++ b/data/rscripts_for_data_analysis/rscripts_for_data_analysisbioschemas.jsonld @@ -17,13 +17,13 @@ "sc:license": "GPL-3.0", "sc:name": "Rscripts for data analysis", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ - "Lab Roderic Guigo Group", - "crg.eu" + "crg.eu", + "Lab Roderic Guigo Group" ], "sc:url": "https://github.com/abreschi/Rscripts", "sc:version": "1" diff --git a/data/rsd/rsdbioschemas.jsonld b/data/rsd/rsdbioschemas.jsonld index baaa7788b1de8..46460253f65a9 100644 --- a/data/rsd/rsdbioschemas.jsonld +++ b/data/rsd/rsdbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Reciprocal Smallest Distance (RSD)", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/todddeluca/reciprocal_smallest_distance", "sc:version": "v1.1.7" diff --git a/data/rseg/rsegbioschemas.jsonld b/data/rseg/rsegbioschemas.jsonld index 2d118c04f93bc..6016c722e3fb7 100644 --- a/data/rseg/rsegbioschemas.jsonld +++ b/data/rseg/rsegbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool allows the user to define sample-specific thresholds to call gains and losses in an interactive way. It also allows the user to correct for RMA induced normalization artifacts in case of imbalance between losses and gains.", "sc:name": "Rseg", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.cs.au.dk/~plamy/Rseg/" } \ No newline at end of file diff --git a/data/rseqan/rseqanbioschemas.jsonld b/data/rseqan/rseqanbioschemas.jsonld index c44f0686bd1e3..6d3deb078bee3 100644 --- a/data/rseqan/rseqanbioschemas.jsonld +++ b/data/rseqan/rseqanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "RSeqAn", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RSeqAn.html", "sc:version": "1.0.0" diff --git a/data/rseqc/rseqcbioschemas.jsonld b/data/rseqc/rseqcbioschemas.jsonld index 811a558da15bc..64ae22ca004ce 100644 --- a/data/rseqc/rseqcbioschemas.jsonld +++ b/data/rseqc/rseqcbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.", "sc:name": "RSeQC", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://rseqc.sourceforge.net" } \ No newline at end of file diff --git a/data/rseqrep/rseqrepbioschemas.jsonld b/data/rseqrep/rseqrepbioschemas.jsonld index 4f5402b8b74e0..641c65d67970f 100644 --- a/data/rseqrep/rseqrepbioschemas.jsonld +++ b/data/rseqrep/rseqrepbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "RSEQREP", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/emmesgit/RSEQREP" diff --git a/data/rseqtu-a/rseqtu-abioschemas.jsonld b/data/rseqtu-a/rseqtu-abioschemas.jsonld index 07d9b581cb691..59e4865f2cfc6 100644 --- a/data/rseqtu-a/rseqtu-abioschemas.jsonld +++ b/data/rseqtu-a/rseqtu-abioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3389/fgene.2019.00374", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rSeqTU-A", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:31156694", - "pmcid:PMC6529933", { "@id": "https://doi.org/10.3389/fgene.2019.00374" - } + }, + "pmcid:PMC6529933" ], "sc:description": "Machine learning based R package for prediction of bacterial transcription units.", "sc:featureList": [ @@ -31,21 +27,25 @@ "@id": "edam:operation_0435" }, { - "@id": "edam:operation_0438" + "@id": "edam:operation_2495" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_0438" } ], "sc:license": "MIT", "sc:name": "rSeqTU-A", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://s18692001.github.io/rSeqTU/", "sc:version": "0.1.0" + }, + { + "@id": "https://doi.org/10.3389/fgene.2019.00374", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rsffreader/rsffreaderbioschemas.jsonld b/data/rsffreader/rsffreaderbioschemas.jsonld index 9d52e8a4ac0ad..862714f89d6ce 100644 --- a/data/rsffreader/rsffreaderbioschemas.jsonld +++ b/data/rsffreader/rsffreaderbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Matt Settles", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers into similar classes as are present for fastq files.", "sc:license": "Artistic-2.0", "sc:name": "rSFFreader", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rSFFreader.html", "sc:version": "0.22.0" diff --git a/data/rsi/rsibioschemas.jsonld b/data/rsi/rsibioschemas.jsonld index 555800c3788bb..6812bc8d1a329 100644 --- a/data/rsi/rsibioschemas.jsonld +++ b/data/rsi/rsibioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "RSI", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://rsi.hulilab.org/" } \ No newline at end of file diff --git a/data/rsite/rsitebioschemas.jsonld b/data/rsite/rsitebioschemas.jsonld index d6e13bc7598c5..d9aafd7fb914e 100644 --- a/data/rsite/rsitebioschemas.jsonld +++ b/data/rsite/rsitebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A computational tool to identify the functional sites of noncoding RNAs", "sc:name": "Rsite", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.cuilab.cn/rsite" } \ No newline at end of file diff --git a/data/rsnp_guide/rsnp_guidebioschemas.jsonld b/data/rsnp_guide/rsnp_guidebioschemas.jsonld index cf4db12a9fdb9..9039ae2b5aa36 100644 --- a/data/rsnp_guide/rsnp_guidebioschemas.jsonld +++ b/data/rsnp_guide/rsnp_guidebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A system of databases documenting the influence of mutations in regulatory gene regions.", "sc:name": "rSNP_Guide", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/" } \ No newline at end of file diff --git a/data/rspred/rspredbioschemas.jsonld b/data/rspred/rspredbioschemas.jsonld index b78ba626572b8..ee8c01bef629a 100644 --- a/data/rspred/rspredbioschemas.jsonld +++ b/data/rspred/rspredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RSpred", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "bils.se", "sc:url": "http://persson-group.scilifelab.se/rspred/" diff --git a/data/rsssite/rsssitebioschemas.jsonld b/data/rsssite/rsssitebioschemas.jsonld index 298f70060e84a..fa1b20fc39cd5 100644 --- a/data/rsssite/rsssitebioschemas.jsonld +++ b/data/rsssite/rsssitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RSSsite", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.itb.cnr.it/rss" } \ No newline at end of file diff --git a/data/rstoolbox/rstoolboxbioschemas.jsonld b/data/rstoolbox/rstoolboxbioschemas.jsonld index dbdee0854c37c..c34e39c7983db 100644 --- a/data/rstoolbox/rstoolboxbioschemas.jsonld +++ b/data/rstoolbox/rstoolboxbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2796-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rstoolbox", "@type": "sc:SoftwareApplication", @@ -29,13 +25,13 @@ "sc:description": "large-scale analysis of computational protein design data and structural bioinformatics.", "sc:featureList": [ { - "@id": "edam:operation_0476" + "@id": "edam:operation_3216" }, { - "@id": "edam:operation_0478" + "@id": "edam:operation_0476" }, { - "@id": "edam:operation_3216" + "@id": "edam:operation_0478" } ], "sc:license": "MIT", @@ -46,6 +42,10 @@ "Windows" ], "sc:url": "https://github.com/jaumebonet/RosettaSilentToolbox" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2796-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rstudio/rstudiobioschemas.jsonld b/data/rstudio/rstudiobioschemas.jsonld index 4a866ec508a11..85f3e88b3b67a 100644 --- a/data/rstudio/rstudiobioschemas.jsonld +++ b/data/rstudio/rstudiobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Integrated development environment (IDE) for the R programming language.", "sc:name": "RStudio", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://www.rstudio.com/" } \ No newline at end of file diff --git a/data/rsubread/rsubreadbioschemas.jsonld b/data/rsubread/rsubreadbioschemas.jsonld index 002a67fa41586..1db8fe554859f 100644 --- a/data/rsubread/rsubreadbioschemas.jsonld +++ b/data/rsubread/rsubreadbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkt214", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/rsubread", "@type": "sc:SoftwareApplication", @@ -20,26 +24,26 @@ "@id": "edam:data_0863" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ - { - "@id": "edam:topic_3168" - }, { "@id": "edam:topic_0204" }, { "@id": "edam:topic_3053" + }, + { + "@id": "edam:topic_3168" } ], "sc:citation": [ - "pmcid:PMC3664803", "pubmed:23558742", { "@id": "https://doi.org/10.1093/nar/gkt214" - } + }, + "pmcid:PMC3664803" ], "sc:description": "Provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. Includes quality assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.", "sc:featureList": { @@ -54,10 +58,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rsubread.html", "sc:version": "1.24.1" - }, - { - "@id": "https://doi.org/10.1093/nar/gkt214", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rsvsim/rsvsimbioschemas.jsonld b/data/rsvsim/rsvsimbioschemas.jsonld index 892769545171f..ea4b439b416fc 100644 --- a/data/rsvsim/rsvsimbioschemas.jsonld +++ b/data/rsvsim/rsvsimbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christoph Bartenhagen", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.", "sc:license": "GPL-3.0", "sc:name": "RSVSim", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RSVSim.html", diff --git a/data/rswebtool/rswebtoolbioschemas.jsonld b/data/rswebtool/rswebtoolbioschemas.jsonld index 5ad62e83886bd..649b6555a5442 100644 --- a/data/rswebtool/rswebtoolbioschemas.jsonld +++ b/data/rswebtool/rswebtoolbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "R. S. WebTool is a web server for random sampling-based significance evaluation of pairwise distances.", "sc:name": "R. S. WebTool", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://rswebtool.kwaklab.org" } \ No newline at end of file diff --git a/data/rt/rtbioschemas.jsonld b/data/rt/rtbioschemas.jsonld index f7b37ebb9d662..4cc461f6b1115 100644 --- a/data/rt/rtbioschemas.jsonld +++ b/data/rt/rtbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "rt", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.ms-utils.org/rt.html" } \ No newline at end of file diff --git a/data/rtanalyzer-retro/rtanalyzer-retrobioschemas.jsonld b/data/rtanalyzer-retro/rtanalyzer-retrobioschemas.jsonld index ca608992a522c..d24186fe55327 100644 --- a/data/rtanalyzer-retro/rtanalyzer-retrobioschemas.jsonld +++ b/data/rtanalyzer-retro/rtanalyzer-retrobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "It looks for a target site duplication, a polyA in 3′ and an endonuclease cleavage site in 5′ to calculate an overall score of retrotransposition. The tool will be useful for indepth analysis of non-autonomous retrotransposons in sequenced mammals to help us understand retrotransosition in our evolutionary tree.", "sc:name": "RTanalyzer", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://biotools.riboclub.org/cgi-bin/RTAnalyzer/index.pl" diff --git a/data/rtanalyzer/rtanalyzerbioschemas.jsonld b/data/rtanalyzer/rtanalyzerbioschemas.jsonld index 4f669182ae12d..a67d977012548 100644 --- a/data/rtanalyzer/rtanalyzerbioschemas.jsonld +++ b/data/rtanalyzer/rtanalyzerbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "RTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures.", "sc:name": "RTAnalyzer", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://ismailoglu.github.io/RT-analyzer/" } \ No newline at end of file diff --git a/data/rtandem/rtandembioschemas.jsonld b/data/rtandem/rtandembioschemas.jsonld index cc2fcbe3e5fe4..47973fc6c59d8 100644 --- a/data/rtandem/rtandembioschemas.jsonld +++ b/data/rtandem/rtandembioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Frederic Fournier", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package interfaces the tandem protein identification algorithm in R. Identification can be launched in the X!Tandem style, by using as sole parameter the path to a parameter file. But it also provides extended syntax and functions to streamline launching analyses, as well as function to convert results, parameters and taxonomy to/from R. A related package, shinyTANDEM, provides visualization interface for result objects.", "sc:license": "Artistic-1.0", "sc:name": "rTANDEM", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rTANDEM.html", "sc:version": "1.14.0" diff --git a/data/rtcga/bioconda_rtcga.yaml b/data/rtcga/bioconda_rtcga.yaml index 9f7b40c2fcb01..4f41d4a856cc5 100644 --- a/data/rtcga/bioconda_rtcga.yaml +++ b/data/rtcga/bioconda_rtcga.yaml @@ -11,7 +11,6 @@ description: The Cancer Genome Atlas (TCGA) Data Portal provides a platform for home: https://bioconductor.org/packages/3.10/bioc/html/RTCGA.html identifiers: - biotools:rtcga -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-rtcga diff --git a/data/rtcga/rtcgabioschemas.jsonld b/data/rtcga/rtcgabioschemas.jsonld index 827e36559244a..ddb14c4a61d0e 100644 --- a/data/rtcga/rtcgabioschemas.jsonld +++ b/data/rtcga/rtcgabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Marcin Kosinski", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data and high level sequence analysis of the tumor genomes.", "sc:license": "GPL-2.0", "sc:name": "RTCGA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RTCGA.html", "sc:version": "1.4.0" diff --git a/data/rtcgatoolbox/rtcgatoolboxbioschemas.jsonld b/data/rtcgatoolbox/rtcgatoolboxbioschemas.jsonld index a55c585034ce9..1e6c16249a78c 100644 --- a/data/rtcgatoolbox/rtcgatoolboxbioschemas.jsonld +++ b/data/rtcgatoolbox/rtcgatoolboxbioschemas.jsonld @@ -18,8 +18,8 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4152273", "pubmed:25181531", + "pmcid:PMC4152273", { "@id": "https://doi.org/10.1371/journal.pone.0106397" } @@ -31,9 +31,9 @@ "sc:license": "GPL-2.0", "sc:name": "RTCGAToolbox", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RTCGAToolbox.html", "sc:version": "2.4.0" diff --git a/data/rtk/rtkbioschemas.jsonld b/data/rtk/rtkbioschemas.jsonld index 9c0a2f34ee22d..e70927333cccb 100644 --- a/data/rtk/rtkbioschemas.jsonld +++ b/data/rtk/rtkbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Efficient rarefaction analysis of large datasets.", "sc:name": "RTK", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/rtk/index.html" diff --git a/data/rtn/rtnbioschemas.jsonld b/data/rtn/rtnbioschemas.jsonld index 18dd27b93692c..fa7ff566d85ff 100644 --- a/data/rtn/rtnbioschemas.jsonld +++ b/data/rtn/rtnbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/ncomms3464", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0003-4942-8131", "@type": "schema:Person" @@ -20,15 +24,15 @@ "@id": "http://orcid.org/0000-0003-4942-8131" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:24043118", - "pmcid:PMC3778544", { "@id": "https://doi.org/10.1038/ncomms3464" - } + }, + "pmcid:PMC3778544", + "pubmed:24043118" ], "sc:description": "This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies. Additionally, master regulators can be linked to genetic markers using eQTL/VSE analysis, taking advantage of the haplotype block structure mapped to the human genome in order to explore risk-associated SNPs identified in GWAS studies.", "sc:featureList": { @@ -43,10 +47,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RTN.html", "sc:version": "1.12.0" - }, - { - "@id": "https://doi.org/10.1038/ncomms3464", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rtnduals/rtndualsbioschemas.jsonld b/data/rtnduals/rtndualsbioschemas.jsonld index f368f26bfa06f..3ea0db20c6cca 100644 --- a/data/rtnduals/rtndualsbioschemas.jsonld +++ b/data/rtnduals/rtndualsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/rtnduals", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Clarice Groeneveld", - "Mauro Castro" + "Mauro Castro", + "Clarice Groeneveld" ], "sc:additionalType": "Library", "sc:description": "RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer 'dual regulons', a new concept that tests whether regulon pairs agree on the predicted downstream effects.", @@ -20,8 +20,8 @@ "sc:name": "RTNduals", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RTNduals.html", "sc:version": "1.4.0" diff --git a/data/rtopper/rtopperbioschemas.jsonld b/data/rtopper/rtopperbioschemas.jsonld index eda7f32975a6e..b08414ecbf1aa 100644 --- a/data/rtopper/rtopperbioschemas.jsonld +++ b/data/rtopper/rtopperbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/gb-2011-12-10-r105", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-7336-8071", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/rtopper", "@type": "sc:SoftwareApplication", @@ -24,12 +16,12 @@ "@id": "http://orcid.org/0000-0002-7336-8071" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pmcid:PMC3333775", "pubmed:22018358", + "pmcid:PMC3333775", { "@id": "https://doi.org/10.1186/gb-2011-12-10-r105" } @@ -41,12 +33,20 @@ "sc:license": "GPL-3.0", "sc:name": "RTopper", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RTopper.html", "sc:version": "1.20.0" + }, + { + "@id": "https://doi.org/10.1186/gb-2011-12-10-r105", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-7336-8071", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/rtp/rtpbioschemas.jsonld b/data/rtp/rtpbioschemas.jsonld index bc8a5697c7a95..c0fbe6cad2087 100644 --- a/data/rtp/rtpbioschemas.jsonld +++ b/data/rtp/rtpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A C code for calculating significance of truncated products of P-values", "sc:name": "RTP", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://sites.google.com/site/fdudbridge/software" } \ No newline at end of file diff --git a/data/rtracklayer/rtracklayerbioschemas.jsonld b/data/rtracklayer/rtracklayerbioschemas.jsonld index ae30c7feccc9c..7d2b924d5b66b 100644 --- a/data/rtracklayer/rtracklayerbioschemas.jsonld +++ b/data/rtracklayer/rtracklayerbioschemas.jsonld @@ -20,8 +20,8 @@ "@id": "edam:data_3002" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { @@ -50,8 +50,8 @@ "sc:license": "Artistic-2.0", "sc:name": "rtracklayer", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rtracklayer.html", diff --git a/data/rtree/rtreebioschemas.jsonld b/data/rtree/rtreebioschemas.jsonld index 1ed94c9c0933a..9290eb57c0c09 100644 --- a/data/rtree/rtreebioschemas.jsonld +++ b/data/rtree/rtreebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Analyze relative risk and conducts sib pair linkage analysis using tree-based methods.", "sc:name": "RTREE", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://c2s2.yale.edu/software/rtree/" diff --git a/data/rtreemix/rtreemixbioschemas.jsonld b/data/rtreemix/rtreemixbioschemas.jsonld index 28d8547a85591..3bb246e871e4d 100644 --- a/data/rtreemix/rtreemixbioschemas.jsonld +++ b/data/rtreemix/rtreemixbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "Rtreemix", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Rtreemix.html", "sc:version": "1.36.0" diff --git a/data/rtrm/rtrmbioschemas.jsonld b/data/rtrm/rtrmbioschemas.jsonld index 574a6144337b7..33f6dfdb1740f 100644 --- a/data/rtrm/rtrmbioschemas.jsonld +++ b/data/rtrm/rtrmbioschemas.jsonld @@ -28,11 +28,11 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:24137002", { "@id": "https://doi.org/10.1093/nar/gkt913" }, - "pmcid:PMC3874207", - "pubmed:24137002" + "pmcid:PMC3874207" ], "sc:description": "Identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.", "sc:featureList": { @@ -41,9 +41,9 @@ "sc:license": "GPL-3.0", "sc:name": "rTRM", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rTRM.html", "sc:version": "1.12.0" diff --git a/data/rtrmui/bioconda_rtrmui.yaml b/data/rtrmui/bioconda_rtrmui.yaml index e0a4b19cb5d56..9c3a20987b614 100644 --- a/data/rtrmui/bioconda_rtrmui.yaml +++ b/data/rtrmui/bioconda_rtrmui.yaml @@ -4,7 +4,6 @@ description: This package provides a web interface to compute transcriptional re home: https://bioconductor.org/packages/3.10/bioc/html/rTRMui.html identifiers: - biotools:rtrmui -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rtrmui diff --git a/data/rtrmui/rtrmuibioschemas.jsonld b/data/rtrmui/rtrmuibioschemas.jsonld index a4db8213db975..a20ff9a9c161e 100644 --- a/data/rtrmui/rtrmuibioschemas.jsonld +++ b/data/rtrmui/rtrmuibioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Diego Diez", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides a web interface to compute transcriptional regulatory modules with rTRM.", "sc:license": "GPL-3.0", "sc:name": "rTRMui", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rTRMui.html", "sc:version": "1.12.0" diff --git a/data/rtxi/rtxibioschemas.jsonld b/data/rtxi/rtxibioschemas.jsonld index 4718db3ca8943..4d315512191c8 100644 --- a/data/rtxi/rtxibioschemas.jsonld +++ b/data/rtxi/rtxibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "RTXI", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://rtxi.org/" } \ No newline at end of file diff --git a/data/rubi/rubibioschemas.jsonld b/data/rubi/rubibioschemas.jsonld index b0063a3e3aa42..5d3f6bfcc8f72 100644 --- a/data/rubi/rubibioschemas.jsonld +++ b/data/rubi/rubibioschemas.jsonld @@ -20,9 +20,9 @@ "sc:description": "New web server to detect regions of proteins which are thought to contain ubiquitinated lysines.", "sc:name": "RUBI", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/rubi/", diff --git a/data/rubioseq/rubioseqbioschemas.jsonld b/data/rubioseq/rubioseqbioschemas.jsonld index f8a9135f82fcc..21182d2716791 100644 --- a/data/rubioseq/rubioseqbioschemas.jsonld +++ b/data/rubioseq/rubioseqbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact form", "sc:additionalType": [ - "Suite", - "Workflow" + "Workflow", + "Suite" ], "sc:citation": "pubmed:23630175", "sc:description": "Primary and secondary analysis of resequencing projects by an integrated software suite of parallelized pipelines to detect exome variants (SNVs and CNVs) and to perform Bisulfite-seq analyses automatically.", diff --git a/data/rucs/rucsbioschemas.jsonld b/data/rucs/rucsbioschemas.jsonld index 1ab37ea1f289d..a3160613c4c2d 100644 --- a/data/rucs/rucsbioschemas.jsonld +++ b/data/rucs/rucsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "RUCS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cge.cbs.dtu.dk/services/RUCS/" } \ No newline at end of file diff --git a/data/rum/rumbioschemas.jsonld b/data/rum/rumbioschemas.jsonld index d69433f8db36a..535756fc9c328 100644 --- a/data/rum/rumbioschemas.jsonld +++ b/data/rum/rumbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-0139-7658", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btr427", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/rum", "@type": "sc:SoftwareApplication", @@ -26,10 +18,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC3167048", + "pubmed:21775302", { "@id": "https://doi.org/10.1093/bioinformatics/btr427" - }, - "pubmed:21775302" + } ], "sc:description": "RNA-Seq alignment pipeline.", "sc:featureList": { @@ -42,6 +34,14 @@ "Mac" ], "sc:url": "http://cbil.upenn.edu/RUM/" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btr427", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-0139-7658", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/runibic/runibicbioschemas.jsonld b/data/runibic/runibicbioschemas.jsonld index 1a198fc35a250..8bca61bfd952a 100644 --- a/data/runibic/runibicbioschemas.jsonld +++ b/data/runibic/runibicbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "runibic", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/runibic.html", "sc:version": "1.2.3" diff --git a/data/runsbml/runsbmlbioschemas.jsonld b/data/runsbml/runsbmlbioschemas.jsonld index 8d1b4dba5925a..15ba74c913aa2 100644 --- a/data/runsbml/runsbmlbioschemas.jsonld +++ b/data/runsbml/runsbmlbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.", "sc:name": "runSBML", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sourceforge.net/projects/runsbml/", "sc:version": "1.11" diff --git a/data/rust-bio/rust-biobioschemas.jsonld b/data/rust-bio/rust-biobioschemas.jsonld index 8e5326657cd12..dc51ec582c8e0 100644 --- a/data/rust-bio/rust-biobioschemas.jsonld +++ b/data/rust-bio/rust-biobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Rust-Bio", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://rust-bio.github.io/" } \ No newline at end of file diff --git a/data/ruv-iii/ruv-iiibioschemas.jsonld b/data/ruv-iii/ruv-iiibioschemas.jsonld index 3d82f02a60d54..13aa2248da250 100644 --- a/data/ruv-iii/ruv-iiibioschemas.jsonld +++ b/data/ruv-iii/ruv-iiibioschemas.jsonld @@ -9,26 +9,22 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKZ433", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/RUV-III", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Johann Gagnon-Bartsch", { "@id": "https://orcid.org/0000-0002-5403-7998" - } + }, + "Johann Gagnon-Bartsch" ], "sc:additionalType": "Library", "sc:citation": [ - "pubmed:31114909", - "pmcid:PMC6614807", { "@id": "https://doi.org/10.1093/NAR/GKZ433" - } + }, + "pmcid:PMC6614807", + "pubmed:31114909" ], "sc:description": "Removing Unwanted Variation-III (RUV-III) - normalization for Nanostring nCounter gene expression data.", "sc:featureList": [ @@ -36,21 +32,25 @@ "@id": "edam:operation_2940" }, { - "@id": "edam:operation_2939" + "@id": "edam:operation_3891" }, { - "@id": "edam:operation_3891" + "@id": "edam:operation_2939" } ], "sc:license": "GPL-2.0", "sc:name": "RUV-III", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/package=ruv" }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ433", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0002-5403-7998", "@type": "schema:Person" diff --git a/data/ruvnormalize/ruvnormalizebioschemas.jsonld b/data/ruvnormalize/ruvnormalizebioschemas.jsonld index d1c221471032b..8e536fc52e778 100644 --- a/data/ruvnormalize/ruvnormalizebioschemas.jsonld +++ b/data/ruvnormalize/ruvnormalizebioschemas.jsonld @@ -14,14 +14,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laurent Jacob", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:26286812", { "@id": "https://doi.org/10.1093/biostatistics/kxv026" }, + "pubmed:26286812", "pmcid:PMC4679071" ], "sc:description": "Removes unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis.", @@ -31,9 +31,9 @@ "sc:license": "GPL-3.0", "sc:name": "RUVnormalize", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RUVnormalize.html", "sc:version": "1.8.0" diff --git a/data/ruvseq/ruvseqbioschemas.jsonld b/data/ruvseq/ruvseqbioschemas.jsonld index d35e5b7730d48..acdf2e23350c0 100644 --- a/data/ruvseq/ruvseqbioschemas.jsonld +++ b/data/ruvseq/ruvseqbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "Artistic-2.0", "sc:name": "RUVSeq", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/RUVSeq.html", "sc:version": "1.8.0" diff --git a/data/rv-typer/rv-typerbioschemas.jsonld b/data/rv-typer/rv-typerbioschemas.jsonld index b63c668c3aaf0..b5a3f09edd956 100644 --- a/data/rv-typer/rv-typerbioschemas.jsonld +++ b/data/rv-typer/rv-typerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Assign serotype to Rhinovirus -A, -B & -C using geomic/protein sequences.", "sc:name": "RV-Typer", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfo.net.in/RV-Typer/home.html" } \ No newline at end of file diff --git a/data/rvboost/rvboostbioschemas.jsonld b/data/rvboost/rvboostbioschemas.jsonld index 7d2066d533720..c77355c758c85 100644 --- a/data/rvboost/rvboostbioschemas.jsonld +++ b/data/rvboost/rvboostbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/rvboost", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Saurabh Baheti", - "Chen Wang" + "Chen Wang", + "Saurabh Baheti" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:25170027", "sc:description": "RNA-seq variant prioritization approach for Illumina next-generation sequencing data.", "sc:name": "RVboost", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinformaticstools.mayo.edu/research/rvboost/" } \ No newline at end of file diff --git a/data/rvista/rvistabioschemas.jsonld b/data/rvista/rvistabioschemas.jsonld index 37b48f993ae98..e6d2e7e06a68d 100644 --- a/data/rvista/rvistabioschemas.jsonld +++ b/data/rvista/rvistabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This tool combines TFBS predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are evolutionarily conserved and present in a specific configuration within genomic sequences. The newly developed version 2.0 of the tool can process alignments generated by both the zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from the ECR Browser and GALA database.", "sc:name": "rVista", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://rvista.dcode.org/" } \ No newline at end of file diff --git a/data/rvpedigree/rvpedigreebioschemas.jsonld b/data/rvpedigree/rvpedigreebioschemas.jsonld index bfdeb67b28d4d..159a73a72ed9b 100644 --- a/data/rvpedigree/rvpedigreebioschemas.jsonld +++ b/data/rvpedigree/rvpedigreebioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/ije/dyw047", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/rvpedigree", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Karim Oualkacha", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5841637", { "@id": "https://doi.org/10.1093/ije/dyw047" }, - "pmcid:PMC5841637", "pubmed:27085080" ], "sc:description": "Family-based rare variant association tests for normally and non-normally distributed quantitative traits. Calculation of kinship matrices, various options for coping with non-normality, three different ways of estimating statistical significance incorporating triaging to enable efficient use of the most computationally-intensive calculations, and a parallelization option for genome-wide analysis.", @@ -29,10 +33,6 @@ "sc:name": "RVPedigree", "sc:url": "https://github.com/GreenwoodLab/RVPedigree", "sc:version": "0.0.3" - }, - { - "@id": "https://doi.org/10.1093/ije/dyw047", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/rvs/rvsbioschemas.jsonld b/data/rvs/rvsbioschemas.jsonld index e168292b5c728..27d5dd72dc811 100644 --- a/data/rvs/rvsbioschemas.jsonld +++ b/data/rvs/rvsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "RVS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://strug.ccb.sickkids.ca/rvs/index.html" } \ No newline at end of file diff --git a/data/rvsharing/rvsharingbioschemas.jsonld b/data/rvsharing/rvsharingbioschemas.jsonld index 51a050b58eddb..634a112b05ad0 100644 --- a/data/rvsharing/rvsharingbioschemas.jsonld +++ b/data/rvsharing/rvsharingbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool computes the probability that a rare variant is shared by related subjects, given that the variant was observed in any of them.", "sc:name": "RVsharing", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.crulrg.ulaval.ca/pages_perso_chercheurs/bureau_a/software.html" } \ No newline at end of file diff --git a/data/rvtests/rvtestsbioschemas.jsonld b/data/rvtests/rvtestsbioschemas.jsonld index ffff95876bb03..7fa187ff4af77 100644 --- a/data/rvtests/rvtestsbioschemas.jsonld +++ b/data/rvtests/rvtestsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A flexible software package for genetic association studies. It is designed to support unrelated individual or related (family-based) individuals. Both quantitative trait and binary trait are supported", "sc:name": "RvTests", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://zhanxw.github.io/rvtests/" } \ No newline at end of file diff --git a/data/rwikipathways/rwikipathwaysbioschemas.jsonld b/data/rwikipathways/rwikipathwaysbioschemas.jsonld index 0ba7530e8bd58..9d0f556cafd43 100644 --- a/data/rwikipathways/rwikipathwaysbioschemas.jsonld +++ b/data/rwikipathways/rwikipathwaysbioschemas.jsonld @@ -23,9 +23,9 @@ "sc:license": "MIT", "sc:name": "rWikiPathways", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/rWikiPathways.html", "sc:version": "1.0.0" diff --git a/data/rxa/rxabioschemas.jsonld b/data/rxa/rxabioschemas.jsonld index 25d2d8ec980f4..6b6f6f94ace7d 100644 --- a/data/rxa/rxabioschemas.jsonld +++ b/data/rxa/rxabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An R Package for Relative expression analysis of gene expession profiles.", "sc:name": "RXA", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://jshare.johnshopkins.edu/dnaiman1/public_html/rxa/" } \ No newline at end of file diff --git a/data/rxnsim/rxnsimbioschemas.jsonld b/data/rxnsim/rxnsimbioschemas.jsonld index 83853fe6d8311..2e5b642405e93 100644 --- a/data/rxnsim/rxnsimbioschemas.jsonld +++ b/data/rxnsim/rxnsimbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/RxnSim", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Varun Giri", "Tae Yong Kim", - "Anirban Bhaduri" + "Anirban Bhaduri", + "Varun Giri" ], "sc:additionalType": "Library", "sc:description": "Tool computes reaction similarity based on the molecular signatures of participating molecules.", @@ -21,8 +21,8 @@ "sc:name": "RxnSim", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/package=RxnSim" } \ No newline at end of file diff --git a/data/s-mart/s-martbioschemas.jsonld b/data/s-mart/s-martbioschemas.jsonld index 321c1e4ea83ae..37ae04c6808b1 100644 --- a/data/s-mart/s-martbioschemas.jsonld +++ b/data/s-mart/s-martbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "S-MART", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://urgi.versailles.inra.fr/Tools/S-MART" } \ No newline at end of file diff --git a/data/s-psorter/s-psorterbioschemas.jsonld b/data/s-psorter/s-psorterbioschemas.jsonld index 9db289b510707..5d960ddda0ab8 100644 --- a/data/s-psorter/s-psorterbioschemas.jsonld +++ b/data/s-psorter/s-psorterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A novel cell structure-driven classifier construction approach for predicting image-based protein subcellular location by employing the prior biological structural information.", "sc:name": "S-PSorter", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/shaoweinuaa/S-PSorter" diff --git a/data/s2o/s2obioschemas.jsonld b/data/s2o/s2obioschemas.jsonld index 17e570ffa5d3c..4f14b91fc517b 100644 --- a/data/s2o/s2obioschemas.jsonld +++ b/data/s2o/s2obioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12911-016-0402-4", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/s2o", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Martin Dugas", - "Philipp Bruland" + "Philipp Bruland", + "Martin Dugas" ], "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:28061771", { "@id": "https://doi.org/10.1186/s12911-016-0402-4" }, - "pmcid:PMC5219713" + "pmcid:PMC5219713", + "pubmed:28061771" ], "sc:description": "Convert data collections based on IBM SPSS Statistics to the data standard for definition and exchange of clinical trials.", "sc:featureList": { @@ -31,15 +35,11 @@ "sc:license": "LGPL-2.0", "sc:name": "S2O", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://sourceforge.net/projects/s2o/" - }, - { - "@id": "https://doi.org/10.1186/s12911-016-0402-4", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/s2p/s2pbioschemas.jsonld b/data/s2p/s2pbioschemas.jsonld index 168d13dcfcb7e..0d6cfdc3a7798 100644 --- a/data/s2p/s2pbioschemas.jsonld +++ b/data/s2p/s2pbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "S2P", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://sing-group.org/s2p", "sc:version": "1.2.1" diff --git a/data/s4te/s4tebioschemas.jsonld b/data/s4te/s4tebioschemas.jsonld index e12d54fd8a867..e34320696cc1a 100644 --- a/data/s4te/s4tebioschemas.jsonld +++ b/data/s4te/s4tebioschemas.jsonld @@ -14,8 +14,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6448907", "pubmed:30908487", + "pmcid:PMC6448907", { "@id": "https://doi.org/10.1371/journal.pcbi.1006847" } diff --git a/data/s4vectors/bioconda_s4vectors.yaml b/data/s4vectors/bioconda_s4vectors.yaml index 0e9d9d5ceb3cb..2f16d72645396 100644 --- a/data/s4vectors/bioconda_s4vectors.yaml +++ b/data/s4vectors/bioconda_s4vectors.yaml @@ -9,7 +9,6 @@ description: The S4Vectors package defines the Vector and List virtual classes a home: https://bioconductor.org/packages/3.10/bioc/html/S4Vectors.html identifiers: - biotools:s4vectors -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-s4vectors summary: Foundation of vector-like and list-like containers in Bioconductor diff --git a/data/s4vectors/s4vectorsbioschemas.jsonld b/data/s4vectors/s4vectorsbioschemas.jsonld index 9737fe8225f61..052a52813f264 100644 --- a/data/s4vectors/s4vectorsbioschemas.jsonld +++ b/data/s4vectors/s4vectorsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "S4Vectors", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/S4Vectors.html", "sc:version": "0.12.1" diff --git a/data/sa-conf/sa-confbioschemas.jsonld b/data/sa-conf/sa-confbioschemas.jsonld index 5e037eb0ed993..e7f2a7d34f706 100644 --- a/data/sa-conf/sa-confbioschemas.jsonld +++ b/data/sa-conf/sa-confbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Quantify the structural variability of a multiple target conformations (MTC) set and localize the structural variable positions and regions of the target.", "sc:name": "SA-CONF", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels" } \ No newline at end of file diff --git a/data/sa-mot/sa-motbioschemas.jsonld b/data/sa-mot/sa-motbioschemas.jsonld index 7b3329982468b..5b8c8a8370d8e 100644 --- a/data/sa-mot/sa-motbioschemas.jsonld +++ b/data/sa-mot/sa-motbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/sa-mot", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Leslie Regad", "Adrien Saladin", + "Leslie Regad", "Julien Maupetit" ], "sc:additionalType": "Web application", @@ -21,8 +21,8 @@ "sc:name": "SA-Mot", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://sa-mot.mti.univ-paris-diderot.fr" } \ No newline at end of file diff --git a/data/sa-search/sa-searchbioschemas.jsonld b/data/sa-search/sa-searchbioschemas.jsonld index c4070af407147..e81e1637e4e2a 100644 --- a/data/sa-search/sa-searchbioschemas.jsonld +++ b/data/sa-search/sa-searchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool which first converts a PDB structure file into a one-dimensional representation using a structural alphabet, and then searches for similarities using standard methods for sequence alignment.", "sc:name": "SA-Search", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search" } \ No newline at end of file diff --git a/data/sabbac/sabbacbioschemas.jsonld b/data/sabbac/sabbacbioschemas.jsonld index bbdb59e352cb7..7dc44a60d7de7 100644 --- a/data/sabbac/sabbacbioschemas.jsonld +++ b/data/sabbac/sabbacbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-1033-9895", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/sabbac", "@type": "sc:SoftwareApplication", @@ -22,10 +26,6 @@ "sc:name": "SABBAC", "sc:url": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC", "sc:version": "1.3" - }, - { - "@id": "https://orcid.org/0000-0003-1033-9895", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/saber/saberbioschemas.jsonld b/data/saber/saberbioschemas.jsonld index eee633ccc1e25..c663447fb1a5c 100644 --- a/data/saber/saberbioschemas.jsonld +++ b/data/saber/saberbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool implements a Markov-Hidden Markov Model for inferring locus-specific ancestry in admixed individuals", "sc:name": "SABER", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://med.stanford.edu/tanglab/software/saber.html" } \ No newline at end of file diff --git a/data/sable/sablebioschemas.jsonld b/data/sable/sablebioschemas.jsonld index 488dec7c6fa99..7755f65877510 100644 --- a/data/sable/sablebioschemas.jsonld +++ b/data/sable/sablebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This server can be used for predicting real valued relative solvent possibilities of amino acid residues in proteins, and for improved prediction of secondary structures using evolutionary profiles and predicted relative solvent accessibility of an amino acid residue as a fingerprint of the overall packing.", "sc:name": "SABLE", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://sable.cchmc.org/" } \ No newline at end of file diff --git a/data/sabund/sabundbioschemas.jsonld b/data/sabund/sabundbioschemas.jsonld index 2845f3e0da902..4e56fca436f21 100644 --- a/data/sabund/sabundbioschemas.jsonld +++ b/data/sabund/sabundbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Make Sabund and Rabund files from a CD-HIT cluster output.", "sc:name": "sabund", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/Sabund/0.1%20beta", "sc:version": "0.1 beta" diff --git a/data/sadmama/sadmamabioschemas.jsonld b/data/sadmama/sadmamabioschemas.jsonld index 5c45be5789a16..41acb020d58aa 100644 --- a/data/sadmama/sadmamabioschemas.jsonld +++ b/data/sadmama/sadmamabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Computational detection of significant variation in binding affinity across two sets of sequences. The binding sites are modeled as matches to a, possibly gapped, position weight matrix (PWM) which is presumed to be known.", "sc:name": "SADMAMA", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.maths.usyd.edu.au/u/uri/SADMAMA/", "sc:version": "20110410" diff --git a/data/safe/safebioschemas.jsonld b/data/safe/safebioschemas.jsonld index ca2e17d9cb696..ac579c61fdda6 100644 --- a/data/safe/safebioschemas.jsonld +++ b/data/safe/safebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "William T. Barry", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Resampling-based method for testing functional categories in gene expression experiments. It can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.", "sc:license": "GPL-2.0", "sc:name": "safe", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/safe.html", "sc:version": "3.14.0" diff --git a/data/safeec/safeecbioschemas.jsonld b/data/safeec/safeecbioschemas.jsonld index 1555db8cbae7d..28c67629fae8d 100644 --- a/data/safeec/safeecbioschemas.jsonld +++ b/data/safeec/safeecbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web applicatin for calculating folding free energy changes caused by missense mutations in proteins.", "sc:name": "SAFEEC", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://compbio.clemson.edu/SAAFEC/" } \ No newline at end of file diff --git a/data/sagat/sagatbioschemas.jsonld b/data/sagat/sagatbioschemas.jsonld index 68e4d7311b249..e1b4740e9cf86 100644 --- a/data/sagat/sagatbioschemas.jsonld +++ b/data/sagat/sagatbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "R package enabling the integration of currently existing microarray data from repositories like NCBI’s Gene Expression Omnibus (GEO) with microarray data querying conditions of interest. The goal of this integration is to better identify differentially expressed genes in the query conditions.", "sc:name": "SAGAT", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://simtk.org/home/sagat", "sc:version": "1.0" diff --git a/data/sagemap/sagemapbioschemas.jsonld b/data/sagemap/sagemapbioschemas.jsonld index 2030215e35cc1..e5a5777bda62c 100644 --- a/data/sagemap/sagemapbioschemas.jsonld +++ b/data/sagemap/sagemapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SAGE tag to gene mapping by NCBI.", "sc:name": "SAGEmap", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.ncbi.nlm.nih.gov/SAGE/" diff --git a/data/sagenhaft/bioconda_sagenhaft.yaml b/data/sagenhaft/bioconda_sagenhaft.yaml index c6d33afea8e77..4045acc69307e 100644 --- a/data/sagenhaft/bioconda_sagenhaft.yaml +++ b/data/sagenhaft/bioconda_sagenhaft.yaml @@ -7,7 +7,6 @@ description: This package implements several functions useful for analysis of ge home: https://bioconductor.org/packages/3.10/bioc/html/sagenhaft.html identifiers: - biotools:sagenhaft -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-sagenhaft diff --git a/data/sagenhaft/sagenhaftbioschemas.jsonld b/data/sagenhaft/sagenhaftbioschemas.jsonld index 94aa9789a0003..c2d430deb06c1 100644 --- a/data/sagenhaft/sagenhaftbioschemas.jsonld +++ b/data/sagenhaft/sagenhaftbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "sagenhaft", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sagenhaft.html", "sc:version": "1.44.0" diff --git a/data/sagexplore/sagexplorebioschemas.jsonld b/data/sagexplore/sagexplorebioschemas.jsonld index 96f80a29ce1bf..67b6abe01d470 100644 --- a/data/sagexplore/sagexplorebioschemas.jsonld +++ b/data/sagexplore/sagexplorebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A server for the mapping of SAGE tags against a genomic annotation.", "sc:name": "SAGExplore", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://melolab.org/sagexplore/home.php" } \ No newline at end of file diff --git a/data/sagpar/sagparbioschemas.jsonld b/data/sagpar/sagparbioschemas.jsonld index de903bc0307cb..1c33f9f0c49e6 100644 --- a/data/sagpar/sagparbioschemas.jsonld +++ b/data/sagpar/sagparbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A fast and robust algorithm that generates any metabolic pathway using some given structural representations of metabolites.", "sc:name": "SAGPAR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.isical.ac.in/~rajat/" } \ No newline at end of file diff --git a/data/sagx/bioconda_sagx.yaml b/data/sagx/bioconda_sagx.yaml index 05728146b857b..34e8c0b895977 100644 --- a/data/sagx/bioconda_sagx.yaml +++ b/data/sagx/bioconda_sagx.yaml @@ -5,7 +5,6 @@ description: A package for retrieval, preparation and analysis of data from the home: https://bioconductor.org/packages/3.10/bioc/html/SAGx.html identifiers: - biotools:sagx -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-sagx diff --git a/data/sahg/sahgbioschemas.jsonld b/data/sahg/sahgbioschemas.jsonld index 92477bd23b323..3a55a6c0c6dcc 100644 --- a/data/sahg/sahgbioschemas.jsonld +++ b/data/sahg/sahgbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SAHG", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bird.cbrc.jp/sahg" } \ No newline at end of file diff --git a/data/salad/saladbioschemas.jsonld b/data/salad/saladbioschemas.jsonld index 68f3598b2bdf7..c388ae2929331 100644 --- a/data/salad/saladbioschemas.jsonld +++ b/data/salad/saladbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "It is a unique comparative genomics database from plant-genome-based proteome data sets. Evolutionarily conserved motifs were extracted by MEME software from protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences.", "sc:name": "SALAD", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://salad.dna.affrc.go.jp/salad/en/" } \ No newline at end of file diff --git a/data/salmobase/salmobasebioschemas.jsonld b/data/salmobase/salmobasebioschemas.jsonld index e9f596cc6daa6..3a079e1c6608e 100644 --- a/data/salmobase/salmobasebioschemas.jsonld +++ b/data/salmobase/salmobasebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Integrated molecular resource for Salmonid species.", "sc:name": "SalmoBase", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://salmonbase.org/" diff --git a/data/salmonella_crispr_typing/salmonella_crispr_typingbioschemas.jsonld b/data/salmonella_crispr_typing/salmonella_crispr_typingbioschemas.jsonld index a7f6a06e34c7e..8ab58bbb57e75 100644 --- a/data/salmonella_crispr_typing/salmonella_crispr_typingbioschemas.jsonld +++ b/data/salmonella_crispr_typing/salmonella_crispr_typingbioschemas.jsonld @@ -11,22 +11,22 @@ "@id": "https://bio.tools/salmonella_crispr_typing", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kenzo Hugo Hillion", - "Laetitia Fabre" + "Laetitia Fabre", + "Kenzo Hugo Hillion" ], "sc:additionalType": "Command-line tool", "sc:description": "This tool gets a CRISPR profile by identifying the presence of known spacers and direct repeats (DRs) in a given sequence based on a catalogue.", "sc:license": "GPL-3.0", "sc:name": "Salmonella CRISPR typing", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "Enteric Bacterial Pathogens", - "Bioinformatics and Biostatistics Hub", "C3BI", - "Institut Pasteur" + "Institut Pasteur", + "Bioinformatics and Biostatistics Hub" ], "sc:url": "https://research.pasteur.fr/team/enteric-bacterial-pathogens/", "sc:version": "v.1.0.0" diff --git a/data/sam/sambioschemas.jsonld b/data/sam/sambioschemas.jsonld index 570a24d9a14ac..869cb0e3a57da 100644 --- a/data/sam/sambioschemas.jsonld +++ b/data/sam/sambioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool is a statistical technique for finding significant genes in a set of microarray experiments, a supervised learning software for genomic expression data mining.", "sc:name": "SAM", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://statweb.stanford.edu/~tibs/SAM/index.html" } \ No newline at end of file diff --git a/data/sam2tsv/sam2tsvbioschemas.jsonld b/data/sam2tsv/sam2tsvbioschemas.jsonld index 44548e8adfd56..e749d18c72267 100644 --- a/data/sam2tsv/sam2tsvbioschemas.jsonld +++ b/data/sam2tsv/sam2tsvbioschemas.jsonld @@ -21,8 +21,8 @@ "Linux" ], "sc:provider": [ - "Institut du Thorax, Nantes, France", - "univ-nantes.fr" + "univ-nantes.fr", + "Institut du Thorax, Nantes, France" ], "sc:url": "https://github.com/lindenb/jvarkit/wiki/Sam2Tsv", "sc:version": "1.0" diff --git a/data/sam_to_bam/sam_to_bambioschemas.jsonld b/data/sam_to_bam/sam_to_bambioschemas.jsonld index 5868139b59f0d..28b6ba5b478f9 100644 --- a/data/sam_to_bam/sam_to_bambioschemas.jsonld +++ b/data/sam_to_bam/sam_to_bambioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Converts SAM format to BAM format.", "sc:name": "sam_to_bam", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.htslib.org/", "sc:version": "0.1.19" diff --git a/data/sam_wga/sam_wgabioschemas.jsonld b/data/sam_wga/sam_wgabioschemas.jsonld index 9881531dad2b6..c9ead14b483e1 100644 --- a/data/sam_wga/sam_wgabioschemas.jsonld +++ b/data/sam_wga/sam_wgabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SAM is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type.", "sc:name": "SAM - Sequence Assembly Manager", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.bcgsc.ca/platform/bioinfo/software/sam" diff --git a/data/sambamba/sambambabioschemas.jsonld b/data/sambamba/sambambabioschemas.jsonld index 60bd53e96f3a2..bf8132c65a766 100644 --- a/data/sambamba/sambambabioschemas.jsonld +++ b/data/sambamba/sambambabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats.", "sc:name": "Sambamba", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.open-bio.org/wiki/Sambamba" } \ No newline at end of file diff --git a/data/sambinder/sambinderbioschemas.jsonld b/data/sambinder/sambinderbioschemas.jsonld index 28c035bbeec37..80ce9a5d147ba 100644 --- a/data/sambinder/sambinderbioschemas.jsonld +++ b/data/sambinder/sambinderbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "G.P.S. Raghava", "sc:additionalType": [ - "Web service", "Web application", - "Command-line tool" + "Command-line tool", + "Web service" ], "sc:description": "Web server for predicting SAM binding residues of a protein from its amino acid sequence.", "sc:license": "GPL-3.0", "sc:name": "SAMbinder", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://webs.iiitd.edu.in/raghava/sambinder/" } \ No newline at end of file diff --git a/data/samblaster/samblasterbioschemas.jsonld b/data/samblaster/samblasterbioschemas.jsonld index ddd29b7b170d8..c249d0278f849 100644 --- a/data/samblaster/samblasterbioschemas.jsonld +++ b/data/samblaster/samblasterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool to mark duplicates and extract discordant and split reads from SAM files.", "sc:name": "SAMBLASTER", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/GregoryFaust/samblaster" } \ No newline at end of file diff --git a/data/samcluster/samclusterbioschemas.jsonld b/data/samcluster/samclusterbioschemas.jsonld index 3b46dd6f48245..dc17c363fe0d6 100644 --- a/data/samcluster/samclusterbioschemas.jsonld +++ b/data/samcluster/samclusterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An integrated scheme and corresponding program for automatic discovery of sample classes based on gene expression profile.", "sc:name": "SamCluster", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.biosun.org.cn/SamCluster/index.htm" } \ No newline at end of file diff --git a/data/samexplorer/samexplorerbioschemas.jsonld b/data/samexplorer/samexplorerbioschemas.jsonld index dda79d2ce7b38..cb65ce53657f3 100644 --- a/data/samexplorer/samexplorerbioschemas.jsonld +++ b/data/samexplorer/samexplorerbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "samExploreR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/samExploreR.html", "sc:version": "1.4.0" diff --git a/data/samjavascript/samjavascriptbioschemas.jsonld b/data/samjavascript/samjavascriptbioschemas.jsonld index 82fb5c43df53c..1e0b5fcb232dc 100644 --- a/data/samjavascript/samjavascriptbioschemas.jsonld +++ b/data/samjavascript/samjavascriptbioschemas.jsonld @@ -17,12 +17,12 @@ "sc:license": "MIT", "sc:name": "SamJavascript", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "Institut du Thorax, Nantes, France", - "univ-nantes.fr" + "univ-nantes.fr", + "Institut du Thorax, Nantes, France" ], "sc:url": "https://github.com/lindenb/jvarkit/wiki/SamJavascript", "sc:version": "1.0" diff --git a/data/samnetweb/samnetwebbioschemas.jsonld b/data/samnetweb/samnetwebbioschemas.jsonld index e399099c13bdc..75f6bcf512803 100644 --- a/data/samnetweb/samnetwebbioschemas.jsonld +++ b/data/samnetweb/samnetwebbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SAMNetWeb", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://fraenkel-nsf.csbi.mit.edu/samnetweb/" } \ No newline at end of file diff --git a/data/sampdi/sampdibioschemas.jsonld b/data/sampdi/sampdibioschemas.jsonld index 5095cd9d52b8b..67d1ea3cc5f14 100644 --- a/data/sampdi/sampdibioschemas.jsonld +++ b/data/sampdi/sampdibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Single Amino acid Mutation binding free energy change of Protein–DNA Interaction.", "sc:name": "SAMPDI", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://compbio.clemson.edu/SAMPDI/" } \ No newline at end of file diff --git a/data/sampleclassifier/sampleclassifierbioschemas.jsonld b/data/sampleclassifier/sampleclassifierbioschemas.jsonld index aeef93f8efde2..6f52ef609937c 100644 --- a/data/sampleclassifier/sampleclassifierbioschemas.jsonld +++ b/data/sampleclassifier/sampleclassifierbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "sampleClassifier", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sampleClassifier.html", "sc:version": "1.4.0" diff --git a/data/sampleseq2/sampleseq2bioschemas.jsonld b/data/sampleseq2/sampleseq2bioschemas.jsonld index 4cf37639db54c..1a8dd96ba3510 100644 --- a/data/sampleseq2/sampleseq2bioschemas.jsonld +++ b/data/sampleseq2/sampleseq2bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A probability-based algorithm for selecting samples for a targeted resequencing experiment.", "sc:name": "SampleSeq2", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://biostat.mc.vanderbilt.edu/wiki/Main/SampleSeq" } \ No newline at end of file diff --git a/data/sampletrees/sampletreesbioschemas.jsonld b/data/sampletrees/sampletreesbioschemas.jsonld index a3676d646107f..7b8eb6390546b 100644 --- a/data/sampletrees/sampletreesbioschemas.jsonld +++ b/data/sampletrees/sampletreesbioschemas.jsonld @@ -9,39 +9,39 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btv763", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/sampletrees", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Kelly Burkett", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5860401", + "pubmed:26787665", { "@id": "https://doi.org/10.1093/bioinformatics/btv763" - }, - "pubmed:26787665", - "pmcid:PMC5860401" + } ], "sc:description": "Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.", "sc:featureList": [ { - "@id": "edam:operation_0484" + "@id": "edam:operation_3197" }, { - "@id": "edam:operation_3197" + "@id": "edam:operation_0484" } ], "sc:license": "GPL-3.0", "sc:name": "sampletrees", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://stat.sfu.ca/statgen/research/sampletrees.html" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btv763", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/samsa2/samsa2bioschemas.jsonld b/data/samsa2/samsa2bioschemas.jsonld index 159b7e290587d..73be66c4781c6 100644 --- a/data/samsa2/samsa2bioschemas.jsonld +++ b/data/samsa2/samsa2bioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SAMSA2", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://transcript.github.io/samsa2/", "sc:version": "2.0" diff --git a/data/samselect/samselectbioschemas.jsonld b/data/samselect/samselectbioschemas.jsonld index bda5337b3af7b..e8f7f86f752b7 100644 --- a/data/samselect/samselectbioschemas.jsonld +++ b/data/samselect/samselectbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Solver for sample sequence selection from large DNA datasets for quorum planted motif search", "sc:name": "SamSelect", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/qyu071/samselect" } \ No newline at end of file diff --git a/data/samspectral/samspectralbioschemas.jsonld b/data/samspectral/samspectralbioschemas.jsonld index e54d88a257690..768df6d2f3c04 100644 --- a/data/samspectral/samspectralbioschemas.jsonld +++ b/data/samspectral/samspectralbioschemas.jsonld @@ -20,8 +20,8 @@ "Library" ], "sc:citation": [ - "pmcid:PMC2923634", "pubmed:20667133", + "pmcid:PMC2923634", { "@id": "https://doi.org/10.1186/1471-2105-11-403" } @@ -34,8 +34,8 @@ "sc:name": "SamSPECTRAL", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SamSPECTRAL.html", "sc:version": "1.28.0" diff --git a/data/samtools/samtoolsbioschemas.jsonld b/data/samtools/samtoolsbioschemas.jsonld index 29a43aaac9f15..96a5634f4d47a 100644 --- a/data/samtools/samtoolsbioschemas.jsonld +++ b/data/samtools/samtoolsbioschemas.jsonld @@ -26,26 +26,26 @@ "sc:additionalType": "Suite", "sc:applicationSubCategory": [ { - "@id": "edam:topic_3168" + "@id": "edam:topic_0080" }, { - "@id": "edam:topic_0102" + "@id": "edam:topic_3168" }, { - "@id": "edam:topic_0080" + "@id": "edam:topic_0102" } ], "sc:citation": [ + "pubmed:19505943", { "@id": "https://doi.org/10.1093/bioinformatics/btp352" }, - "pubmed:19505943", "pmcid:PMC2723002" ], "sc:description": "A software package with various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.", "sc:featureList": [ { - "@id": "edam:operation_0227" + "@id": "edam:operation_1812" }, { "@id": "edam:operation_0337" @@ -54,19 +54,19 @@ "@id": "edam:operation_0335" }, { - "@id": "edam:operation_1812" + "@id": "edam:operation_3096" }, { - "@id": "edam:operation_3096" + "@id": "edam:operation_0227" } ], "sc:isAccessibleForFree": true, "sc:license": "MIT", "sc:name": "SAMtools", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:softwareHelp": [ { diff --git a/data/samtools_filter/samtools_filterbioschemas.jsonld b/data/samtools_filter/samtools_filterbioschemas.jsonld index ad7e0556c96e9..fddd49738663a 100644 --- a/data/samtools_filter/samtools_filterbioschemas.jsonld +++ b/data/samtools_filter/samtools_filterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Uses the samtools view command in SAMTools toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region.", "sc:name": "samtools_filter", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.htslib.org/", diff --git a/data/samtools_flagstat/samtools_flagstatbioschemas.jsonld b/data/samtools_flagstat/samtools_flagstatbioschemas.jsonld index 563fd877b0d27..8bf612321a121 100644 --- a/data/samtools_flagstat/samtools_flagstatbioschemas.jsonld +++ b/data/samtools_flagstat/samtools_flagstatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "samtools_flagstat", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.htslib.org/", "sc:version": "1.0.0" diff --git a/data/samtools_idxstats/samtools_idxstatsbioschemas.jsonld b/data/samtools_idxstats/samtools_idxstatsbioschemas.jsonld index 2b0333a9cf2ab..e3f73dfdf171c 100644 --- a/data/samtools_idxstats/samtools_idxstatsbioschemas.jsonld +++ b/data/samtools_idxstats/samtools_idxstatsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Run the samtools idxstats command in the SAMtools toolkit.", "sc:name": "samtools_idxstats", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.htslib.org/", diff --git a/data/samtools_slice_bam/samtools_slice_bambioschemas.jsonld b/data/samtools_slice_bam/samtools_slice_bambioschemas.jsonld index 650e45fff4351..7081f100b71a0 100644 --- a/data/samtools_slice_bam/samtools_slice_bambioschemas.jsonld +++ b/data/samtools_slice_bam/samtools_slice_bambioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Slice BAM by provided regions.", "sc:name": "samtools_slice_bam", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.htslib.org/", "sc:version": "0.0.1" diff --git a/data/samtools_sort/samtools_sortbioschemas.jsonld b/data/samtools_sort/samtools_sortbioschemas.jsonld index 9747ef22534db..7e3425f0eabe0 100644 --- a/data/samtools_sort/samtools_sortbioschemas.jsonld +++ b/data/samtools_sort/samtools_sortbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool uses the SAMTools toolkit to produce an indexed BAM file based on a sorted input SAM file.", "sc:name": "samtools_sort", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.htslib.org/", "sc:version": "0.1.18" diff --git a/data/sana-aligner/sana-alignerbioschemas.jsonld b/data/sana-aligner/sana-alignerbioschemas.jsonld index c7f6c285bceca..ecf6120f305d5 100644 --- a/data/sana-aligner/sana-alignerbioschemas.jsonld +++ b/data/sana-aligner/sana-alignerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Simulated annealing far outperforms many other search algorithms for biological network alignment.", "sc:name": "SANA", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://sana.ics.uci.edu/" diff --git a/data/sandpuma/sandpumabioschemas.jsonld b/data/sandpuma/sandpumabioschemas.jsonld index c5c6c62eb15da..ceb7393ff563a 100644 --- a/data/sandpuma/sandpumabioschemas.jsonld +++ b/data/sandpuma/sandpumabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/sandpuma", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Marnix H. Medema", - "Marc G. Chevrette" + "Marc G. Chevrette", + "Marnix H. Medema" ], "sc:additionalType": "Command-line tool", "sc:description": "Specificity of AdenylatioN Domain Prediction Using Multiple Algorithms.", diff --git a/data/sangerseqr/sangerseqrbioschemas.jsonld b/data/sangerseqr/sangerseqrbioschemas.jsonld index 417eed025ac3a..b53d31a5e421f 100644 --- a/data/sangerseqr/sangerseqrbioschemas.jsonld +++ b/data/sangerseqr/sangerseqrbioschemas.jsonld @@ -24,15 +24,15 @@ "@id": "http://orcid.org/0000-0003-1190-6302" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pubmed:25160973", + "pmcid:PMC4525701", { "@id": "https://doi.org/10.1002/dvdy.24183" - }, - "pmcid:PMC4525701", - "pubmed:25160973" + } ], "sc:description": "This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.", "sc:featureList": { @@ -41,9 +41,9 @@ "sc:license": "GPL-2.0", "sc:name": "sangerseqR", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sangerseqR.html", "sc:version": "1.10.0" diff --git a/data/sann/sannbioschemas.jsonld b/data/sann/sannbioschemas.jsonld index 8bb392b8476db..5df9219c5a3aa 100644 --- a/data/sann/sannbioschemas.jsonld +++ b/data/sann/sannbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Sann", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://lee.kias.re.kr/~newton/sann/" } \ No newline at end of file diff --git a/data/sansparallel/sansparallelbioschemas.jsonld b/data/sansparallel/sansparallelbioschemas.jsonld index 1a200e4a12ebe..e915c5cea6273 100644 --- a/data/sansparallel/sansparallelbioschemas.jsonld +++ b/data/sansparallel/sansparallelbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool takes a protein sequence as input and returns a set of similar sequences from Uniprot databases.", "sc:name": "SANSparallel", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi" diff --git a/data/santa/santabioschemas.jsonld b/data/santa/santabioschemas.jsonld index f022dd0e978bd..405ca94ad6df5 100644 --- a/data/santa/santabioschemas.jsonld +++ b/data/santa/santabioschemas.jsonld @@ -32,8 +32,8 @@ "sc:name": "SANTA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SANTA.html", "sc:version": "2.12.0" diff --git a/data/sanxot/sanxotbioschemas.jsonld b/data/sanxot/sanxotbioschemas.jsonld index 454f03b9bcd16..495926db7baba 100644 --- a/data/sanxot/sanxotbioschemas.jsonld +++ b/data/sanxot/sanxotbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/bty815", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/SanXoT", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ ], "sc:additionalType": "Script", "sc:citation": [ + "pubmed:30252043", { "@id": "https://doi.org/10.1093/bioinformatics/bty815" }, - "pmcid:PMC6499250", - "pubmed:30252043" + "pmcid:PMC6499250" ], "sc:description": "Modular and versatile package for the quantitative analysis of high-throughput proteomics experiments.", "sc:featureList": { @@ -36,10 +32,14 @@ "sc:name": "SanXoT", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.cnic.es/wiki/proteomica/index.php/SanXoT_software_package" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/bty815", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sapfinder/sapfinderbioschemas.jsonld b/data/sapfinder/sapfinderbioschemas.jsonld index 1374700454ce5..a6b579fb4d15e 100644 --- a/data/sapfinder/sapfinderbioschemas.jsonld +++ b/data/sapfinder/sapfinderbioschemas.jsonld @@ -22,9 +22,9 @@ "sc:license": "GPL-2.0", "sc:name": "sapFinder", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sapFinder.html", "sc:version": "1.12.0" diff --git a/data/saps/sapsbioschemas.jsonld b/data/saps/sapsbioschemas.jsonld index 2f8f20526358e..5915daf3dcddb 100644 --- a/data/saps/sapsbioschemas.jsonld +++ b/data/saps/sapsbioschemas.jsonld @@ -13,16 +13,16 @@ "biotools:primaryContact": "Daniel Schmolze", "sc:additionalType": "Command-line tool", "sc:author": [ - "Daniel Schmolze [aut", - "cre]", "Andrew Beck [aut]", + "cre]", + "Daniel Schmolze [aut", "Benjamin Haibe-Kains [aut]" ], "sc:description": "Functions implementing the Significance Analysis of Prognostic Signatures method that provides a robust method for identifying biologically significant gene sets associated with patient survival. Three basic statistics are computed: P_pure, P_random and a pre-ranked Gene Set Enrichment Analysis (GSEA). A score is calculated to summarize the three statistics, and optionally a Q-value is computed to estimate the significance.", "sc:name": "saps", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "BioConductor", diff --git a/data/saps_ebi/saps_ebibioschemas.jsonld b/data/saps_ebi/saps_ebibioschemas.jsonld index 17b25f3c578a4..752d87e8ef309 100644 --- a/data/saps_ebi/saps_ebibioschemas.jsonld +++ b/data/saps_ebi/saps_ebibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "SAPS (Statistical Analysis of Protein Sequences) evaluates a wide variety of protein sequence properties using statistics. Properties considered include compositional biases, clusters and runs of charge and other amino acid types, different kinds and extents of repetitive structures, locally periodic motifs, and anomalous spacings between identical residue types.", "sc:name": "SAPS (EBI)", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.ebi.ac.uk/Tools/seqstats/saps/" } \ No newline at end of file diff --git a/data/sara-cnv/sara-cnvbioschemas.jsonld b/data/sara-cnv/sara-cnvbioschemas.jsonld index 83ac1a10d68ba..ccd45365599fb 100644 --- a/data/sara-cnv/sara-cnvbioschemas.jsonld +++ b/data/sara-cnv/sara-cnvbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A program to detect chromosome copy number variations.", "sc:name": "SaRa", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://c2s2.yale.edu/software/SaRa/" } \ No newline at end of file diff --git a/data/sarek/sarekbioschemas.jsonld b/data/sarek/sarekbioschemas.jsonld index 0ed40bc35cc33..e4d91866f8659 100644 --- a/data/sarek/sarekbioschemas.jsonld +++ b/data/sarek/sarekbioschemas.jsonld @@ -17,20 +17,20 @@ "@id": "https://bio.tools/sarek", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Szilvester Juhos", { "@id": "https://orcid.org/0000-0003-2827-9261" - }, - "Szilvester Juhos" + } ], "sc:additionalType": [ "Command-line tool", "Workflow" ], "sc:author": [ - "Szilvester Juhos", { "@id": "https://orcid.org/0000-0003-2827-9261" - } + }, + "Szilvester Juhos" ], "sc:description": "Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing", "sc:license": "MIT", @@ -38,16 +38,16 @@ "sc:operatingSystem": "Linux", "sc:url": "https://nf-co.re/sarek", "sc:version": [ - "2.0.0", - "2.5", - "2.5.1", "2.2.2", - "2.2.0", - "2.3", + "2.5.2", + "2.1.0", "2.2.1", + "2.5", + "2.5.1", "2.3.FIX1", - "2.5.2", - "2.1.0" + "2.3", + "2.2.0", + "2.0.0" ] } ] diff --git a/data/sarotup/sarotupbioschemas.jsonld b/data/sarotup/sarotupbioschemas.jsonld index b36bdf99e33b8..df306a0237207 100644 --- a/data/sarotup/sarotupbioschemas.jsonld +++ b/data/sarotup/sarotupbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SAROTUP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://i.uestc.edu.cn/sarotup/index.html", "sc:version": "2.0" diff --git a/data/sarpred/sarpredbioschemas.jsonld b/data/sarpred/sarpredbioschemas.jsonld index 7d94d0c987fe6..d2ba187c41586 100644 --- a/data/sarpred/sarpredbioschemas.jsonld +++ b/data/sarpred/sarpredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment. In this method, two feed forward, back-propagation networks are used. The first sequence-to-structure network is trained with PSI-BLAST generated position specific scoring matrices. Further, the initial predictions from the first network and PSIPRED predicted secondary structure are used as input to the second structure-to-structure network.", "sc:name": "SARpred", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/sarpred/" } \ No newline at end of file diff --git a/data/sartools/sartoolsbioschemas.jsonld b/data/sartools/sartoolsbioschemas.jsonld index 571bf9804a655..d5ba01bdb2484 100644 --- a/data/sartools/sartoolsbioschemas.jsonld +++ b/data/sartools/sartoolsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SARTools", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "Institut Pasteur", "sc:url": "https://github.com/PF2-pasteur-fr/SARTools", diff --git a/data/sartools_deseq2/sartools_deseq2bioschemas.jsonld b/data/sartools_deseq2/sartools_deseq2bioschemas.jsonld index 82145a0bcc477..4dca74e1bcd75 100644 --- a/data/sartools_deseq2/sartools_deseq2bioschemas.jsonld +++ b/data/sartools_deseq2/sartools_deseq2bioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "sartools_deseq2", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/PF2-pasteur-fr/SARTools", "sc:version": "0.99.2" diff --git a/data/sartools_edger/sartools_edgerbioschemas.jsonld b/data/sartools_edger/sartools_edgerbioschemas.jsonld index aea80575af811..1535730bb4fcd 100644 --- a/data/sartools_edger/sartools_edgerbioschemas.jsonld +++ b/data/sartools_edger/sartools_edgerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Compare two or more biological conditions in a RNA-Seq framework with edgeR.", "sc:name": "sartools_edger", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/PF2-pasteur-fr/SARTools", "sc:version": "0.99.2" diff --git a/data/sas/sasbioschemas.jsonld b/data/sas/sasbioschemas.jsonld index 325b0ee1b5fa7..ad59e81aa4e20 100644 --- a/data/sas/sasbioschemas.jsonld +++ b/data/sas/sasbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "SAS", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/thornton-srv/databases/sas", diff --git a/data/sase-hunter/sase-hunterbioschemas.jsonld b/data/sase-hunter/sase-hunterbioschemas.jsonld index 2c265ddd1cfd3..88661d50c9eb3 100644 --- a/data/sase-hunter/sase-hunterbioschemas.jsonld +++ b/data/sase-hunter/sase-hunterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software to identify regions of interest with a higher than expected number of mutations than the near-by regions.", "sc:name": "SASE-hunter", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.sjdlab.org/resources/" } \ No newline at end of file diff --git a/data/sasgene/sasgenebioschemas.jsonld b/data/sasgene/sasgenebioschemas.jsonld index 16bc0c543d096..a45707beb234f 100644 --- a/data/sasgene/sasgenebioschemas.jsonld +++ b/data/sasgene/sasgenebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SASGene", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html", "sc:version": "1.2" diff --git a/data/sasm-vgwas/sasm-vgwasbioschemas.jsonld b/data/sasm-vgwas/sasm-vgwasbioschemas.jsonld index 69a49f2493698..a88534c1e20e1 100644 --- a/data/sasm-vgwas/sasm-vgwasbioschemas.jsonld +++ b/data/sasm-vgwas/sasm-vgwasbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "Unlicense", "sc:name": "SASM-VGWAS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/Meiyan88/SASM-VGWAS" } \ No newline at end of file diff --git a/data/sasquant/sasquantbioschemas.jsonld b/data/sasquant/sasquantbioschemas.jsonld index b817106d2da56..7377ae33c8425 100644 --- a/data/sasquant/sasquantbioschemas.jsonld +++ b/data/sasquant/sasquantbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A SAS computer program for analysis of quantitative genetic data.", "sc:name": "SASQuant", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html" diff --git a/data/satellog/satellogbioschemas.jsonld b/data/satellog/satellogbioschemas.jsonld index 5a564130adce3..29c73c5f31f3a 100644 --- a/data/satellog/satellogbioschemas.jsonld +++ b/data/satellog/satellogbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database for the identification and prioritization of satellite repeats in disease association studies.", "sc:name": "Satellog", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://satellog.bcgsc.ca/" } \ No newline at end of file diff --git a/data/sativa/sativabioschemas.jsonld b/data/sativa/sativabioschemas.jsonld index 3432a7cf8036e..3433b514268b2 100644 --- a/data/sativa/sativabioschemas.jsonld +++ b/data/sativa/sativabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A pipeline that uses Evolutionary Placement Algorithm (EPA) to identify taxonomically mislabeled sequences and suggest corrections.", "sc:name": "SATIVA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/amkozlov/sativa" } \ No newline at end of file diff --git a/data/saucie/sauciebioschemas.jsonld b/data/saucie/sauciebioschemas.jsonld index 0080ff94051e2..8a95302af3c7d 100644 --- a/data/saucie/sauciebioschemas.jsonld +++ b/data/saucie/sauciebioschemas.jsonld @@ -18,8 +18,8 @@ "sc:license": "Not licensed", "sc:name": "SAUCIE", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/KrishnaswamyLab/SAUCIE/" diff --git a/data/savant_genome_browser/savant_genome_browserbioschemas.jsonld b/data/savant_genome_browser/savant_genome_browserbioschemas.jsonld index 9c1f9d3950438..4c2fdf0284bf5 100644 --- a/data/savant_genome_browser/savant_genome_browserbioschemas.jsonld +++ b/data/savant_genome_browser/savant_genome_browserbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Savant Genome Browser", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.savantbrowser.com" } \ No newline at end of file diff --git a/data/savor/savorbioschemas.jsonld b/data/savor/savorbioschemas.jsonld index f39a98bed3c0b..51cea5a9c36e9 100644 --- a/data/savor/savorbioschemas.jsonld +++ b/data/savor/savorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SAVoR webserver allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures. SAVoR is designed to help researchers visualize sequencing data in the context of RNA secondary structures. Useful if you want to see the distribution of smRNA-seq reads along a microRNA precursor, how a set of SNPs might impact RNA structure, or in a control vs. treatment sequencing experiments you would like to see regions of enrichment along an RNA structure.", "sc:name": "SAVoR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://tesla.pcbi.upenn.edu/savor" } \ No newline at end of file diff --git a/data/savr/bioconda_savr.yaml b/data/savr/bioconda_savr.yaml index 3a88e059bb2b7..de30c49f41ecd 100644 --- a/data/savr/bioconda_savr.yaml +++ b/data/savr/bioconda_savr.yaml @@ -4,7 +4,6 @@ description: Parse Illumina Sequence Analysis Viewer (SAV) files, access data, a home: https://bioconductor.org/packages/3.10/bioc/html/savR.html identifiers: - biotools:savr -- doi:10.1038/nmeth.3252 license: AGPL-3 license_file: /lib/R/share/licenses/AGPL-3 name: bioconductor-savr diff --git a/data/savr/savrbioschemas.jsonld b/data/savr/savrbioschemas.jsonld index 3219044849b98..592d1a311e7ab 100644 --- a/data/savr/savrbioschemas.jsonld +++ b/data/savr/savrbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "savR", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/savR.html", "sc:version": "1.12.0" diff --git a/data/savvycnv/savvycnvbioschemas.jsonld b/data/savvycnv/savvycnvbioschemas.jsonld index 9f5c02954f3c0..814ee4b983c71 100644 --- a/data/savvycnv/savvycnvbioschemas.jsonld +++ b/data/savvycnv/savvycnvbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "SavvyCNV", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/rdemolgen/SavvySuite" diff --git a/data/saxster/saxsterbioschemas.jsonld b/data/saxster/saxsterbioschemas.jsonld index 349e18a93eb74..91339ba3d6359 100644 --- a/data/saxster/saxsterbioschemas.jsonld +++ b/data/saxster/saxsterbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A new algorithm to combine small-angle x-ray scattering data and threading for high-resolution protein structure determination.", "sc:name": "SAXSTER", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://zhanglab.ccmb.med.umich.edu/SAXSTER/" diff --git a/data/sbetoolbox/sbetoolboxbioschemas.jsonld b/data/sbetoolbox/sbetoolboxbioschemas.jsonld index 1a5b11a34a758..455e78c3c1059 100644 --- a/data/sbetoolbox/sbetoolboxbioschemas.jsonld +++ b/data/sbetoolbox/sbetoolboxbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SBEToolbox", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/biocoder/SBEToolbox" } \ No newline at end of file diff --git a/data/sbgntikz/sbgntikzbioschemas.jsonld b/data/sbgntikz/sbgntikzbioschemas.jsonld index e41583e14886d..23516b485cdde 100644 --- a/data/sbgntikz/sbgntikzbioschemas.jsonld +++ b/data/sbgntikz/sbgntikzbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "sbgntikz", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/Adrienrougny/sbgntikz/" } \ No newline at end of file diff --git a/data/sbgr/sbgrbioschemas.jsonld b/data/sbgr/sbgrbioschemas.jsonld index 4dc0441adc942..0dbf9f20ba7c5 100644 --- a/data/sbgr/sbgrbioschemas.jsonld +++ b/data/sbgr/sbgrbioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Nan Xiao", "sc:additionalType": "Command-line tool", "sc:author": [ - "Tengfei Yin ", - "Nan Xiao " + "Nan Xiao ", + "Tengfei Yin " ], "sc:description": "R client for Seven Bridges Genomics API.", "sc:name": "sbgr", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "BioConductor", "sc:url": "https://www.bioconductor.org/packages/3.2/bioc/html/sbgr.html", diff --git a/data/sbl/sblbioschemas.jsonld b/data/sbl/sblbioschemas.jsonld index 8a2dafcb41b91..6913f65b1e181 100644 --- a/data/sbl/sblbioschemas.jsonld +++ b/data/sbl/sblbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "SBL", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/MeiyueComputBio/sbl/tree/master/R%20packge" } \ No newline at end of file diff --git a/data/sbml/sbmlbioschemas.jsonld b/data/sbml/sbmlbioschemas.jsonld index 0bdd5c8320c54..fc93799d6b795 100644 --- a/data/sbml/sbmlbioschemas.jsonld +++ b/data/sbml/sbmlbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Project that develops and makes available a number of software resources in addition to the homonimous .org portal.", "sc:name": "SBML", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://sbml.org/Software" } \ No newline at end of file diff --git a/data/sbml2latex/sbml2latexbioschemas.jsonld b/data/sbml2latex/sbml2latexbioschemas.jsonld index 1b8bcc9738952..1e3c098df0a2b 100644 --- a/data/sbml2latex/sbml2latexbioschemas.jsonld +++ b/data/sbml2latex/sbml2latexbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool to convert files in the System Biology Markup Language (SBML) format into LATEX files.", "sc:name": "SBML2LATEX", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://sourceforge.net/projects/sbml2latex/" diff --git a/data/sbmleditor/sbmleditorbioschemas.jsonld b/data/sbmleditor/sbmleditorbioschemas.jsonld index 4f8673732614f..4ec7f1618f80d 100644 --- a/data/sbmleditor/sbmleditorbioschemas.jsonld +++ b/data/sbmleditor/sbmleditorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SBMLeditor", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.ebi.ac.uk/compneur-srv/SBMLeditor.html", "sc:version": "2.0-b1" diff --git a/data/sbmlmod/sbmlmodbioschemas.jsonld b/data/sbmlmod/sbmlmodbioschemas.jsonld index 08b2872306af3..4dfa76de43bc4 100644 --- a/data/sbmlmod/sbmlmodbioschemas.jsonld +++ b/data/sbmlmod/sbmlmodbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-017-1722-9", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/sbmlmod", "@type": "sc:SoftwareApplication", @@ -18,8 +22,8 @@ { "@id": "https://doi.org/10.1186/S12859-017-1722-9" }, - "pubmed:28646877", - "pmcid:PMC5483284" + "pmcid:PMC5483284", + "pubmed:28646877" ], "sc:description": "A web application that allows the integration of various data into a given SBML model. Accepted data cover common gene expression, proteomics or metabolomics data.", "sc:featureList": { @@ -28,14 +32,10 @@ "sc:name": "SBMLmod", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sbmlmod.uit.no:8000/sbmlmod/" - }, - { - "@id": "https://doi.org/10.1186/S12859-017-1722-9", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sbmlr/sbmlrbioschemas.jsonld b/data/sbmlr/sbmlrbioschemas.jsonld index 612ea27dcbdca..9ece58358f807 100644 --- a/data/sbmlr/sbmlrbioschemas.jsonld +++ b/data/sbmlr/sbmlrbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "SBMLR", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SBMLR.html", "sc:version": "1.70.0" diff --git a/data/sbmlsqueezer/sbmlsqueezerbioschemas.jsonld b/data/sbmlsqueezer/sbmlsqueezerbioschemas.jsonld index ce1cc8bb71973..9b06cdbae2667 100644 --- a/data/sbmlsqueezer/sbmlsqueezerbioschemas.jsonld +++ b/data/sbmlsqueezer/sbmlsqueezerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Generates kinetic equations for biochemical networks according to context of each reaction.", "sc:name": "SBMLsqueezer", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer/" diff --git a/data/sbpks2/sbpks2bioschemas.jsonld b/data/sbpks2/sbpks2bioschemas.jsonld index 0ac0155b18968..7de53a1de8c31 100644 --- a/data/sbpks2/sbpks2bioschemas.jsonld +++ b/data/sbpks2/sbpks2bioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkx344", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/sbpks2", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:28460065", - "pmcid:PMC5570206", { "@id": "https://doi.org/10.1093/nar/gkx344" - } + }, + "pmcid:PMC5570206" ], "sc:description": "Structure-based genome mining and analysis of polyketide and non-ribosomal peptide biosynthetic pathways in chemical space.", "sc:featureList": { @@ -27,10 +31,6 @@ }, "sc:name": "SBPKS2", "sc:url": "http://www.nii.ac.in/sbspks2.html" - }, - { - "@id": "https://doi.org/10.1093/nar/gkx344", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sbscl/sbsclbioschemas.jsonld b/data/sbscl/sbsclbioschemas.jsonld index aa250482e0405..fd4afd56c1fd6 100644 --- a/data/sbscl/sbsclbioschemas.jsonld +++ b/data/sbscl/sbsclbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Systems Biology Simulation Core Library", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://draeger-lab.github.io/SBSCL/" } \ No newline at end of file diff --git a/data/sbw/sbwbioschemas.jsonld b/data/sbw/sbwbioschemas.jsonld index ba7ece6a2dee6..e95872867d6e6 100644 --- a/data/sbw/sbwbioschemas.jsonld +++ b/data/sbw/sbwbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An open source framework connecting heterogeneous software application components-written in diverse programming languages and running on different platforms-to communicate and use each others' capabilities via a fast binary encoded-message system.", "sc:name": "SBW", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sbw.sourceforge.net/" } \ No newline at end of file diff --git a/data/sc3/sc3bioschemas.jsonld b/data/sc3/sc3bioschemas.jsonld index 0310a676d244f..f6516cc618910 100644 --- a/data/sc3/sc3bioschemas.jsonld +++ b/data/sc3/sc3bioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-1893-2255", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1038/nmeth.4236", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/sc3", "@type": "sc:SoftwareApplication", @@ -28,30 +20,38 @@ "Library" ], "sc:citation": [ + "pmcid:PMC5410170", "pubmed:28346451", { "@id": "https://doi.org/10.1038/nmeth.4236" - }, - "pmcid:PMC5410170" + } ], "sc:description": "A tool for unsupervised clustering and analysis of single cell RNA-Seq data.", "sc:featureList": [ { - "@id": "edam:operation_3680" + "@id": "edam:operation_0291" }, { - "@id": "edam:operation_0291" + "@id": "edam:operation_3680" } ], "sc:license": "GPL-3.0", "sc:name": "SC3", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SC3.html", "sc:version": "1.3.11" + }, + { + "@id": "http://orcid.org/0000-0003-1893-2255", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1038/nmeth.4236", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/scaffold_hunter/scaffold_hunterbioschemas.jsonld b/data/scaffold_hunter/scaffold_hunterbioschemas.jsonld index a8a32d757a26a..fa5eafdf913cc 100644 --- a/data/scaffold_hunter/scaffold_hunterbioschemas.jsonld +++ b/data/scaffold_hunter/scaffold_hunterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "ava-based open source tool for the visual analysis of data sets with a focus on data from the life sciences, aiming at an intuitive access to large and complex data sets. The tool offers a variety of views, e.g. graph, dendrogram, and plot view, as well as analysis methods, e.g. for clustering and classification.", "sc:name": "Scaffold Hunter", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://scaffoldhunter.sourceforge.net/index.html" } \ No newline at end of file diff --git a/data/scaffold_viewer/scaffold_viewerbioschemas.jsonld b/data/scaffold_viewer/scaffold_viewerbioschemas.jsonld index a0c90b05c7a24..ec76a4950b6e6 100644 --- a/data/scaffold_viewer/scaffold_viewerbioschemas.jsonld +++ b/data/scaffold_viewer/scaffold_viewerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Free viewer to share and visualize Scaffold-analyzed data.", "sc:name": "Scaffold Viewer", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.proteomesoftware.com/Scaffold/Scaffold_viewer.htm" } \ No newline at end of file diff --git a/data/scale4c/scale4cbioschemas.jsonld b/data/scale4c/scale4cbioschemas.jsonld index f3c3f7a454a9a..4161547e22856 100644 --- a/data/scale4c/scale4cbioschemas.jsonld +++ b/data/scale4c/scale4cbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "LGPL-3.0", "sc:name": "Scale4C", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Scale4C.html", diff --git a/data/scaleus/scaleusbioschemas.jsonld b/data/scaleus/scaleusbioschemas.jsonld index e9b1807bc6065..4693cfae58cc6 100644 --- a/data/scaleus/scaleusbioschemas.jsonld +++ b/data/scaleus/scaleusbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/scaleus", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Workbench", "Web API", + "Workbench", + "Web application", "SPARQL endpoint" ], "sc:citation": "pubmed:28214993", @@ -21,9 +21,9 @@ "sc:license": "MIT", "sc:name": "Scaleus", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinformatics-ua.github.io/scaleus/" } \ No newline at end of file diff --git a/data/scallop-lr/scallop-lrbioschemas.jsonld b/data/scallop-lr/scallop-lrbioschemas.jsonld index 21f95f3c73c13..195a30c0d3569 100644 --- a/data/scallop-lr/scallop-lrbioschemas.jsonld +++ b/data/scallop-lr/scallop-lrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "Scallop-LR", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/Kingsford-Group/scallop" } \ No newline at end of file diff --git a/data/scampi/scampibioschemas.jsonld b/data/scampi/scampibioschemas.jsonld index f31a20ec7672a..c3fb0ecc991ba 100644 --- a/data/scampi/scampibioschemas.jsonld +++ b/data/scampi/scampibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Prediction of membrane protein topology from first principles.", "sc:name": "SCAMPI", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://scampi.cbr.su.se/", diff --git a/data/scampi2/scampi2bioschemas.jsonld b/data/scampi2/scampi2bioschemas.jsonld index 1cc052faf5734..68ec59c766db9 100644 --- a/data/scampi2/scampi2bioschemas.jsonld +++ b/data/scampi2/scampi2bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Given the amino acid sequence of a putative alpha-helical membrane protein, this tool predicts the topology of the protein, i.e. a specification of the membrane spanning segments and their IN/OUT orientation relative to the membrane.", "sc:name": "SCAMPI2", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://scampi.bioinfo.se" } \ No newline at end of file diff --git a/data/scanaflp/scanaflpbioschemas.jsonld b/data/scanaflp/scanaflpbioschemas.jsonld index 0fe34e60e4b8c..176824221b78c 100644 --- a/data/scanaflp/scanaflpbioschemas.jsonld +++ b/data/scanaflp/scanaflpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A R script to evaluate AFLP electropherograms for phenotyping and marker selection based on peak height distribution and repeatability using blind controls.", "sc:name": "ScanAFLP", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www-leca.ujf-grenoble.fr/moyens-techniques/logiciels/article/population-genomics-software#ScanAFLP" } \ No newline at end of file diff --git a/data/scanmot/scanmotbioschemas.jsonld b/data/scanmot/scanmotbioschemas.jsonld index 6a990afac8384..d594db9397c1f 100644 --- a/data/scanmot/scanmotbioschemas.jsonld +++ b/data/scanmot/scanmotbioschemas.jsonld @@ -11,10 +11,10 @@ "@id": "https://bio.tools/scanmot", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Prem Anand A.", + "Sowdhamini R.", "Pugalenthi G.", "Nitin Bhardwaj", - "Sowdhamini R.", - "Prem Anand A.", "Saikat Chakrabarti" ], "sc:additionalType": "Web application", @@ -22,9 +22,9 @@ "sc:description": "SCANMOT is a sequence similarity searching tool that adds the additional constraints of simultaneous matching of multiple motifs.", "sc:name": "SCANMOT", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://caps.ncbs.res.in/scanmot/scanmot.html" } \ No newline at end of file diff --git a/data/scanprosite/scanprositebioschemas.jsonld b/data/scanprosite/scanprositebioschemas.jsonld index ddfb9c98b8771..eb28563f314f1 100644 --- a/data/scanprosite/scanprositebioschemas.jsonld +++ b/data/scanprosite/scanprositebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "ScanProsite is a tool for detecting PROSITE signature matches in protein sequences. Users can also search protein databases for specific motifs.", "sc:name": "ScanProsite", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://prosite.expasy.org/scanprosite/" diff --git a/data/scanpy/scanpybioschemas.jsonld b/data/scanpy/scanpybioschemas.jsonld index ca8c415899475..0e8f51f166fa2 100644 --- a/data/scanpy/scanpybioschemas.jsonld +++ b/data/scanpy/scanpybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "SCANPY", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/theislab/Scanpy" } \ No newline at end of file diff --git a/data/scansite/scansitebioschemas.jsonld b/data/scansite/scansitebioschemas.jsonld index c5cc0b1d852d9..7bba0820bbaed 100644 --- a/data/scansite/scansitebioschemas.jsonld +++ b/data/scansite/scansitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "Scansite", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://scansite.mit.edu/", diff --git a/data/scanstat/scanstatbioschemas.jsonld b/data/scanstat/scanstatbioschemas.jsonld index 7674768961c0a..ce5b73c90107d 100644 --- a/data/scanstat/scanstatbioschemas.jsonld +++ b/data/scanstat/scanstatbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool finds a set of contiguous SNPs that jointly are associated with disease.", "sc:name": "SCANSTAT", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.jurgott.org/linkage/scanstat.html" } \ No newline at end of file diff --git a/data/scapd/scapdbioschemas.jsonld b/data/scapd/scapdbioschemas.jsonld index e45c347c093c3..5926e7ff59243 100644 --- a/data/scapd/scapdbioschemas.jsonld +++ b/data/scapd/scapdbioschemas.jsonld @@ -22,11 +22,11 @@ "Web application" ], "sc:citation": [ - "pubmed:28984188", + "pmcid:PMC5629588", { "@id": "https://doi.org/10.1186/s12859-017-1806-6" }, - "pmcid:PMC5629588" + "pubmed:28984188" ], "sc:description": "Database for human scaffold proteins.", "sc:featureList": [ @@ -39,8 +39,8 @@ ], "sc:name": "ScaPD", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioinfo.wilmer.jhu.edu/ScaPD/" diff --git a/data/scarf/scarfbioschemas.jsonld b/data/scarf/scarfbioschemas.jsonld index 3844787b23a8f..97cde884363b3 100644 --- a/data/scarf/scarfbioschemas.jsonld +++ b/data/scarf/scarfbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "SCARF", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://evopipes.net/scarf.html" } \ No newline at end of file diff --git a/data/scater/scaterbioschemas.jsonld b/data/scater/scaterbioschemas.jsonld index 5c2b985156913..875326146b6f9 100644 --- a/data/scater/scaterbioschemas.jsonld +++ b/data/scater/scaterbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Davis McCarthy", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.", "sc:name": "scater", diff --git a/data/scbio/scbiobioschemas.jsonld b/data/scbio/scbiobioschemas.jsonld index e5efca8c2ec84..26abe8bfe0c94 100644 --- a/data/scbio/scbiobioschemas.jsonld +++ b/data/scbio/scbiobioschemas.jsonld @@ -13,8 +13,8 @@ "biotools:primaryContact": "Amit Frishberg", "sc:additionalType": "Library", "sc:author": [ - "Amit Frishberg", "Irit Gat-Viks", + "Amit Frishberg", "Naama Peshes-Yaloz" ], "sc:citation": "pubmed:30886410", @@ -22,9 +22,9 @@ "sc:license": "GPL-2.0", "sc:name": "scBio", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/amitfrish/scBio/blob/master/README.md", "sc:version": "0.1.5" diff --git a/data/sccmecfinder/sccmecfinderbioschemas.jsonld b/data/sccmecfinder/sccmecfinderbioschemas.jsonld index ea239c9aad423..78563b92f28fa 100644 --- a/data/sccmecfinder/sccmecfinderbioschemas.jsonld +++ b/data/sccmecfinder/sccmecfinderbioschemas.jsonld @@ -13,8 +13,8 @@ "@id": "https://bio.tools/sccmecfinder", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Technical support", - "Scientific Support" + "Scientific Support", + "Technical support" ], "sc:additionalType": "Web application", "sc:citation": [ @@ -30,9 +30,9 @@ }, "sc:name": "SCCmecFinder", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://cge.cbs.dtu.dk/services/SCCmecFinder/" }, diff --git a/data/scdd/scddbioschemas.jsonld b/data/scdd/scddbioschemas.jsonld index ce20ff83e32a8..ad40021873000 100644 --- a/data/scdd/scddbioschemas.jsonld +++ b/data/scdd/scddbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "scDD", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/scDD.html", diff --git a/data/scde/scdebioschemas.jsonld b/data/scde/scdebioschemas.jsonld index 5c27cc74680a9..d5cf9c536c158 100644 --- a/data/scde/scdebioschemas.jsonld +++ b/data/scde/scdebioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jean Fan", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package implements a set of statistical methods for analyzing single-cell RNA-seq data by fitting individual error models for single-cell RNA-seq measurements. These models can then be used for the assessment of DE between groups of cells, as well as other types of analysis. This package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures.", "sc:license": "GPL-2.0", diff --git a/data/scde_discovery/scde_discoverybioschemas.jsonld b/data/scde_discovery/scde_discoverybioschemas.jsonld index c251f6dc699e0..516fc52d960a9 100644 --- a/data/scde_discovery/scde_discoverybioschemas.jsonld +++ b/data/scde_discovery/scde_discoverybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework.", "sc:name": "Stem Cell Discovery Engine (SCDE)", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://discovery.hsci.harvard.edu/" } \ No newline at end of file diff --git a/data/scec/scecbioschemas.jsonld b/data/scec/scecbioschemas.jsonld index c030a850ee060..819225a836ce1 100644 --- a/data/scec/scecbioschemas.jsonld +++ b/data/scec/scecbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This server is designed for the prediction of 4 types of structural classes (all-α,all-β,α/β, and α+β) based on a protein sequence.", "sc:name": "SCEC", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://biomine.ece.ualberta.ca/Structural_Class/SCEC.html" } \ No newline at end of file diff --git a/data/scenery/scenerybioschemas.jsonld b/data/scenery/scenerybioschemas.jsonld index ec02a239bdbbf..a4ca9ad6e113d 100644 --- a/data/scenery/scenerybioschemas.jsonld +++ b/data/scenery/scenerybioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkx448", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/scenery", "@type": "sc:SoftwareApplication", @@ -29,36 +25,39 @@ "sc:additionalType": "Web service", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0804" + "@id": "edam:topic_2269" }, { - "@id": "edam:topic_2269" + "@id": "edam:topic_0121" }, { "@id": "edam:topic_0602" }, { - "@id": "edam:topic_0121" + "@id": "edam:topic_0804" }, { "@id": "edam:topic_3307" } ], "sc:citation": [ - "pmcid:PMC5570263", "pubmed:28525568", { "@id": "https://doi.org/10.1093/nar/gkx448" - } + }, + "pmcid:PMC5570263" ], "sc:contributor": "European Research Council within the CausalPath project", "sc:description": "Apply standard pre-processing, statistical analysis, advanced visualization methods and network reconstruction methods on single-cell cytometry data. It has an open architecture that allows power users to extend its functionalities by submitting their own machine learning methods.", "sc:featureList": [ + { + "@id": "edam:operation_3435" + }, { "@id": "edam:operation_3658" }, { - "@id": "edam:operation_3083" + "@id": "edam:operation_3439" }, { "@id": "edam:operation_3664" @@ -67,10 +66,7 @@ "@id": "edam:operation_3659" }, { - "@id": "edam:operation_3439" - }, - { - "@id": "edam:operation_3435" + "@id": "edam:operation_3083" } ], "sc:funder": "European Research Council within the CausalPath project", @@ -82,6 +78,10 @@ }, "sc:url": "http://scenery.csd.uoc.gr", "sc:version": "1.0" + }, + { + "@id": "https://doi.org/10.1093/nar/gkx448", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/scenic/scenicbioschemas.jsonld b/data/scenic/scenicbioschemas.jsonld index 9b94ef70e0694..1f72a4853c787 100644 --- a/data/scenic/scenicbioschemas.jsonld +++ b/data/scenic/scenicbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "SCENIC", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://scenic.aertslab.org" } \ No newline at end of file diff --git a/data/scepath/scepathbioschemas.jsonld b/data/scepath/scepathbioschemas.jsonld index c57728f7117ad..311ffda50fe10 100644 --- a/data/scepath/scepathbioschemas.jsonld +++ b/data/scepath/scepathbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "scEpath", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/sqjin/scEpath" } \ No newline at end of file diff --git a/data/scertf/scertfbioschemas.jsonld b/data/scertf/scertfbioschemas.jsonld index 54da60031b8df..573530beeb5c0 100644 --- a/data/scertf/scertfbioschemas.jsonld +++ b/data/scertf/scertfbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ScerTF catalogs over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors.", "sc:name": "ScerTF", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://stormo.wustl.edu/ScerTF/" } \ No newline at end of file diff --git a/data/scfba/scfbabioschemas.jsonld b/data/scfba/scfbabioschemas.jsonld index bba0723c3b3db..53ead11e9e182 100644 --- a/data/scfba/scfbabioschemas.jsonld +++ b/data/scfba/scfbabioschemas.jsonld @@ -19,29 +19,29 @@ "biotools:primaryContact": "BIMIB", "sc:additionalType": "Suite", "sc:citation": [ + "pmcid:PMC6413955", { "@id": "https://doi.org/10.1371/journal.pcbi.1006733" }, - "pmcid:PMC6413955", "pubmed:30818329" ], "sc:description": "Suite of MATLAB functions to perform a single-cell Flux Balance Analysis (scFBA)", "sc:featureList": [ - { - "@id": "edam:operation_3660" - }, { "@id": "edam:operation_3803" }, { "@id": "edam:operation_2495" + }, + { + "@id": "edam:operation_3660" } ], "sc:name": "scFBA", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/BIMIB-DISCo/scFBA" } diff --git a/data/scfeaturefilter/scfeaturefilterbioschemas.jsonld b/data/scfeaturefilter/scfeaturefilterbioschemas.jsonld index bbc19a66f8493..92b243d1baadb 100644 --- a/data/scfeaturefilter/scfeaturefilterbioschemas.jsonld +++ b/data/scfeaturefilter/scfeaturefilterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "scFeatureFilter", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/scFeatureFilter.html", diff --git a/data/scfind/scfindbioschemas.jsonld b/data/scfind/scfindbioschemas.jsonld index f3736a1ab1f82..e1a7fefe3afc5 100644 --- a/data/scfind/scfindbioschemas.jsonld +++ b/data/scfind/scfindbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "scfind", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/scfind.html", "sc:version": "1.2.0" diff --git a/data/scg/scgbioschemas.jsonld b/data/scg/scgbioschemas.jsonld index 38d801d1187d6..0c7e0373331ba 100644 --- a/data/scg/scgbioschemas.jsonld +++ b/data/scg/scgbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "Single Cell Genotyper (SCG)", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://shahlab.ca/projects/scg/" } \ No newline at end of file diff --git a/data/schicnorm/schicnormbioschemas.jsonld b/data/schicnorm/schicnormbioschemas.jsonld index 6cd22f5038276..4747b42c4a1d3 100644 --- a/data/schicnorm/schicnormbioschemas.jsonld +++ b/data/schicnorm/schicnormbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Zheng Wang", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5860379", "pubmed:29186290", { "@id": "https://doi.org/10.1093/bioinformatics/btx747" - } + }, + "pmcid:PMC5860379" ], "sc:description": "Software package for eliminating systematic biases in single-cell Hi-C data. Considering that single-cell Hi-C data are zero-inflated, here we use zero-inflated (Poisson and Negative Binomial) and hurdle (Poisson and Negative Binomial) models to remove biases, including cutting sites, GC content, and mappability.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "scHiCNorm", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://dna.cs.miami.edu/scHiCNorm/" diff --git a/data/schmutzi/schmutzibioschemas.jsonld b/data/schmutzi/schmutzibioschemas.jsonld index 0a1c1cbbc9922..1b53907d90438 100644 --- a/data/schmutzi/schmutzibioschemas.jsonld +++ b/data/schmutzi/schmutzibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "schmutzi", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://grenaud.github.io/schmutzi/" } \ No newline at end of file diff --git a/data/sci-lmm/sci-lmmbioschemas.jsonld b/data/sci-lmm/sci-lmmbioschemas.jsonld index db5d2b52d54e6..2270bac4e7b22 100644 --- a/data/sci-lmm/sci-lmmbioschemas.jsonld +++ b/data/sci-lmm/sci-lmmbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://orcid.org/0000-0003-1432-7461", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PGEN.1008124", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Sci-LMM", "@type": "sc:SoftwareApplication", @@ -21,33 +25,29 @@ }, "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC6529016", - "pubmed:31071088", { "@id": "https://doi.org/10.1371/JOURNAL.PGEN.1008124" - } + }, + "pubmed:31071088", + "pmcid:PMC6529016" ], "sc:description": "Modeling framework for studying population-scale family trees that combines techniques from the animal and plant breeding literature and from human genetics literature.", "sc:featureList": [ { - "@id": "edam:operation_3659" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3196" + "@id": "edam:operation_3659" } ], "sc:license": "GPL-3.0", "sc:name": "Sci-LMM", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/TalShor/SciLMM" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PGEN.1008124", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sciluigi/sciluigibioschemas.jsonld b/data/sciluigi/sciluigibioschemas.jsonld index d5dfd4089528f..5c9387e0044f6 100644 --- a/data/sciluigi/sciluigibioschemas.jsonld +++ b/data/sciluigi/sciluigibioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13321-016-0179-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/sciluigi", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Samuel Lampa", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC5123367", { "@id": "https://doi.org/10.1186/s13321-016-0179-6" }, - "pubmed:27942268", - "pmcid:PMC5123367" + "pubmed:27942268" ], "sc:description": "Scientific Luigi (SciLuigi for short) is a light-weight wrapper library around Spotify's Luigi workflow system that aims to make writing scientific workflows more fluent, flexible and modular.", "sc:featureList": { @@ -35,12 +31,16 @@ "sc:license": "MIT", "sc:name": "SciLuigi", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/pharmbio/sciluigi", "sc:version": "0.9.5" + }, + { + "@id": "https://doi.org/10.1186/s13321-016-0179-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/scimo/scimobioschemas.jsonld b/data/scimo/scimobioschemas.jsonld index e2f38a5135ac6..f867f12a6e121 100644 --- a/data/scimo/scimobioschemas.jsonld +++ b/data/scimo/scimobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "SCIMO a prototype of a 2-D Gel Electrophoresis image analysis system. Being a prototype, some errors may be found that we would appreciate to be informed of. Currently, this software detects the protein spots in the gel and will present the area and volume of each spot.", "sc:name": "SCIMO", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://w3.ualg.pt/~aanjos/prototypes.html", "sc:version": "20100824" diff --git a/data/scipion/scipionbioschemas.jsonld b/data/scipion/scipionbioschemas.jsonld index d593e06e70919..92f3b8d8375b6 100644 --- a/data/scipion/scipionbioschemas.jsonld +++ b/data/scipion/scipionbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Scipion", "sc:additionalType": [ - "Desktop application", "Command-line tool", + "Desktop application", "Workbench" ], "sc:description": "A software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from http://scipion.cnb.csic.es.", diff --git a/data/scipion_web_tools/scipion_web_toolsbioschemas.jsonld b/data/scipion_web_tools/scipion_web_toolsbioschemas.jsonld index e6c570f13b8fc..47240b27f612f 100644 --- a/data/scipion_web_tools/scipion_web_toolsbioschemas.jsonld +++ b/data/scipion_web_tools/scipion_web_toolsbioschemas.jsonld @@ -16,12 +16,12 @@ "sc:name": "SCIPION WEB TOOLS", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "INB", "cnb.csic.es", + "INB", "ELIXIR-ES" ], "sc:url": "http://scipion.cnb.csic.es/m/services/", diff --git a/data/sciroko/scirokobioschemas.jsonld b/data/sciroko/scirokobioschemas.jsonld index f5b99cd6e58b3..cdcedf790284a 100644 --- a/data/sciroko/scirokobioschemas.jsonld +++ b/data/sciroko/scirokobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SciRoKo", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.kofler.or.at/bioinformatics/SciRoKo/index.html", "sc:version": "3.4" diff --git a/data/scisi/bioconda_scisi.yaml b/data/scisi/bioconda_scisi.yaml index e94dbb327d9ee..8f40ae83ffc7e 100644 --- a/data/scisi/bioconda_scisi.yaml +++ b/data/scisi/bioconda_scisi.yaml @@ -3,7 +3,6 @@ description: Package to create In Silico Interactomes home: https://bioconductor.org/packages/3.10/bioc/html/ScISI.html identifiers: - biotools:scisi -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-scisi diff --git a/data/scisi/scisibioschemas.jsonld b/data/scisi/scisibioschemas.jsonld index 8e3b2e729fff8..34a57c44242cc 100644 --- a/data/scisi/scisibioschemas.jsonld +++ b/data/scisi/scisibioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Tony Chiang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Package to create In Silico Interactomes.", "sc:license": "GPL-3.0", "sc:name": "ScISI", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ScISI.html", "sc:version": "1.46.0" diff --git a/data/scite/scitebioschemas.jsonld b/data/scite/scitebioschemas.jsonld index acc17b4e1a9c5..de3776b09d4f0 100644 --- a/data/scite/scitebioschemas.jsonld +++ b/data/scite/scitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "SCITE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/cbg-ethz/SCITE" } \ No newline at end of file diff --git a/data/scitrack/scitrackbioschemas.jsonld b/data/scitrack/scitrackbioschemas.jsonld index f3beb6c724b81..9697365ca0505 100644 --- a/data/scitrack/scitrackbioschemas.jsonld +++ b/data/scitrack/scitrackbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Library aimed at application developers writing scientific software to support this tracking of scientific computation. The library provides elementary functionality to support logging. The primary capabilities concern generating checksums on input and output files and facilitating logging of the computational environment. If the optional dependency mpiutils is installed, then logging can be done safely in a parallel computation environment.", "sc:name": "SciTrack", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "unimelb.edu.au", "sc:url": "https://bitbucket.org/gavin.huttley/scitrack", diff --git a/data/sclvm/sclvmbioschemas.jsonld b/data/sclvm/sclvmbioschemas.jsonld index b48c7b50ca3ba..2c85ef722abfb 100644 --- a/data/sclvm/sclvmbioschemas.jsonld +++ b/data/sclvm/sclvmbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation.", "sc:name": "scLVM", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/PMBio/scLVM" diff --git a/data/scmap/scmapbioschemas.jsonld b/data/scmap/scmapbioschemas.jsonld index 3a9eb3ce476d3..8d301c08fa4aa 100644 --- a/data/scmap/scmapbioschemas.jsonld +++ b/data/scmap/scmapbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "scmap", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://www.sanger.ac.uk/science/tools/scmap" } \ No newline at end of file diff --git a/data/scmd/scmdbioschemas.jsonld b/data/scmd/scmdbioschemas.jsonld index 35cd98ad6de7b..831c10651cc1a 100644 --- a/data/scmd/scmdbioschemas.jsonld +++ b/data/scmd/scmdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Collection of micrographs of budding yeast mutants, visualization and data mining tools are provided.", "sc:name": "SCMD", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://scmd.gi.k.u-tokyo.ac.jp/" } \ No newline at end of file diff --git a/data/scmeth/scmethbioschemas.jsonld b/data/scmeth/scmethbioschemas.jsonld index 53809687e75ca..6a6274c2dd3ee 100644 --- a/data/scmeth/scmethbioschemas.jsonld +++ b/data/scmeth/scmethbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "scmeth", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/scmeth.html", "sc:version": "1.0.1" diff --git a/data/scmfdd/scmfddbioschemas.jsonld b/data/scmfdd/scmfddbioschemas.jsonld index 4174266280c61..38da9470baee4 100644 --- a/data/scmfdd/scmfddbioschemas.jsonld +++ b/data/scmfdd/scmfddbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "SCMFDD", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bioinfotech.cn/SCMFDD/" } \ No newline at end of file diff --git a/data/scmmtp/scmmtpbioschemas.jsonld b/data/scmmtp/scmmtpbioschemas.jsonld index dc43fe8c10633..ba25e3edffeec 100644 --- a/data/scmmtp/scmmtpbioschemas.jsonld +++ b/data/scmmtp/scmmtpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A novel method  based on the scoring card method (SCM) using dipeptide composition to identify and characterize MTPs from an existing dataset.", "sc:name": "SCMMTP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://iclab.life.nctu.edu.tw/iclab_webtools/SCMMTP/" } \ No newline at end of file diff --git a/data/scmpsp/scmpspbioschemas.jsonld b/data/scmpsp/scmpspbioschemas.jsonld index f5d1fbcb24943..bb59c80a92ba5 100644 --- a/data/scmpsp/scmpspbioschemas.jsonld +++ b/data/scmpsp/scmpspbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A novel bioinformatics method of predicting and characterizing PSPs based on scoring card method.", "sc:name": "SCMPSP", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://iclab.life.nctu.edu.tw/SCMPSP/" } \ No newline at end of file diff --git a/data/scnpf/scnpfbioschemas.jsonld b/data/scnpf/scnpfbioschemas.jsonld index 8b2bd14a2bb74..a36eb438a6809 100644 --- a/data/scnpf/scnpfbioschemas.jsonld +++ b/data/scnpf/scnpfbioschemas.jsonld @@ -9,45 +9,45 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12864-019-5747-5", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/scNPF", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wenbin Ye", - "Xiaohui Wu" + "Xiaohui Wu", + "Wenbin Ye" ], "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6505295", "pubmed:31068142", + "pmcid:PMC6505295", { "@id": "https://doi.org/10.1186/S12864-019-5747-5" } ], "sc:description": "R package for pre-processing of single-cell RNA-seq data by leveraging the context-specific topology inherent in the given data and the network information from priori gene-gene interaction networks.", "sc:featureList": [ - { - "@id": "edam:operation_3557" - }, { "@id": "edam:operation_3463" }, { "@id": "edam:operation_3766" + }, + { + "@id": "edam:operation_3557" } ], "sc:license": "GPL-2.0", "sc:name": "scNPF", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/BMILAB/scNPF" - }, - { - "@id": "https://doi.org/10.1186/S12864-019-5747-5", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/scones/sconesbioschemas.jsonld b/data/scones/sconesbioschemas.jsonld index 8c19729fbcd12..7241022d3fe45 100644 --- a/data/scones/sconesbioschemas.jsonld +++ b/data/scones/sconesbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SConES", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.bsse.ethz.ch/mlcb/research/bioinformatics-and-computational-biology/scones.html" } \ No newline at end of file diff --git a/data/sconify/sconifybioschemas.jsonld b/data/sconify/sconifybioschemas.jsonld index 93385954edc94..09af3eaafe8c5 100644 --- a/data/sconify/sconifybioschemas.jsonld +++ b/data/sconify/sconifybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "Sconify", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Sconify.html", "sc:version": "1.0.0" diff --git a/data/scop/scopbioschemas.jsonld b/data/scop/scopbioschemas.jsonld index fbad41c91f19b..e9db8e4c0b14d 100644 --- a/data/scop/scopbioschemas.jsonld +++ b/data/scop/scopbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Database created by a combination of manual inspection and automated methods. Comprehensive ordering of all proteins of known structure, according to evolutionary and structural relationships.", "sc:name": "SCOP", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://scop.mrc-lmb.cam.ac.uk/scop/" } \ No newline at end of file diff --git a/data/scop3d/scop3dbioschemas.jsonld b/data/scop3d/scop3dbioschemas.jsonld index 699875338f6d0..c9eec325375c3 100644 --- a/data/scop3d/scop3dbioschemas.jsonld +++ b/data/scop3d/scop3dbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/scop3d", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "Sequence Conservation On Protein 3D structure allows the visualization of sequence variation of a protein on its structure.", "sc:name": "Scop3d", diff --git a/data/scopa/scopabioschemas.jsonld b/data/scopa/scopabioschemas.jsonld index 1d7e340125264..fe053d245aa2f 100644 --- a/data/scopa/scopabioschemas.jsonld +++ b/data/scopa/scopabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-016-1437-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/SCOPA", "@type": "sc:SoftwareApplication", @@ -18,11 +22,11 @@ ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:28077070", - "pmcid:PMC5225593", { "@id": "https://doi.org/10.1186/s12859-016-1437-3" - } + }, + "pubmed:28077070", + "pmcid:PMC5225593" ], "sc:description": "Software for COrrelated Phenotype Analysis.", "sc:featureList": [ @@ -39,15 +43,11 @@ "sc:license": "Other", "sc:name": "SCOPA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.geenivaramu.ee/en/tools/scopa", "sc:version": "1.0.14" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-1437-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/scope-scrna/scope-scrnabioschemas.jsonld b/data/scope-scrna/scope-scrnabioschemas.jsonld index 7032ed84f0dd4..c255ee3b8ac87 100644 --- a/data/scope-scrna/scope-scrnabioschemas.jsonld +++ b/data/scope-scrna/scope-scrnabioschemas.jsonld @@ -18,9 +18,9 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:author": [ - "Kristofer Davie", + "Lukasz Kreft", "Maxime De Waegeneer", - "Lukasz Kreft" + "Kristofer Davie" ], "sc:contributor": { "@id": "https://orcid.org/0000-0002-8006-0315" diff --git a/data/scor/scorbioschemas.jsonld b/data/scor/scorbioschemas.jsonld index a7f318b527ce2..06cbef27a79c0 100644 --- a/data/scor/scorbioschemas.jsonld +++ b/data/scor/scorbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SCOR", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://scor.berkeley.edu/" } \ No newline at end of file diff --git a/data/scorange/scorangebioschemas.jsonld b/data/scorange/scorangebioschemas.jsonld index db1277cfd12c8..4a51207242d9f 100644 --- a/data/scorange/scorangebioschemas.jsonld +++ b/data/scorange/scorangebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "scOrange", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://singlecell.biolab.si/" } \ No newline at end of file diff --git a/data/scorecons/scoreconsbioschemas.jsonld b/data/scorecons/scoreconsbioschemas.jsonld index e4d4287f78549..e6c3e6c3ff22c 100644 --- a/data/scorecons/scoreconsbioschemas.jsonld +++ b/data/scorecons/scoreconsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Scorecons", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl", diff --git a/data/scoreinvhap/scoreinvhapbioschemas.jsonld b/data/scoreinvhap/scoreinvhapbioschemas.jsonld index 9a5cf0a3ee310..a8706f7aaae8b 100644 --- a/data/scoreinvhap/scoreinvhapbioschemas.jsonld +++ b/data/scoreinvhap/scoreinvhapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "scoreInvHap", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/scoreInvHap.html", "sc:version": "1.2.1" diff --git a/data/scoria/scoriabioschemas.jsonld b/data/scoria/scoriabioschemas.jsonld index a0594c3855036..bd28f5730d5ab 100644 --- a/data/scoria/scoriabioschemas.jsonld +++ b/data/scoria/scoriabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Apache-2.0", "sc:name": "Scoria", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://durrantlab.com/scoria/" } \ No newline at end of file diff --git a/data/scotti/scottibioschemas.jsonld b/data/scotti/scottibioschemas.jsonld index 9475e75d2a711..40073e086c6f3 100644 --- a/data/scotti/scottibioschemas.jsonld +++ b/data/scotti/scottibioschemas.jsonld @@ -9,36 +9,36 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pcbi.1005184", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/scotti", "@type": "sc:SoftwareApplication", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5106001", "pubmed:27835644", { "@id": "https://doi.org/10.1371/journal.pcbi.1005184" - } + }, + "pmcid:PMC5106001" ], "sc:description": "Structured COalescent Transmission Tree Inference. BEAST 2 package to reconstruct transmission trees from genetic data of the pathogen and epidemiological data simultaneously.", "sc:featureList": [ - { - "@id": "edam:operation_3501" - }, { "@id": "edam:operation_0323" }, { "@id": "edam:operation_2426" + }, + { + "@id": "edam:operation_3501" } ], "sc:license": "GPL-3.0", "sc:name": "SCOTTI", "sc:url": "https://bitbucket.org/nicofmay/scotti/" + }, + { + "@id": "https://doi.org/10.1371/journal.pcbi.1005184", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/scotty/scottybioschemas.jsonld b/data/scotty/scottybioschemas.jsonld index 2c20514fa293d..5a9ab4a2bed37 100644 --- a/data/scotty/scottybioschemas.jsonld +++ b/data/scotty/scottybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims.", "sc:name": "Scotty", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://scotty.genetics.utah.edu/" diff --git a/data/scpipe/scpipebioschemas.jsonld b/data/scpipe/scpipebioschemas.jsonld index 41d2dc1cf52bd..a2093cf3d76c2 100644 --- a/data/scpipe/scpipebioschemas.jsonld +++ b/data/scpipe/scpipebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "scPipe", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/scPipe.html", "sc:version": "1.2.1" diff --git a/data/scpsrm/scpsrmbioschemas.jsonld b/data/scpsrm/scpsrmbioschemas.jsonld index 2de6c9429e53c..ab075c3019085 100644 --- a/data/scpsrm/scpsrmbioschemas.jsonld +++ b/data/scpsrm/scpsrmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Cyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. This tool contains the scripts used to search for CDK clusters.", "sc:name": "SCPSRM", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.moseslab.csb.utoronto.ca/alan/protein_motifs.html" } \ No newline at end of file diff --git a/data/scr_find/scr_findbioschemas.jsonld b/data/scr_find/scr_findbioschemas.jsonld index 47b99df074a80..05b8123445366 100644 --- a/data/scr_find/scr_findbioschemas.jsonld +++ b/data/scr_find/scr_findbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SCR_FIND is a tool to analyze structurally conserved regions (SCRs) from superimposed structures and multiple sequence alignments.", "sc:name": "SCR_FIND", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://schubert.bio.uniroma1.it/scr_find.html" diff --git a/data/scrabble/scrabblebioschemas.jsonld b/data/scrabble/scrabblebioschemas.jsonld index 6783c611d068d..0c88e45de9795 100644 --- a/data/scrabble/scrabblebioschemas.jsonld +++ b/data/scrabble/scrabblebioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Tao Peng", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:31060596", + "pmcid:PMC6501316", { "@id": "https://doi.org/10.1186/s13059-019-1681-8" - }, - "pubmed:31060596", - "pmcid:PMC6501316" + } ], "sc:description": "Single-cell RNA-seq imputation constrained by bulk RNA-seq data.", "sc:featureList": [ @@ -37,8 +37,8 @@ "sc:license": "GPL-3.0", "sc:name": "SCRABBLE", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://rdrr.io/cran/SCRABBLE/" diff --git a/data/scran/scranbioschemas.jsonld b/data/scran/scranbioschemas.jsonld index 51491908865f7..93d871101833c 100644 --- a/data/scran/scranbioschemas.jsonld +++ b/data/scran/scranbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-3564-4813", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/scran", "@type": "sc:SoftwareApplication", @@ -20,11 +24,11 @@ "Command-line tool" ], "sc:citation": [ - "pubmed:27909575", + "pmcid:PMC5112579", { "@id": "https://doi.org/10.12688/f1000research.9501.1" }, - "pmcid:PMC5112579" + "pubmed:27909575" ], "sc:description": "Implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.", "sc:featureList": { @@ -43,10 +47,6 @@ { "@id": "https://doi.org/10.12688/f1000research.9501.1", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-3564-4813", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/scrat/scratbioschemas.jsonld b/data/scrat/scratbioschemas.jsonld index 9e0cef91ae225..3c4258f18a961 100644 --- a/data/scrat/scratbioschemas.jsonld +++ b/data/scrat/scratbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Single-cell regulome data analysis.", "sc:name": "SCRAT", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://zhiji.shinyapps.io/scrat/" } \ No newline at end of file diff --git a/data/scratch/scratchbioschemas.jsonld b/data/scratch/scratchbioschemas.jsonld index 027d49e3a3187..6eb55fa9ecdd1 100644 --- a/data/scratch/scratchbioschemas.jsonld +++ b/data/scratch/scratchbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC1160157", + "pubmed:15980571", { "@id": "https://doi.org/10.1093/nar/gki396" }, - "pubmed:15980571" + "pmcid:PMC1160157" ], "sc:description": "Suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta-residue and beta-strand pairings, amino acid contact maps, and tertiary structure.", "sc:featureList": [ @@ -30,10 +30,10 @@ "@id": "edam:operation_0471" }, { - "@id": "edam:operation_2488" + "@id": "edam:operation_0267" }, { - "@id": "edam:operation_0267" + "@id": "edam:operation_2488" }, { "@id": "edam:operation_0303" @@ -42,9 +42,9 @@ "sc:license": "Other", "sc:name": "SCRATCH", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://scratch.proteomics.ics.uci.edu/explanation.html" } diff --git a/data/scratch_protein_predictor/scratch_protein_predictorbioschemas.jsonld b/data/scratch_protein_predictor/scratch_protein_predictorbioschemas.jsonld index 501b5d9eef551..c5ec263d5b7e8 100644 --- a/data/scratch_protein_predictor/scratch_protein_predictorbioschemas.jsonld +++ b/data/scratch_protein_predictor/scratch_protein_predictorbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gki396", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/scratch_protein_predictor", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Scratch Protein Predictor Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:15980571", { "@id": "https://doi.org/10.1093/nar/gki396" }, - "pmcid:PMC1160157" + "pmcid:PMC1160157", + "pubmed:15980571" ], "sc:description": "Server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "Scratch Protein Predictor", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://scratch.proteomics.ics.uci.edu/index.html" + }, + { + "@id": "https://doi.org/10.1093/nar/gki396", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/screenbeam/screenbeambioschemas.jsonld b/data/screenbeam/screenbeambioschemas.jsonld index f94283f60ed20..c03b6e43cb260 100644 --- a/data/screenbeam/screenbeambioschemas.jsonld +++ b/data/screenbeam/screenbeambioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data. Both microarray and NGS data are supported", "sc:name": "ScreenBEAM", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/jyyu/ScreenBEAM" } \ No newline at end of file diff --git a/data/scribl/scriblbioschemas.jsonld b/data/scribl/scriblbioschemas.jsonld index 5ab9faffa96fb..5d02e1855f7ac 100644 --- a/data/scribl/scriblbioschemas.jsonld +++ b/data/scribl/scriblbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. It can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file.", "sc:name": "Scribl", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://chmille4.github.com/Scribl/", "sc:version": "1.1.4" diff --git a/data/scripture/scripturebioschemas.jsonld b/data/scripture/scripturebioschemas.jsonld index a3e62b5110788..1ef474bdab58d 100644 --- a/data/scripture/scripturebioschemas.jsonld +++ b/data/scripture/scripturebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/scripture", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Manuel Garber", - "Mitchell Guttman" + "Mitchell Guttman", + "Manuel Garber" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:20436462", diff --git a/data/scruff/scruffbioschemas.jsonld b/data/scruff/scruffbioschemas.jsonld index 2186670367bf7..fe6abb946b2de 100644 --- a/data/scruff/scruffbioschemas.jsonld +++ b/data/scruff/scruffbioschemas.jsonld @@ -14,11 +14,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:31046658", + "pmcid:PMC6498700", { "@id": "https://doi.org/10.1186/s12859-019-2797-2" }, - "pmcid:PMC6498700" + "pubmed:31046658" ], "sc:description": "R/Bioconductor package for preprocessing single-cell RNA-sequencing data.", "sc:featureList": [ @@ -26,10 +26,10 @@ "@id": "edam:operation_3563" }, { - "@id": "edam:operation_3198" + "@id": "edam:operation_3219" }, { - "@id": "edam:operation_3219" + "@id": "edam:operation_3198" } ], "sc:license": "MIT", diff --git a/data/scrwl/scrwlbioschemas.jsonld b/data/scrwl/scrwlbioschemas.jsonld index 88b67d2974483..87bc8d87b2d2c 100644 --- a/data/scrwl/scrwlbioschemas.jsonld +++ b/data/scrwl/scrwlbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Proprietary", "sc:name": "SCRWL", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://dunbrack.fccc.edu/scwrl4/SCWRL4.php", "sc:version": "4.0" diff --git a/data/scry/scrybioschemas.jsonld b/data/scry/scrybioschemas.jsonld index 5370eac1a2339..c292f4a4cac2e 100644 --- a/data/scry/scrybioschemas.jsonld +++ b/data/scry/scrybioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bas Stringer", "sc:additionalType": [ - "Web API", "Command-line tool", "Workbench", + "Web API", "SPARQL endpoint" ], "sc:author": "Bas Stringer", @@ -23,13 +23,13 @@ "sc:license": "MIT", "sc:name": "SCRY", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ - "Vrije Universiteit Amsterdam", - "Centre for Integrative Bioinformatics" + "Centre for Integrative Bioinformatics", + "Vrije Universiteit Amsterdam" ], "sc:url": "https://pypi.python.org/pypi/scry", "sc:version": "1.2.5" diff --git a/data/scscope/scscopebioschemas.jsonld b/data/scscope/scscopebioschemas.jsonld index 1be6e5655de36..381f2fa6d0068 100644 --- a/data/scscope/scscopebioschemas.jsonld +++ b/data/scscope/scscopebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Apache-2.0", "sc:name": "scScope", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/AltschulerWu-Lab/scScope" } \ No newline at end of file diff --git a/data/scsr/scsrbioschemas.jsonld b/data/scsr/scsrbioschemas.jsonld index 93807eb80c30d..1a2e7ddd9b8c7 100644 --- a/data/scsr/scsrbioschemas.jsonld +++ b/data/scsr/scsrbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/scsr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Roger Meier", "Andrea Franceschini", - "Christian von Mering" + "Christian von Mering", + "Roger Meier" ], "sc:additionalType": [ "Command-line tool", @@ -23,9 +23,9 @@ "sc:license": "GPL-2.0", "sc:name": "scsR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/scsR.html", "sc:version": "1.10.0" diff --git a/data/sctree/sctreebioschemas.jsonld b/data/sctree/sctreebioschemas.jsonld index 6780b64d2bcf7..22af8257fb886 100644 --- a/data/sctree/sctreebioschemas.jsonld +++ b/data/sctree/sctreebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/SCTree", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Liang Ma", - "Lin Wan" + "Lin Wan", + "Liang Ma" ], "sc:additionalType": "Library", "sc:citation": "pubmed:31116393", @@ -20,9 +20,9 @@ "sc:license": "Unlicense", "sc:name": "SCTree", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/XQBai/SCTree-test" } \ No newline at end of file diff --git a/data/scudo/scudobioschemas.jsonld b/data/scudo/scudobioschemas.jsonld index 76929b3fd59d3..46a897482f397 100644 --- a/data/scudo/scudobioschemas.jsonld +++ b/data/scudo/scudobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool for clustering gene expression profiles for diagnostic purposes using a new type of rank-based signatures.", "sc:name": "SCUDO", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.cosbi.eu/research/prototypes/scudo" } \ No newline at end of file diff --git a/data/sculptor/sculptorbioschemas.jsonld b/data/sculptor/sculptorbioschemas.jsonld index 506cd74703535..f51425cff97be 100644 --- a/data/sculptor/sculptorbioschemas.jsonld +++ b/data/sculptor/sculptorbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures. GUI-based extension of the Situs docking programs, to allow an interactive exploration and analysis of volumetric maps. Combines 3D rendering with advanced mathematical concepts like clustering techniques and pattern matching algorithms to permit an almost instantaneous fitting of the high-resolution structures.", "sc:name": "Sculptor", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sculptor.biomachina.org/", "sc:version": "2.1.1" diff --git a/data/sczewas/sczewasbioschemas.jsonld b/data/sczewas/sczewasbioschemas.jsonld index 1f82f181fffb2..fb9411550ed2e 100644 --- a/data/sczewas/sczewasbioschemas.jsonld +++ b/data/sczewas/sczewasbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "SCZEWAS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/ejh243/SCZEWAS" diff --git a/data/sda/sdabioschemas.jsonld b/data/sda/sdabioschemas.jsonld index 9373b0b13f29c..c09f114013da4 100644 --- a/data/sda/sdabioschemas.jsonld +++ b/data/sda/sdabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This is a Java-application for the statistical analysis of data from 2-Dimensional Difference Gel Electrophoresis (DIGE).", "sc:name": "SDA (Statistical DIGE Analyzer)", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "Medizinisches Proteom-Center", "sc:url": "http://www.ruhr-uni-bochum.de/mpc/software/SDA/index.html.en", diff --git a/data/sdams/sdamsbioschemas.jsonld b/data/sdams/sdamsbioschemas.jsonld index 03709ac0743e2..283b62f6dd091 100644 --- a/data/sdams/sdamsbioschemas.jsonld +++ b/data/sdams/sdamsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-1.0", "sc:name": "SDAMS", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SDAMS.html", "sc:version": "1.0.0" diff --git a/data/sde/sdebioschemas.jsonld b/data/sde/sdebioschemas.jsonld index e93687b6c9a24..2f96abb126c1a 100644 --- a/data/sde/sdebioschemas.jsonld +++ b/data/sde/sdebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "SDE", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/rowaniskandar/SDE" } \ No newline at end of file diff --git a/data/sdeap/sdeapbioschemas.jsonld b/data/sdeap/sdeapbioschemas.jsonld index 314bfb71edede..725479acf93c4 100644 --- a/data/sdeap/sdeapbioschemas.jsonld +++ b/data/sdeap/sdeapbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/SDEAP", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ei-Wen Yang", - "Tao Jian" + "Tao Jian", + "Ei-Wen Yang" ], "sc:additionalType": "Command-line tool", "sc:description": "Splice graph based differential transcript expression analysis tool for population data.", diff --git a/data/sdef/sdefbioschemas.jsonld b/data/sdef/sdefbioschemas.jsonld index bb3af0999dddf..ac1f87f7517a3 100644 --- a/data/sdef/sdefbioschemas.jsonld +++ b/data/sdef/sdefbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool performs two tests to evaluate if the experiments are associated and returns a list of interesting features common to all the experiments.", "sc:name": "sdef", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/sdef/index.html" diff --git a/data/sdmdata/sdmdatabioschemas.jsonld b/data/sdmdata/sdmdatabioschemas.jsonld index 55a8f94438ec1..8924a6ef35cac 100644 --- a/data/sdmdata/sdmdatabioschemas.jsonld +++ b/data/sdmdata/sdmdatabioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0128295", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/sdmdata", "@type": "sc:SoftwareApplication", @@ -32,10 +36,6 @@ "Mac" ], "sc:url": "http://www.sdmserialsoftware.org/" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0128295", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sdmtoolbox/sdmtoolboxbioschemas.jsonld b/data/sdmtoolbox/sdmtoolboxbioschemas.jsonld index fb4ab234f105d..58992d3a496fa 100644 --- a/data/sdmtoolbox/sdmtoolboxbioschemas.jsonld +++ b/data/sdmtoolbox/sdmtoolboxbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.7717/peerj.4095", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/sdmtoolbox", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:29230356", + "pmcid:PMC5721907", { "@id": "https://doi.org/10.7717/peerj.4095" }, - "pmcid:PMC5721907" + "pubmed:29230356" ], "sc:description": "Next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses.", "sc:featureList": { @@ -31,12 +27,16 @@ }, "sc:name": "SDMtoolbox", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://sdmtoolbox.org/", "sc:version": "2.0" + }, + { + "@id": "https://doi.org/10.7717/peerj.4095", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sdphapinfer/sdphapinferbioschemas.jsonld b/data/sdphapinfer/sdphapinferbioschemas.jsonld index 87cf3464a6e4b..604c908800868 100644 --- a/data/sdphapinfer/sdphapinferbioschemas.jsonld +++ b/data/sdphapinfer/sdphapinferbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool formulates the haplotype inference problem as the following integer quadratic programming (IQP) problem. The objective function is to minimize the number of haplotypes, and the constraint functions are to resolve each genotype.", "sc:name": "SDPHapInfer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.csie.ntu.edu.tw/~kmchao/tools/HapInfer/index.htm#SDPHapInfer" } \ No newline at end of file diff --git a/data/sdppred/sdppredbioschemas.jsonld b/data/sdppred/sdppredbioschemas.jsonld index bf20c867fe8f8..83726ff378127 100644 --- a/data/sdppred/sdppredbioschemas.jsonld +++ b/data/sdppred/sdppredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SDPpred is a tool for predicting which residues of a protein determine functional differences relative to its homologues. It takes as input an multiple sequence alignment of a protein family divided into groups based on the perceived functional differences.", "sc:name": "SDPpred", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioinf.fbb.msu.ru/SDPpred/" diff --git a/data/sea-archive/sea-archivebioschemas.jsonld b/data/sea-archive/sea-archivebioschemas.jsonld index 3efc32371b376..08ac69d8816c0 100644 --- a/data/sea-archive/sea-archivebioschemas.jsonld +++ b/data/sea-archive/sea-archivebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkv1243", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/sea-archive", "@type": "sc:SoftwareApplication", @@ -31,6 +27,10 @@ }, "sc:name": "SEA", "sc:url": "http://sea.edbc.org" + }, + { + "@id": "https://doi.org/10.1093/nar/gkv1243", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sea/seabioschemas.jsonld b/data/sea/seabioschemas.jsonld index f0c8d7e09c37f..5667a816d7eb0 100644 --- a/data/sea/seabioschemas.jsonld +++ b/data/sea/seabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SEA", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sea.bioinfo.cipf.es" } \ No newline at end of file diff --git a/data/seagrass_zmu_genome/seagrass_zmu_genomebioschemas.jsonld b/data/seagrass_zmu_genome/seagrass_zmu_genomebioschemas.jsonld index b67fd105ebe21..4e293f0b591a2 100644 --- a/data/seagrass_zmu_genome/seagrass_zmu_genomebioschemas.jsonld +++ b/data/seagrass_zmu_genome/seagrass_zmu_genomebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This page provides access to Zostera muelleri genome assembly and annotation data.", "sc:name": "Seagrass Zmu Genome", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "unimelb.edu.au", "sc:url": "http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome" diff --git a/data/seamote/seamotebioschemas.jsonld b/data/seamote/seamotebioschemas.jsonld index 96296ae887bae..5f958169c4dcb 100644 --- a/data/seamote/seamotebioschemas.jsonld +++ b/data/seamote/seamotebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Fast and accurate large-scale de novo motif discovery in nucleic acid sequences.", "sc:name": "SeAMotE", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://s.tartaglialab.com/new_submission/seamote" diff --git a/data/seance/seancebioschemas.jsonld b/data/seance/seancebioschemas.jsonld index 22e4803349dfd..30b01ec326680 100644 --- a/data/seance/seancebioschemas.jsonld +++ b/data/seance/seancebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12862-014-0235-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/seance", "@type": "sc:SoftwareApplication", @@ -39,10 +43,6 @@ "Mac" ], "sc:url": "http://wasabiapp.org/software/seance/" - }, - { - "@id": "https://doi.org/10.1186/S12862-014-0235-7", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sear/searbioschemas.jsonld b/data/sear/searbioschemas.jsonld index 407da809b0621..4381a9fdf5174 100644 --- a/data/sear/searbioschemas.jsonld +++ b/data/sear/searbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Will Rowe", "sc:additionalType": [ - "Web application", + "Command-line tool", "Database portal", - "Command-line tool" + "Web application" ], "sc:description": "Construct full-length, horizontally acquired Antibiotic Resistance Genes (ARGs) from sequencing datasets. It has been designed with environmental metagenomics and microbiome experiments in mind, where the diversity and relative abundance of ARGs need to be determined both quickly and easily.", "sc:name": "SEAR: Search Engine for Antimicrobial Resistance", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "cam.ac.uk", "sc:url": "http://www.github.com/wpmr2/SEAR" diff --git a/data/searchgtr/searchgtrbioschemas.jsonld b/data/searchgtr/searchgtrbioschemas.jsonld index 34e8d1382bd8b..c2199831db097 100644 --- a/data/searchgtr/searchgtrbioschemas.jsonld +++ b/data/searchgtr/searchgtrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Apache-2.0", "sc:name": "SEARCHGTr", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://clustermine360.ca/antiSMASH/Sequences/116/searchgtr/" } \ No newline at end of file diff --git a/data/searchgui/searchguibioschemas.jsonld b/data/searchgui/searchguibioschemas.jsonld index a42e4b07a4b61..3ce530579612a 100644 --- a/data/searchgui/searchguibioschemas.jsonld +++ b/data/searchgui/searchguibioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/searchgui", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Graphical user interface for proteomics identification search engines", "sc:name": "SearchGUI", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://compomics.github.io/projects/searchgui.html", diff --git a/data/seas/seasbioschemas.jsonld b/data/seas/seasbioschemas.jsonld index ab8786afe8174..cfb194583bc80 100644 --- a/data/seas/seasbioschemas.jsonld +++ b/data/seas/seasbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A computational tool for pathway enrichment analysis over a given set of genes in a specified organism against pathways (or subsystems) in the SEED database, a popular pathway database for bacteria. SEAS maps a given set of genes in a bacterium to genes currently covered by SEED through gene ID and/or orthology mapping, and then calculates the statistical significance of the enrichment of each relevant SEED pathway by the mapped genes.", "sc:name": "SEAS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://csbl.bmb.uga.edu/~xizeng/research/seas/" } \ No newline at end of file diff --git a/data/seaview/seaviewbioschemas.jsonld b/data/seaview/seaviewbioschemas.jsonld index 8cc45e58aaecb..6c13a9f52898a 100644 --- a/data/seaview/seaviewbioschemas.jsonld +++ b/data/seaview/seaviewbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Multiplatform graphical user interface designed to facilitate alignment and phylogenic tree building from molecular sequences.", "sc:name": "SeaView", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "IFB ELIXIR-FR", diff --git a/data/sebnif/sebnifbioschemas.jsonld b/data/sebnif/sebnifbioschemas.jsonld index c0fabd7684fa6..cc56b3f64e60f 100644 --- a/data/sebnif/sebnifbioschemas.jsonld +++ b/data/sebnif/sebnifbioschemas.jsonld @@ -28,32 +28,32 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0659" + "@id": "edam:topic_3170" }, { - "@id": "edam:topic_3170" + "@id": "edam:topic_0659" }, { "@id": "edam:topic_3512" } ], "sc:citation": [ - "pmcid:PMC3882232", { "@id": "https://doi.org/10.1371/journal.pone.0084500" }, + "pmcid:PMC3882232", "pubmed:24400097" ], "sc:description": "Self-Estimation Based Novel lincRNA Filter. Discovery of bona fide novel lincRNAs that are suitable for further functional characterization. Specifically, it implements an algorithm for identifying high-quality single-exonic lincRNAs that were often omitted in many studies.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_3192" }, { - "@id": "edam:operation_0314" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3192" + "@id": "edam:operation_0314" } ], "sc:license": "BSL-1.0", diff --git a/data/seca/secabioschemas.jsonld b/data/seca/secabioschemas.jsonld index f6b3829b8ea5e..604e9ea00290d 100644 --- a/data/seca/secabioschemas.jsonld +++ b/data/seca/secabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A user-friendly web-based application to perform SNP effect concordance analysis using GWA summary results.", "sc:name": "SECA", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://neurogenetics.qimrberghofer.edu.au/SECA/" } \ No newline at end of file diff --git a/data/secisaln/secisalnbioschemas.jsonld b/data/secisaln/secisalnbioschemas.jsonld index 1dd14d54757ef..af9d6b15f55f3 100644 --- a/data/secisaln/secisalnbioschemas.jsonld +++ b/data/secisaln/secisalnbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:description": "Predict a SECIS element in the query sequence, split it into its constituent parts and align these against a precompiled database of eukaryotic SECIS elements.", "sc:name": "SECISaln", "sc:provider": [ - "crg.eu", - "Lab Roderic Guigo Group" + "Lab Roderic Guigo Group", + "crg.eu" ], "sc:url": "http://big.crg.cat/services/secisaln", "sc:version": "1" diff --git a/data/secisdesign/secisdesignbioschemas.jsonld b/data/secisdesign/secisdesignbioschemas.jsonld index eb5ee22b9ef3b..1a32a1e5c65bd 100644 --- a/data/secisdesign/secisdesignbioschemas.jsonld +++ b/data/secisdesign/secisdesignbioschemas.jsonld @@ -13,10 +13,10 @@ "@id": "https://bio.tools/secisdesign", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Anke Busch", { "@id": "http://orcid.org/0000-0001-8231-3323" - }, - "Anke Busch" + } ], "sc:additionalType": "Web application", "sc:author": [ @@ -29,8 +29,8 @@ "sc:description": "Insert SECIS-elements in coding mRNAs.", "sc:name": "SECISDesign web server", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": [ diff --git a/data/secisearch3_seblastian/secisearch3_seblastianbioschemas.jsonld b/data/secisearch3_seblastian/secisearch3_seblastianbioschemas.jsonld index ca94ddb8146cc..284ee5d95b5aa 100644 --- a/data/secisearch3_seblastian/secisearch3_seblastianbioschemas.jsonld +++ b/data/secisearch3_seblastian/secisearch3_seblastianbioschemas.jsonld @@ -23,8 +23,8 @@ "Linux" ], "sc:provider": [ - "Lab Roderic Guigo Group", - "crg.eu" + "crg.eu", + "Lab Roderic Guigo Group" ], "sc:url": "http://seblastian.crg.es/", "sc:version": "1" diff --git a/data/seclaf/seclafbioschemas.jsonld b/data/seclaf/seclafbioschemas.jsonld index 777d499a6b2bb..195bcd351e3dc 100644 --- a/data/seclaf/seclafbioschemas.jsonld +++ b/data/seclaf/seclafbioschemas.jsonld @@ -15,17 +15,17 @@ "Balázs Szalkai" ], "sc:additionalType": [ - "Command-line tool", + "Web application", "Web service", - "Web application" + "Command-line tool" ], "sc:description": "Webserver and deep neural network design tool for hierarchical biological sequence classification.", "sc:license": "Unlicense", "sc:name": "SECLAF", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://pitgroup.org/seclaf/" } \ No newline at end of file diff --git a/data/secretomep/secretomepbioschemas.jsonld b/data/secretomep/secretomepbioschemas.jsonld index 39322a95dc7ac..10b566ebdbbe9 100644 --- a/data/secretomep/secretomepbioschemas.jsonld +++ b/data/secretomep/secretomepbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Henrik Nielsen", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:description": "Predictions of non-classical (i.e. not signal peptide triggered) protein secretion.", "sc:license": "Other", diff --git a/data/secstrannotator/secstrannotatorbioschemas.jsonld b/data/secstrannotator/secstrannotatorbioschemas.jsonld index d366f1743e1fb..789528496ae08 100644 --- a/data/secstrannotator/secstrannotatorbioschemas.jsonld +++ b/data/secstrannotator/secstrannotatorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SecStrAnnotator", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://webchem.ncbr.muni.cz/API/SecStr" } \ No newline at end of file diff --git a/data/securema/securemabioschemas.jsonld b/data/securema/securemabioschemas.jsonld index 1b2e42e3cb057..7ecb68cb9f1e7 100644 --- a/data/securema/securemabioschemas.jsonld +++ b/data/securema/securemabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SecureMA", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/XieConnect/SecureMA" } \ No newline at end of file diff --git a/data/seder/sederbioschemas.jsonld b/data/seder/sederbioschemas.jsonld index 65a50a837e016..69506d47c855c 100644 --- a/data/seder/sederbioschemas.jsonld +++ b/data/seder/sederbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A global machine learning based scoring function for protein structure prediction. The package was designed using the GEneral Neural Network program.", "sc:name": "Seder", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mamiris.com/services.html" } \ No newline at end of file diff --git a/data/sedus/sedusbioschemas.jsonld b/data/sedus/sedusbioschemas.jsonld index 7897f2fbc975e..62c42b7823406 100644 --- a/data/sedus/sedusbioschemas.jsonld +++ b/data/sedus/sedusbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A forward-in-time simulator of segmental duplications undergoing concerted evolution.", "sc:name": "SeDuS", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.biologiaevolutiva.org/sedus/" } \ No newline at end of file diff --git a/data/seealso/seealsobioschemas.jsonld b/data/seealso/seealsobioschemas.jsonld index f285f7e2840bb..4a2c87cd96f2d 100644 --- a/data/seealso/seealsobioschemas.jsonld +++ b/data/seealso/seealsobioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "EMBOSS Contributors", + "UK MRC", + "Wellcome Trust" ], "sc:description": "Find programs with similar function to a specified program.", "sc:funder": [ "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "seealso", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/seealso.html", "sc:version": "r6" diff --git a/data/seecer/seecerbioschemas.jsonld b/data/seecer/seecerbioschemas.jsonld index 84023dfb13734..f9000ec1a6d73 100644 --- a/data/seecer/seecerbioschemas.jsonld +++ b/data/seecer/seecerbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/seecer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ziv Bar-Joseph", + "Hai-Son Le", "Marcel H. Schulz", - "Hai-Son Le" + "Ziv Bar-Joseph" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:23558750", "sc:description": "Sequence error correction for RNA-Seq data.", "sc:name": "SEECER", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sb.cs.cmu.edu/seecer/" } \ No newline at end of file diff --git a/data/seed/seedbioschemas.jsonld b/data/seed/seedbioschemas.jsonld index 910e3b847a72c..726332dcaa81b 100644 --- a/data/seed/seedbioschemas.jsonld +++ b/data/seed/seedbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool to cluster sequence reads prior to assembly or other operations.", "sc:name": "SEED", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://manuals.bioinformatics.ucr.edu/home/seed" } \ No newline at end of file diff --git a/data/seedgff/seedgffbioschemas.jsonld b/data/seedgff/seedgffbioschemas.jsonld index adcbe631a8e3b..0dac342585be7 100644 --- a/data/seedgff/seedgffbioschemas.jsonld +++ b/data/seedgff/seedgffbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Creates the seed from -15 to -25 bp before ATG.", "sc:name": "seedgff", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/seedy/seedybioschemas.jsonld b/data/seedy/seedybioschemas.jsonld index 8425952ffe84d..4f8b4f7b148ba 100644 --- a/data/seedy/seedybioschemas.jsonld +++ b/data/seedy/seedybioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Colin J. Worby", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:26075402", + "pmcid:PMC4467979", { "@id": "https://doi.org/10.1371/journal.pone.0129745" - }, - "pmcid:PMC4467979", - "pubmed:26075402" + } ], "sc:description": "SEEDY (Simulation of Evolutionary and Epidemiological Dynamics) is an R package that can be used to follow the accumulation of within-host mutation in pathogens.", "sc:featureList": { diff --git a/data/seek/seekbioschemas.jsonld b/data/seek/seekbioschemas.jsonld index ac59ee366a705..04f2972e00fe8 100644 --- a/data/seek/seekbioschemas.jsonld +++ b/data/seek/seekbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-2-Clause", "sc:name": "SEEK", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.seek4science.org/" } \ No newline at end of file diff --git a/data/seekr/seekrbioschemas.jsonld b/data/seekr/seekrbioschemas.jsonld index 09759d21c48d9..5b2b08570a3a9 100644 --- a/data/seekr/seekrbioschemas.jsonld +++ b/data/seekr/seekrbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1021/acs.jpcb.6b09388", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/seekr", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5562489", + "pubmed:28191969", { "@id": "https://doi.org/10.1021/acs.jpcb.6b09388" - }, - "pubmed:28191969" + } ], "sc:description": "Simulation Enabled Estimation of Kinetic Rates- A Computational Tool to Estimate Molecular Kinetics and its Application to Trypsin-Benzamidine Binding.", "sc:featureList": { @@ -28,10 +32,6 @@ "sc:name": "SEEKR", "sc:operatingSystem": "Linux", "sc:url": "https://amarolab.ucsd.edu/seekr/" - }, - { - "@id": "https://doi.org/10.1021/acs.jpcb.6b09388", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/segmentseq/segmentseqbioschemas.jsonld b/data/segmentseq/segmentseqbioschemas.jsonld index 8a6a7d23684d5..f8c175bb43551 100644 --- a/data/segmentseq/segmentseqbioschemas.jsonld +++ b/data/segmentseq/segmentseqbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "segmentSeq", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/segmentSeq.html", "sc:version": "2.8.0" diff --git a/data/segmer/segmerbioschemas.jsonld b/data/segmer/segmerbioschemas.jsonld index 4197ba8c0d515..ac894867a8ea2 100644 --- a/data/segmer/segmerbioschemas.jsonld +++ b/data/segmer/segmerbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "SEGMER", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://zhanglab.ccmb.med.umich.edu/SEGMER/" } \ No newline at end of file diff --git a/data/segtools/segtoolsbioschemas.jsonld b/data/segtools/segtoolsbioschemas.jsonld index a0cb6d800d625..72588f4fe83e6 100644 --- a/data/segtools/segtoolsbioschemas.jsonld +++ b/data/segtools/segtoolsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Tools for exploratory analysis of genomic segmentations.", "sc:name": "Segtools", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://www.pmgenomics.ca/hoffmanlab/proj/segtools/" diff --git a/data/segtor/segtorbioschemas.jsonld b/data/segtor/segtorbioschemas.jsonld index d522279c79dda..fce3e05f90edf 100644 --- a/data/segtor/segtorbioschemas.jsonld +++ b/data/segtor/segtorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A software tool to annotate large sets of genomic coordinates, intervals, SNVs, indels and translocations with respect to known genes.", "sc:name": "Segtor", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/BioNica/Segtor" } \ No newline at end of file diff --git a/data/segway/segwaybioschemas.jsonld b/data/segway/segwaybioschemas.jsonld index 49aff776f4df9..9f555034d6fab 100644 --- a/data/segway/segwaybioschemas.jsonld +++ b/data/segway/segwaybioschemas.jsonld @@ -14,18 +14,18 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Eric Roberts", { "@id": "http://orcid.org/0000-0002-4517-1562" - } + }, + "Eric Roberts" ], "sc:citation": [ - "pmcid:PMC3340533", - "pubmed:22426492", "pubmed:23221638", { "@id": "https://doi.org/10.1038/nmeth.1937" - } + }, + "pubmed:22426492", + "pmcid:PMC3340533" ], "sc:description": "Novel method for analyzing multiple tracks of functional genomics data which uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling.", "sc:license": "GPL-2.0", @@ -38,13 +38,13 @@ "sc:url": "http://segway.hoffmanlab.org/", "sc:version": "1.4.0" }, - { - "@id": "https://doi.org/10.1038/nmeth.1937", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-4517-1562", "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1038/nmeth.1937", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/selansi/selansibioschemas.jsonld b/data/selansi/selansibioschemas.jsonld index 5ccf1fc5ded0a..229cf4647f8b9 100644 --- a/data/selansi/selansibioschemas.jsonld +++ b/data/selansi/selansibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Simulation of stochastic multidimensional Gene Regulatory Networks (GRNs).", "sc:name": "SELANSI", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://sites.google.com/view/selansi" } \ No newline at end of file diff --git a/data/selectbesthit/selectbesthitbioschemas.jsonld b/data/selectbesthit/selectbesthitbioschemas.jsonld index 891cbd4ad2ac3..6b78d5d035e7b 100644 --- a/data/selectbesthit/selectbesthitbioschemas.jsonld +++ b/data/selectbesthit/selectbesthitbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "selectbesthit", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/SelectBestHit/0.1%20beta", "sc:version": "0.1 beta" diff --git a/data/selecthitscore/selecthitscorebioschemas.jsonld b/data/selecthitscore/selecthitscorebioschemas.jsonld index ca8a1e18ada67..997fc593a87b9 100644 --- a/data/selecthitscore/selecthitscorebioschemas.jsonld +++ b/data/selecthitscore/selecthitscorebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Blast-hits filter for each line in a Blast file.", "sc:name": "selecthitscore", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/SelectHitScore/0.1%20beta", "sc:version": "0.1 beta" diff --git a/data/selectome/selectomebioschemas.jsonld b/data/selectome/selectomebioschemas.jsonld index 8bc9b7263687c..44681d8673320 100644 --- a/data/selectome/selectomebioschemas.jsonld +++ b/data/selectome/selectomebioschemas.jsonld @@ -9,18 +9,22 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkt1065", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/selectome", "@type": "sc:SoftwareApplication", "edam:has_input": [ { - "@id": "edam:data_1075" + "@id": "edam:data_1868" }, { - "@id": "edam:data_0842" + "@id": "edam:data_1075" }, { - "@id": "edam:data_1868" + "@id": "edam:data_0842" } ], "edam:has_output": [ @@ -39,11 +43,11 @@ "@id": "edam:topic_3293" }, "sc:citation": [ - "pubmed:24225318", "pmcid:PMC3964977", { "@id": "https://doi.org/10.1093/nar/gkt1065" - } + }, + "pubmed:24225318" ], "sc:description": "Database of positive selection based on a rigorous branch-site specific likelihood test.", "sc:featureList": { @@ -57,10 +61,6 @@ ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://selectome.unil.ch/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkt1065", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/selecton/selectonbioschemas.jsonld b/data/selecton/selectonbioschemas.jsonld index d59ca25927b3d..d7cd7d73a7bec 100644 --- a/data/selecton/selectonbioschemas.jsonld +++ b/data/selecton/selectonbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Selecton is a server for the identification of site-specific positive selection and purifying selection.", "sc:name": "Selecton", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://selecton.tau.ac.il/" } \ No newline at end of file diff --git a/data/selectpro/selectprobioschemas.jsonld b/data/selectpro/selectprobioschemas.jsonld index 9f647682d02b5..b27df79c389af 100644 --- a/data/selectpro/selectprobioschemas.jsonld +++ b/data/selectpro/selectprobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A novel structure-based model selection method derived from an energy function comprising physical, statistical, and predicted structural terms. Novel and unique energy terms include predicted secondary structure, predicted solvent accessibility, predicted contact map, beta-strand pairing, and side-chain hydrogen bonding.", "sc:name": "SELECTpro", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.igb.uci.edu/~baldig/selectpro.html" diff --git a/data/selene/selenebioschemas.jsonld b/data/selene/selenebioschemas.jsonld index cd7ee1a830c30..48a2b8c8dac02 100644 --- a/data/selene/selenebioschemas.jsonld +++ b/data/selene/selenebioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Troyanskaya Laborator", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:30923381", "sc:description": "PyTorch-based deep learning library for sequence data.", "sc:license": "BSD-3-Clause", "sc:name": "Selene", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://selene.flatironinstitute.org/", "sc:version": "0.3.1" diff --git a/data/selenoprofiles3/selenoprofiles3bioschemas.jsonld b/data/selenoprofiles3/selenoprofiles3bioschemas.jsonld index 37caa7be0bea2..eef50df81a733 100644 --- a/data/selenoprofiles3/selenoprofiles3bioschemas.jsonld +++ b/data/selenoprofiles3/selenoprofiles3bioschemas.jsonld @@ -18,8 +18,8 @@ "sc:license": "GPL-3.0", "sc:name": "Selenoprofiles3", "sc:provider": [ - "Lab Roderic Guigo Group", - "crg.eu" + "crg.eu", + "Lab Roderic Guigo Group" ], "sc:url": "http://big.crg.cat/services/selenoprofiles", "sc:version": "3.0" diff --git a/data/selenzyme/selenzymebioschemas.jsonld b/data/selenzyme/selenzymebioschemas.jsonld index 0c473fff85722..b373bd9b3c999 100644 --- a/data/selenzyme/selenzymebioschemas.jsonld +++ b/data/selenzyme/selenzymebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Enzyme selection tool for pathway design.", "sc:name": "Selenzyme", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://selenzyme.synbiochem.co.uk/" } \ No newline at end of file diff --git a/data/selex/selexbioschemas.jsonld b/data/selex/selexbioschemas.jsonld index 9721df8839c61..52831f91804d4 100644 --- a/data/selex/selexbioschemas.jsonld +++ b/data/selex/selexbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Harmen Bussemaker", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Tools for quantifying DNA binding specificities based on SELEX-seq data.", "sc:license": "GPL-2.0", "sc:name": "SELEX", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SELEX.html", "sc:version": "1.6.0" diff --git a/data/selftarget/selftargetbioschemas.jsonld b/data/selftarget/selftargetbioschemas.jsonld index c2642216aa0ba..192b217d6f0fb 100644 --- a/data/selftarget/selftargetbioschemas.jsonld +++ b/data/selftarget/selftargetbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SelfTarget", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/felicityallen/SelfTarget" } \ No newline at end of file diff --git a/data/selphi/selphibioschemas.jsonld b/data/selphi/selphibioschemas.jsonld index 3ef80f79a0206..147f33a84ea19 100644 --- a/data/selphi/selphibioschemas.jsonld +++ b/data/selphi/selphibioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKV459", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/selphi", "@type": "sc:SoftwareApplication", @@ -27,15 +31,11 @@ }, "sc:name": "SELPHI", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://rothwebprod.mshri.on.ca:8081/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKV459", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/seltarbase/seltarbasebioschemas.jsonld b/data/seltarbase/seltarbasebioschemas.jsonld index 3f4e1935fe8fc..c788c7277657a 100644 --- a/data/seltarbase/seltarbasebioschemas.jsonld +++ b/data/seltarbase/seltarbasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Curated database of a growing number of public mononucleotide repeat tracts (MNR) mutation data in microsatellite unstable human tumors. Regression calculations for various microsatellite instability (MSI) -H tumor entities indicating statistically deviant mutation frequencies predict genes that are shown or highly suspected to be involved in MSI tumorigenesis.", "sc:name": "SelTarbase", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.seltarbase.org" } \ No newline at end of file diff --git a/data/selva/selvabioschemas.jsonld b/data/selva/selvabioschemas.jsonld index 460c679c91b94..671eb95b3c201 100644 --- a/data/selva/selvabioschemas.jsonld +++ b/data/selva/selvabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "SELVa", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/bazykinlab/SELVa" } \ No newline at end of file diff --git a/data/sem/sembioschemas.jsonld b/data/sem/sembioschemas.jsonld index bfcb7260026f0..081bb72697e15 100644 --- a/data/sem/sembioschemas.jsonld +++ b/data/sem/sembioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization, some configuration necessary.", "sc:name": "SEM", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://dicsoft2.physics.iisc.ernet.in/sem/" } \ No newline at end of file diff --git a/data/sema/semabioschemas.jsonld b/data/sema/semabioschemas.jsonld index 426ea8984f321..a01bd820d1a76 100644 --- a/data/sema/semabioschemas.jsonld +++ b/data/sema/semabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "SEMA", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://sema.research.cchmc.org/" } \ No newline at end of file diff --git a/data/semantic_body_browser/semantic_body_browserbioschemas.jsonld b/data/semantic_body_browser/semantic_body_browserbioschemas.jsonld index bfef68c6c5876..8a9f8ed5e613d 100644 --- a/data/semantic_body_browser/semantic_body_browserbioschemas.jsonld +++ b/data/semantic_body_browser/semantic_body_browserbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web application for intuitively exploring the body of an organism from the organ to the sub-cellular level and visualising expression profiles by means of semantically annotated illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users.", "sc:name": "Semantic Body Browser", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://sbb.cellfinder.org/" } \ No newline at end of file diff --git a/data/semdist/bioconda_semdist.yaml b/data/semdist/bioconda_semdist.yaml index ff99139e514ac..0b396049c1be0 100644 --- a/data/semdist/bioconda_semdist.yaml +++ b/data/semdist/bioconda_semdist.yaml @@ -6,7 +6,6 @@ description: This package implements methods to calculate information accretion home: https://bioconductor.org/packages/3.10/bioc/html/SemDist.html identifiers: - biotools:semdist -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-semdist diff --git a/data/semdist/semdistbioschemas.jsonld b/data/semdist/semdistbioschemas.jsonld index a95baa5a96446..b919ca129c9c2 100644 --- a/data/semdist/semdistbioschemas.jsonld +++ b/data/semdist/semdistbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ian Gonzalez", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor.", "sc:license": "GPL-2.0", "sc:name": "SemDist", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SemDist.html", "sc:version": "1.8.0" diff --git a/data/seme/semebioschemas.jsonld b/data/seme/semebioschemas.jsonld index d5e1109a6ef95..75b7a046e0053 100644 --- a/data/seme/semebioschemas.jsonld +++ b/data/seme/semebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SEME", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://biogpu.ddns.comp.nus.edu.sg/~chipseq/SEME/" } \ No newline at end of file diff --git a/data/semgen/semgenbioschemas.jsonld b/data/semgen/semgenbioschemas.jsonld index eff011c45433d..8360672217ac9 100644 --- a/data/semgen/semgenbioschemas.jsonld +++ b/data/semgen/semgenbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An experimental software tool for automating the modular composition and decomposition of biosimulation models.", "sc:name": "SemGen", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://sbp.bhi.washington.edu/projects/semgen" } \ No newline at end of file diff --git a/data/semisup/semisupbioschemas.jsonld b/data/semisup/semisupbioschemas.jsonld index e5cd35fa708d8..bcf60c2ab03b5 100644 --- a/data/semisup/semisupbioschemas.jsonld +++ b/data/semisup/semisupbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "semisup", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/semisup.html", "sc:version": "1.4.0" diff --git a/data/sensa/sensabioschemas.jsonld b/data/sensa/sensabioschemas.jsonld index b171603bb961a..0fcf2198839f6 100644 --- a/data/sensa/sensabioschemas.jsonld +++ b/data/sensa/sensabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web-based application for sensitivity analysis of mathematical models. The sensitivity analysis is based on metabolic control analysis, computing the local, global and time-dependent properties of model components. Interactive visualisation facilitates interpretation of usually complex results.", "sc:name": "SensA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://gofid.biologie.hu-berlin.de/" } \ No newline at end of file diff --git a/data/sensipath/sensipathbioschemas.jsonld b/data/sensipath/sensipathbioschemas.jsonld index 28354d80eb9f1..5a01a44d756f9 100644 --- a/data/sensipath/sensipathbioschemas.jsonld +++ b/data/sensipath/sensipathbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool will help you design Sensing-Enabling Metabolic Pathways for synthetic biology applications in prokaryotes.", "sc:name": "SensiPath", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sensipath.micalis.fr/" } \ No newline at end of file diff --git a/data/sepa/bioconda_sepa.yaml b/data/sepa/bioconda_sepa.yaml index 8c30c1cb1e5cd..9d47d54475c5c 100644 --- a/data/sepa/bioconda_sepa.yaml +++ b/data/sepa/bioconda_sepa.yaml @@ -2,7 +2,6 @@ biotools_id: sepa home: https://bioconductor.org/packages/3.9/bioc/html/SEPA.html identifiers: - biotools:sepa -- doi:10.1038/nmeth.3252 license: GPL(>=2) name: bioconductor-sepa summary: Given single-cell RNA-seq data and true experiment time of cells or pseudo-time diff --git a/data/sepira/sepirabioschemas.jsonld b/data/sepira/sepirabioschemas.jsonld index afbb2db49cb41..8bdad139e7a1c 100644 --- a/data/sepira/sepirabioschemas.jsonld +++ b/data/sepira/sepirabioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Yuting Chen", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5738803", "pubmed:29262847", { "@id": "https://doi.org/10.1186/s13059-017-1366-0" - }, - "pmcid:PMC5738803" + } ], "sc:description": "Systems EPigenomics Inference of Regulatory Activity is an algorithm that infers sample-specific transcription factor activity from the genome-wide expression or DNA methylation profile of the sample.", "sc:featureList": { @@ -29,8 +29,8 @@ "sc:name": "SEPIRA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SEPIRA.html", "sc:version": "1.0.0" diff --git a/data/seq2feature/seq2featurebioschemas.jsonld b/data/seq2feature/seq2featurebioschemas.jsonld index cdb3bc85795d8..5f392cd8f34fb 100644 --- a/data/seq2feature/seq2featurebioschemas.jsonld +++ b/data/seq2feature/seq2featurebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Unlicense", "sc:name": "Seq2Feature", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://www.iitm.ac.in/bioinfo/SBFE/index.html" } \ No newline at end of file diff --git a/data/seq2logo/seq2logobioschemas.jsonld b/data/seq2logo/seq2logobioschemas.jsonld index e43aac82a6b30..d7452dbf5fae2 100644 --- a/data/seq2logo/seq2logobioschemas.jsonld +++ b/data/seq2logo/seq2logobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/seq2logo", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Scientific problems: Morten Nielsen", - "Technical problems and suggestions: Martin Thomsen" + "Technical problems and suggestions: Martin Thomsen", + "Scientific problems: Morten Nielsen" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:22638583", @@ -20,9 +20,9 @@ "sc:license": "Other", "sc:name": "Seq2Logo", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.cbs.dtu.dk/biotools/Seq2Logo/" } \ No newline at end of file diff --git a/data/seq2pathway/seq2pathwaybioschemas.jsonld b/data/seq2pathway/seq2pathwaybioschemas.jsonld index da58ec40a4f66..edd205964aeb0 100644 --- a/data/seq2pathway/seq2pathwaybioschemas.jsonld +++ b/data/seq2pathway/seq2pathwaybioschemas.jsonld @@ -13,57 +13,57 @@ "@id": "https://bio.tools/seq2pathway", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Xinan Yang", - "Ana Marija Sokovic" + "Ana Marija Sokovic", + "Xinan Yang" ], "edam:has_input": { "@id": "edam:data_2012" }, "edam:has_output": [ { - "@id": "edam:data_1772" + "@id": "edam:data_2725" }, { - "@id": "edam:data_2725" + "@id": "edam:data_1772" } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3169" + "@id": "edam:topic_3517" }, { - "@id": "edam:topic_3517" + "@id": "edam:topic_3169" }, { "@id": "edam:topic_3170" } ], "sc:citation": [ + "pmcid:PMC3266878", + "pubmed:22291585", { "@id": "https://doi.org/10.1371/journal.pcbi.1002350" - }, - "pubmed:22291585", - "pmcid:PMC3266878" + } ], "sc:description": "This functional gene-set tool for the analysis of NGS data consists of \"seq2gene\" and \"gene2path\" components. The seq2gene component links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2path feature summarizes gene scores to pathway-scores for each sample.", "sc:featureList": [ { - "@id": "edam:operation_2497" + "@id": "edam:operation_3680" }, { - "@id": "edam:operation_3680" + "@id": "edam:operation_2497" } ], "sc:license": "GPL-2.0", "sc:name": "seq2pathway", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seq2pathway.html", "sc:version": "1.6.0" diff --git a/data/seq2ref/seq2refbioschemas.jsonld b/data/seq2ref/seq2refbioschemas.jsonld index ae741612806ab..b2b6b34a7d274 100644 --- a/data/seq2ref/seq2refbioschemas.jsonld +++ b/data/seq2ref/seq2refbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web server designed to facilitate functional interpretation by retrieving and ranking the reference proteins in the BLAST result.", "sc:name": "Seq2Ref", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://prodata.swmed.edu/seq2ref/" } \ No newline at end of file diff --git a/data/seqacademy/seqacademybioschemas.jsonld b/data/seqacademy/seqacademybioschemas.jsonld index 91771572ed369..c3870c8cf66d7 100644 --- a/data/seqacademy/seqacademybioschemas.jsonld +++ b/data/seqacademy/seqacademybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Syed Hussain Ather", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Jupyter notebook-based educational pipeline for RNA-Seq and epigenomic data analysis. Easy-to-use tutorial that outlines the complete RNA-Seq and ChIP-Seq analysis workflow and requires no prior programming experience.", "sc:license": "MIT", "sc:name": "SeqAcademy", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.seqacademy.org/" } \ No newline at end of file diff --git a/data/seqan/seqanbioschemas.jsonld b/data/seqan/seqanbioschemas.jsonld index 13ada1c4c220d..118fb3bb88c82 100644 --- a/data/seqan/seqanbioschemas.jsonld +++ b/data/seqan/seqanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "SeqAn", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "Freie Universität Berlin", "sc:url": "http://www.seqan.de", diff --git a/data/seqarray/seqarraybioschemas.jsonld b/data/seqarray/seqarraybioschemas.jsonld index 9cf3f0db1c722..4a11144d9bb78 100644 --- a/data/seqarray/seqarraybioschemas.jsonld +++ b/data/seqarray/seqarraybioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1093/bioinformatics/btx145", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0002-1390-0708", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/seqarray", "@type": "sc:SoftwareApplication", @@ -28,11 +24,11 @@ "Command-line tool" ], "sc:citation": [ + "pubmed:28334390", + "pmcid:PMC5860110", { "@id": "https://doi.org/10.1093/bioinformatics/btx145" - }, - "pubmed:28334390", - "pmcid:PMC5860110" + } ], "sc:description": "Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in the corresponding files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.", "sc:featureList": { @@ -47,6 +43,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SeqArray.html", "sc:version": "1.14.0" + }, + { + "@id": "http://orcid.org/0000-0002-1390-0708", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/seqassist/seqassistbioschemas.jsonld b/data/seqassist/seqassistbioschemas.jsonld index a45bc7b757282..cf11cb74a25d9 100644 --- a/data/seqassist/seqassistbioschemas.jsonld +++ b/data/seqassist/seqassistbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4251038", "pubmed:25349885", { "@id": "https://doi.org/10.1186/1471-2105-15-S11-S10" - } + }, + "pmcid:PMC4251038" ], "sc:description": "Valuable “assistant” to a broad range of investigators who conduct genome re-sequencing, RNA-Seq, or de novo genome sequencing and assembly experiments. It takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for sequence alignment, and aims to provide a quick overview and basic statistics of NGS data.", "sc:featureList": [ diff --git a/data/seqatoms/seqatomsbioschemas.jsonld b/data/seqatoms/seqatomsbioschemas.jsonld index 8d478191caa7d..61ce17db1c1f2 100644 --- a/data/seqatoms/seqatomsbioschemas.jsonld +++ b/data/seqatoms/seqatomsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SEQATOMS is a web tool for identifying missing regions in PDB sequence. To visualize these regions in their sequence context, a BLAST interface is used that is able to show the lower-case masked regions in the output (hits in the BLAST output are replaced with the corresponding subsequence from the original FASTA files).", "sc:name": "SEQATOMS", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.bioinformatics.nl/tools/seqatoms" } \ No newline at end of file diff --git a/data/seqbench/seqbenchbioschemas.jsonld b/data/seqbench/seqbenchbioschemas.jsonld index 96c219501774d..8a90409106279 100644 --- a/data/seqbench/seqbenchbioschemas.jsonld +++ b/data/seqbench/seqbenchbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1756-0500-7-43", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/seqbench", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:24444368", + "pmcid:PMC3898724", { "@id": "https://doi.org/10.1186/1756-0500-7-43" - }, - "pmcid:PMC3898724", - "pubmed:24444368" + } ], "sc:description": "Management and analysis of exome sequencing data. Provides a user friendly data acquisition module to facilitate comprehensive and intuitive data handling. Provides also direct access to the analysis pipeline SIMPLEX, which can be configured to run locally, on a cluster, or in the cloud.", "sc:featureList": { @@ -32,10 +36,6 @@ "Linux" ], "sc:url": "http://www.icbi.at/software/seqbench/seqbench.shtml" - }, - { - "@id": "https://doi.org/10.1186/1756-0500-7-43", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/seqbias/seqbiasbioschemas.jsonld b/data/seqbias/seqbiasbioschemas.jsonld index bac7960c5ec0a..986c88a2546d9 100644 --- a/data/seqbias/seqbiasbioschemas.jsonld +++ b/data/seqbias/seqbiasbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Daniel Jones", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:22285831", { "@id": "https://doi.org/10.1093/bioinformatics/bts055" }, - "pmcid:PMC3315719" + "pmcid:PMC3315719", + "pubmed:22285831" ], "sc:description": "This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.", "sc:featureList": { @@ -35,8 +35,8 @@ "sc:license": "GPL-3.0", "sc:name": "seqbias", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seqbias.html", diff --git a/data/seqbuster/seqbusterbioschemas.jsonld b/data/seqbuster/seqbusterbioschemas.jsonld index 5b6f0ada7589c..f1453df14a3c8 100644 --- a/data/seqbuster/seqbusterbioschemas.jsonld +++ b/data/seqbuster/seqbusterbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SeqBuster, a web-based bioinformatic tool offering a custom analysis of deep sequencing data at different levels, with special emphasis on the analysis of miRNA variants or isomiRs and the discovering of new small RNAs.", "sc:name": "SeqBuster", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/lpantano/seqbuster" } \ No newline at end of file diff --git a/data/seqcat/seqcatbioschemas.jsonld b/data/seqcat/seqcatbioschemas.jsonld index 8a3c4bf3b90bb..0690a80c0f5ed 100644 --- a/data/seqcat/seqcatbioschemas.jsonld +++ b/data/seqcat/seqcatbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "seqCAT", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seqCAT.html", "sc:version": "1.2.1" diff --git a/data/seqcksum/seqcksumbioschemas.jsonld b/data/seqcksum/seqcksumbioschemas.jsonld index e70ee6c78d7e9..9ef27befb9649 100644 --- a/data/seqcksum/seqcksumbioschemas.jsonld +++ b/data/seqcksum/seqcksumbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Generation of checksums for protein and nucleotide sequences.", "sc:name": "SeqCksum", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/so/seqcksum/", diff --git a/data/seqcluster/seqclusterbioschemas.jsonld b/data/seqcluster/seqclusterbioschemas.jsonld index 2d78fe4782565..64192bf4d8a08 100644 --- a/data/seqcluster/seqclusterbioschemas.jsonld +++ b/data/seqcluster/seqclusterbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Francisco Pantano Rubino", - "Judith Flo Gaya" + "Judith Flo Gaya", + "Francisco Pantano Rubino" ], "sc:citation": "pubmed:26530722", "sc:description": "Analysis of small RNA sequencing data. It detect unit of transcription over the genome, annotate them and create an HTML interactive report that helps to explore the data quickly.", @@ -22,8 +22,8 @@ "sc:operatingSystem": "Linux", "sc:provider": [ "hsph.harvard.edu", - "Harvard Chan School", - "Center of Genomic Regulation" + "Center of Genomic Regulation", + "Harvard Chan School" ], "sc:url": "http://seqcluster.readthedocs.org", "sc:version": "1.1.14" diff --git a/data/seqcna/seqcnabioschemas.jsonld b/data/seqcna/seqcnabioschemas.jsonld index 80a4f56a1cba4..62a332e36d130 100644 --- a/data/seqcna/seqcnabioschemas.jsonld +++ b/data/seqcna/seqcnabioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2164-15-178", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/seqcna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David Mosen-Ansorena", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC4022175", + "pubmed:24597965", { "@id": "https://doi.org/10.1186/1471-2164-15-178" - }, - "pubmed:24597965" + } ], "sc:description": "Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization.", "sc:featureList": { @@ -35,12 +31,16 @@ "sc:license": "GPL-3.0", "sc:name": "seqCNA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seqCNA.html", "sc:version": "1.20.0" + }, + { + "@id": "https://doi.org/10.1186/1471-2164-15-178", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/seqcombo/seqcombobioschemas.jsonld b/data/seqcombo/seqcombobioschemas.jsonld index 60b7a8e4ae18c..400599067cea0 100644 --- a/data/seqcombo/seqcombobioschemas.jsonld +++ b/data/seqcombo/seqcombobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "seqcombo", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seqcombo.html", "sc:version": "1.2.0" diff --git a/data/seqcons/seqconsbioschemas.jsonld b/data/seqcons/seqconsbioschemas.jsonld index 045e0e0f30ffb..6bba917faede4 100644 --- a/data/seqcons/seqconsbioschemas.jsonld +++ b/data/seqcons/seqconsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SeqCons is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly.", "sc:name": "SeqCons", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/gkno/seqan/tree/master/core/apps/seqcons" } \ No newline at end of file diff --git a/data/seqcount/seqcountbioschemas.jsonld b/data/seqcount/seqcountbioschemas.jsonld index 83cd7c95edeb5..8b7e83c486310 100644 --- a/data/seqcount/seqcountbioschemas.jsonld +++ b/data/seqcount/seqcountbioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", + "EMBOSS Contributors", "Wellcome Trust", - "UK MRC", - "EMBOSS Contributors" + "UK MRC" ], "sc:description": "Read and count sequences.", "sc:funder": [ - "UK MRC", "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "seqcount", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/seqcount.html", "sc:version": "r6" diff --git a/data/seqdepot/seqdepotbioschemas.jsonld b/data/seqdepot/seqdepotbioschemas.jsonld index 6b065e7b3d3b9..6b80bfb749023 100644 --- a/data/seqdepot/seqdepotbioschemas.jsonld +++ b/data/seqdepot/seqdepotbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Novel database that focuses solely on two primary goals: (i) assimilating known primary sequences with predicted feature data and (ii) providing the most simple and straightforward means to procure and readily use this information.", "sc:name": "SeqDepot", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://seqdepot.net/", "sc:version": "1" diff --git a/data/seqfam/seqfambioschemas.jsonld b/data/seqfam/seqfambioschemas.jsonld index beb85c505c884..2ce4ba64dc344 100644 --- a/data/seqfam/seqfambioschemas.jsonld +++ b/data/seqfam/seqfambioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "seqfam", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/mframpton/seqfam", "sc:version": "1.0" diff --git a/data/seqfeatr/seqfeatrbioschemas.jsonld b/data/seqfeatr/seqfeatrbioschemas.jsonld index bccb2e8d84cd5..60761de4a837f 100644 --- a/data/seqfeatr/seqfeatrbioschemas.jsonld +++ b/data/seqfeatr/seqfeatrbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1371/journal.pone.0146409", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0002-9313-8636", + "@type": "schema:Person" }, { "@id": "https://bio.tools/seqfeatr", @@ -20,8 +20,8 @@ "@id": "http://orcid.org/0000-0002-9313-8636" }, "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": [ { @@ -38,15 +38,15 @@ "sc:name": "SeqFeatR", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://seqfeatr.zmb.uni-due.de/", "sc:version": "0.2.7" }, { - "@id": "http://orcid.org/0000-0002-9313-8636", - "@type": "schema:Person" + "@id": "https://doi.org/10.1371/journal.pone.0146409", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/seqfire/seqfirebioschemas.jsonld b/data/seqfire/seqfirebioschemas.jsonld index f229f1e308e2a..6d6d8b66cd14c 100644 --- a/data/seqfire/seqfirebioschemas.jsonld +++ b/data/seqfire/seqfirebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SeqFIRE", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.seqfire.org" } \ No newline at end of file diff --git a/data/seqfold/seqfoldbioschemas.jsonld b/data/seqfold/seqfoldbioschemas.jsonld index 3916b0a7fda8a..8961f604f93a6 100644 --- a/data/seqfold/seqfoldbioschemas.jsonld +++ b/data/seqfold/seqfoldbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "RNA secondary structure prediction from experimental data. Given high-throughput data, it can reconstruct the secondary structures of the whole transcriptome, termed the RNA structurome.", "sc:name": "SeqFold", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://ouyanglab.jax.org/seqfold/" } \ No newline at end of file diff --git a/data/seqgsea/seqgseabioschemas.jsonld b/data/seqgsea/seqgseabioschemas.jsonld index 885d58cb74420..72d334ed90cae 100644 --- a/data/seqgsea/seqgseabioschemas.jsonld +++ b/data/seqgsea/seqgseabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-7572-6354", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/seqgsea", "@type": "sc:SoftwareApplication", @@ -20,20 +16,24 @@ "@id": "http://orcid.org/0000-0002-7572-6354" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:24535097", "sc:description": "The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.", "sc:license": "GPL-3.0", "sc:name": "SeqGSEA", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SeqGSEA.html", "sc:version": "1.14.0" + }, + { + "@id": "http://orcid.org/0000-0002-7572-6354", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/seqhound/seqhoundbioschemas.jsonld b/data/seqhound/seqhoundbioschemas.jsonld index 6c3af2300c42b..36844fd101e86 100644 --- a/data/seqhound/seqhoundbioschemas.jsonld +++ b/data/seqhound/seqhoundbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A freely available bioinformatics database warehouse resource that collects bioinformatics data from a number of sources including the National Center for Biotechnology Information and the Gene Ontology Consortium. It is designed for programmers who need unrestricted access to up-to-date data.", "sc:name": "SeqHound", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://sourceforge.net/projects/slritools/" } \ No newline at end of file diff --git a/data/seql-nrps/seql-nrpsbioschemas.jsonld b/data/seql-nrps/seql-nrpsbioschemas.jsonld index 67b19c64b2e05..5ac77c2642d84 100644 --- a/data/seql-nrps/seql-nrpsbioschemas.jsonld +++ b/data/seql-nrps/seql-nrpsbioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-6294-2517", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/seql-nrps", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Dan Søndergaard", { "@id": "http://orcid.org/0000-0002-6294-2517" - }, - "Dan Søndergaard" + } ], "sc:additionalType": "Web service", "sc:citation": "pubmed:26471456", @@ -33,6 +29,10 @@ ], "sc:url": "http://services.birc.au.dk/seql-nrps/", "sc:version": "1.0" + }, + { + "@id": "http://orcid.org/0000-0002-6294-2517", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/seqlm/seqlmbioschemas.jsonld b/data/seqlm/seqlmbioschemas.jsonld index 3983e611b389b..7a57fff5a39d1 100644 --- a/data/seqlm/seqlmbioschemas.jsonld +++ b/data/seqlm/seqlmbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "seqlm", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ELIXIR-EE", "sc:url": "https://github.com/raivokolde/seqlm", diff --git a/data/seqlogo/bioconda_seqlogo.yaml b/data/seqlogo/bioconda_seqlogo.yaml index f21984e193c6e..99f2c5f8b051f 100644 --- a/data/seqlogo/bioconda_seqlogo.yaml +++ b/data/seqlogo/bioconda_seqlogo.yaml @@ -4,7 +4,6 @@ description: seqLogo takes the position weight matrix of a DNA sequence motif an home: https://bioconductor.org/packages/3.10/bioc/html/seqLogo.html identifiers: - biotools:seqlogo -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-seqlogo diff --git a/data/seqlogo/seqlogobioschemas.jsonld b/data/seqlogo/seqlogobioschemas.jsonld index 51be285587b7d..15caa502cb194 100644 --- a/data/seqlogo/seqlogobioschemas.jsonld +++ b/data/seqlogo/seqlogobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Oliver Bembom", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This tool takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).", "sc:license": "GPL-2.0", "sc:name": "seqLogo", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seqLogo.html", "sc:version": "1.40.0" diff --git a/data/seqman_ngen/seqman_ngenbioschemas.jsonld b/data/seqman_ngen/seqman_ngenbioschemas.jsonld index f4ad38ec90526..6dae9a1336f84 100644 --- a/data/seqman_ngen/seqman_ngenbioschemas.jsonld +++ b/data/seqman_ngen/seqman_ngenbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Sequence assembly software using traditional and next-gen techonologies. Subsequent analysis of the assembly, including variant discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene.", "sc:name": "SeqMan NGen", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.dnastar.com/t-nextgen-seqman-ngen.aspx" } \ No newline at end of file diff --git a/data/seqmap/seqmapbioschemas.jsonld b/data/seqmap/seqmapbioschemas.jsonld index e044e4efdfbe9..98e32dfe2d73c 100644 --- a/data/seqmap/seqmapbioschemas.jsonld +++ b/data/seqmap/seqmapbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SeqMap", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www-personal.umich.edu/~jianghui/seqmap/" } \ No newline at end of file diff --git a/data/seqmatchall/seqmatchallbioschemas.jsonld b/data/seqmatchall/seqmatchallbioschemas.jsonld index 905aebd0f6d43..57ab57b67c0da 100644 --- a/data/seqmatchall/seqmatchallbioschemas.jsonld +++ b/data/seqmatchall/seqmatchallbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", + "EMBOSS Contributors", "UK MRC", "UK BBSRC", - "EMBOSS Contributors" + "Wellcome Trust" ], "sc:description": "All-against-all word comparison of a sequence set.", "sc:funder": [ - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "seqmatchall", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/seqmatchall.html", "sc:version": "r6" diff --git a/data/seqminer-variant/seqminer-variantbioschemas.jsonld b/data/seqminer-variant/seqminer-variantbioschemas.jsonld index 8de2c356a2900..90f550f21d158 100644 --- a/data/seqminer-variant/seqminer-variantbioschemas.jsonld +++ b/data/seqminer-variant/seqminer-variantbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An R package for annotating and querying files of sequence variants (e.g., VCF/BCF files) and summary association statistics (e.g., METAL/RAREMETAL files), and for integrating bioinformatics databases.", "sc:name": "SEQMINER", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://seqminer.genomic.codes/" } \ No newline at end of file diff --git a/data/seqminer/seqminerbioschemas.jsonld b/data/seqminer/seqminerbioschemas.jsonld index 126898c5dabaf..e43dc7128d7dc 100644 --- a/data/seqminer/seqminerbioschemas.jsonld +++ b/data/seqminer/seqminerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "seqMINER", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bips.u-strasbg.fr/seqminer/tiki-index.php" } \ No newline at end of file diff --git a/data/seqpattern/bioconda_seqpattern.yaml b/data/seqpattern/bioconda_seqpattern.yaml index 2f975c5b12e3b..18cfed960957e 100644 --- a/data/seqpattern/bioconda_seqpattern.yaml +++ b/data/seqpattern/bioconda_seqpattern.yaml @@ -5,7 +5,6 @@ description: Visualising oligonucleotide patterns and sequence motifs occurrence home: https://bioconductor.org/packages/3.10/bioc/html/seqPattern.html identifiers: - biotools:seqpattern -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-seqpattern diff --git a/data/seqpattern/seqpatternbioschemas.jsonld b/data/seqpattern/seqpatternbioschemas.jsonld index d2323d3f8faf0..49c1b246a2356 100644 --- a/data/seqpattern/seqpatternbioschemas.jsonld +++ b/data/seqpattern/seqpatternbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "seqPattern", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seqPattern.html", "sc:version": "1.6.0" diff --git a/data/seqplots/seqplotsbioschemas.jsonld b/data/seqplots/seqplotsbioschemas.jsonld index 5c5cfeed71b8a..5bfd8b6143cd6 100644 --- a/data/seqplots/seqplotsbioschemas.jsonld +++ b/data/seqplots/seqplotsbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "seqplots", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seqplots.html", diff --git a/data/seqpower/seqpowerbioschemas.jsonld b/data/seqpower/seqpowerbioschemas.jsonld index af105b88f25cb..d9df3abc2a756 100644 --- a/data/seqpower/seqpowerbioschemas.jsonld +++ b/data/seqpower/seqpowerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool that provides statistical power analysis and sample size estimation for sequence-based association studies.", "sc:name": "SEQPower", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinformatics.org/spower/" } \ No newline at end of file diff --git a/data/seqprocess/seqprocessbioschemas.jsonld b/data/seqprocess/seqprocessbioschemas.jsonld index 8260f39e32c22..32904dcdf8dbf 100644 --- a/data/seqprocess/seqprocessbioschemas.jsonld +++ b/data/seqprocess/seqprocessbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "SEQprocess", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/omicsCore/SEQprocess" } \ No newline at end of file diff --git a/data/seqret-ebi/seqret-ebibioschemas.jsonld b/data/seqret-ebi/seqret-ebibioschemas.jsonld index 676fb0e2f7ef5..cdb276a39b6f6 100644 --- a/data/seqret-ebi/seqret-ebibioschemas.jsonld +++ b/data/seqret-ebi/seqret-ebibioschemas.jsonld @@ -13,14 +13,14 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "EMBOSS", - "Web Production" + "Web Production", + "EMBOSS" ], "sc:description": "Sequence format coversion tool.", "sc:name": "seqret (EBI)", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "EMBL-EBI", diff --git a/data/seqret/seqretbioschemas.jsonld b/data/seqret/seqretbioschemas.jsonld index f7d7d31a82f18..cb6f69221f575 100644 --- a/data/seqret/seqretbioschemas.jsonld +++ b/data/seqret/seqretbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "Wellcome Trust", - "UK MRC", - "EMBOSS Contributors" + "UK BBSRC", + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Read and write (return) sequences.", "sc:funder": [ - "UK BBSRC", "UK MRC", + "UK BBSRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "seqret", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/seqret.html", "sc:version": "r6" diff --git a/data/seqretsetall/seqretsetallbioschemas.jsonld b/data/seqretsetall/seqretsetallbioschemas.jsonld index 09ee41c06c2a1..f4dd1b2f51a9a 100644 --- a/data/seqretsetall/seqretsetallbioschemas.jsonld +++ b/data/seqretsetall/seqretsetallbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "Wellcome Trust", "UK MRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Read and write (return) many sets of sequences.", "sc:funder": [ - "Wellcome Trust", "UK MRC", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "seqretsetall", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/seqretsplit/seqretsplitbioschemas.jsonld b/data/seqretsplit/seqretsplitbioschemas.jsonld index 8e8554841625a..ae42d73d10933 100644 --- a/data/seqretsplit/seqretsplitbioschemas.jsonld +++ b/data/seqretsplit/seqretsplitbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "Wellcome Trust", + "UK BBSRC", "EMBOSS Contributors", - "UK BBSRC" + "Wellcome Trust", + "UK MRC" ], "sc:description": "Read sequences and write them to individual files.", "sc:funder": [ - "UK MRC", "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "seqretsplit", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/seqseg/seqsegbioschemas.jsonld b/data/seqseg/seqsegbioschemas.jsonld index 4fb27724b83e6..274cb7feda652 100644 --- a/data/seqseg/seqsegbioschemas.jsonld +++ b/data/seqseg/seqsegbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "SeqSeg", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=182" } \ No newline at end of file diff --git a/data/seqsetvis/seqsetvisbioschemas.jsonld b/data/seqsetvis/seqsetvisbioschemas.jsonld index 905f0cc6671a3..c654fcf916472 100644 --- a/data/seqsetvis/seqsetvisbioschemas.jsonld +++ b/data/seqsetvis/seqsetvisbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "seqsetvis", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seqsetvis.html", "sc:version": "1.0.2" diff --git a/data/seqsimla/seqsimlabioschemas.jsonld b/data/seqsimla/seqsimlabioschemas.jsonld index 87add9c9c9233..d0213693fed26 100644 --- a/data/seqsimla/seqsimlabioschemas.jsonld +++ b/data/seqsimla/seqsimlabioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "SeqSIMLA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://seqsimla.sourceforge.net/" } \ No newline at end of file diff --git a/data/seqsite/seqsitebioschemas.jsonld b/data/seqsite/seqsitebioschemas.jsonld index 84d91f887f8e7..3af2e8aabd183 100644 --- a/data/seqsite/seqsitebioschemas.jsonld +++ b/data/seqsite/seqsitebioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "SeqSite", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinfo.au.tsinghua.edu.cn/software/seqsite/" } \ No newline at end of file diff --git a/data/seqspark/seqsparkbioschemas.jsonld b/data/seqspark/seqsparkbioschemas.jsonld index 33b682f905354..32c769c460e7c 100644 --- a/data/seqspark/seqsparkbioschemas.jsonld +++ b/data/seqspark/seqsparkbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1016/j.ajhg.2017.05.017", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/seqspark", "@type": "sc:SoftwareApplication", @@ -28,14 +32,10 @@ "sc:license": "Apache-2.0", "sc:name": "SEQSpark", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/statgenetics/seqspark" - }, - { - "@id": "https://doi.org/10.1016/j.ajhg.2017.05.017", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/seqsqc/seqsqcbioschemas.jsonld b/data/seqsqc/seqsqcbioschemas.jsonld index 1285c68c6e48f..3b218233736e1 100644 --- a/data/seqsqc/seqsqcbioschemas.jsonld +++ b/data/seqsqc/seqsqcbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SeqSQC", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SeqSQC.html", "sc:version": "1.2.0" diff --git a/data/seqstrap/seqstrapbioschemas.jsonld b/data/seqstrap/seqstrapbioschemas.jsonld index 0cd0fa8c4b865..5f51143af5080 100644 --- a/data/seqstrap/seqstrapbioschemas.jsonld +++ b/data/seqstrap/seqstrapbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "“Extrapolating” partial or fragmentary nucleic acid sequences prior to assay design. It works by first loading a set of user specified sequences in FASTA format, iteratively comparing every sequence to every other sequence, and using the best matching sequence as a template for adding additional sequence at the 5′ and 3′ ends of the sequence.", "sc:name": "SeqStrap", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://public.lanl.gov/jgans/", "sc:version": "1.0" diff --git a/data/seqtailor/seqtailorbioschemas.jsonld b/data/seqtailor/seqtailorbioschemas.jsonld index bf84e4b6f7648..0e68ef021c7f3 100644 --- a/data/seqtailor/seqtailorbioschemas.jsonld +++ b/data/seqtailor/seqtailorbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-6129-567X", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ326", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/SeqTailor", "@type": "sc:SoftwareApplication", @@ -16,24 +24,24 @@ "@id": "https://orcid.org/0000-0002-6129-567X" }, "sc:additionalType": [ - "Web application", + "Command-line tool", "Web service", - "Command-line tool" + "Web application" ], "sc:citation": [ { "@id": "https://doi.org/10.1093/NAR/GKZ326" }, - "pubmed:31045209", - "pmcid:PMC6602489" + "pmcid:PMC6602489", + "pubmed:31045209" ], "sc:description": "Web server for the extraction of DNA or protein sequences from next-generation sequencing data.", "sc:featureList": [ { - "@id": "edam:operation_0433" + "@id": "edam:operation_3227" }, { - "@id": "edam:operation_3227" + "@id": "edam:operation_0433" }, { "@id": "edam:operation_3216" @@ -42,19 +50,11 @@ "sc:license": "Unlicense", "sc:name": "SeqTailor", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://shiva.rockefeller.edu/SeqTailor/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ326", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0002-6129-567X", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/seqtk/seqtkbioschemas.jsonld b/data/seqtk/seqtkbioschemas.jsonld index 850cc712e767a..6082e8d38f7e5 100644 --- a/data/seqtk/seqtkbioschemas.jsonld +++ b/data/seqtk/seqtkbioschemas.jsonld @@ -15,18 +15,18 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:28701181", - "pmcid:PMC5508660", { "@id": "https://doi.org/10.1186/s13104-017-2616-7" - } + }, + "pmcid:PMC5508660" ], "sc:description": "A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.", "sc:featureList": [ { - "@id": "edam:operation_2409" + "@id": "edam:operation_2121" }, { - "@id": "edam:operation_2121" + "@id": "edam:operation_2409" } ], "sc:license": "MIT", diff --git a/data/seqtools/bioconda_seqtools.yaml b/data/seqtools/bioconda_seqtools.yaml index 97b736314c5da..ed91f60298439 100644 --- a/data/seqtools/bioconda_seqtools.yaml +++ b/data/seqtools/bioconda_seqtools.yaml @@ -4,7 +4,6 @@ description: Analyze read length, phred scores and alphabet frequency and DNA k- home: https://bioconductor.org/packages/3.10/bioc/html/seqTools.html identifiers: - biotools:seqtools -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-seqtools summary: Analysis of nucleotide, sequence and quality content on fastq files diff --git a/data/seqtools/seqtoolsbioschemas.jsonld b/data/seqtools/seqtoolsbioschemas.jsonld index e2f893b470bd5..bfc702b55ec47 100644 --- a/data/seqtools/seqtoolsbioschemas.jsonld +++ b/data/seqtools/seqtoolsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Wolfgang Kaisers", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files.", "sc:license": "Artistic-2.0", "sc:name": "seqTools", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/seqTools.html", "sc:version": "1.8.0" diff --git a/data/seqtrace/seqtracebioschemas.jsonld b/data/seqtrace/seqtracebioschemas.jsonld index 415c1c4a7e928..aee954f04c7d9 100644 --- a/data/seqtrace/seqtracebioschemas.jsonld +++ b/data/seqtrace/seqtracebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Application for viewing and processing DNA sequencing chromatograms (trace files). SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA.", "sc:name": "SeqTrace", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://code.google.com/p/seqtrace/" diff --git a/data/seqtrim/seqtrimbioschemas.jsonld b/data/seqtrim/seqtrimbioschemas.jsonld index c573ba9ef711b..9e99b332513bc 100644 --- a/data/seqtrim/seqtrimbioschemas.jsonld +++ b/data/seqtrim/seqtrimbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A pipeline for preprocessing sequences from Sanger sequencing.", "sc:name": "SeqTrim", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.scbi.uma.es/ingebiol/session/new/seqtrimnext" } \ No newline at end of file diff --git a/data/sequalyzer/sequalyzerbioschemas.jsonld b/data/sequalyzer/sequalyzerbioschemas.jsonld index cee5e3b7258b2..b8c3d7288983d 100644 --- a/data/sequalyzer/sequalyzerbioschemas.jsonld +++ b/data/sequalyzer/sequalyzerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "SEQualyzer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bme.ucdavis.edu/aviranlab/SEQualyzer" } \ No newline at end of file diff --git a/data/sequana_coverage/sequana_coveragebioschemas.jsonld b/data/sequana_coverage/sequana_coveragebioschemas.jsonld index d8b0fed87fc3d..ac7b61042c888 100644 --- a/data/sequana_coverage/sequana_coveragebioschemas.jsonld +++ b/data/sequana_coverage/sequana_coveragebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Dimitri Desvillechabrol", - "Thomas Cokelaer" + "Thomas Cokelaer", + "Dimitri Desvillechabrol" ], "sc:description": "Show coverage and interval of confidence to identify under and over represented genomic regions. The tool also creates an HTML report with various images showing the coverage and GC versus coverage plots. It also provides a set of CSV files with low or high coverage regions (as compared to the average coverage).", "sc:license": "BSD-3-Clause", "sc:name": "sequana_coverage", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "Institut Pasteur", diff --git a/data/sequanix/sequanixbioschemas.jsonld b/data/sequanix/sequanixbioschemas.jsonld index 4f8fa62f8d920..481cb5b291977 100644 --- a/data/sequanix/sequanixbioschemas.jsonld +++ b/data/sequanix/sequanixbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "sequanix", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sequana.readthedocs.io", "sc:version": "0.5.0" diff --git a/data/sequence_harmony/sequence_harmonybioschemas.jsonld b/data/sequence_harmony/sequence_harmonybioschemas.jsonld index 151b1eb3c3aef..998b37714c9f5 100644 --- a/data/sequence_harmony/sequence_harmonybioschemas.jsonld +++ b/data/sequence_harmony/sequence_harmonybioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Sequence Harmony", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ibi.vu.nl/programs/seqharmwww/" } \ No newline at end of file diff --git a/data/sequence_maneuverer/sequence_maneuvererbioschemas.jsonld b/data/sequence_maneuverer/sequence_maneuvererbioschemas.jsonld index 399ee72ff4950..073bf2d8ecf15 100644 --- a/data/sequence_maneuverer/sequence_maneuvererbioschemas.jsonld +++ b/data/sequence_maneuverer/sequence_maneuvererbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool efficiently extracts sequences from large datasets with few simple steps. It can efficiently extract multiple sequences of any desired length from a genome of any organism.", "sc:name": "Sequence Maneuverer", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://ww3.comsats.edu.pk/bio/SequenceManeuverer.aspx" diff --git a/data/sequence_searcher/sequence_searcherbioschemas.jsonld b/data/sequence_searcher/sequence_searcherbioschemas.jsonld index 0dd7e41239ddb..2f0d69fef1a79 100644 --- a/data/sequence_searcher/sequence_searcherbioschemas.jsonld +++ b/data/sequence_searcher/sequence_searcherbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Sequence Searcher", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://athena.bioc.uvic.ca/virology-ca-tools/sequence-searcher/" } \ No newline at end of file diff --git a/data/sequencher/sequencherbioschemas.jsonld b/data/sequencher/sequencherbioschemas.jsonld index 98a0e11ff2e79..4e04f20b6e943 100644 --- a/data/sequencher/sequencherbioschemas.jsonld +++ b/data/sequencher/sequencherbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/sequencher", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Contact Form", - "Technical support" + "Technical support", + "Contact Form" ], "sc:additionalType": "Desktop application", "sc:description": "Desktop alignment software now with plugins to MAQ and GSNAP for NGS sequence date", diff --git a/data/sequins/sequinsbioschemas.jsonld b/data/sequins/sequinsbioschemas.jsonld index 48a5963780551..75d5f40f20348 100644 --- a/data/sequins/sequinsbioschemas.jsonld +++ b/data/sequins/sequinsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Performs sequence validation by comparing the model side chains against the electron density. It may be run with phases from experimental phasing, or it can calculate its own phases using a side-chain-omit process. In this case it can be used after molecular replacement, or to validate structures in the PDB.", "sc:name": "sequins", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ysbl.york.ac.uk/~cowtan/sequins/sequins.html", "sc:version": "20070909" diff --git a/data/seqvartools/seqvartoolsbioschemas.jsonld b/data/seqvartools/seqvartoolsbioschemas.jsonld index d27665142d030..9d00ad14f3279 100644 --- a/data/seqvartools/seqvartoolsbioschemas.jsonld +++ b/data/seqvartools/seqvartoolsbioschemas.jsonld @@ -16,16 +16,16 @@ "Adrienne Stilp" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.", "sc:license": "GPL-3.0", "sc:name": "SeqVarTools", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SeqVarTools.html", "sc:version": "1.12.0" diff --git a/data/seqvista/seqvistabioschemas.jsonld b/data/seqvista/seqvistabioschemas.jsonld index a85f6653443de..355ba573efc61 100644 --- a/data/seqvista/seqvistabioschemas.jsonld +++ b/data/seqvista/seqvistabioschemas.jsonld @@ -11,10 +11,10 @@ "@id": "https://bio.tools/seqvista", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Martin Frith", "Tianhua Niu", - "Zhiping Weng", - "Zhenjun Hu" + "Zhenjun Hu", + "Martin Frith", + "Zhiping Weng" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:12513700", diff --git a/data/seqware/seqwarebioschemas.jsonld b/data/seqware/seqwarebioschemas.jsonld index e97ba47258008..e7a03aeb08594 100644 --- a/data/seqware/seqwarebioschemas.jsonld +++ b/data/seqware/seqwarebioschemas.jsonld @@ -11,27 +11,27 @@ "@id": "https://bio.tools/seqware", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Denis Yuen", - "Brian O'Connor" + "Brian O'Connor", + "Denis Yuen" ], "sc:additionalType": [ - "Web API", "Workbench", - "Command-line tool" + "Command-line tool", + "Web API" ], "sc:author": [ - "Denis Yuen", + "Brian O'Connor", "Morgan Taschuk", - "Solomon Shorser", - "Brian O'Connor" + "Denis Yuen", + "Solomon Shorser" ], "sc:description": "Portable software infrastructure designed to analyze massive genomics datasets produced by contemporary and emerging technologies, in particular Next Generation Sequencing (NGS) platforms.", "sc:license": "LGPL-2.1", "sc:name": "SeqWare", "sc:operatingSystem": "Linux", "sc:provider": [ - "Ontario Institute for Cancer Research", - "ucla.edu" + "ucla.edu", + "Ontario Institute for Cancer Research" ], "sc:url": "http://seqware.io/", "sc:version": "1.1.1" diff --git a/data/seqxref/seqxrefbioschemas.jsonld b/data/seqxref/seqxrefbioschemas.jsonld index 3ce4e1fe4163a..b009968062b74 100644 --- a/data/seqxref/seqxrefbioschemas.jsonld +++ b/data/seqxref/seqxrefbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "Wellcome Trust", - "EMBOSS Contributors", - "UK BBSRC" + "UK BBSRC", + "UK MRC", + "EMBOSS Contributors" ], "sc:description": "Retrieve all database cross-references for a sequence entry.", "sc:funder": [ "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "seqxref", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/seqxref.html", "sc:version": "r6" diff --git a/data/seqxrefget/seqxrefgetbioschemas.jsonld b/data/seqxrefget/seqxrefgetbioschemas.jsonld index 3f8bd8bf10d94..62b9bd68041d0 100644 --- a/data/seqxrefget/seqxrefgetbioschemas.jsonld +++ b/data/seqxrefget/seqxrefgetbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Retrieve all cross-referenced data for a sequence entry.", "sc:funder": [ - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "seqxrefget", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/seqxrefget.html", "sc:version": "r6" diff --git a/data/serendip/serendipbioschemas.jsonld b/data/serendip/serendipbioschemas.jsonld index 29b2eab2287d0..4330d2a47d49e 100644 --- a/data/serendip/serendipbioschemas.jsonld +++ b/data/serendip/serendipbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/SeRenDIP", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Q. Hou", "Paul de Geest", - "K. Anton Feenstra" + "K. Anton Feenstra", + "Q. Hou" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:31116381", @@ -22,8 +22,8 @@ "sc:name": "SeRenDIP", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ibi.vu.nl/programs/serendipwww/" } \ No newline at end of file diff --git a/data/servertell/servertellbioschemas.jsonld b/data/servertell/servertellbioschemas.jsonld index 961f5da51b5a0..1d8432786c532 100644 --- a/data/servertell/servertellbioschemas.jsonld +++ b/data/servertell/servertellbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "EMBOSS Contributors", + "UK MRC", "Wellcome Trust", "UK BBSRC" ], "sc:description": "Display information about a public server.", "sc:funder": [ - "UK BBSRC", "UK MRC", + "UK BBSRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", diff --git a/data/seten/setenbioschemas.jsonld b/data/seten/setenbioschemas.jsonld index 3e3801f6982d5..01aca82ae9e0e 100644 --- a/data/seten/setenbioschemas.jsonld +++ b/data/seten/setenbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1261/RNA.059089.116", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/seten", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Gungor Budak", - "Sarath Chandra Janga" + "Sarath Chandra Janga", + "Gungor Budak" ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28336542", { "@id": "https://doi.org/10.1261/RNA.059089.116" }, - "pmcid:PMC5435856" + "pmcid:PMC5435856", + "pubmed:28336542" ], "sc:description": "A tool for systematic identification and comparison of processes, phenotypes and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles.", "sc:featureList": { @@ -35,10 +39,6 @@ "Windows" ], "sc:url": "http://www.iupui.edu/~sysbio/seten/" - }, - { - "@id": "https://doi.org/10.1261/RNA.059089.116", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/setsapp/setsappbioschemas.jsonld b/data/setsapp/setsappbioschemas.jsonld index 036dda4f21c05..f620095bebff5 100644 --- a/data/setsapp/setsappbioschemas.jsonld +++ b/data/setsapp/setsappbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A Cytoscape 3 app allowing the user to create and manipulate sets of nodes or edges (but not sets with both nodes and edges, at least in the current version) in Cytoscape. Sets can be created for different networks.", "sc:name": "setsApp", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://apps.cytoscape.org/apps/setsapp" diff --git a/data/setter/setterbioschemas.jsonld b/data/setter/setterbioschemas.jsonld index 6c87e0faec7e0..da380180ad09b 100644 --- a/data/setter/setterbioschemas.jsonld +++ b/data/setter/setterbioschemas.jsonld @@ -13,8 +13,8 @@ "sc:additionalType": "Web application", "sc:author": [ "Petr Čech", - "Daniel Svozil", - "David Hoksza" + "David Hoksza", + "Daniel Svozil" ], "sc:contributor": "Daniel Svozil", "sc:description": "A web application for RNA structure comparison.", diff --git a/data/setuppromoter/setuppromoterbioschemas.jsonld b/data/setuppromoter/setuppromoterbioschemas.jsonld index 08c301a3db053..e7513b252c44a 100644 --- a/data/setuppromoter/setuppromoterbioschemas.jsonld +++ b/data/setuppromoter/setuppromoterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Builds a fasta file of sequences from a reference genome using promoter region coordinates.", "sc:name": "setuppromoter", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/promoteur_tools/setuppromoter/1.0", "sc:version": "1.0" diff --git a/data/sevenc/sevencbioschemas.jsonld b/data/sevenc/sevencbioschemas.jsonld index c0f89d5af1d9e..822d163a4068d 100644 --- a/data/sevenc/sevencbioschemas.jsonld +++ b/data/sevenc/sevencbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "sevenC", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sevenC.html", "sc:version": "1.0.0" diff --git a/data/sewer/sewerbioschemas.jsonld b/data/sewer/sewerbioschemas.jsonld index e137cb68511dd..d96d25f191892 100644 --- a/data/sewer/sewerbioschemas.jsonld +++ b/data/sewer/sewerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Sequence analysis tools on the web; includes nucleic acid, protein, PCR and alignment tools.", "sc:name": "SeWeR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinformatics.org/sewer/" } \ No newline at end of file diff --git a/data/sexy/sexybioschemas.jsonld b/data/sexy/sexybioschemas.jsonld index 506b2f0c59b61..b355db303f5c1 100644 --- a/data/sexy/sexybioschemas.jsonld +++ b/data/sexy/sexybioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Unlicense", "sc:name": "seXY", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/Christopher-Amos-Lab/seXY" } \ No newline at end of file diff --git a/data/sfdr/sfdrbioschemas.jsonld b/data/sfdr/sfdrbioschemas.jsonld index 743f8c24d24ed..4d00dfea4bb93 100644 --- a/data/sfdr/sfdrbioschemas.jsonld +++ b/data/sfdr/sfdrbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A program to compute FDR q-values of genome-wide SNP association analysis within each stratum. Especialy the SFDR program is taylored to directly use genome-wide linkage scan results to assign strata. Weighted FDR q-values can be also computed as an alternative to SFDR.", "sc:name": "SFDR", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://fisher.utstat.toronto.edu/sun/Software/SFDR/index.html" diff --git a/data/sfesa/sfesabioschemas.jsonld b/data/sfesa/sfesabioschemas.jsonld index 685e1df28690a..8d0468bb5ef11 100644 --- a/data/sfesa/sfesabioschemas.jsonld +++ b/data/sfesa/sfesabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SFESA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://prodata.swmed.edu/sfesa/sfesa.php" } \ No newline at end of file diff --git a/data/sfinx/sfinxbioschemas.jsonld b/data/sfinx/sfinxbioschemas.jsonld index 4226d0902654b..9013f8f6c3204 100644 --- a/data/sfinx/sfinxbioschemas.jsonld +++ b/data/sfinx/sfinxbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Straightforward filtering index for affinity purification mass spectrometry data analysis.", "sc:name": "SFINX", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://sfinx.ugent.be/", diff --git a/data/sfmap/sfmapbioschemas.jsonld b/data/sfmap/sfmapbioschemas.jsonld index 3ac629f04e52a..0d7300f9159b2 100644 --- a/data/sfmap/sfmapbioschemas.jsonld +++ b/data/sfmap/sfmapbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SFmap is a web server for predicting putative splicing factor (SF) binding sites in genomic data. Sequences are input in FASTA format.", "sc:name": "SFmap", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://sfmap.technion.ac.il" } \ No newline at end of file diff --git a/data/sfold/sfoldbioschemas.jsonld b/data/sfold/sfoldbioschemas.jsonld index 9bc22dcacfb86..aec45434038b4 100644 --- a/data/sfold/sfoldbioschemas.jsonld +++ b/data/sfold/sfoldbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.", "sc:name": "Sfold", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://sfold.wadsworth.org" } \ No newline at end of file diff --git a/data/sfs_code/sfs_codebioschemas.jsonld b/data/sfs_code/sfs_codebioschemas.jsonld index 9696469b4087c..23f69ecdc9763 100644 --- a/data/sfs_code/sfs_codebioschemas.jsonld +++ b/data/sfs_code/sfs_codebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects.", "sc:name": "SFS_CODE", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sfscode.sourceforge.net/SFS_CODE/index/index.html" } \ No newline at end of file diff --git a/data/sgatools/sgatoolsbioschemas.jsonld b/data/sgatools/sgatoolsbioschemas.jsonld index 7b002a63bf03d..3eb3b8dd30b94 100644 --- a/data/sgatools/sgatoolsbioschemas.jsonld +++ b/data/sgatools/sgatoolsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A single stop solution for analysing data from genetic screens. There are three steps to the analysis pipeline, each of which can also be run separately from the rest. First, images of plates with colonies are processed to give quantified colony sizes for the screen. Next, the colony sizes are normalised and filtered within plates, taking into account position effects and other confounding factors.", "sc:name": "SGAtools", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://sgatools.ccbr.utoronto.ca/" } \ No newline at end of file diff --git a/data/sgd/sgdbioschemas.jsonld b/data/sgd/sgdbioschemas.jsonld index 3af4d23d7a88c..7aaf32538b3fb 100644 --- a/data/sgd/sgdbioschemas.jsonld +++ b/data/sgd/sgdbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae. The information in it includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Phenotypes and genetic interaction data are also annotated and displayed.", "sc:name": "Saccharomyces genome database (SGD)", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.yeastgenome.org/" diff --git a/data/sgi/sgibioschemas.jsonld b/data/sgi/sgibioschemas.jsonld index efe39d42e0436..af4cfdabaf09e 100644 --- a/data/sgi/sgibioschemas.jsonld +++ b/data/sgi/sgibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software for detecting positive and negative selection at single codon sites.", "sc:name": "SGI", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.personal.psu.edu/nxm2/sgi2.htm" } \ No newline at end of file diff --git a/data/sgp2/sgp2bioschemas.jsonld b/data/sgp2/sgp2bioschemas.jsonld index 0efad7f6e366c..2f7a3cfbb2bce 100644 --- a/data/sgp2/sgp2bioschemas.jsonld +++ b/data/sgp2/sgp2bioschemas.jsonld @@ -12,21 +12,21 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Francisco Camara", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": [ - "Roderic Guigo", "Genis Parra", + "Roderic Guigo", "Josep Abril" ], "sc:description": "Program to predict genes by comparing anonymous genomic sequences from different species. It combines tblastx, a sequence similarity search program, with geneid, an ab initio gene prediction program.", "sc:license": "GPL-3.0", "sc:name": "SGP2", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ "crg.eu", diff --git a/data/sgrp_blast_server/sgrp_blast_serverbioschemas.jsonld b/data/sgrp_blast_server/sgrp_blast_serverbioschemas.jsonld index 8038c9ce28c41..22240149a8a8c 100644 --- a/data/sgrp_blast_server/sgrp_blast_serverbioschemas.jsonld +++ b/data/sgrp_blast_server/sgrp_blast_serverbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/sgrp_blast_server", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Richard Durbin", - "Edward J. Louis" + "Edward J. Louis", + "Richard Durbin" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:19212322", "sc:description": "One to fourfold more coverage of the genome sequences of over seventy isolates of the yeast S. cerevisiae and its closest relative, S. paradoxus are presented here. BLAST tool, and sequence retrieval option.", "sc:name": "SGRP Blast Server", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.moseslab.csb.utoronto.ca/sgrp/" } \ No newline at end of file diff --git a/data/sgseq/sgseqbioschemas.jsonld b/data/sgseq/sgseqbioschemas.jsonld index cae5c5af7bb07..5ada7b9ac003f 100644 --- a/data/sgseq/sgseqbioschemas.jsonld +++ b/data/sgseq/sgseqbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0156132", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/sgseq", "@type": "sc:SoftwareApplication", @@ -30,18 +34,18 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3320" + "@id": "edam:topic_3170" }, { - "@id": "edam:topic_3170" + "@id": "edam:topic_3320" } ], "sc:citation": [ - "pmcid:PMC4878813", "pubmed:27218464", { "@id": "https://doi.org/10.1371/journal.pone.0156132" - } + }, + "pmcid:PMC4878813" ], "sc:description": "Package for analyzing splice events from RNA-seq data. Input data are sequence reads mapped to a reference genome in BAM format. Genes are represented as a genome-wide splice graph, which can be obtained from existing annotation or can be predicted from the data. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant.", "sc:featureList": { @@ -50,16 +54,12 @@ "sc:license": "Artistic-2.0", "sc:name": "SGSeq", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SGSeq.html", "sc:version": "1.8.1" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0156132", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sgtarget/sgtargetbioschemas.jsonld b/data/sgtarget/sgtargetbioschemas.jsonld index ff69bd9a1f9c4..8102433721b67 100644 --- a/data/sgtarget/sgtargetbioschemas.jsonld +++ b/data/sgtarget/sgtargetbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a range of physiochemical properties.", "sc:name": "sgTarget", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.ysbl.york.ac.uk/sgTarget/" } \ No newline at end of file diff --git a/data/sh3-hunter/sh3-hunterbioschemas.jsonld b/data/sh3-hunter/sh3-hunterbioschemas.jsonld index 7f1973931d534..03e6f288e3eca 100644 --- a/data/sh3-hunter/sh3-hunterbioschemas.jsonld +++ b/data/sh3-hunter/sh3-hunterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.", "sc:name": "SH3-Hunter", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://cbm.bio.uniroma2.it/SH3-Hunter/" } \ No newline at end of file diff --git a/data/shaep/shaepbioschemas.jsonld b/data/shaep/shaepbioschemas.jsonld index 2a79ec3522894..d6b57a07cd9f5 100644 --- a/data/shaep/shaepbioschemas.jsonld +++ b/data/shaep/shaepbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay. It can be used for the virtual screening of libraries of chemical structures against a known active molecule, or as a preparative step for 3D QSAR methods.", "sc:name": "ShaEP", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://users.abo.fi/mivainio/shaep/" diff --git a/data/shaman/shamanbioschemas.jsonld b/data/shaman/shamanbioschemas.jsonld index 34445925ea436..384ce4d50f1b7 100644 --- a/data/shaman/shamanbioschemas.jsonld +++ b/data/shaman/shamanbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:author": [ - "Stevenn Volant", - "Pierre Lechat", "Hugo Varet", + "Pierre Lechat", + "Stevenn Volant", "Amine Ghozlane" ], "sc:description": "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].", @@ -22,8 +22,8 @@ "sc:name": "SHAMAN", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "Institut Pasteur", "sc:url": "http://shaman.c3bi.pasteur.fr/" diff --git a/data/shambhala/shambhalabioschemas.jsonld b/data/shambhala/shambhalabioschemas.jsonld index 72b468dbc719a..ff77e6fe77d58 100644 --- a/data/shambhala/shambhalabioschemas.jsonld +++ b/data/shambhala/shambhalabioschemas.jsonld @@ -9,24 +9,28 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2641-8", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Shambhala", "@type": "sc:SoftwareApplication", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6366102", + "pubmed:30727942", { "@id": "https://doi.org/10.1186/s12859-019-2641-8" - }, - "pmcid:PMC6366102", - "pubmed:30727942" + } ], "sc:description": "Platform-agnostic data harmonizer for gene expression data.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_0533" }, { - "@id": "edam:operation_0533" + "@id": "edam:operation_3431" }, { "@id": "edam:operation_0313" @@ -35,15 +39,11 @@ "sc:license": "GPL-3.0", "sc:name": "Shambhala", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/oncobox-admin/harmony" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2641-8", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/shatterproof/shatterproofbioschemas.jsonld b/data/shatterproof/shatterproofbioschemas.jsonld index 900501f7b98ea..e0d58576fadc7 100644 --- a/data/shatterproof/shatterproofbioschemas.jsonld +++ b/data/shatterproof/shatterproofbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Contact list", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:24646301", + "pmcid:PMC3999944", { "@id": "https://doi.org/10.1186/1471-2105-15-78" }, - "pmcid:PMC3999944" + "pubmed:24646301" ], "sc:description": "Operational detection and quantification of chromothripsis.", "sc:featureList": { diff --git a/data/she-ra/she-rabioschemas.jsonld b/data/she-ra/she-rabioschemas.jsonld index 7bd35f4d01877..004b1f3d27bdb 100644 --- a/data/she-ra/she-rabioschemas.jsonld +++ b/data/she-ra/she-rabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/she-ra", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Shandrina Burns", - "Eric Alm" + "Eric Alm", + "Shandrina Burns" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:20676378", diff --git a/data/shear/shearbioschemas.jsonld b/data/shear/shearbioschemas.jsonld index f6f04bbbe4005..9ae3352f59bc8 100644 --- a/data/shear/shearbioschemas.jsonld +++ b/data/shear/shearbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool for next-generation sequencing data analysis that predicts sequence variations, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis.", "sc:name": "SHEAR", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://vk.cs.umn.edu/SHEAR/" } \ No newline at end of file diff --git a/data/sheep/sheepbioschemas.jsonld b/data/sheep/sheepbioschemas.jsonld index b5559766ffa78..74f400b198f6e 100644 --- a/data/sheep/sheepbioschemas.jsonld +++ b/data/sheep/sheepbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool displays schemes of β-sheet called, draws β-sheet maps.", "sc:name": "SheeP", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=sheep" } \ No newline at end of file diff --git a/data/sherman/shermanbioschemas.jsonld b/data/sherman/shermanbioschemas.jsonld index c51a975f36d57..eec1b30dcff8a 100644 --- a/data/sherman/shermanbioschemas.jsonld +++ b/data/sherman/shermanbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Sherman", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.bioinformatics.babraham.ac.uk/projects/sherman/" } \ No newline at end of file diff --git a/data/shiftcor/shiftcorbioschemas.jsonld b/data/shiftcor/shiftcorbioschemas.jsonld index 9570524918ca3..b05bf9aa54f87 100644 --- a/data/shiftcor/shiftcorbioschemas.jsonld +++ b/data/shiftcor/shiftcorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool compares, identifies, corrects and re-referencs 1H, 13C and 15N backbone chemical shifts of peptides and proteins by comparing the observed chemical shifts with the predicted chemical shifts derived from the 3D structure (PDB corrdinates) of the protein(s)of interest.", "sc:name": "Shiftcor", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://shifty.wishartlab.com/" } \ No newline at end of file diff --git a/data/shiftor/shiftorbioschemas.jsonld b/data/shiftor/shiftorbioschemas.jsonld index fe1d09032f43d..307956ca5858f 100644 --- a/data/shiftor/shiftorbioschemas.jsonld +++ b/data/shiftor/shiftorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A program for predicting φ, ψ, χ1, and ω torsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology.", "sc:name": "SHIFTOR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://wishart.biology.ualberta.ca/shiftor/cgi-bin/shiftor_1f.py" } \ No newline at end of file diff --git a/data/shifty/shiftybioschemas.jsonld b/data/shifty/shiftybioschemas.jsonld index 3de14d760ff9d..b0ce3d7bd96da 100644 --- a/data/shifty/shiftybioschemas.jsonld +++ b/data/shifty/shiftybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "With this tool you can predict 1H, 13C, and 15N chemical shifts for your favourite protein using only its amino acid sequence as input. The technique uses dynamic programming to detect sequence homologies between your query and sequences of hundreds of previously assigned protiens in the BioMagResBank.", "sc:name": "Shifty", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://shifty.wishartlab.com/" } \ No newline at end of file diff --git a/data/shinycircos/shinycircosbioschemas.jsonld b/data/shinycircos/shinycircosbioschemas.jsonld index fb80f5d460792..10c627b494591 100644 --- a/data/shinycircos/shinycircosbioschemas.jsonld +++ b/data/shinycircos/shinycircosbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:name": "shinyCircos", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/venyao/shinyCircos" } \ No newline at end of file diff --git a/data/shinydiversity/shinydiversitybioschemas.jsonld b/data/shinydiversity/shinydiversitybioschemas.jsonld index 10f140f130152..0762491a88d2d 100644 --- a/data/shinydiversity/shinydiversitybioschemas.jsonld +++ b/data/shinydiversity/shinydiversitybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "ShinyDiversity", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://erictleung.shinyapps.io/shinydiversity" } \ No newline at end of file diff --git a/data/shinygeo/shinygeobioschemas.jsonld b/data/shinygeo/shinygeobioschemas.jsonld index 955594466b15c..bf037df6c3301 100644 --- a/data/shinygeo/shinygeobioschemas.jsonld +++ b/data/shinygeo/shinygeobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "shinyGEO", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://gdancik.github.io/shinyGEO/" } \ No newline at end of file diff --git a/data/shinyheatmap/shinyheatmapbioschemas.jsonld b/data/shinyheatmap/shinyheatmapbioschemas.jsonld index 125abbe9e3711..6ed88748925f4 100644 --- a/data/shinyheatmap/shinyheatmapbioschemas.jsonld +++ b/data/shinyheatmap/shinyheatmapbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Bohdan Khomtchouk", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC5426587", + "pubmed:28493881", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0176334" - }, - "pmcid:PMC5426587", - "pubmed:28493881" + } ], "sc:description": "Ultra fast low memory heatmap web interface for big data genomics.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "shinyheatmap", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://shinyheatmap.com/" } diff --git a/data/shinymethyl/shinymethylbioschemas.jsonld b/data/shinymethyl/shinymethylbioschemas.jsonld index 18ad79b962efc..ac520c5daf04b 100644 --- a/data/shinymethyl/shinymethylbioschemas.jsonld +++ b/data/shinymethyl/shinymethylbioschemas.jsonld @@ -9,28 +9,32 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/f1000research.4680.2", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/shinymethyl", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jean-Philippe Fortin", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ { "@id": "https://doi.org/10.12688/f1000research.4680.2" }, - "pubmed:25285208", - "pmcid:PMC4176427" + "pmcid:PMC4176427", + "pubmed:25285208" ], "sc:description": "Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.", "sc:featureList": [ { - "@id": "edam:operation_3204" + "@id": "edam:operation_2939" }, { - "@id": "edam:operation_2939" + "@id": "edam:operation_3204" } ], "sc:license": "Artistic-2.0", @@ -42,10 +46,6 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/shinyMethyl.html", "sc:version": "1.16.0" - }, - { - "@id": "https://doi.org/10.12688/f1000research.4680.2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/shinysom/shinysombioschemas.jsonld b/data/shinysom/shinysombioschemas.jsonld index 3309a7f61b69c..91937469a20d4 100644 --- a/data/shinysom/shinysombioschemas.jsonld +++ b/data/shinysom/shinysombioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0001-7356-4075", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/ShinySOM", "@type": "sc:SoftwareApplication", @@ -23,15 +27,11 @@ "sc:license": "GPL-3.0", "sc:name": "ShinySOM", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://gitlab.com/exaexa/ShinySOM" - }, - { - "@id": "http://orcid.org/0000-0001-7356-4075", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/shinytandem/shinytandembioschemas.jsonld b/data/shinytandem/shinytandembioschemas.jsonld index 5f00cb00607dc..62768865b7e09 100644 --- a/data/shinytandem/shinytandembioschemas.jsonld +++ b/data/shinytandem/shinytandembioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Frederic Fournier", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides a GUI interface for rTANDEM. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.", "sc:license": "GPL-3.0", "sc:name": "shinyTANDEM", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/shinyTANDEM.html", "sc:version": "1.12.0" diff --git a/data/shiprec/shiprecbioschemas.jsonld b/data/shiprec/shiprecbioschemas.jsonld index 538e1920ca3c2..76faff9c5a745 100644 --- a/data/shiprec/shiprecbioschemas.jsonld +++ b/data/shiprec/shiprecbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A Salmonella/Host Protein-Protein Interaction predictions browser.", "sc:name": "SHIPREC", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://sbi.imim.es/web/index.php/research/databases/shiprec" } \ No newline at end of file diff --git a/data/shorah/shorahbioschemas.jsonld b/data/shorah/shorahbioschemas.jsonld index 67c41395e58cc..9e06942101d16 100644 --- a/data/shorah/shorahbioschemas.jsonld +++ b/data/shorah/shorahbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "ShoRAH", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ozagordi/shorah" } \ No newline at end of file diff --git a/data/shore/shorebioschemas.jsonld b/data/shore/shorebioschemas.jsonld index 96742d8a73e23..4910208f952bf 100644 --- a/data/shore/shorebioschemas.jsonld +++ b/data/shore/shorebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Analysis suite for short read data.", "sc:name": "Shore", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://1001genomes.org/downloads/shore.html" } \ No newline at end of file diff --git a/data/shoremap/shoremapbioschemas.jsonld b/data/shoremap/shoremapbioschemas.jsonld index dfc7252e7d1c2..db4143aeeb493 100644 --- a/data/shoremap/shoremapbioschemas.jsonld +++ b/data/shoremap/shoremapbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/shoremap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Contact form", + "Korbinian Schneeberger", "Hequan Sun", - "Korbinian Schneeberger" + "Contact form" ], "sc:additionalType": "Suite", "sc:citation": "pubmed:19644454", @@ -21,9 +21,9 @@ "sc:license": "GPL-3.0", "sc:name": "SHOREmap", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://1001genomes.org/software/shoremap.html" } \ No newline at end of file diff --git a/data/shortread/shortreadbioschemas.jsonld b/data/shortread/shortreadbioschemas.jsonld index 159e707d84db3..e9883c18b2935 100644 --- a/data/shortread/shortreadbioschemas.jsonld +++ b/data/shortread/shortreadbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btp450", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/shortread", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ "pmcid:PMC2752612", + "pubmed:19654119", { "@id": "https://doi.org/10.1093/bioinformatics/btp450" - }, - "pubmed:19654119" + } ], "sc:description": "This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.", "sc:featureList": [ @@ -36,16 +40,12 @@ "sc:license": "Artistic-2.0", "sc:name": "ShortRead", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ShortRead.html", "sc:version": "1.32.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btp450", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/shorty/shortybioschemas.jsonld b/data/shorty/shortybioschemas.jsonld index 99df02443f022..b9551226e1587 100644 --- a/data/shorty/shortybioschemas.jsonld +++ b/data/shorty/shortybioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/shorty", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Bala Nagi Reddy M", "Anand Sagar Kothapalli", - "Chandrakanth Reddy B", - "Bala Nagi Reddy M" + "Chandrakanth Reddy B" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:19208115", diff --git a/data/shot/shotbioschemas.jsonld b/data/shot/shotbioschemas.jsonld index 2aa5b1186666e..f14fcff73dc1b 100644 --- a/data/shot/shotbioschemas.jsonld +++ b/data/shot/shotbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A web server for the classification of genomes on the basis of shared gene content or the conservation of gene order that reflects the dominant, phylogenetic signal in these genomic properties. In general, the genome trees are consistent with classical gene-based phylogenies, although some interesting exceptions indicate massive horizontal gene transfer.", "sc:name": "SHOT", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.bork.embl-heidelberg.de/~korbel/SHOT_v2/" diff --git a/data/shovill/shovillbioschemas.jsonld b/data/shovill/shovillbioschemas.jsonld index f347f95a911b0..0f8406082950d 100644 --- a/data/shovill/shovillbioschemas.jsonld +++ b/data/shovill/shovillbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-6046-610X", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/shovill", "@type": "sc:SoftwareApplication", @@ -25,21 +29,17 @@ ], "sc:url": "https://github.com/tseemann/shovill", "sc:version": [ - "1.0.7", + "1.0.1", + "1.0.2", "1.0.8", "1.0.5", - "1.0.0", - "1.0.1", - "1.0.4", "1.0.6", - "1.0.9", - "1.0.2", - "1.0.3" + "1.0.4", + "1.0.0", + "1.0.3", + "1.0.7", + "1.0.9" ] - }, - { - "@id": "https://orcid.org/0000-0001-6046-610X", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/show_emfit/show_emfitbioschemas.jsonld b/data/show_emfit/show_emfitbioschemas.jsonld index 3efc756490bdc..abd4628dd9a1c 100644 --- a/data/show_emfit/show_emfitbioschemas.jsonld +++ b/data/show_emfit/show_emfitbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool enables to fit an Hiden Markov Model on sequences using EM algorithm (learning) and to reconstruct the hidden state path using forward-backward algorithm (segmentation). When used with fixed parameters, it only produces the sequence segmentation with the forward-backward algorithm.", "sc:name": "show_emfit", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "IFB ELIXIR-FR", "sc:url": "http://genome.jouy.inra.fr/ssb/SHOW/", diff --git a/data/show_simul/show_simulbioschemas.jsonld b/data/show_simul/show_simulbioschemas.jsonld index 59e2c2dccbbf0..24d82d2dbeb70 100644 --- a/data/show_simul/show_simulbioschemas.jsonld +++ b/data/show_simul/show_simulbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This tool enables to simulate a hidden state sequence and a DNA sequence under a specified Hidden Markov Model.", "sc:name": "show_simul", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "IFB ELIXIR-FR", "sc:url": "http://genome.jouy.inra.fr/ssb/SHOW/", diff --git a/data/showalign/showalignbioschemas.jsonld b/data/showalign/showalignbioschemas.jsonld index df8c7841fa394..eed53bce54ec2 100644 --- a/data/showalign/showalignbioschemas.jsonld +++ b/data/showalign/showalignbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", "EMBOSS Contributors", + "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:description": "Display a multiple sequence alignment in pretty format.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", + "UK BBSRC", "UK MRC" ], "sc:license": "GPL-3.0", diff --git a/data/showalign_ws_husar/showalign_ws_husarbioschemas.jsonld b/data/showalign_ws_husar/showalign_ws_husarbioschemas.jsonld index d7a7a9276e357..40fbf96f0fb20 100644 --- a/data/showalign_ws_husar/showalign_ws_husarbioschemas.jsonld +++ b/data/showalign_ws_husar/showalign_ws_husarbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This tool displays an aligned set of protein or a nucleic acid sequences in a style suitable for publication.", "sc:name": "showalign WS (husar)", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/showalign.html", "sc:version": "1" diff --git a/data/showdb/showdbbioschemas.jsonld b/data/showdb/showdbbioschemas.jsonld index 4d3f65508b637..88cc2356201e7 100644 --- a/data/showdb/showdbbioschemas.jsonld +++ b/data/showdb/showdbbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "UK MRC", - "EMBOSS Contributors", - "Wellcome Trust" + "UK BBSRC", + "Wellcome Trust", + "EMBOSS Contributors" ], "sc:description": "Display information on configured databases.", "sc:funder": [ @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "showdb", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/showdb.html", "sc:version": "r6" diff --git a/data/showfeat/showfeatbioschemas.jsonld b/data/showfeat/showfeatbioschemas.jsonld index 5e901dbf66a7c..97ef77979509a 100644 --- a/data/showfeat/showfeatbioschemas.jsonld +++ b/data/showfeat/showfeatbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK BBSRC", "Wellcome Trust", "EMBOSS Contributors", - "UK MRC", - "UK BBSRC" + "UK MRC" ], "sc:description": "Display features of a sequence in pretty format.", "sc:funder": [ - "Wellcome Trust", "UK MRC", + "Wellcome Trust", "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "showfeat", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBOSS", diff --git a/data/showorf/showorfbioschemas.jsonld b/data/showorf/showorfbioschemas.jsonld index 56d180674b71e..d8a6242678858 100644 --- a/data/showorf/showorfbioschemas.jsonld +++ b/data/showorf/showorfbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", - "Wellcome Trust", "UK MRC", + "Wellcome Trust", "UK BBSRC" ], "sc:description": "Display a nucleotide sequence and translation in pretty format.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", + "UK BBSRC", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "showorf", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/showpep/showpepbioschemas.jsonld b/data/showpep/showpepbioschemas.jsonld index a93b9da412df2..423957427cf4d 100644 --- a/data/showpep/showpepbioschemas.jsonld +++ b/data/showpep/showpepbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK BBSRC", "UK MRC", - "EMBOSS Contributors" + "Wellcome Trust", + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Display protein sequences with features in pretty format.", "sc:funder": [ @@ -27,8 +27,8 @@ "sc:name": "showpep", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/showseq/showseqbioschemas.jsonld b/data/showseq/showseqbioschemas.jsonld index a96be98614b86..8e99ad051a160 100644 --- a/data/showseq/showseqbioschemas.jsonld +++ b/data/showseq/showseqbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:contributor": [ "EMBOSS Contributors", "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Display sequences with features in pretty format.", "sc:funder": [ diff --git a/data/showserver/showserverbioschemas.jsonld b/data/showserver/showserverbioschemas.jsonld index ad76ff23a5a64..e1a54c83e93a9 100644 --- a/data/showserver/showserverbioschemas.jsonld +++ b/data/showserver/showserverbioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "EMBOSS Contributors", + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:description": "Display information on configured servers.", "sc:funder": [ - "UK BBSRC", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "showserver", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/showserver.html", "sc:version": "r6" diff --git a/data/shrimpgpat/shrimpgpatbioschemas.jsonld b/data/shrimpgpat/shrimpgpatbioschemas.jsonld index 24cde78741fb7..710a986c7ea23 100644 --- a/data/shrimpgpat/shrimpgpatbioschemas.jsonld +++ b/data/shrimpgpat/shrimpgpatbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Contact form", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:24952385", "pmcid:PMC4094775", { "@id": "https://doi.org/10.1186/1471-2164-15-506" - } + }, + "pubmed:24952385" ], "sc:description": "Gene and protein annotation tool for knowledge sharing and gene discovery in shrimp.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:name": "ShrimpGPAT", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://shrimpgpat.sc.mahidol.ac.th/ShrimpGPATV2/" }, diff --git a/data/shuffleseq/shuffleseqbioschemas.jsonld b/data/shuffleseq/shuffleseqbioschemas.jsonld index d639e62c460c9..f56005f20e4b9 100644 --- a/data/shuffleseq/shuffleseqbioschemas.jsonld +++ b/data/shuffleseq/shuffleseqbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "Wellcome Trust", "UK MRC", - "UK BBSRC", "EMBOSS Contributors", - "Wellcome Trust" + "UK BBSRC" ], "sc:description": "Shuffle a set of sequences maintaining composition.", "sc:funder": [ - "UK BBSRC", "UK MRC", + "UK BBSRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "shuffleseq", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/siamcat/siamcatbioschemas.jsonld b/data/siamcat/siamcatbioschemas.jsonld index e792428e64b9a..48a16b046f965 100644 --- a/data/siamcat/siamcatbioschemas.jsonld +++ b/data/siamcat/siamcatbioschemas.jsonld @@ -39,21 +39,21 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_2269" + "@id": "edam:topic_0622" }, { "@id": "edam:topic_3174" }, { - "@id": "edam:topic_0622" + "@id": "edam:topic_2269" } ], "sc:citation": [ - "pmcid:PMC4299606", - "pubmed:25432777", { "@id": "https://doi.org/10.15252/msb.20145645" - } + }, + "pubmed:25432777", + "pmcid:PMC4299606" ], "sc:description": "Modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. It is based on LASSO models, which offer distinctive advantages for model interpretation and microbial biomarker selection and avoid overfitting issues that can arise in naive combinations of feature selection and cross-validation.", "sc:featureList": { @@ -64,8 +64,8 @@ "sc:name": "SIAMCAT", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "HD-HuB", diff --git a/data/sian/sianbioschemas.jsonld b/data/sian/sianbioschemas.jsonld index 75ca640d729f7..0b4d3fa5c8aa9 100644 --- a/data/sian/sianbioschemas.jsonld +++ b/data/sian/sianbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "SIAN", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/pogudingleb/SIAN" } \ No newline at end of file diff --git a/data/siapopr/siapoprbioschemas.jsonld b/data/siapopr/siapoprbioschemas.jsonld index 02bc852cea708..fb30d7c2da824 100644 --- a/data/siapopr/siapoprbioschemas.jsonld +++ b/data/siapopr/siapoprbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.", "sc:name": "SIApopr", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/olliemcdonald/siapopr" } \ No newline at end of file diff --git a/data/sib-blast/sib-blastbioschemas.jsonld b/data/sib-blast/sib-blastbioschemas.jsonld index 9afc7bfb71058..a4250a3c9d969 100644 --- a/data/sib-blast/sib-blastbioschemas.jsonld +++ b/data/sib-blast/sib-blastbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SIB-BLAST is a web server for improved delineation of true and false positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for sequence based homology detection.", "sc:name": "SIB-BLAST", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioserv.mps.ohio-state.edu/sib-blast/" } \ No newline at end of file diff --git a/data/sibelia/sibeliabioschemas.jsonld b/data/sibelia/sibeliabioschemas.jsonld index c74ccb72820a3..da15ecd03dcb5 100644 --- a/data/sibelia/sibeliabioschemas.jsonld +++ b/data/sibelia/sibeliabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "Sibelia", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioinf.spbau.ru/sibelia" diff --git a/data/sibmed/sibmedbioschemas.jsonld b/data/sibmed/sibmedbioschemas.jsonld index 3b95708048c9e..7c4c3bc4baf49 100644 --- a/data/sibmed/sibmedbioschemas.jsonld +++ b/data/sibmed/sibmedbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Identifiy likely genotyping errors and mutations for a sib pair in the context of multipoint mapping. Using a hidden Markov model, the program calculates the posterior probability of genotyping error or mutation for each sib-pair-marker combination, given all the available marker data, an assumed genotype-error rate, and a known genetic map.", "sc:name": "SIBMED", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://csg.sph.umich.edu/boehnke/sibmed.php", "sc:version": "1.0" diff --git a/data/sibsim4/sibsim4bioschemas.jsonld b/data/sibsim4/sibsim4bioschemas.jsonld index 4bfac6d5b4c16..dec51154567ca 100644 --- a/data/sibsim4/sibsim4bioschemas.jsonld +++ b/data/sibsim4/sibsim4bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "SIBsim4 is a modified version of the sim4 program, which is a similarity-based tool for spliced alignments, i.e. for aligning an expressed DNA sequence (EST, mRNA) with a genomic sequence.", "sc:name": "SIBsim4", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/sibsim4/" } \ No newline at end of file diff --git a/data/sictools/sictoolsbioschemas.jsonld b/data/sictools/sictoolsbioschemas.jsonld index 62e48ecbc35e0..4e6327519571c 100644 --- a/data/sictools/sictoolsbioschemas.jsonld +++ b/data/sictools/sictoolsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xiaobin Xing", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.", "sc:license": "GPL-2.0", "sc:name": "SICtools", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SICtools.html", "sc:version": "1.4.0" diff --git a/data/side-effects/side-effectsbioschemas.jsonld b/data/side-effects/side-effectsbioschemas.jsonld index 8f654d09b0936..430f6baa6ec93 100644 --- a/data/side-effects/side-effectsbioschemas.jsonld +++ b/data/side-effects/side-effectsbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/side-effects", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Aleksandar Poleksic", - "Lei Xie" + "Lei Xie", + "Aleksandar Poleksic" ], "sc:additionalType": "Library", "sc:description": "Algorithm for predicting adverse drug reactions.", "sc:name": "side-effects", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/poleksic/side-effects" } \ No newline at end of file diff --git a/data/sider/siderbioschemas.jsonld b/data/sider/siderbioschemas.jsonld index 946eb20348abb..17ca637031429 100644 --- a/data/sider/siderbioschemas.jsonld +++ b/data/sider/siderbioschemas.jsonld @@ -20,12 +20,12 @@ "sc:additionalType": "Database portal", "sc:author": "Michael Kuhn", "sc:citation": [ - "pubmed:23632385", - "pubmed:26481350", "pmcid:PMC4702794", { "@id": "https://doi.org/10.1093/nar/gkv1075" - } + }, + "pubmed:23632385", + "pubmed:26481350" ], "sc:contributor": "Peer Bork", "sc:description": "Contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations.", diff --git a/data/sidirect/sidirectbioschemas.jsonld b/data/sidirect/sidirectbioschemas.jsonld index bd05e6d1ec1b8..a42d92958a891 100644 --- a/data/sidirect/sidirectbioschemas.jsonld +++ b/data/sidirect/sidirectbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.", "sc:name": "siDirect", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://design.RNAi.jp/" } \ No newline at end of file diff --git a/data/sidr/sidrbioschemas.jsonld b/data/sidr/sidrbioschemas.jsonld index 9c1d8727c34b6..d413e3cc0940b 100644 --- a/data/sidr/sidrbioschemas.jsonld +++ b/data/sidr/sidrbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Tool to filter Next Generation Sequencing (NGS) data based on a chosen target organism. It uses data fron BLAST (or similar classifiers) to train a Decision Tree model to classify sequence data as either belonging to the target organism, or belonging to something else. This classification can be used to filter the data for later assembly.", "sc:name": "SIDR", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sidr.readthedocs.io/en/latest/" } \ No newline at end of file diff --git a/data/siena/sienabioschemas.jsonld b/data/siena/sienabioschemas.jsonld index db89080909190..8f6d9424bd097 100644 --- a/data/siena/sienabioschemas.jsonld +++ b/data/siena/sienabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Search for homologous protein binding sites structures in the Protein Data Bank. The tool allows an automated assembly and preprocessing of protein structure ensembles supporting protein flexibility and point mutation analyses as well as structure-based virtual screening.", "sc:name": "SIENA", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "University of Hamburg - Center for Bioinformatics", "sc:url": "http://proteinsplus.zbh.uni-hamburg.de/#siena" diff --git a/data/sievesifter/sievesifterbioschemas.jsonld b/data/sievesifter/sievesifterbioschemas.jsonld index 558ecbd51b0e7..d572db922daf3 100644 --- a/data/sievesifter/sievesifterbioschemas.jsonld +++ b/data/sievesifter/sievesifterbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Unlicense", "sc:name": "SieveSifter", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://sieve.fredhutch.org/viz" diff --git a/data/sift/siftbioschemas.jsonld b/data/sift/siftbioschemas.jsonld index 9926acb25891b..50df03a004f7c 100644 --- a/data/sift/siftbioschemas.jsonld +++ b/data/sift/siftbioschemas.jsonld @@ -22,32 +22,32 @@ "Desktop application" ], "sc:citation": [ - "pmcid:PMC3394338", - "pubmed:22689647", { "@id": "https://doi.org/10.1093/nar/gks539" - } + }, + "pubmed:22689647", + "pmcid:PMC3394338" ], "sc:description": "Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.", "sc:featureList": [ { - "@id": "edam:operation_0484" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_1777" + "@id": "edam:operation_0477" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_0484" }, { - "@id": "edam:operation_0477" + "@id": "edam:operation_1777" } ], "sc:license": "Other", "sc:name": "SIFT", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://sift-dna.org" diff --git a/data/sig2biopax/sig2biopaxbioschemas.jsonld b/data/sig2biopax/sig2biopaxbioschemas.jsonld index 73e309013838a..39cf5d9d31741 100644 --- a/data/sig2biopax/sig2biopaxbioschemas.jsonld +++ b/data/sig2biopax/sig2biopaxbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "A Java program that can be used to convert structured text files describing molecular interactions into the BioPAX Level 3 standard format.", "sc:name": "Sig2BioPAX", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://code.google.com/p/sig2biopax/" } \ No newline at end of file diff --git a/data/sigar/bioconda_sigar.yaml b/data/sigar/bioconda_sigar.yaml index d708fde122784..554f1805b0783 100644 --- a/data/sigar/bioconda_sigar.yaml +++ b/data/sigar/bioconda_sigar.yaml @@ -5,7 +5,6 @@ description: Facilitates the joint analysis of high-throughput data from multipl home: https://bioconductor.org/packages/3.10/bioc/html/sigaR.html identifiers: - biotools:sigar -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-sigar diff --git a/data/sigar/sigarbioschemas.jsonld b/data/sigar/sigarbioschemas.jsonld index 6bd69e08a4578..b0152bc7d7532 100644 --- a/data/sigar/sigarbioschemas.jsonld +++ b/data/sigar/sigarbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "sigaR", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sigaR.html", "sc:version": "1.22.0" diff --git a/data/sigcheck/sigcheckbioschemas.jsonld b/data/sigcheck/sigcheckbioschemas.jsonld index b62407cb85491..082020db54ead 100644 --- a/data/sigcheck/sigcheckbioschemas.jsonld +++ b/data/sigcheck/sigcheckbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Rory Stark", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "While gene signatures are frequently used to predict phenotypes, it is not always clear how optimal or meaningful they are. Based on suggestions in that paper, this tool accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata.", "sc:license": "Artistic-2.0", "sc:name": "SigCheck", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SigCheck.html", "sc:version": "2.6.0" diff --git a/data/sigcleave/sigcleavebioschemas.jsonld b/data/sigcleave/sigcleavebioschemas.jsonld index 913c94c37d29d..503925e821e13 100644 --- a/data/sigcleave/sigcleavebioschemas.jsonld +++ b/data/sigcleave/sigcleavebioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "EMBOSS Contributors", - "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "UK MRC", + "Wellcome Trust" ], "sc:description": "Report on signal cleavage sites in a protein sequence.", "sc:funder": [ @@ -27,12 +27,12 @@ "sc:name": "sigcleave", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/sigcleave.html", "sc:version": "r6" diff --git a/data/sigfuge/sigfugebioschemas.jsonld b/data/sigfuge/sigfugebioschemas.jsonld index 9d99796e1a375..4de19aae46100 100644 --- a/data/sigfuge/sigfugebioschemas.jsonld +++ b/data/sigfuge/sigfugebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "SigFuge", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SigFuge.html", diff --git a/data/siggenes/siggenesbioschemas.jsonld b/data/siggenes/siggenesbioschemas.jsonld index 4a71328f5dc8a..9d093de24ed45 100644 --- a/data/siggenes/siggenesbioschemas.jsonld +++ b/data/siggenes/siggenesbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Holger Schwender", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).", "sc:license": "GPL-2.0", "sc:name": "siggenes", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/siggenes.html", "sc:version": "1.48.0" diff --git a/data/sights/sightsbioschemas.jsonld b/data/sights/sightsbioschemas.jsonld index 70a8ba08be11e..4f3253028f0f3 100644 --- a/data/sights/sightsbioschemas.jsonld +++ b/data/sights/sightsbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Elika Garg", "sc:additionalType": [ - "Library", + "Suite", "Command-line tool", - "Suite" + "Library" ], "sc:description": "Suite of normalization methods, statistical tests, and diagnostic graphical tools for high throughput screening (HTS) assays. HTS assays use microtitre plates to screen large libraries of compounds for their biological, chemical, or biochemical activity.", "sc:license": "GPL-3.0", "sc:name": "sights", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sights.html", "sc:version": "1.0.0" diff --git a/data/sighunt/sighuntbioschemas.jsonld b/data/sighunt/sighuntbioschemas.jsonld index a73ca5981d290..a2b7f7cde696d 100644 --- a/data/sighunt/sighuntbioschemas.jsonld +++ b/data/sighunt/sighuntbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool that analyses genomic signature of a DNA sequence and outputs the score DIAS.", "sc:name": "SigHunt", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.iba.muni.cz/index-en.php?pg=research--data-analysis-tools--sighunt" } \ No newline at end of file diff --git a/data/sigma/sigmabioschemas.jsonld b/data/sigma/sigmabioschemas.jsonld index b4106569426c5..fd611a4041f8f 100644 --- a/data/sigma/sigmabioschemas.jsonld +++ b/data/sigma/sigmabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A novel sequence similarity-based approach for strain-level identification of genomes from metagenomic analysis for biosurveillance.", "sc:name": "SIGMA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sigma.omicsbio.org/" } \ No newline at end of file diff --git a/data/sigmod/sigmodbioschemas.jsonld b/data/sigmod/sigmodbioschemas.jsonld index c6734c073b665..92743bd100b2d 100644 --- a/data/sigmod/sigmodbioschemas.jsonld +++ b/data/sigmod/sigmodbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SigMod", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/YuanlongLiu/SigMod" } \ No newline at end of file diff --git a/data/signal-3l/signal-3lbioschemas.jsonld b/data/signal-3l/signal-3lbioschemas.jsonld index 64d58dc947b2e..e72f3da00e6c1 100644 --- a/data/signal-3l/signal-3lbioschemas.jsonld +++ b/data/signal-3l/signal-3lbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Signal-3L", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/" } \ No newline at end of file diff --git a/data/signal-cf/signal-cfbioschemas.jsonld b/data/signal-cf/signal-cfbioschemas.jsonld index 008d864c1a280..90af16fd25ea6 100644 --- a/data/signal-cf/signal-cfbioschemas.jsonld +++ b/data/signal-cf/signal-cfbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Automated method for predicting signal peptide sequences and their cleavage sites in eukaryotic and bacterial protein sequences", "sc:name": "Signal-CF", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/Signal-CF/" } \ No newline at end of file diff --git a/data/signalp/signalpbioschemas.jsonld b/data/signalp/signalpbioschemas.jsonld index d242d077801c2..9322f03b068f4 100644 --- a/data/signalp/signalpbioschemas.jsonld +++ b/data/signalp/signalpbioschemas.jsonld @@ -16,20 +16,20 @@ "@id": "http://orcid.org/0000-0002-9412-9643" }, "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": [ - "Henrik Nielsen", - "TN Petersen" + "TN Petersen", + "Henrik Nielsen" ], "sc:citation": "pubmed:21959131", "sc:description": "Prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms.", "sc:license": "Other", "sc:name": "SignalP", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/SignalP/", diff --git a/data/signalspider/signalspiderbioschemas.jsonld b/data/signalspider/signalspiderbioschemas.jsonld index 2ab2299f332ee..4eb0c792b1bca 100644 --- a/data/signalspider/signalspiderbioschemas.jsonld +++ b/data/signalspider/signalspiderbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/signalspider", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Script", - "Desktop application" + "Desktop application", + "Script" ], "sc:citation": "pubmed:25192742", "sc:description": "A probabilistic model for deciphering the combinatorial binding of DNA-binding proteins. The model (SignalSpider) aims at modeling and extracting patterns from multiple ChIP-Seq profiles.", "sc:name": "SignalSpider", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.cs.toronto.edu/~wkc/SignalSpider/" } \ No newline at end of file diff --git a/data/signature/signaturebioschemas.jsonld b/data/signature/signaturebioschemas.jsonld index 35fca02338cc8..7b12233392d67 100644 --- a/data/signature/signaturebioschemas.jsonld +++ b/data/signature/signaturebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Signature", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.cmbi.ru.nl/signature" } \ No newline at end of file diff --git a/data/signer/signerbioschemas.jsonld b/data/signer/signerbioschemas.jsonld index 82beba7f1e427..ee5093adcfbd8 100644 --- a/data/signer/signerbioschemas.jsonld +++ b/data/signer/signerbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Renan Valieris", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:27591080", "sc:description": "This package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variaton (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.", @@ -21,8 +21,8 @@ "sc:name": "signeR", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/signeR.html", "sc:version": "1.0.1" diff --git a/data/signor/signorbioschemas.jsonld b/data/signor/signorbioschemas.jsonld index 25914e86c9779..514b392c54fc9 100644 --- a/data/signor/signorbioschemas.jsonld +++ b/data/signor/signorbioschemas.jsonld @@ -13,27 +13,27 @@ "biotools:primaryContact": "Luana Licata", "sc:additionalType": "Database portal", "sc:author": [ + "Alberto Calderone", "Prisca Lo Surdo", - "Leonardo Briganti", - "Alberto Calderone" + "Leonardo Briganti" ], "sc:contributor": [ - "Elena Santonico", - "Livia Perfetto", "Gianni Cesareni", + "Livia Perfetto", + "Elena Santonico", "Marta Iannuccelli" ], "sc:description": "A tool collects manually-annotated logic relationships between molecules that participate in signal transduction.", "sc:license": "CC-BY-SA-4.0", "sc:name": "SIGNOR", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ - "ELIXIR-ITA-TORVERGATA", - "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" + "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy", + "ELIXIR-ITA-TORVERGATA" ], "sc:url": "http://signor.uniroma2.it/" } \ No newline at end of file diff --git a/data/sigpathway/bioconda_sigpathway.yaml b/data/sigpathway/bioconda_sigpathway.yaml index e4a5df9afa87a..7cde1e4b925a3 100644 --- a/data/sigpathway/bioconda_sigpathway.yaml +++ b/data/sigpathway/bioconda_sigpathway.yaml @@ -4,7 +4,6 @@ description: Conducts pathway analysis by calculating the NT_k and NE_k statisti home: https://bioconductor.org/packages/3.10/bioc/html/sigPathway.html identifiers: - biotools:sigpathway -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-sigpathway diff --git a/data/sigpathway/sigpathwaybioschemas.jsonld b/data/sigpathway/sigpathwaybioschemas.jsonld index f42003b9c54b5..3a883e2c81ae2 100644 --- a/data/sigpathway/sigpathwaybioschemas.jsonld +++ b/data/sigpathway/sigpathwaybioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "sigPathway", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sigPathway.html", diff --git a/data/sigprofilermatrixgenerator/sigprofilermatrixgeneratorbioschemas.jsonld b/data/sigprofilermatrixgenerator/sigprofilermatrixgeneratorbioschemas.jsonld index c610f316dc843..3f5e038bd03a6 100644 --- a/data/sigprofilermatrixgenerator/sigprofilermatrixgeneratorbioschemas.jsonld +++ b/data/sigprofilermatrixgenerator/sigprofilermatrixgeneratorbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-2-Clause", "sc:name": "SigProfilerMatrixGenerator", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/AlexandrovLab/SigProfilerMatrixGenerator" } \ No newline at end of file diff --git a/data/sigqc/sigqcbioschemas.jsonld b/data/sigqc/sigqcbioschemas.jsonld index 78cbbb34cecd0..0612ca01097a8 100644 --- a/data/sigqc/sigqcbioschemas.jsonld +++ b/data/sigqc/sigqcbioschemas.jsonld @@ -13,18 +13,18 @@ "biotools:primaryContact": "Francesca Buffa", "sc:additionalType": "Library", "sc:author": [ - "Wei-Chen Cheng", - "Andrew Dhawan", + "Alessandro Barberis", "Francesca Buffa", - "Alessandro Barberis" + "Andrew Dhawan", + "Wei-Chen Cheng" ], "sc:description": "R package enabling a streamlined methodological and standardised approach for the quality control validation of gene signatures on independent data sets.", "sc:license": "Unlicense", "sc:name": "sigQC", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://cran.r-project.org/package=sigQC", "sc:version": "0.1.21" diff --git a/data/sigreannot-mart/sigreannot-martbioschemas.jsonld b/data/sigreannot-mart/sigreannot-martbioschemas.jsonld index 32cd84651130f..2a568227196bd 100644 --- a/data/sigreannot-mart/sigreannot-martbioschemas.jsonld +++ b/data/sigreannot-mart/sigreannot-martbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Re-annotating oligo sets used for expression microarrays is essential to supply biologists with up-to-date annotations. The tool is a query environment populated with regularly updated annotations for different oligo sets. It permits easy extraction in different formats using filters. It is used to compare probe sets on different criteria, to choose the set for a given experiment to mix probe sets in order to create a new one.", "sc:name": "SigReannot-mart", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://sigreannot-mart.toulouse.inra.fr/biomart/martview/430b028768948e41c781761b26ba2cc6" } \ No newline at end of file diff --git a/data/sigsquared/sigsquaredbioschemas.jsonld b/data/sigsquared/sigsquaredbioschemas.jsonld index 04701d5d0d905..8b7f678b96f8a 100644 --- a/data/sigsquared/sigsquaredbioschemas.jsonld +++ b/data/sigsquared/sigsquaredbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "sigsquared", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sigsquared.html", "sc:version": "1.12.0" diff --git a/data/sigtree/sigtreebioschemas.jsonld b/data/sigtree/sigtreebioschemas.jsonld index e36c45d4bdaaa..9a1f8161d970b 100644 --- a/data/sigtree/sigtreebioschemas.jsonld +++ b/data/sigtree/sigtreebioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "John R. Stevens", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:28748045", + "pmcid:PMC5512180", { "@id": "https://doi.org/10.1016/j.csbj.2017.06.002" - }, - "pmcid:PMC5512180", - "pubmed:28748045" + } ], "sc:description": "Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.", "sc:featureList": { @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "SigTree", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/SigTree/index.html" }, diff --git a/data/silactor/silactorbioschemas.jsonld b/data/silactor/silactorbioschemas.jsonld index 11ff1e58ebebc..9c5f5d2065a95 100644 --- a/data/silactor/silactorbioschemas.jsonld +++ b/data/silactor/silactorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software for automated protein turnover analysis and method refinement for SILAC data.", "sc:name": "SILACtor", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://brucelab.gs.washington.edu/software.html" } \ No newline at end of file diff --git a/data/silent/silentbioschemas.jsonld b/data/silent/silentbioschemas.jsonld index 4a0558cedac29..194588185c913 100644 --- a/data/silent/silentbioschemas.jsonld +++ b/data/silent/silentbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", + "UK BBSRC", "Wellcome Trust", "UK MRC", - "UK BBSRC" + "EMBOSS Contributors" ], "sc:description": "Find restriction sites to insert (mutate) with no translation change.", "sc:funder": [ @@ -26,8 +26,8 @@ "sc:license": "GPL-3.0", "sc:name": "silent", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ diff --git a/data/silis-ptoxra/silis-ptoxrabioschemas.jsonld b/data/silis-ptoxra/silis-ptoxrabioschemas.jsonld index 6ea993d4d41b1..80d41d1cd97a5 100644 --- a/data/silis-ptoxra/silis-ptoxrabioschemas.jsonld +++ b/data/silis-ptoxra/silis-ptoxrabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "SiliS-PTOXRA", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://tomocomd.com/apps/ptoxra" } \ No newline at end of file diff --git a/data/silkdb/silkdbbioschemas.jsonld b/data/silkdb/silkdbbioschemas.jsonld index 9aaec68c642f8..e5d17c0d6bd20 100644 --- a/data/silkdb/silkdbbioschemas.jsonld +++ b/data/silkdb/silkdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently.", "sc:name": "SilkDB", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://silkworm.genomics.org.cn/" diff --git a/data/siloco/silocobioschemas.jsonld b/data/siloco/silocobioschemas.jsonld index 212c3afa9afe9..b405c151cedab 100644 --- a/data/siloco/silocobioschemas.jsonld +++ b/data/siloco/silocobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SiLoCo", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://srna-workbench.cmp.uea.ac.uk" } \ No newline at end of file diff --git a/data/silva/silvabioschemas.jsonld b/data/silva/silvabioschemas.jsonld index f417236ca279a..05cb4f503f8d5 100644 --- a/data/silva/silvabioschemas.jsonld +++ b/data/silva/silvabioschemas.jsonld @@ -15,24 +15,24 @@ "Database portal" ], "sc:contributor": [ - "Ribocon GmbH", "DFG", + "MPG", "BMBF", - "MPG" + "Ribocon GmbH" ], "sc:description": "SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).", "sc:funder": [ - "MPG", "BMBF", "Ribocon GmbH", - "DFG" + "DFG", + "MPG" ], "sc:license": "CC-BY-4.0", "sc:name": "SILVA rRNA database", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "SILVA", "sc:url": "http://www.arb-silva.de" diff --git a/data/silva_tree_viewer/silva_tree_viewerbioschemas.jsonld b/data/silva_tree_viewer/silva_tree_viewerbioschemas.jsonld index 75c0977c55d38..91b838849d222 100644 --- a/data/silva_tree_viewer/silva_tree_viewerbioschemas.jsonld +++ b/data/silva_tree_viewer/silva_tree_viewerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Interactive web browsing of the SILVA phylogenetic guide trees.", "sc:name": "SILVA Tree Viewer", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://treeviewer.mpi-bremen.de/tree_viewer_public/" diff --git a/data/silvangs/silvangsbioschemas.jsonld b/data/silvangs/silvangsbioschemas.jsonld index a652e894c2ce2..bc493c994d0b1 100644 --- a/data/silvangs/silvangsbioschemas.jsonld +++ b/data/silvangs/silvangsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:contributor": [ - "BMBF", - "DFG" + "DFG", + "BMBF" ], "sc:description": "SILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon reads from high-throughput sequencing (next-generation sequencing (NGS)) approaches based on an automatic software pipeline. It uses the SILVA rDNA databases, taxonomies, and alignments as a reference. It facilitates the classification of rDNA reads and provides a wealth of results (tables, graphs and sequence files) for download.", "sc:funder": [ @@ -22,9 +22,9 @@ ], "sc:name": "SILVAngs", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "silva", "sc:url": "https://www.arb-silva.de/ngs/", diff --git a/data/sim/simbioschemas.jsonld b/data/sim/simbioschemas.jsonld index 33a20025b5f7f..5b9b6fc1653f8 100644 --- a/data/sim/simbioschemas.jsonld +++ b/data/sim/simbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "SIM", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SIM.html", "sc:version": "1.44.0" diff --git a/data/sim1000g/sim1000gbioschemas.jsonld b/data/sim1000g/sim1000gbioschemas.jsonld index 1341cf4f77e0f..4bb862d498c00 100644 --- a/data/sim1000g/sim1000gbioschemas.jsonld +++ b/data/sim1000g/sim1000gbioschemas.jsonld @@ -19,22 +19,22 @@ "biotools:primaryContact": "Apostolos Dimitromanolakis", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:30646839", { "@id": "https://doi.org/10.1186/s12859-019-2611-1" }, - "pubmed:30646839", "pmcid:PMC6332552" ], "sc:description": "Genetic variant simulator in R for unrelated individuals and family-based designs.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_0487" }, { - "@id": "edam:operation_0488" + "@id": "edam:operation_3196" }, { - "@id": "edam:operation_0487" + "@id": "edam:operation_0488" } ], "sc:license": "GPL-3.0", diff --git a/data/sim_expasy/sim_expasybioschemas.jsonld b/data/sim_expasy/sim_expasybioschemas.jsonld index 29b516a9d739d..1f16eebb83e1b 100644 --- a/data/sim_expasy/sim_expasybioschemas.jsonld +++ b/data/sim_expasy/sim_expasybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "SIM finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence. Results can be viewed with LALNVIEW, a graphical viewer program for pairwise alignments.", "sc:name": "SIM (ExPASy)", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://web.expasy.org/sim/" diff --git a/data/simap/simapbioschemas.jsonld b/data/simap/simapbioschemas.jsonld index f45ca6c7e6425..20903be02ba9f 100644 --- a/data/simap/simapbioschemas.jsonld +++ b/data/simap/simapbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkt970", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/simap", "@type": "sc:SoftwareApplication", @@ -28,11 +32,11 @@ "@id": "edam:topic_0080" }, "sc:citation": [ + "pmcid:PMC3965014", + "pubmed:24165881", { "@id": "https://doi.org/10.1093/nar/gkt970" - }, - "pubmed:24165881", - "pmcid:PMC3965014" + } ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-7496-7578" @@ -57,10 +61,6 @@ { "@id": "http://orcid.org/0000-0002-7496-7578", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/nar/gkt970", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/simat/simatbioschemas.jsonld b/data/simat/simatbioschemas.jsonld index 20562c1f0c191..46560142fb795 100644 --- a/data/simat/simatbioschemas.jsonld +++ b/data/simat/simatbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mo R. Nezami Ranjbar", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.", "sc:license": "GPL-2.0", "sc:name": "SIMAT", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SIMAT.html", "sc:version": "1.6.1" diff --git a/data/simba-cractools/simba-cractoolsbioschemas.jsonld b/data/simba-cractools/simba-cractoolsbioschemas.jsonld index dcd689fba48b4..dde81beccee6f 100644 --- a/data/simba-cractools/simba-cractoolsbioschemas.jsonld +++ b/data/simba-cractools/simba-cractoolsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines.", "sc:name": "SimBA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://cractools.gforge.inria.fr/softwares/simba/" } \ No newline at end of file diff --git a/data/simba/simbabioschemas.jsonld b/data/simba/simbabioschemas.jsonld index 7abb1e6a529e3..3fe9639994fde 100644 --- a/data/simba/simbabioschemas.jsonld +++ b/data/simba/simbabioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-016-1344-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/simba", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Vasco A. C. Azevedo", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5249034", { "@id": "https://doi.org/10.1186/S12859-016-1344-7" }, - "pubmed:28105921" + "pubmed:28105921", + "pmcid:PMC5249034" ], "sc:description": "Web interface for managing assembly projects of bacterial genomes. It was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively.", "sc:featureList": { @@ -28,14 +32,10 @@ "sc:name": "SIMBA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://ufmg-simba.sourceforge.net/" - }, - { - "@id": "https://doi.org/10.1186/S12859-016-1344-7", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/simbindprofiles/bioconda_simbindprofiles.yaml b/data/simbindprofiles/bioconda_simbindprofiles.yaml index 6ac40c2030725..185f1c8314d5d 100644 --- a/data/simbindprofiles/bioconda_simbindprofiles.yaml +++ b/data/simbindprofiles/bioconda_simbindprofiles.yaml @@ -7,7 +7,6 @@ description: SimBindProfiles identifies common and unique binding regions in gen home: https://bioconductor.org/packages/3.10/bioc/html/SimBindProfiles.html identifiers: - biotools:simbindprofiles -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-simbindprofiles diff --git a/data/simbindprofiles/simbindprofilesbioschemas.jsonld b/data/simbindprofiles/simbindprofilesbioschemas.jsonld index bde8e1b3e58c5..5f9985d0ef7aa 100644 --- a/data/simbindprofiles/simbindprofilesbioschemas.jsonld +++ b/data/simbindprofiles/simbindprofilesbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "SimBindProfiles", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SimBindProfiles.html", "sc:version": "1.12.0" diff --git a/data/simboost/simboostbioschemas.jsonld b/data/simboost/simboostbioschemas.jsonld index cf96072d9c39d..c96dfc35ac918 100644 --- a/data/simboost/simboostbioschemas.jsonld +++ b/data/simboost/simboostbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Read-across approach for predicting drug–target binding affinities using gradient boosting machines.", "sc:name": "SimBoost", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://zenodo.org/record/164436#.W4aXJZP7TGI" } \ No newline at end of file diff --git a/data/simcal/simcalbioschemas.jsonld b/data/simcal/simcalbioschemas.jsonld index 1bcc96bc023b8..af52affa53c02 100644 --- a/data/simcal/simcalbioschemas.jsonld +++ b/data/simcal/simcalbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "LGPL-2.0", "sc:name": "SimCAL", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://sourceforge.net/projects/simcal/files/?source=navbar" } \ No newline at end of file diff --git a/data/simcep/simcepbioschemas.jsonld b/data/simcep/simcepbioschemas.jsonld index 3560b6142a84f..4cf68189e0640 100644 --- a/data/simcep/simcepbioschemas.jsonld +++ b/data/simcep/simcepbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A simulation platform for generating synthetic images of fluorescence-stained cell populations with realistic properties. Moreover, the synthetic images can be used for validating analysis methods for automated image cytometry, and for comparing their performance.", "sc:name": "SIMCEP", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.cs.tut.fi/sgn/csb/simcep/index.html" } \ No newline at end of file diff --git a/data/simcluster/simclusterbioschemas.jsonld b/data/simcluster/simclusterbioschemas.jsonld index 8014a4590da79..2b8273912093c 100644 --- a/data/simcluster/simclusterbioschemas.jsonld +++ b/data/simcluster/simclusterbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/simcluster", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:17625017", "sc:description": "A package for clustering analysis of transcript enumeration data on the simplex space.", diff --git a/data/simcomp-subcomp/simcomp-subcompbioschemas.jsonld b/data/simcomp-subcomp/simcomp-subcompbioschemas.jsonld index b56d4a0ee0d89..820f95792d725 100644 --- a/data/simcomp-subcomp/simcomp-subcompbioschemas.jsonld +++ b/data/simcomp-subcomp/simcomp-subcompbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Computes chemical similarity searches and SUBstructure matching of COMPounds (SUBCOMP) computes chemical substructure searches. Outputs are linked to the KEGG pathway and BRITE databases for interpretation of biological meanings of chemical structures.", "sc:name": "SIMCOMP-SUBCOMP", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.genome.jp/tools/simcomp/" } \ No newline at end of file diff --git a/data/simconcept/simconceptbioschemas.jsonld b/data/simconcept/simconceptbioschemas.jsonld index 733c4d090da7b..1a8cdabcae819 100644 --- a/data/simconcept/simconceptbioschemas.jsonld +++ b/data/simconcept/simconceptbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A hybrid approach by integrating a machine learning model  with a pattern identification strategy to identify individual mentions from a composite named entity.", "sc:name": "SimConcept", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/SimConcept" } \ No newline at end of file diff --git a/data/simexpr2sampledata/simexpr2sampledatabioschemas.jsonld b/data/simexpr2sampledata/simexpr2sampledatabioschemas.jsonld index bcf22a4d469f3..75a0291e5edc6 100644 --- a/data/simexpr2sampledata/simexpr2sampledatabioschemas.jsonld +++ b/data/simexpr2sampledata/simexpr2sampledatabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Methodologies for the discovery of biomarkers related to diseases using microarray data often provide limited results, due to the dataset size, the heterogeneity of the disease and the heterogeneity of experimental protocols and computational pipelines employed in the analysis. Focusing on the first two issues, a simulation schema was developed to outline advantages and drawbacks of classification and feature selection methods on a benchmark with known biomarkers.", "sc:name": "SimExpr2SampleData", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://sysbiobig.dei.unipd.it/?q=Software#SimExpr2SampleData", diff --git a/data/simextargid/simextargidbioschemas.jsonld b/data/simextargid/simextargidbioschemas.jsonld index 84db269d0b3ea..ad5bedfea4a27 100644 --- a/data/simextargid/simextargidbioschemas.jsonld +++ b/data/simextargid/simextargidbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "SimExTargId", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/JosieLHayes/simExTargId" } \ No newline at end of file diff --git a/data/simflu/simflubioschemas.jsonld b/data/simflu/simflubioschemas.jsonld index ca6fe867954a0..ab1caf25bca8d 100644 --- a/data/simflu/simflubioschemas.jsonld +++ b/data/simflu/simflubioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool performs the sequence simulations using the codon variation patterns of influenza A viruses over time.", "sc:name": "SimFlu", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://lcbb.snu.ac.kr/simflu/" } \ No newline at end of file diff --git a/data/similarpeak/similarpeakbioschemas.jsonld b/data/similarpeak/similarpeakbioschemas.jsonld index 3d7d522f24fc4..b5beb97bac7e2 100644 --- a/data/similarpeak/similarpeakbioschemas.jsonld +++ b/data/similarpeak/similarpeakbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Astrid Louise Deschenes", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package calculates metrics which assign a level of similarity between ChIP-Seq profiles.", "sc:license": "Artistic-2.0", "sc:name": "similaRpeak", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/similaRpeak.html", "sc:version": "1.6.0" diff --git a/data/simlr/simlrbioschemas.jsonld b/data/simlr/simlrbioschemas.jsonld index 22034498e56fe..5adc2fa046109 100644 --- a/data/simlr/simlrbioschemas.jsonld +++ b/data/simlr/simlrbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Novel similarity-learning framework, which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization. It can separate known subpopulations more accurately in single-cell data sets than do existing dimension reduction methods. Additionally, it demonstrates high sensitivity and accuracy on high-throughput peripheral blood mononuclear cells (PBMC) data sets generated by the GemCode single-cell.", "sc:name": "SIMLR", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SIMLR.html", diff --git a/data/simmap/simmapbioschemas.jsonld b/data/simmap/simmapbioschemas.jsonld index e9dde54117a7c..206310e4ece4f 100644 --- a/data/simmap/simmapbioschemas.jsonld +++ b/data/simmap/simmapbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "The SiMMap server statistically derives site-moiety maps which describe the relationship between moiety preferences and the physico-chemical properties of the binding site. Users input the interaction profiles of a query target protein and its docked compound.", "sc:name": "SiMMap", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://simfam.life.nctu.edu.tw/" } \ No newline at end of file diff --git a/data/simmune/simmunebioschemas.jsonld b/data/simmune/simmunebioschemas.jsonld index d6d5098fa0ff9..e3dd8db0bbbe4 100644 --- a/data/simmune/simmunebioschemas.jsonld +++ b/data/simmune/simmunebioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Suite of software tools that guides the user through the multiple hierarchical scales of cellular behavior, facilitating the generation of comprehensive models. It was originally created to simulate immunological phenomena, but it is applicable to a very broad class of cell biological models.", "sc:name": "Simmune", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.niaid.nih.gov/labsandresources/labs/aboutlabs/lsb/Pages/simmuneproject.aspx" diff --git a/data/simped/simpedbioschemas.jsonld b/data/simped/simpedbioschemas.jsonld index 6025ce178e7f3..61357e5086c54 100644 --- a/data/simped/simpedbioschemas.jsonld +++ b/data/simped/simpedbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies.", "sc:name": "SimPed", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioinformatics.org/simped/" } \ No newline at end of file diff --git a/data/simphospho/simphosphobioschemas.jsonld b/data/simphospho/simphosphobioschemas.jsonld index 9d1c669d38009..0efc37fca8e32 100644 --- a/data/simphospho/simphosphobioschemas.jsonld +++ b/data/simphospho/simphosphobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/SimPhospho", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Garry L Corthals", - "Veronika Suni" + "Veronika Suni", + "Garry L Corthals" ], "sc:additionalType": "Desktop application", "sc:description": "Software tool enabling confident phosphosite assignment.", diff --git a/data/simple_clinvar/simple_clinvarbioschemas.jsonld b/data/simple_clinvar/simple_clinvarbioschemas.jsonld index 9cd5d29a3e756..baab66f74a0ee 100644 --- a/data/simple_clinvar/simple_clinvarbioschemas.jsonld +++ b/data/simple_clinvar/simple_clinvarbioschemas.jsonld @@ -22,34 +22,34 @@ "Marie Gramm" ], "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": [ + "pubmed:31114901", + "pmcid:PMC6602488", { "@id": "https://doi.org/10.1093/NAR/GKZ411" - }, - "pubmed:31114901", - "pmcid:PMC6602488" + } ], "sc:description": "Interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database.", "sc:featureList": [ - { - "@id": "edam:operation_3436" - }, { "@id": "edam:operation_3197" }, { "@id": "edam:operation_3461" + }, + { + "@id": "edam:operation_3436" } ], "sc:license": "Unlicense", "sc:name": "Simple ClinVar", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://simple-clinvar.broadinstitute.org/" } diff --git a/data/simpleaffy/simpleaffybioschemas.jsonld b/data/simpleaffy/simpleaffybioschemas.jsonld index 2e780d02cdadd..0d6f1c1bf74a6 100644 --- a/data/simpleaffy/simpleaffybioschemas.jsonld +++ b/data/simpleaffy/simpleaffybioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "simpleaffy", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/simpleaffy.html", "sc:version": "2.50.0" diff --git a/data/simplesynteny/simplesyntenybioschemas.jsonld b/data/simplesynteny/simplesyntenybioschemas.jsonld index 5175bfd648ca3..104f6fefe18fa 100644 --- a/data/simplesynteny/simplesyntenybioschemas.jsonld +++ b/data/simplesynteny/simplesyntenybioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKW330", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/simplesynteny", "@type": "sc:SoftwareApplication", @@ -32,10 +28,14 @@ "sc:name": "SimpleSynteny", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.dveltri.com/simplesynteny/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKW330", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/simplifier/simplifierbioschemas.jsonld b/data/simplifier/simplifierbioschemas.jsonld index 9334b62ee83b7..e6fe43e75ee99 100644 --- a/data/simplifier/simplifierbioschemas.jsonld +++ b/data/simplifier/simplifierbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/simplifier", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Prof. Rommel Ramos", - "Prof. Artur Silva" + "Prof. Artur Silva", + "Prof. Rommel Ramos" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:23275695", diff --git a/data/simrare/simrarebioschemas.jsonld b/data/simrare/simrarebioschemas.jsonld index 8fca6ea4f3e79..f3c9968a06550 100644 --- a/data/simrare/simrarebioschemas.jsonld +++ b/data/simrare/simrarebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SimRare", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://code.google.com/p/simrare/" } \ No newline at end of file diff --git a/data/simreg/simregbioschemas.jsonld b/data/simreg/simregbioschemas.jsonld index 6a626c7cf2ff3..a3069d8594541 100644 --- a/data/simreg/simregbioschemas.jsonld +++ b/data/simreg/simregbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool to perform maker-set association analysis. Association analysis at gene, pathway, or exon levels (here by marker-set analysis) hold great promise in evaluating modest etiological effects of genes with GWAS or sequence data.", "sc:name": "SIMreg", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www4.stat.ncsu.edu/~jytzeng/software.php" } \ No newline at end of file diff --git a/data/simtoolbox/simtoolboxbioschemas.jsonld b/data/simtoolbox/simtoolboxbioschemas.jsonld index 3a96a48195f8a..1e6341e7ce1c0 100644 --- a/data/simtoolbox/simtoolboxbioschemas.jsonld +++ b/data/simtoolbox/simtoolboxbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An open-source, modular set of functions for MATLAB designed for processing data acquired by structured illumination microscopy.", "sc:name": "SIMToolbox", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://mmtg.fel.cvut.cz/SIMToolbox/" diff --git a/data/simug/simugbioschemas.jsonld b/data/simug/simugbioschemas.jsonld index b36a439698380..588fb49e7b4fe 100644 --- a/data/simug/simugbioschemas.jsonld +++ b/data/simug/simugbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "simuG", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/yjx1217/simuG" } \ No newline at end of file diff --git a/data/simulatorz/simulatorzbioschemas.jsonld b/data/simulatorz/simulatorzbioschemas.jsonld index 82bf580685751..6746e15050c05 100644 --- a/data/simulatorz/simulatorzbioschemas.jsonld +++ b/data/simulatorz/simulatorzbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "simulatorZ", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/simulatorZ.html", "sc:version": "1.8.0" diff --git a/data/simwalk/simwalkbioschemas.jsonld b/data/simwalk/simwalkbioschemas.jsonld index 9a9e9e3f70221..9c2088419bf2e 100644 --- a/data/simwalk/simwalkbioschemas.jsonld +++ b/data/simwalk/simwalkbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Statistical analysis for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. Uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms.", "sc:name": "SimWalk", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://watson.hgen.pitt.edu/docs/simwalk2.html", diff --git a/data/sina/sinabioschemas.jsonld b/data/sina/sinabioschemas.jsonld index f2e921d06c093..0d58b36b03612 100644 --- a/data/sina/sinabioschemas.jsonld +++ b/data/sina/sinabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "SINA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://sina.readthedocs.io", "sc:version": [ diff --git a/data/sinbase/sinbasebioschemas.jsonld b/data/sinbase/sinbasebioschemas.jsonld index bac134aa11f8a..b0f83a6520844 100644 --- a/data/sinbase/sinbasebioschemas.jsonld +++ b/data/sinbase/sinbasebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Sinbase", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://ocri-genomics.org/Sinbase/" } \ No newline at end of file diff --git a/data/sincell/sincellbioschemas.jsonld b/data/sincell/sincellbioschemas.jsonld index 417a5a9d84585..11d4562a4831c 100644 --- a/data/sincell/sincellbioschemas.jsonld +++ b/data/sincell/sincellbioschemas.jsonld @@ -13,23 +13,31 @@ "@id": "http://orcid.org/0000-0002-4832-6101", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv368", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-4403-1840", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/sincell", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "http://orcid.org/0000-0002-4832-6101" + "@id": "http://orcid.org/0000-0002-4403-1840" }, { - "@id": "http://orcid.org/0000-0002-4403-1840" + "@id": "http://orcid.org/0000-0002-4832-6101" } ], "edam:has_input": [ { - "@id": "edam:data_0863" + "@id": "edam:data_0872" }, { - "@id": "edam:data_0872" + "@id": "edam:data_0863" } ], "edam:has_output": { @@ -41,24 +49,24 @@ ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_0637" + "@id": "edam:topic_3308" }, { - "@id": "edam:topic_0099" + "@id": "edam:topic_3170" }, { - "@id": "edam:topic_3308" + "@id": "edam:topic_0099" }, { - "@id": "edam:topic_3170" + "@id": "edam:topic_0637" } ], "sc:citation": [ - "pmcid:PMC4595899", "pubmed:26099264", { "@id": "https://doi.org/10.1093/bioinformatics/btv368" - } + }, + "pmcid:PMC4595899" ], "sc:description": "This package implements a methodological toolbox allowing flexible workflows under such framework and it contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.", "sc:featureList": { @@ -67,20 +75,12 @@ "sc:license": "GPL-2.0", "sc:name": "sincell", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sincell.html", "sc:version": "1.6.0" - }, - { - "@id": "http://orcid.org/0000-0002-4403-1840", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btv368", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/singlecellexperiment/singlecellexperimentbioschemas.jsonld b/data/singlecellexperiment/singlecellexperimentbioschemas.jsonld index 11e2abc7cd92c..f4d80d83fcb26 100644 --- a/data/singlecellexperiment/singlecellexperimentbioschemas.jsonld +++ b/data/singlecellexperiment/singlecellexperimentbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "SingleCellExperiment", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html", diff --git a/data/singscore/singscorebioschemas.jsonld b/data/singscore/singscorebioschemas.jsonld index 664b7f1ecd7ae..a03a0c97d6582 100644 --- a/data/singscore/singscorebioschemas.jsonld +++ b/data/singscore/singscorebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "singscore", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/singscore.html", "sc:version": "1.0.0" diff --git a/data/singularity_hub/singularity_hubbioschemas.jsonld b/data/singularity_hub/singularity_hubbioschemas.jsonld index 9c439ef2542bf..b8cb1cb323f9b 100644 --- a/data/singularity_hub/singularity_hubbioschemas.jsonld +++ b/data/singularity_hub/singularity_hubbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers.", "sc:name": "Singularity Hub", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://singularity-hub.org/" } \ No newline at end of file diff --git a/data/sinuscor/sinuscorbioschemas.jsonld b/data/sinuscor/sinuscorbioschemas.jsonld index e90ca782097bd..7ff6aec12e9e8 100644 --- a/data/sinuscor/sinuscorbioschemas.jsonld +++ b/data/sinuscor/sinuscorbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Rhenan Bartels", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5604194", + "pubmed:28923061", { "@id": "https://doi.org/10.1186/s12938-017-0401-4" }, - "pubmed:28923061" + "pmcid:PMC5604194" ], "sc:description": "Advanced tool for heart rate variability analysis.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "SinusCor", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://rhenanbartels.github.io/SinusCor/" } diff --git a/data/sipred/sipredbioschemas.jsonld b/data/sipred/sipredbioschemas.jsonld index 094ef3db09b24..5a118bea16717 100644 --- a/data/sipred/sipredbioschemas.jsonld +++ b/data/sipred/sipredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool utilizes two layers of support vector regression (SVR) to predict the efficacy of an siRNA.", "sc:name": "siPRED", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://predictor.nchu.edu.tw/siPRED/" } \ No newline at end of file diff --git a/data/sipros/siprosbioschemas.jsonld b/data/sipros/siprosbioschemas.jsonld index 348e6ee784cec..e7e31e36568c4 100644 --- a/data/sipros/siprosbioschemas.jsonld +++ b/data/sipros/siprosbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A database-searching algorithm for peptide and protein identification in shotgun proteomics/metaproteomics.", "sc:name": "Sipros", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://siprosensemble.omicsbio.org/" } \ No newline at end of file diff --git a/data/sirah/sirahbioschemas.jsonld b/data/sirah/sirahbioschemas.jsonld index 00869829656cf..064977f47ab96 100644 --- a/data/sirah/sirahbioschemas.jsonld +++ b/data/sirah/sirahbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool comprises a set of utilities to convert all-atoms coordinates to arbitrary residue-based CG schemes, write GROMACS’ topological information at any resolution into PSF format and a VMD plugin to visualize, analyze and retrieve pseudo-atomistic information from CG trajectories performed with the force field.", "sc:name": "SIRAH", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.sirahff.com/" } \ No newline at end of file diff --git a/data/sircah/sircahbioschemas.jsonld b/data/sircah/sircahbioschemas.jsonld index 3fab6acba9d8e..8ff853bea8635 100644 --- a/data/sircah/sircahbioschemas.jsonld +++ b/data/sircah/sircahbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An application written in python that detects and visualises alternative splicing events using spliced alignments.Sircah takes as input transcript models in the GFF3 format allowing the user the flexibility to choose the sources of evidence for the use in detecting alternative transcription. Such transcript models may come from the gene prediction pipelines of genome databases or from spliced alignments of ESTs or proteins against the genome.", "sc:name": "Sircah", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.bork.embl.de/Sircah/" } \ No newline at end of file diff --git a/data/sires/siresbioschemas.jsonld b/data/sires/siresbioschemas.jsonld index 4b68bf6133984..036f899076f9e 100644 --- a/data/sires/siresbioschemas.jsonld +++ b/data/sires/siresbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/sires", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ildefonso Cases (For questions regarding IREs prediction Algorithm or the Web Server)", - "Mayka Sanchez (For questions regarding IREs)" + "Mayka Sanchez (For questions regarding IREs)", + "Ildefonso Cases (For questions regarding IREs prediction Algorithm or the Web Server)" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:20460462", "sc:description": "SIREs is an iron responsive element prediction tool. From input data, SIREs produces structure analysis, predicted RNA folds, folding energy data and overall quality flags.", "sc:name": "SIREs", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://ccbg.imppc.org/sires/index.html" } \ No newline at end of file diff --git a/data/sirius/siriusbioschemas.jsonld b/data/sirius/siriusbioschemas.jsonld index b019ebd82ea6d..e0d6bb12a810d 100644 --- a/data/sirius/siriusbioschemas.jsonld +++ b/data/sirius/siriusbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Sirius", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bio.informatik.uni-jena.de/sirius" } \ No newline at end of file diff --git a/data/sirna/sirnabioschemas.jsonld b/data/sirna/sirnabioschemas.jsonld index 909083413c1ec..385d05cdfe93d 100644 --- a/data/sirna/sirnabioschemas.jsonld +++ b/data/sirna/sirnabioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK BBSRC", "EMBOSS Contributors", - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:description": "Find siRNA duplexes in mRNA.", "sc:funder": [ - "UK MRC", "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "sirna", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/sirna.html", "sc:version": "r6" diff --git a/data/sirna_selection/sirna_selectionbioschemas.jsonld b/data/sirna_selection/sirna_selectionbioschemas.jsonld index 4989b4e36bc3e..8454439243a11 100644 --- a/data/sirna_selection/sirna_selectionbioschemas.jsonld +++ b/data/sirna_selection/sirna_selectionbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of a potential siRNA.", "sc:name": "siRNA Selection Server", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://jura.wi.mit.edu/bioc/siRNA" } \ No newline at end of file diff --git a/data/sirw/sirwbioschemas.jsonld b/data/sirw/sirwbioschemas.jsonld index a35bfea96b141..89a8e945d76fd 100644 --- a/data/sirw/sirwbioschemas.jsonld +++ b/data/sirw/sirwbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search protein/nucleotide databases with keywords and a sequence motif.", "sc:name": "SIRW", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://sirw.embl.de/" } \ No newline at end of file diff --git a/data/siseq/siseqbioschemas.jsonld b/data/siseq/siseqbioschemas.jsonld index f5bca58771eda..f2d37cdf6ccd0 100644 --- a/data/siseq/siseqbioschemas.jsonld +++ b/data/siseq/siseqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "SISEQ has been developed to extract sequence informations from large database entries and to manipulate sequence informations for input to various sequence analysis software.", "sc:name": "SISEQ", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://nsato4.c.u-tokyo.ac.jp/old/Siseq.html", "sc:version": "1.59.4" diff --git a/data/sispa/sispabioschemas.jsonld b/data/sispa/sispabioschemas.jsonld index 0c30e431a9588..4c7e5753c61f7 100644 --- a/data/sispa/sispabioschemas.jsonld +++ b/data/sispa/sispabioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Bhakti Dwivedi", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Sample Integrated Set Profile Analysis is a method designed to define sample groups with similar gene set enrichment profiles.", "sc:license": "GPL-2.0", "sc:name": "SISPA", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SISPA.html", diff --git a/data/sissrs/sissrsbioschemas.jsonld b/data/sissrs/sissrsbioschemas.jsonld index 1fc61aa7bbfdb..ae3020e79ffcc 100644 --- a/data/sissrs/sissrsbioschemas.jsonld +++ b/data/sissrs/sissrsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Produce a list of peakmaxima from aligned positions.", "sc:name": "SISSRs", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://sissrs.rajajothi.com/" } \ No newline at end of file diff --git a/data/sitar/sitarbioschemas.jsonld b/data/sitar/sitarbioschemas.jsonld index 67f687a6dd1c5..ac35685eba8ef 100644 --- a/data/sitar/sitarbioschemas.jsonld +++ b/data/sitar/sitarbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Novel tool for transcription factor binding site prediction.", "sc:name": "SiTaR", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://sbi.hki-jena.de/sitar/index.php" } \ No newline at end of file diff --git a/data/sitebinder/sitebinderbioschemas.jsonld b/data/sitebinder/sitebinderbioschemas.jsonld index 3606db93e001c..c1bbd56f03890 100644 --- a/data/sitebinder/sitebinderbioschemas.jsonld +++ b/data/sitebinder/sitebinderbioschemas.jsonld @@ -13,15 +13,15 @@ "sc:additionalType": "Web application", "sc:author": "David Sehnal", "sc:contributor": [ - "Crina-Maria Ionescu", - "Radka Svobodová Vařeková" + "Radka Svobodová Vařeková", + "Crina-Maria Ionescu" ], "sc:description": "A web based tool for superimposing and analyzing structural fragments in molecules.", "sc:name": "SiteBinder", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "Masaryk University, Brno, Czech Republic", "sc:url": "http://webchem.ncbr.muni.cz/Platform/App/SiteBinder", diff --git a/data/sitecon/siteconbioschemas.jsonld b/data/sitecon/siteconbioschemas.jsonld index 935e568a18787..22ed40688f9e8 100644 --- a/data/sitecon/siteconbioschemas.jsonld +++ b/data/sitecon/siteconbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.", "sc:name": "SITECON", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/" } \ No newline at end of file diff --git a/data/siteengine/siteenginebioschemas.jsonld b/data/siteengine/siteenginebioschemas.jsonld index f3b6e8248cf5f..bc0361af8bffc 100644 --- a/data/siteengine/siteenginebioschemas.jsonld +++ b/data/siteengine/siteenginebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool predicts regions that can potentially function as binding sites. The methods is based on recognition of geometrical and physico-chemical environments that are similar to known binding sites.", "sc:name": "SiteEngine", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/SiteEngine/" } \ No newline at end of file diff --git a/data/sitehound-web/sitehound-webbioschemas.jsonld b/data/sitehound-web/sitehound-webbioschemas.jsonld index 532bd822d1ff7..a24d9be6f82cf 100644 --- a/data/sitehound-web/sitehound-webbioschemas.jsonld +++ b/data/sitehound-web/sitehound-webbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SITEHOUND-web", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sitehound.sanchezlab.org" } \ No newline at end of file diff --git a/data/sitesampler/sitesamplerbioschemas.jsonld b/data/sitesampler/sitesamplerbioschemas.jsonld index af22c9aa76742..84bb1e912f238 100644 --- a/data/sitesampler/sitesamplerbioschemas.jsonld +++ b/data/sitesampler/sitesamplerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Java application that can sample the sites of a sequence alignment to produce replicate data sets.", "sc:name": "SiteSampler", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/simon-ho/sitesampler/" } \ No newline at end of file diff --git a/data/siteseer/siteseerbioschemas.jsonld b/data/siteseer/siteseerbioschemas.jsonld index 8f72a15f2adc7..788c8404a2195 100644 --- a/data/siteseer/siteseerbioschemas.jsonld +++ b/data/siteseer/siteseerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.", "sc:name": "SiteSeer", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://rocky.bms.umist.ac.uk/SiteSeer/" } \ No newline at end of file diff --git a/data/sitex/sitexbioschemas.jsonld b/data/sitex/sitexbioschemas.jsonld index 985064a0bc537..bc37d85e65f21 100644 --- a/data/sitex/sitexbioschemas.jsonld +++ b/data/sitex/sitexbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database that contains information on functional site amino acid positions in the exon structure of encoding gene. It contains BLAST and 3DExonScan programs. BLAST is used for searching sequence similarity between the query protein and polypeptides encoded by single exons stored in it. The 3DExonScan program is used for searching for structural similarity of the given protein with these polypeptides using superimpositions.", "sc:name": "SitEx", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www-bionet.sscc.ru/sitex/" } \ No newline at end of file diff --git a/data/sivirus/sivirusbioschemas.jsonld b/data/sivirus/sivirusbioschemas.jsonld index 7a09e89620b91..58ab5901889bf 100644 --- a/data/sivirus/sivirusbioschemas.jsonld +++ b/data/sivirus/sivirusbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "siVirus", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://sivirus.rnai.jp/" } \ No newline at end of file diff --git a/data/sixpac/sixpacbioschemas.jsonld b/data/sixpac/sixpacbioschemas.jsonld index f90a47dbdbd8b..6b453073bb729 100644 --- a/data/sixpac/sixpacbioschemas.jsonld +++ b/data/sixpac/sixpacbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Scalable search algorithm that finds synergy between pairs of physically unlinked SNPs (genome-wide) in large case-control datasets.", "sc:name": "SIXPAC", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.cs.columbia.edu/~snehitp/sixpac/", "sc:version": "1.0.2" diff --git a/data/sixpack-ebi/sixpack-ebibioschemas.jsonld b/data/sixpack-ebi/sixpack-ebibioschemas.jsonld index 66481a9e446f8..36e966e25986d 100644 --- a/data/sixpack-ebi/sixpack-ebibioschemas.jsonld +++ b/data/sixpack-ebi/sixpack-ebibioschemas.jsonld @@ -12,18 +12,18 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Web Production", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:author": [ - "Web Production", - "EMBOSS" + "EMBOSS", + "Web Production" ], "sc:description": "Six frame nucleotide sequence translation, with ORF finding. The tool reads a DNA sequence and outputs the three forward and (optionally) three reverse translations in a visual manner.", "sc:name": "sixpack (EBI)", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "EMBL-EBI", diff --git a/data/sixpack/sixpackbioschemas.jsonld b/data/sixpack/sixpackbioschemas.jsonld index 0cad2518d88d5..9c12fe218c90a 100644 --- a/data/sixpack/sixpackbioschemas.jsonld +++ b/data/sixpack/sixpackbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "Wellcome Trust", - "UK MRC", - "EMBOSS Contributors" + "UK BBSRC", + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Display a DNA sequence with 6-frame translation and ORFs.", "sc:funder": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "sixpack", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/sizepower/bioconda_sizepower.yaml b/data/sizepower/bioconda_sizepower.yaml index 1443425b5012b..0869c3af96b62 100644 --- a/data/sizepower/bioconda_sizepower.yaml +++ b/data/sizepower/bioconda_sizepower.yaml @@ -8,7 +8,6 @@ description: This package has been prepared to assist users in computing either home: https://bioconductor.org/packages/3.10/bioc/html/sizepower.html identifiers: - biotools:sizepower -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-sizepower diff --git a/data/sizepower/sizepowerbioschemas.jsonld b/data/sizepower/sizepowerbioschemas.jsonld index c3344a072de50..dfd6b161967b5 100644 --- a/data/sizepower/sizepowerbioschemas.jsonld +++ b/data/sizepower/sizepowerbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Weiliang Qiu", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice.", "sc:license": "GPL-3.0", "sc:name": "sizepower", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sizepower.html", "sc:version": "1.44.0" diff --git a/data/sizeseq/sizeseqbioschemas.jsonld b/data/sizeseq/sizeseqbioschemas.jsonld index 2b8caeeea9b69..ea73075418a0b 100644 --- a/data/sizeseq/sizeseqbioschemas.jsonld +++ b/data/sizeseq/sizeseqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "Wellcome Trust", "UK BBSRC", - "EMBOSS Contributors" + "Wellcome Trust", + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Sort sequences by size.", "sc:funder": [ "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "sizeseq", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/sizeseq.html", "sc:version": "r6" diff --git a/data/sjcount/sjcountbioschemas.jsonld b/data/sjcount/sjcountbioschemas.jsonld index 219e387f2c5ac..355de8da35a9f 100644 --- a/data/sjcount/sjcountbioschemas.jsonld +++ b/data/sjcount/sjcountbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "SJcount", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "crg.eu", diff --git a/data/skat/skatbioschemas.jsonld b/data/skat/skatbioschemas.jsonld index 1fe8ddd7fdcca..48bf9d8fcddc5 100644 --- a/data/skat/skatbioschemas.jsonld +++ b/data/skat/skatbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "SKAT", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://www.hsph.harvard.edu/skat/" diff --git a/data/skelesim/skelesimbioschemas.jsonld b/data/skelesim/skelesimbioschemas.jsonld index 57780895239da..cb04c629a4dc6 100644 --- a/data/skelesim/skelesimbioschemas.jsonld +++ b/data/skelesim/skelesimbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Allan Strand", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5161633", "pubmed:27736016", { "@id": "https://doi.org/10.1111/1755-0998.12607" - } + }, + "pmcid:PMC5161633" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-4511-3493" @@ -31,8 +31,8 @@ "sc:license": "GPL-2.0", "sc:name": "skeleSim", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/skeleSim/index.html" }, diff --git a/data/skewr/skewrbioschemas.jsonld b/data/skewr/skewrbioschemas.jsonld index d8cf6ab474d17..01872d0cf5e41 100644 --- a/data/skewr/skewrbioschemas.jsonld +++ b/data/skewr/skewrbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ryan Putney", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II. The remaining three distributions give the density of the Beta-values for these same three subsets.", "sc:license": "GPL-2.0", "sc:name": "skewr", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/skewr.html", "sc:version": "1.6.0" diff --git a/data/skink/skinkbioschemas.jsonld b/data/skink/skinkbioschemas.jsonld index 5331b2cce4d62..a73b6d1fc9847 100644 --- a/data/skink/skinkbioschemas.jsonld +++ b/data/skink/skinkbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SKINK", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://biows-inf.zdv.uni-mainz.de/skink/index.php" } \ No newline at end of file diff --git a/data/skipredundant/skipredundantbioschemas.jsonld b/data/skipredundant/skipredundantbioschemas.jsonld index 17065c5c9f4fc..cb7f8238a9ab1 100644 --- a/data/skipredundant/skipredundantbioschemas.jsonld +++ b/data/skipredundant/skipredundantbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "EMBOSS Contributors", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC", + "UK MRC" ], "sc:description": "Remove redundant sequences from an input set.", "sc:funder": [ @@ -26,8 +26,8 @@ "sc:license": "GPL-3.0", "sc:name": "skipredundant", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": [ diff --git a/data/skipseq/skipseqbioschemas.jsonld b/data/skipseq/skipseqbioschemas.jsonld index 313748c4fb9cf..e6734a05e9d9d 100644 --- a/data/skipseq/skipseqbioschemas.jsonld +++ b/data/skipseq/skipseqbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK MRC", "UK BBSRC", + "UK MRC", + "Wellcome Trust", "EMBOSS Contributors" ], "sc:description": "Read and write (return) sequences, skipping first few.", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", + "UK BBSRC", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "skipseq", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/skylign/skylignbioschemas.jsonld b/data/skylign/skylignbioschemas.jsonld index 006de5d00d04e..97926b6dabdd1 100644 --- a/data/skylign/skylignbioschemas.jsonld +++ b/data/skylign/skylignbioschemas.jsonld @@ -14,15 +14,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Skylign Support", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": [ + "pmcid:PMC3893531", + "pubmed:24410852", { "@id": "https://doi.org/10.1186/1471-2105-15-7" - }, - "pmcid:PMC3893531", - "pubmed:24410852" + } ], "sc:description": "Create informative, interactive logos representing sequence alignments and profile hidden Markov models.", "sc:featureList": { @@ -31,8 +31,8 @@ "sc:name": "Skylign", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://skylign.org/" }, diff --git a/data/skyline/skylinebioschemas.jsonld b/data/skyline/skylinebioschemas.jsonld index 5396219e031d9..3c1248a01cbdb 100644 --- a/data/skyline/skylinebioschemas.jsonld +++ b/data/skyline/skylinebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Skyline", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Skyline/begin.view" } \ No newline at end of file diff --git a/data/slalom/slalombioschemas.jsonld b/data/slalom/slalombioschemas.jsonld index 736a7aa68ef17..964a6ee3d4864 100644 --- a/data/slalom/slalombioschemas.jsonld +++ b/data/slalom/slalombioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "slalom", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/slalom.html", "sc:version": "1.2.0" diff --git a/data/slam-dunk/slam-dunkbioschemas.jsonld b/data/slam-dunk/slam-dunkbioschemas.jsonld index 5c541e503bbf9..18a0a065f9571 100644 --- a/data/slam-dunk/slam-dunkbioschemas.jsonld +++ b/data/slam-dunk/slam-dunkbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-3908-4224", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/S12859-019-2849-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/SLAM-DUNK", "@type": "sc:SoftwareApplication", @@ -20,19 +28,19 @@ ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6528199", { "@id": "https://doi.org/10.1186/S12859-019-2849-7" }, - "pmcid:PMC6528199", "pubmed:31109287" ], "sc:description": "Fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.", "sc:featureList": [ { - "@id": "edam:operation_2495" + "@id": "edam:operation_3799" }, { - "@id": "edam:operation_3799" + "@id": "edam:operation_2495" }, { "@id": "edam:operation_0484" @@ -42,18 +50,10 @@ "sc:name": "SLAM-DUNK", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://t-neumann.github.io/slamdunk" - }, - { - "@id": "https://doi.org/10.1186/S12859-019-2849-7", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0003-3908-4224", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/slda/sldabioschemas.jsonld b/data/slda/sldabioschemas.jsonld index e6fe81e78f0a0..ad3f101461143 100644 --- a/data/slda/sldabioschemas.jsonld +++ b/data/slda/sldabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software for testing the significance of Gene Pathways when signal is relatively weak. Also included is general code for running two-group L1 penalized linear discriminant analysis.", "sc:name": "sLDA", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://research.fhcrc.org/wu/en/software.html#sLDA" diff --git a/data/sleep/sleepbioschemas.jsonld b/data/sleep/sleepbioschemas.jsonld index bbba586f97d3c..d5e192a2dce1b 100644 --- a/data/sleep/sleepbioschemas.jsonld +++ b/data/sleep/sleepbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3389/fninf.2017.00060", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/sleep", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Etienne Combrisson", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:28983246", "pmcid:PMC5613192", { "@id": "https://doi.org/10.3389/fninf.2017.00060" - }, - "pubmed:28983246" + } ], "sc:description": "Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "Sleep", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://visbrain.org/sleep" + }, + { + "@id": "https://doi.org/10.3389/fninf.2017.00060", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sleepeegnet/sleepeegnetbioschemas.jsonld b/data/sleepeegnet/sleepeegnetbioschemas.jsonld index 120419ef8b70b..384e5b09b5ff2 100644 --- a/data/sleepeegnet/sleepeegnetbioschemas.jsonld +++ b/data/sleepeegnet/sleepeegnetbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-3806-8487", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/SleepEEGNet", "@type": "sc:SoftwareApplication", @@ -21,25 +17,29 @@ }, "sc:additionalType": "Script", "sc:citation": [ + "pubmed:31063501", + "pmcid:PMC6504038", { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216456" - }, - "pmcid:PMC6504038", - "pubmed:31063501" + } ], "sc:description": "Automated sleep stage scoring with sequence to sequence deep learning approach.", "sc:license": "Unlicense", "sc:name": "SleepEEGNet", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/SajadMo/SleepEEGNet" }, { "@id": "https://doi.org/10.1371/JOURNAL.PONE.0216456", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-3806-8487", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/sleuth/sleuthbioschemas.jsonld b/data/sleuth/sleuthbioschemas.jsonld index df5962bc44a97..88599819533d5 100644 --- a/data/sleuth/sleuthbioschemas.jsonld +++ b/data/sleuth/sleuthbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "sleuth", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://pachterlab.github.io/sleuth/" } \ No newline at end of file diff --git a/data/slgi/slgibioschemas.jsonld b/data/slgi/slgibioschemas.jsonld index d136d133998f7..7ef09f7893138 100644 --- a/data/slgi/slgibioschemas.jsonld +++ b/data/slgi/slgibioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nolwenn Le Meur", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "A variety of data files and functions for the analysis of genetic interactions.", "sc:license": "Artistic-2.0", "sc:name": "SLGI", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SLGI.html", "sc:version": "1.34.0" diff --git a/data/slicembler/slicemblerbioschemas.jsonld b/data/slicembler/slicemblerbioschemas.jsonld index 9914005eedf22..cd7b676ed1c82 100644 --- a/data/slicembler/slicemblerbioschemas.jsonld +++ b/data/slicembler/slicemblerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A meta-assembler designed for ultra-deep sequencing data.", "sc:name": "SLICEMBLER", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://sites.google.com/a/ucr.edu/slicembler/" diff --git a/data/slide/slidebioschemas.jsonld b/data/slide/slidebioschemas.jsonld index 2cc3b072ac0d3..08b5720303367 100644 --- a/data/slide/slidebioschemas.jsonld +++ b/data/slide/slidebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hyungwon Choi", "sc:additionalType": [ - "Web application", - "Desktop application" + "Desktop application", + "Web application" ], "sc:description": "Systems-Level Interactive Data Exploration (SLIDE) - web-based tool for interactive visualization of large-scale – omics data.", "sc:license": "BSD-2-Clause", "sc:name": "SLIDE", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/soumitag/SLIDE" diff --git a/data/slider/sliderbioschemas.jsonld b/data/slider/sliderbioschemas.jsonld index 7cdec9c48113c..96f8c69bddbeb 100644 --- a/data/slider/sliderbioschemas.jsonld +++ b/data/slider/sliderbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "AFL-3.0", "sc:name": "Slider", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.bcgsc.ca/platform/bioinfo/software/slider" diff --git a/data/slim/slimbioschemas.jsonld b/data/slim/slimbioschemas.jsonld index 94e820589ee67..3e0a861a08aad 100644 --- a/data/slim/slimbioschemas.jsonld +++ b/data/slim/slimbioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2663-2", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/SLIM", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yoann Dufresne", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6381720", "pubmed:30782112", + "pmcid:PMC6381720", { "@id": "https://doi.org/10.1186/s12859-019-2663-2" } @@ -28,10 +24,10 @@ "sc:description": "Web application for the reproducible processing of environmental DNA metabarcoding data.", "sc:featureList": [ { - "@id": "edam:operation_3185" + "@id": "edam:operation_3200" }, { - "@id": "edam:operation_3200" + "@id": "edam:operation_3185" }, { "@id": "edam:operation_0450" @@ -40,11 +36,15 @@ "sc:license": "GPL-3.0", "sc:name": "SLIM", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://trtcrd.github.io/SLIM/" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2663-2", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/slim_software/slim_softwarebioschemas.jsonld b/data/slim_software/slim_softwarebioschemas.jsonld index e3fd571c58430..846b0a8abc538 100644 --- a/data/slim_software/slim_softwarebioschemas.jsonld +++ b/data/slim_software/slim_softwarebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/SLiM_software", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Benjamin C. Haller", - "Philipp Messer" + "Philipp Messer", + "Benjamin C. Haller" ], "sc:additionalType": "Library", "sc:description": "Evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.", diff --git a/data/slimarray/slimarraybioschemas.jsonld b/data/slimarray/slimarraybioschemas.jsonld index 9ad608f3ca7ef..f027054bcae14 100644 --- a/data/slimarray/slimarraybioschemas.jsonld +++ b/data/slimarray/slimarraybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/slimarray", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:citation": "pubmed:17147785", "sc:description": "Web application that allows microarray facilities to track inventories of arrays, hybridizations performed and charge accrued for services by their customers. Beyond just tracking these separate pieces of information, it provides added value by utilizing the relationships between them. For instance, when hybridizations are entered, transactions are automatically created to deduct used microarrays from the proper inventories and appropriate charges are recorded.", diff --git a/data/slimdisc/slimdiscbioschemas.jsonld b/data/slimdisc/slimdiscbioschemas.jsonld index 035118386ab92..2f60ac2ed00dd 100644 --- a/data/slimdisc/slimdiscbioschemas.jsonld +++ b/data/slimdisc/slimdiscbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SLiMDisc", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioware.ucd.ie/~slimdisc/" } \ No newline at end of file diff --git a/data/slimfinder/slimfinderbioschemas.jsonld b/data/slimfinder/slimfinderbioschemas.jsonld index dcfc144b3b9a1..6880d8cea1df6 100644 --- a/data/slimfinder/slimfinderbioschemas.jsonld +++ b/data/slimfinder/slimfinderbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "SLiMFinder", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.slimsuite.unsw.edu.au/servers/slimfinder.php" } \ No newline at end of file diff --git a/data/slimscape/slimscapebioschemas.jsonld b/data/slimscape/slimscapebioschemas.jsonld index cd80e9801a5e7..2fd8acdd7f926 100644 --- a/data/slimscape/slimscapebioschemas.jsonld +++ b/data/slimscape/slimscapebioschemas.jsonld @@ -10,19 +10,19 @@ }, "@graph": [ { - "@id": "https://doi.org/10.12688/F1000RESEARCH.6773.1", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0003-0913-7487", + "@type": "schema:Person" }, { "@id": "https://bio.tools/slimscape", "@type": "sc:SoftwareApplication", "sc:additionalType": "Plug-in", "sc:citation": [ - "pubmed:26674271", "pmcid:PMC4670012", { "@id": "https://doi.org/10.12688/F1000RESEARCH.6773.1" - } + }, + "pubmed:26674271" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-0913-7487" @@ -33,25 +33,25 @@ "@id": "edam:operation_2492" }, { - "@id": "edam:operation_0238" + "@id": "edam:operation_3083" }, { - "@id": "edam:operation_3083" + "@id": "edam:operation_0238" } ], "sc:license": "GPL-3.0", "sc:name": "SLiMScape 3", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://apps.cytoscape.org/apps/slimscape", "sc:version": "3.0.1" }, { - "@id": "http://orcid.org/0000-0003-0913-7487", - "@type": "schema:Person" + "@id": "https://doi.org/10.12688/F1000RESEARCH.6773.1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/slimsearch/slimsearchbioschemas.jsonld b/data/slimsearch/slimsearchbioschemas.jsonld index a4cbe9281e49e..67a19d81bed2d 100644 --- a/data/slimsearch/slimsearchbioschemas.jsonld +++ b/data/slimsearch/slimsearchbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKX238", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/slimsearch", "@type": "sc:SoftwareApplication", @@ -17,20 +21,16 @@ "Suite" ], "sc:citation": [ - "pmcid:PMC5570202", + "pubmed:28387819", + "pubmed:21622654", { "@id": "https://doi.org/10.1093/NAR/GKX238" }, - "pubmed:28387819", - "pubmed:21622654" + "pmcid:PMC5570202" ], "sc:description": "Short Linear Motifs Search. Proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. Scans a motif consensus, representing the specificity determinants of a motif-binding domain, against a proteome to discover putative novel motif instances. It applies several distinct and complementary approaches exploiting the common properties of SLiMs to predict novel motifs.", "sc:name": "SLiMSearch 4", "sc:url": "http://slim.ucd.ie/slimsearch/" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKX238", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/slimsuite/slimsuitebioschemas.jsonld b/data/slimsuite/slimsuitebioschemas.jsonld index b84434b7640c5..49bde6b827fae 100644 --- a/data/slimsuite/slimsuitebioschemas.jsonld +++ b/data/slimsuite/slimsuitebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-3645-5539", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/slimsuite", "@type": "sc:SoftwareApplication", @@ -31,10 +35,6 @@ ], "sc:url": "http://slimsuite.blogspot.com.au/", "sc:version": "1" - }, - { - "@id": "http://orcid.org/0000-0002-3645-5539", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/slink/slinkbioschemas.jsonld b/data/slink/slinkbioschemas.jsonld index 9cb2d9add42d7..53b9f8ecb8198 100644 --- a/data/slink/slinkbioschemas.jsonld +++ b/data/slink/slinkbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The program does calculations by simulating genotypes at one locus given the phenotypes at another locus linked with the first locus.", "sc:name": "SLINK", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://watson.hgen.pitt.edu/docs/SLink.html" diff --git a/data/slinky/slinkybioschemas.jsonld b/data/slinky/slinkybioschemas.jsonld index 7a551c6292a10..8b812fd3e7c7e 100644 --- a/data/slinky/slinkybioschemas.jsonld +++ b/data/slinky/slinkybioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "slinky", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://bioconductor.org/packages/slinky/", "sc:version": "1.3.0" diff --git a/data/sliq/sliqbioschemas.jsonld b/data/sliq/sliqbioschemas.jsonld index 3e3670d623358..e3a10122eb1cb 100644 --- a/data/sliq/sliqbioschemas.jsonld +++ b/data/sliq/sliqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A set of simple linear inequalities derived from the geometry of contigs on the line, can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph.", "sc:name": "SLiQ", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioinformatics.rutgers.edu/Software/SLiQ/" diff --git a/data/slither/slitherbioschemas.jsonld b/data/slither/slitherbioschemas.jsonld index 590da62238547..686b34f0b7690 100644 --- a/data/slither/slitherbioschemas.jsonld +++ b/data/slither/slitherbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.", "sc:name": "SLITHER", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinfo.mc.ntu.edu.tw/slither/" } \ No newline at end of file diff --git a/data/slmsuite/slmsuitebioschemas.jsonld b/data/slmsuite/slmsuitebioschemas.jsonld index b54508a8a573a..c19315ca0d749 100644 --- a/data/slmsuite/slmsuitebioschemas.jsonld +++ b/data/slmsuite/slmsuitebioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Alberto Magi", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5490196", + "pubmed:28659129", { "@id": "https://doi.org/10.1186/S12859-017-1734-5" - }, - "pmcid:PMC5490196", - "pubmed:28659129" + } ], "sc:description": "A suite of algorithms for segmenting genomic profiles.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:name": "SLMSuite", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sourceforge.net/projects/slmsuite/" }, diff --git a/data/slncky/slnckybioschemas.jsonld b/data/slncky/slnckybioschemas.jsonld index 4eae0e0f423e2..1dbb314172860 100644 --- a/data/slncky/slnckybioschemas.jsonld +++ b/data/slncky/slnckybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "slncky", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://slncky.github.io/" } \ No newline at end of file diff --git a/data/slope/slopebioschemas.jsonld b/data/slope/slopebioschemas.jsonld index 01c7b37bceb3c..e472dcd70295d 100644 --- a/data/slope/slopebioschemas.jsonld +++ b/data/slope/slopebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Detects structural variants from targeted short DNA reads", "sc:name": "SLOPE", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www-genepi.med.utah.edu/suppl/SLOPE/index.html" diff --git a/data/slqpcr/bioconda_slqpcr.yaml b/data/slqpcr/bioconda_slqpcr.yaml index d8a9b6e318642..f97c7d4deef79 100644 --- a/data/slqpcr/bioconda_slqpcr.yaml +++ b/data/slqpcr/bioconda_slqpcr.yaml @@ -4,7 +4,6 @@ description: Functions for analysis of real-time quantitative PCR data at SIRS-L home: https://bioconductor.org/packages/3.10/bioc/html/SLqPCR.html identifiers: - biotools:slqpcr -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-slqpcr diff --git a/data/slqpcr/slqpcrbioschemas.jsonld b/data/slqpcr/slqpcrbioschemas.jsonld index 46e9054a1c283..51fe1924548ec 100644 --- a/data/slqpcr/slqpcrbioschemas.jsonld +++ b/data/slqpcr/slqpcrbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "SLqPCR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SLqPCR.html", "sc:version": "1.40.0" diff --git a/data/slr/slrbioschemas.jsonld b/data/slr/slrbioschemas.jsonld index 4b2279bdcfbe0..10af5f7746959 100644 --- a/data/slr/slrbioschemas.jsonld +++ b/data/slr/slrbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A software of fitting smoothed logistic regression with Cauchy-Normal Random Probes Effects with application to aCGH data.", "sc:name": "SLR", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://fafner.meb.ki.se/personal/yudpaw/?page_id=13" diff --git a/data/sltchemdb/sltchemdbbioschemas.jsonld b/data/sltchemdb/sltchemdbbioschemas.jsonld index ea85d352f4cd3..109c0012e554d 100644 --- a/data/sltchemdb/sltchemdbbioschemas.jsonld +++ b/data/sltchemdb/sltchemdbbioschemas.jsonld @@ -21,24 +21,24 @@ { "@id": "https://doi.org/10.1038/S41598-019-43559-Y" }, - "pubmed:31073139", - "pmcid:PMC6509116" + "pmcid:PMC6509116", + "pubmed:31073139" ], "sc:description": "Database of Chemical Constitutents of Smokeless Tobacco Products.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_2421" }, { - "@id": "edam:operation_2421" + "@id": "edam:operation_3431" } ], "sc:license": "Unlicense", "sc:name": "SLTChemDB", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bic.icmr.org.in/sltchem" }, diff --git a/data/slush-biojs/slush-biojsbioschemas.jsonld b/data/slush-biojs/slush-biojsbioschemas.jsonld index 3b9cfdded8e7c..b964091c880d4 100644 --- a/data/slush-biojs/slush-biojsbioschemas.jsonld +++ b/data/slush-biojs/slush-biojsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A slush generator for BioJS modules.", "sc:name": "slush-biojs", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": "BioJS", "sc:url": "https://github.com/biojs/slush-biojs", diff --git a/data/smagexp/smagexpbioschemas.jsonld b/data/smagexp/smagexpbioschemas.jsonld index a1de501e9695f..15a8a7fd83939 100644 --- a/data/smagexp/smagexpbioschemas.jsonld +++ b/data/smagexp/smagexpbioschemas.jsonld @@ -15,8 +15,8 @@ "biotools:primaryContact": "Samuel Blanck", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:30698691", "pmcid:PMC6354025", + "pubmed:30698691", { "@id": "https://doi.org/10.1093/gigascience/giy167" } @@ -24,10 +24,10 @@ "sc:description": "SMAGEXP (Statistical Meta-Analysis for Gene EXPression) - galaxy tool suite for transcriptomics data meta-analysis.", "sc:featureList": [ { - "@id": "edam:operation_3680" + "@id": "edam:operation_3435" }, { - "@id": "edam:operation_3435" + "@id": "edam:operation_3680" }, { "@id": "edam:operation_3223" @@ -36,9 +36,9 @@ "sc:license": "MIT", "sc:name": "SMAGEXP", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/sblanck/smagexp" }, diff --git a/data/smal/smalbioschemas.jsonld b/data/smal/smalbioschemas.jsonld index b4b4e63464288..edfa1e7e23661 100644 --- a/data/smal/smalbioschemas.jsonld +++ b/data/smal/smalbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SMAL", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://haddock6.sfsu.edu/smal/" } \ No newline at end of file diff --git a/data/smallanimalmrghifu/smallanimalmrghifubioschemas.jsonld b/data/smallanimalmrghifu/smallanimalmrghifubioschemas.jsonld index 68c7126e716f3..fac7b83b5d1b2 100644 --- a/data/smallanimalmrghifu/smallanimalmrghifubioschemas.jsonld +++ b/data/smallanimalmrghifu/smallanimalmrghifubioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s40349-016-0066-7", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-5474-8776", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/smallanimalmrghifu", "@type": "sc:SoftwareApplication", @@ -29,10 +21,10 @@ ], "sc:citation": [ "pmcid:PMC5011339", - "pubmed:27597889", { "@id": "https://doi.org/10.1186/s40349-016-0066-7" - } + }, + "pubmed:27597889" ], "sc:description": "smallAnimalMRgHIFU is a hardware and software package that includes closed-loop feedback controlled thermometry code and CAD drawings for a therapy table designed for a preclinical MRI scanner.", "sc:featureList": { @@ -42,6 +34,14 @@ "sc:name": "smallAnimalMRgHIFU", "sc:operatingSystem": "Windows", "sc:url": "https://github.com/poormanme/smallAnimalMRgHIFU" + }, + { + "@id": "https://doi.org/10.1186/s40349-016-0066-7", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0001-5474-8776", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/smallgenometools/smallgenometoolsbioschemas.jsonld b/data/smallgenometools/smallgenometoolsbioschemas.jsonld index d8029743414ce..b352088063940 100644 --- a/data/smallgenometools/smallgenometoolsbioschemas.jsonld +++ b/data/smallgenometools/smallgenometoolsbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Processing, analysis and curation of DNA sequence data. Most of these tools are genome-agnostic, with two tools specifically designed for hepatitis B virus sequence data.", "sc:name": "SmallGenomeTools", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://hvdr.bioinf.wits.ac.za/SmallGenomeTools/" } \ No newline at end of file diff --git a/data/smap/smapbioschemas.jsonld b/data/smap/smapbioschemas.jsonld index cfe461c8716f2..0c3f9800c251d 100644 --- a/data/smap/smapbioschemas.jsonld +++ b/data/smap/smapbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Robin Andersson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Functions and classes for DNA copy number profiling of array-CGH data.", "sc:license": "GPL-2.0", diff --git a/data/smarts/smartsbioschemas.jsonld b/data/smarts/smartsbioschemas.jsonld index 34275c8cab8b5..6689e326a39d8 100644 --- a/data/smarts/smartsbioschemas.jsonld +++ b/data/smarts/smartsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A method integrating static and time series data from multiple individuals to reconstruct condition specific response networks in an unsupervised way.", "sc:name": "SMARTS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://sb.cs.cmu.edu/smarts/" diff --git a/data/smartscan/smartscanbioschemas.jsonld b/data/smartscan/smartscanbioschemas.jsonld index 0773aefee9234..e813ccd226dae 100644 --- a/data/smartscan/smartscanbioschemas.jsonld +++ b/data/smartscan/smartscanbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SMARTscan", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://dsgwebwp.wustl.edu/methods-software/smartscan/" } \ No newline at end of file diff --git a/data/smirnadb/smirnadbbioschemas.jsonld b/data/smirnadb/smirnadbbioschemas.jsonld index 31a1712e67b1c..333d2db6a50fb 100644 --- a/data/smirnadb/smirnadbbioschemas.jsonld +++ b/data/smirnadb/smirnadbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "smiRNAdb is a database containing expression information for human, mouse, rat, zebrafish, worm and fruitfly small RNAs (mostly miRNAs).", "sc:name": "smirnaDB", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://www.mirz.unibas.ch/cloningprofiles/" diff --git a/data/smite/smitebioschemas.jsonld b/data/smite/smitebioschemas.jsonld index 407413ac37a55..da84bdab2304b 100644 --- a/data/smite/smitebioschemas.jsonld +++ b/data/smite/smitebioschemas.jsonld @@ -15,16 +15,16 @@ "Andrew Damon Johnston" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package builds on the Epimods framework which facilitates finding weighted subnetworks (\"modules\") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.", "sc:license": "GPL-2.0", "sc:name": "SMITE", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SMITE.html", "sc:version": "1.2.0" diff --git a/data/smmrna/smmrnabioschemas.jsonld b/data/smmrna/smmrnabioschemas.jsonld index 73203d0dcfd67..6a1d3977d8f31 100644 --- a/data/smmrna/smmrnabioschemas.jsonld +++ b/data/smmrna/smmrnabioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Raman Parkesh", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:24163098", "pmcid:PMC3965028", { "@id": "https://doi.org/10.1093/NAR/GKT976" - } + }, + "pubmed:24163098" ], "sc:description": "An interactive database, with special focus on small molecule ligands targeting RNA.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "SMMRNA", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://rdb.vlifesciences.com/homepage.php" } diff --git a/data/smog/smogbioschemas.jsonld b/data/smog/smogbioschemas.jsonld index a351fca76e3b3..d40798128bde5 100644 --- a/data/smog/smogbioschemas.jsonld +++ b/data/smog/smogbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SMOG@ctbp is a web server for structure based modeling. It is based on the GROMACS molecular dynamics package and comes with tutorials.", "sc:name": "SMOG", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://smog-server.org/" } \ No newline at end of file diff --git a/data/smoldyn/smoldynbioschemas.jsonld b/data/smoldyn/smoldynbioschemas.jsonld index 0d5e29bcb9b80..52724ca8976e7 100644 --- a/data/smoldyn/smoldynbioschemas.jsonld +++ b/data/smoldyn/smoldynbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A spatial stochastic simulator for chemical reaction networks. This tool is a computer program for cell-scale biochemical simulations.", "sc:name": "Smoldyn", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.smoldyn.org/" } \ No newline at end of file diff --git a/data/smolr/smolrbioschemas.jsonld b/data/smolr/smolrbioschemas.jsonld index 2f68d72167684..7207ea86d1b68 100644 --- a/data/smolr/smolrbioschemas.jsonld +++ b/data/smolr/smolrbioschemas.jsonld @@ -16,26 +16,26 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC6334411", + "pubmed:30646838", { "@id": "https://doi.org/10.1186/s12859-018-2578-3" - }, - "pubmed:30646838" + } ], "sc:description": "R package for visualization and analysis of single-molecule localization microscopy data.", "sc:featureList": [ { - "@id": "edam:operation_3799" + "@id": "edam:operation_3457" }, { - "@id": "edam:operation_3457" + "@id": "edam:operation_3799" } ], "sc:license": "LGPL-3.0", "sc:name": "SMoLR", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/maartenpaul/SMoLR" }, diff --git a/data/smrt/smrtbioschemas.jsonld b/data/smrt/smrtbioschemas.jsonld index 81269ee163f91..dcc2791b47ac6 100644 --- a/data/smrt/smrtbioschemas.jsonld +++ b/data/smrt/smrtbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Progressive Approach for SNP Calling and Haplotype Assembly Using SMRT Data.", "sc:name": "SMRT", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/guofeieileen/SMRT/wiki/Software" } \ No newline at end of file diff --git a/data/smrt_analysis/smrt_analysisbioschemas.jsonld b/data/smrt_analysis/smrt_analysisbioschemas.jsonld index 5d454f76af25e..c13e79c773611 100644 --- a/data/smrt_analysis/smrt_analysisbioschemas.jsonld +++ b/data/smrt_analysis/smrt_analysisbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/smrt_analysis", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", + "Suite", "Desktop application", - "Suite" + "Command-line tool" ], "sc:citation": "pubmed:22185597", "sc:description": "Abioinformatics software suite for analyzing single molecule, real-time DNA sequencing data from Pacific Biosciences.", "sc:name": "SMRT Analysis", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/" } \ No newline at end of file diff --git a/data/smrt_view/smrt_viewbioschemas.jsonld b/data/smrt_view/smrt_viewbioschemas.jsonld index 12255236fd3de..50fca4646dcbc 100644 --- a/data/smrt_view/smrt_viewbioschemas.jsonld +++ b/data/smrt_view/smrt_viewbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Open source Genome Browser that visualizes data generated by PacBio® Sequencing Systems.", "sc:name": "SMRT View", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View", diff --git a/data/sms/smsbioschemas.jsonld b/data/sms/smsbioschemas.jsonld index 4363c06dbbc13..b7a7cee6f874f 100644 --- a/data/sms/smsbioschemas.jsonld +++ b/data/sms/smsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/sms", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:10868275", "sc:description": "A collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.", diff --git a/data/smt-genetic/smt-geneticbioschemas.jsonld b/data/smt-genetic/smt-geneticbioschemas.jsonld index 3836e4eb14c65..f659e21faefe3 100644 --- a/data/smt-genetic/smt-geneticbioschemas.jsonld +++ b/data/smt-genetic/smt-geneticbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "SMT-Genetic", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://github.com/dewancse/SMT-Genetic" } \ No newline at end of file diff --git a/data/smurfs/smurfsbioschemas.jsonld b/data/smurfs/smurfsbioschemas.jsonld index 2ad9df1f15c1a..a426b344cf68f 100644 --- a/data/smurfs/smurfsbioschemas.jsonld +++ b/data/smurfs/smurfsbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "Sequential feature selection and inference using multi-variate random forests.", "sc:name": "SMuRFS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/jomayer/SMuRF" diff --git a/data/smut/smutbioschemas.jsonld b/data/smut/smutbioschemas.jsonld index 006c1b2741816..768cc98007cd4 100644 --- a/data/smut/smutbioschemas.jsonld +++ b/data/smut/smutbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-2.0", "sc:name": "SMUT", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://CRAN.R-project.org/package=SMUT" } \ No newline at end of file diff --git a/data/snakemake/snakemakebioschemas.jsonld b/data/snakemake/snakemakebioschemas.jsonld index 0299c9ee91fec..e86dc3a085dc1 100644 --- a/data/snakemake/snakemakebioschemas.jsonld +++ b/data/snakemake/snakemakebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style.", "sc:name": "Snakemake", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://snakemake.readthedocs.io/en/stable/index.html" } \ No newline at end of file diff --git a/data/snakepipes/snakepipesbioschemas.jsonld b/data/snakepipes/snakepipesbioschemas.jsonld index 5623bcf6cf219..c650f6a98df35 100644 --- a/data/snakepipes/snakepipesbioschemas.jsonld +++ b/data/snakepipes/snakepipesbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/snakePipes", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Devon P. Ryan", - "Thomas Manke" + "Thomas Manke", + "Devon P. Ryan" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:31134269", diff --git a/data/snapcgh/snapcghbioschemas.jsonld b/data/snapcgh/snapcghbioschemas.jsonld index f390f9785dc4d..c7fed15ddd254 100644 --- a/data/snapcgh/snapcghbioschemas.jsonld +++ b/data/snapcgh/snapcghbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "John Marioni", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.", "sc:license": "GPL-3.0", "sc:name": "snapCGH", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/snapCGH.html", "sc:version": "1.44.0" diff --git a/data/snapr/snaprbioschemas.jsonld b/data/snapr/snaprbioschemas.jsonld index d17bd419a8c5b..7cf894df0ade7 100644 --- a/data/snapr/snaprbioschemas.jsonld +++ b/data/snapr/snaprbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "New method for RNA-seq analysis, optimized for hundreds or even thousands of RNA-seq libraries. It reads from and writes to BAM format, automatically generates read counts, and accurately identifies viral/bacterial infections and gene fusions.", "sc:name": "SNAPR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://price.systemsbiology.org/research/snapr/" } \ No newline at end of file diff --git a/data/snipa/snipabioschemas.jsonld b/data/snipa/snipabioschemas.jsonld index 484970babb56a..d106d4ead67ae 100644 --- a/data/snipa/snipabioschemas.jsonld +++ b/data/snipa/snipabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool offers both functional annotations and linkage disequilibrium information for bi-allelic genomic variants (SNPs and SNVs). It combines LD data based on the 1000 Genomes Project with various annotation layers, such as gene annotations, phenotypic trait associations, and expression-/metabolic quantitative trait loci.", "sc:name": "SNiPA", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://snipa.helmholtz-muenchen.de/snipa/" } \ No newline at end of file diff --git a/data/snippy/snippybioschemas.jsonld b/data/snippy/snippybioschemas.jsonld index a58f6133bc17f..a68e2a4428edd 100644 --- a/data/snippy/snippybioschemas.jsonld +++ b/data/snippy/snippybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/snippy", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Australia", - "Torsten Seemann" + "Torsten Seemann", + "Australia" ], "sc:additionalType": "Command-line tool", "sc:author": "Torsten Seemann", @@ -24,8 +24,8 @@ "Linux" ], "sc:provider": [ - "University of Melbourne, Australia", - "unimelb.edu.au" + "unimelb.edu.au", + "University of Melbourne, Australia" ], "sc:url": "https://github.com/tseemann/snippy", "sc:version": "1" diff --git a/data/snipviz/snipvizbioschemas.jsonld b/data/snipviz/snipvizbioschemas.jsonld index 81ebc179bf321..2d5608cd7d634 100644 --- a/data/snipviz/snipvizbioschemas.jsonld +++ b/data/snipviz/snipvizbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Michael Riffle", "sc:additionalType": "Plug-in", "sc:citation": [ - "pubmed:25056180", - "pmcid:PMC4118779", { "@id": "https://doi.org/10.1186/1756-0500-7-468" - } + }, + "pubmed:25056180", + "pmcid:PMC4118779" ], "sc:description": "Disseminate multiple versions of related gene and protein sequences on web sites.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "Apache-2.0", "sc:name": "SnipViz", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://github.com/yeastrc/snipviz" } diff --git a/data/snm/snmbioschemas.jsonld b/data/snm/snmbioschemas.jsonld index bfc6df9a6beea..2ee00558c7f06 100644 --- a/data/snm/snmbioschemas.jsonld +++ b/data/snm/snmbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btq118", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/snm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "John D. Storey", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC2865860", + "pubmed:20363728", { "@id": "https://doi.org/10.1093/bioinformatics/btq118" }, - "pubmed:20363728" + "pmcid:PMC2865860" ], "sc:description": "Modeling strategy to normalize high-throughput genomic data, converting them into either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. This approach models all study-specific variables simultaneously in order to more accurately characterize the biological or clinical variables of interest.", "sc:featureList": { @@ -31,16 +35,12 @@ "sc:license": "GPL-3.0", "sc:name": "snm", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/snm.html", "sc:version": "1.22.0" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btq118", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/snmf/snmfbioschemas.jsonld b/data/snmf/snmfbioschemas.jsonld index 5c8a8f995a685..956955259372b 100644 --- a/data/snmf/snmfbioschemas.jsonld +++ b/data/snmf/snmfbioschemas.jsonld @@ -9,15 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1534/genetics.113.160572", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/snmf", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC3982712", { "@id": "https://doi.org/10.1534/genetics.113.160572" }, - "pmcid:PMC3982712", "pubmed:24496008" ], "sc:description": "Fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics.", @@ -31,10 +35,6 @@ "Mac" ], "sc:url": "http://membres-timc.imag.fr/Olivier.Francois/snmf/index.htm" - }, - { - "@id": "https://doi.org/10.1534/genetics.113.160572", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/snn-cliq/snn-cliqbioschemas.jsonld b/data/snn-cliq/snn-cliqbioschemas.jsonld index 4e1faa0e871e9..478ba5efd4015 100644 --- a/data/snn-cliq/snn-cliqbioschemas.jsonld +++ b/data/snn-cliq/snn-cliqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A clustering method designed for high dimensional gene expression data, e.g. single-cell transcriptome data. This method can effectively cluster individual cells based on their transcriptomes, producing clustering outputs highly in accordance with the cell type origins. It utilizes the concept of shared nearest neighbor (SNN) to define similarities between data points (cells) and achieve clustering by a graph theory-based algorithm.", "sc:name": "SNN-Cliq", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinfo.uncc.edu/SNNCliq/" } \ No newline at end of file diff --git a/data/snogps/snogpsbioschemas.jsonld b/data/snogps/snogpsbioschemas.jsonld index d10cb46e8a1a6..978cd13e87984 100644 --- a/data/snogps/snogpsbioschemas.jsonld +++ b/data/snogps/snogpsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "snoGPS allows you to search for H/ACA snoRNA (small nucleolar RNA) genes in a genomic sequence", "sc:name": "snoGPS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://lowelab.ucsc.edu/snoGPS/" diff --git a/data/snomed_ct/snomed_ctbioschemas.jsonld b/data/snomed_ct/snomed_ctbioschemas.jsonld index 9da35358187d5..c9100fc24cc51 100644 --- a/data/snomed_ct/snomed_ctbioschemas.jsonld +++ b/data/snomed_ct/snomed_ctbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/SNOMED_CT", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": "pubmed:17911793", "sc:description": "Web-based browser with comprehensive, scientifically validated clinical healthcare terminology. Enables consistent representation of clinical content in electronic health records.", "sc:license": "Other", "sc:name": "SNOMED CT", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.snomed.org/snomed-ct/five-step-briefing" } \ No newline at end of file diff --git a/data/snoopcgh/snoopcghbioschemas.jsonld b/data/snoopcgh/snoopcghbioschemas.jsonld index af7dbf79355b0..cad63d6c196fd 100644 --- a/data/snoopcgh/snoopcghbioschemas.jsonld +++ b/data/snoopcgh/snoopcghbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A desktop application for visualising and exploring comparative genomic hybridization (CGH) data. The software allows the user to interactively analyse several sets of data simultaneously. The input is based on a tab-, space- or comma-delimited format, containing series of log intensity values corresponding to one or more comparisons or samples.", "sc:name": "SnoopCGH Beta", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://snoopcgh.sourceforge.net/" } \ No newline at end of file diff --git a/data/snooper/snooperbioschemas.jsonld b/data/snooper/snooperbioschemas.jsonld index c363ee665e47a..9827df55f97cd 100644 --- a/data/snooper/snooperbioschemas.jsonld +++ b/data/snooper/snooperbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-3625-6676", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/S12864-016-3281-2", "@type": "sc:CreativeWork" @@ -23,11 +19,11 @@ "biotools:primaryContact": "Jean-Francois Spinella", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5109690", - "pubmed:27842494", { "@id": "https://doi.org/10.1186/S12864-016-3281-2" - } + }, + "pmcid:PMC5109690", + "pubmed:27842494" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-3625-6676" @@ -44,6 +40,10 @@ "Mac" ], "sc:url": "https://www.somaticsnooper.com/" + }, + { + "@id": "http://orcid.org/0000-0003-3625-6676", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/snoopy_hybrid_simulator/snoopy_hybrid_simulatorbioschemas.jsonld b/data/snoopy_hybrid_simulator/snoopy_hybrid_simulatorbioschemas.jsonld index ee61559c319b6..55786bcd1ed18 100644 --- a/data/snoopy_hybrid_simulator/snoopy_hybrid_simulatorbioschemas.jsonld +++ b/data/snoopy_hybrid_simulator/snoopy_hybrid_simulatorbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12918-017-0449-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/snoopy_hybrid_simulator", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mostafa Herajy", "sc:additionalType": "Plug-in", "sc:citation": [ + "pubmed:28754122", { "@id": "https://doi.org/10.1186/s12918-017-0449-6" }, - "pubmed:28754122", "pmcid:PMC5534078" ], "sc:description": "Tool to construct and simulate hybrid biological models.", @@ -36,6 +32,10 @@ "Linux" ], "sc:url": "http://www-dssz.informatik.tu-cottbus.de/DSSZ/Software/Snoopy" + }, + { + "@id": "https://doi.org/10.1186/s12918-017-0449-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/snopy/snopybioschemas.jsonld b/data/snopy/snopybioschemas.jsonld index 50d66d7a4a03b..fc1be150b32ce 100644 --- a/data/snopy/snopybioschemas.jsonld +++ b/data/snopy/snopybioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:24148649", { "@id": "https://doi.org/10.1186/1756-0500-6-426" }, - "pmcid:PMC4015994", - "pubmed:24148649" + "pmcid:PMC4015994" ], "sc:description": "Small nucleolar RNA orthological gene database.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:name": "snOPY", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://snoopy.med.miyazaki-u.ac.jp/" }, diff --git a/data/snoscan/snoscanbioschemas.jsonld b/data/snoscan/snoscanbioschemas.jsonld index 2cfefedbdd162..dfb9a0ecdff10 100644 --- a/data/snoscan/snoscanbioschemas.jsonld +++ b/data/snoscan/snoscanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Snoscan allows you to search for C/D box methylation guide snoRNA (small nucleolar RNA) genes in a genomic sequence", "sc:name": "snoscan", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://lowelab.ucsc.edu/snoscan/" } \ No newline at end of file diff --git a/data/snostrip/snostripbioschemas.jsonld b/data/snostrip/snostripbioschemas.jsonld index dc05820beee21..9b8d57e1d9353 100644 --- a/data/snostrip/snostripbioschemas.jsonld +++ b/data/snostrip/snostripbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A free web server for the analysis of small nucleolar RNAs (snoRNAs) in fungi genomes.", "sc:name": "snoStrip", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://snostrip.bioinf.uni-leipzig.de/index.py" } \ No newline at end of file diff --git a/data/snovault/snovaultbioschemas.jsonld b/data/snovault/snovaultbioschemas.jsonld index ab30ec99d0149..4adf2877d7370 100644 --- a/data/snovault/snovaultbioschemas.jsonld +++ b/data/snovault/snovaultbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata.", "sc:name": "SnoVault", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/ENCODE-DCC/snovault/" } \ No newline at end of file diff --git a/data/snow/snowbioschemas.jsonld b/data/snow/snowbioschemas.jsonld index 30e8917ae90dc..2e466c9b902af 100644 --- a/data/snow/snowbioschemas.jsonld +++ b/data/snow/snowbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SNOW is a web-based tool for the statistical analysis of protein-protein interaction networks. Input is a collection of protein or gene indentifiers onto the interactome scaffold. Output includes statistical significance estimates.", "sc:name": "SNOW", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://snow.bioinfo.cipf.es" } \ No newline at end of file diff --git a/data/snp2sim/snp2simbioschemas.jsonld b/data/snp2sim/snp2simbioschemas.jsonld index ea058564df74b..9804ef82ac2f2 100644 --- a/data/snp2sim/snp2simbioschemas.jsonld +++ b/data/snp2sim/snp2simbioschemas.jsonld @@ -9,29 +9,25 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2774-9", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/SNP2SIM", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Matthew McCoy", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:30943891", + "pmcid:PMC6448223", { "@id": "https://doi.org/10.1186/s12859-019-2774-9" - }, - "pubmed:30943891", - "pmcid:PMC6448223" + } ], "sc:description": "Modular workflow for standardizing molecular simulation and functional analysis of protein variants.", "sc:featureList": [ { - "@id": "edam:operation_2476" + "@id": "edam:operation_3216" }, { - "@id": "edam:operation_3216" + "@id": "edam:operation_2476" }, { "@id": "edam:operation_0478" @@ -43,6 +39,10 @@ "Mac" ], "sc:url": "https://github.com/mccoymd/SNP2SIM" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2774-9", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/snp2tfbs/snp2tfbsbioschemas.jsonld b/data/snp2tfbs/snp2tfbsbioschemas.jsonld index a99d388a6c93e..87e8907441e4e 100644 --- a/data/snp2tfbs/snp2tfbsbioschemas.jsonld +++ b/data/snp2tfbs/snp2tfbsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The resource is based on a new 'in silico' approach for identifying regulatory variants. The transcription factor (TF) binding score is computed in both the reference (hg19) and alternate human genome assemblies. The alternate genome assembly is generated by incorporating the alternate allele of common genetic variants (AF>=0.001) from the 1000 Genomes Project. Interesting candidate variants are those SNPs that disrupt, create or change the TF binding score/affinity between the two genomes.", "sc:name": "SNP2TFBS", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://ccg.vital-it.ch/snp2tfbs/" } \ No newline at end of file diff --git a/data/snp_cutter/snp_cutterbioschemas.jsonld b/data/snp_cutter/snp_cutterbioschemas.jsonld index 66208fa36f786..0874f87441cc5 100644 --- a/data/snp_cutter/snp_cutterbioschemas.jsonld +++ b/data/snp_cutter/snp_cutterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "SNP Cutter", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm" } \ No newline at end of file diff --git a/data/snpadomain/snpadomainbioschemas.jsonld b/data/snpadomain/snpadomainbioschemas.jsonld index 2fbd9cd4a503b..6b69ee0f0886e 100644 --- a/data/snpadomain/snpadomainbioschemas.jsonld +++ b/data/snpadomain/snpadomainbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented.", "sc:name": "SNPaDomain", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://snpnavigator.net/" diff --git a/data/snpassoc/snpassocbioschemas.jsonld b/data/snpassoc/snpassocbioschemas.jsonld index 55f6fcc3fe4f9..58ca648886e37 100644 --- a/data/snpassoc/snpassocbioschemas.jsonld +++ b/data/snpassoc/snpassocbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SNPAssoc", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinfo.iconcologia.net/es/SNPassoc" } \ No newline at end of file diff --git a/data/snpator/snpatorbioschemas.jsonld b/data/snpator/snpatorbioschemas.jsonld index d126a97f9d2ec..895e6c7898256 100644 --- a/data/snpator/snpatorbioschemas.jsonld +++ b/data/snpator/snpatorbioschemas.jsonld @@ -12,12 +12,12 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:author": [ - "Pep Alegre", - "Arcadi Navarro Cuartiellas", - "José Marí­a Heredia Genestar", - "Angel Carreño Torres", "Carlos Morcillo Suarez", + "Arcadi Navarro Cuartiellas", + "Pep Alegre", "Ricard Sangrós", + "Angel Carreño Torres", + "José Marí­a Heredia Genestar", "Tere Páramo Prieto" ], "sc:citation": "pubmed:18515823", @@ -29,8 +29,8 @@ "sc:name": "SNPator", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "upf.edu", diff --git a/data/snpbox/snpboxbioschemas.jsonld b/data/snpbox/snpboxbioschemas.jsonld index f4e77e50def33..c9ed138e9fb0b 100644 --- a/data/snpbox/snpboxbioschemas.jsonld +++ b/data/snpbox/snpboxbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed results for all Ensembl exons are also available on the server.", "sc:name": "SNPbox", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.SNPbox.org" diff --git a/data/snpchip/snpchipbioschemas.jsonld b/data/snpchip/snpchipbioschemas.jsonld index 6f9e10cb3187f..4d59b4aae9246 100644 --- a/data/snpchip/snpchipbioschemas.jsonld +++ b/data/snpchip/snpchipbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "SNPchip", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SNPchip.html", "sc:version": "2.20.0" diff --git a/data/snpdb/snpdbbioschemas.jsonld b/data/snpdb/snpdbbioschemas.jsonld index 4bcac957c739c..f7e1cfddc0880 100644 --- a/data/snpdb/snpdbbioschemas.jsonld +++ b/data/snpdb/snpdbbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/29.1.308", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/snpdb", "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC29783", - "pubmed:11125122", { "@id": "https://doi.org/10.1093/nar/29.1.308" - } + }, + "pubmed:11125122", + "pmcid:PMC29783" ], "sc:description": "Database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants.", "sc:featureList": { @@ -31,11 +27,15 @@ "sc:license": "Other", "sc:name": "SNPdb", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://www.ncbi.nlm.nih.gov/snp" + }, + { + "@id": "https://doi.org/10.1093/nar/29.1.308", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/snpdelscore/snpdelscorebioschemas.jsonld b/data/snpdelscore/snpdelscorebioschemas.jsonld index e6567464db217..dbfe9ef73b4c1 100644 --- a/data/snpdelscore/snpdelscorebioschemas.jsonld +++ b/data/snpdelscore/snpdelscorebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Displays pre-compute deleterious effects of noncoding variants using a large panel of currently available methods and summarizes this information in an interactive, easy to use website.", "sc:name": "SNPDelScore", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://www.ncbi.nlm.nih.gov/research/snpdelscore/" } \ No newline at end of file diff --git a/data/snpduo/snpduobioschemas.jsonld b/data/snpduo/snpduobioschemas.jsonld index e4f0e66e3b9a8..397129fa28beb 100644 --- a/data/snpduo/snpduobioschemas.jsonld +++ b/data/snpduo/snpduobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SNPduo", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://pevsnerlab.kennedykrieger.org/SNPduo/" } \ No newline at end of file diff --git a/data/snpedia/snpediabioschemas.jsonld b/data/snpedia/snpediabioschemas.jsonld index b9c75a9db9901..7ec62274d8bdc 100644 --- a/data/snpedia/snpediabioschemas.jsonld +++ b/data/snpedia/snpediabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA.", "sc:name": "SNPedia", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.snpedia.com/index.php/SNPedia" } \ No newline at end of file diff --git a/data/snpediar/snpediarbioschemas.jsonld b/data/snpediar/snpediarbioschemas.jsonld index ecebcdf0127a8..80198cca06766 100644 --- a/data/snpediar/snpediarbioschemas.jsonld +++ b/data/snpediar/snpediarbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "SNPediaR", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SNPediaR.html", diff --git a/data/snpeff/snpeffbioschemas.jsonld b/data/snpeff/snpeffbioschemas.jsonld index 694c67dbf489b..0297ab5d744e9 100644 --- a/data/snpeff/snpeffbioschemas.jsonld +++ b/data/snpeff/snpeffbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).", "sc:name": "snpEff", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://snpeff.sourceforge.net/" } \ No newline at end of file diff --git a/data/snpeffect/snpeffectbioschemas.jsonld b/data/snpeffect/snpeffectbioschemas.jsonld index 7cbbb7716d084..86a089b99235e 100644 --- a/data/snpeffect/snpeffectbioschemas.jsonld +++ b/data/snpeffect/snpeffectbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "This database uses sequence- and structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins.", "sc:name": "SNPeffect", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://snpeffect.switchlab.org/" } \ No newline at end of file diff --git a/data/snpgenesets/snpgenesetsbioschemas.jsonld b/data/snpgenesets/snpgenesetsbioschemas.jsonld index 50504cc8370b2..22f7bcdef0545 100644 --- a/data/snpgenesets/snpgenesetsbioschemas.jsonld +++ b/data/snpgenesets/snpgenesetsbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1534/g3.116.034694", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/snpgenesets", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hao Mei", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:27807048", { "@id": "https://doi.org/10.1534/g3.116.034694" }, - "pubmed:27807048", "pmcid:PMC5144977" ], "sc:description": "snpGeneSets is a package that simplifies annotation and analysis of GWS results. The package integrates local copies of knowledge bases for SNPs, genes, and gene sets, and implements wrapper functions in the R language to enable transparent access to low-level databases for efficient annotation of large genomic data.", @@ -34,6 +30,10 @@ "sc:operatingSystem": "Windows", "sc:url": "https://www.umc.edu/SoPH/Departments-and-Faculty/Data-Science/Research/Services/Software.html", "sc:version": "V1.12" + }, + { + "@id": "https://doi.org/10.1534/g3.116.034694", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/snpgenie/snpgeniebioschemas.jsonld b/data/snpgenie/snpgeniebioschemas.jsonld index dc1e33eb60f35..e9cb4fd9d5d74 100644 --- a/data/snpgenie/snpgeniebioschemas.jsonld +++ b/data/snpgenie/snpgeniebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SNPGenie", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/hugheslab/snpgenie" } \ No newline at end of file diff --git a/data/snphood/snphoodbioschemas.jsonld b/data/snphood/snphoodbioschemas.jsonld index e76b4b9320caa..75a16c25142fd 100644 --- a/data/snphood/snphoodbioschemas.jsonld +++ b/data/snphood/snphoodbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "SNPhood", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SNPhood.html", diff --git a/data/snphub/snphubbioschemas.jsonld b/data/snphub/snphubbioschemas.jsonld index 51f5afcaf9bfe..85f9d6db5e56c 100644 --- a/data/snphub/snphubbioschemas.jsonld +++ b/data/snphub/snphubbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "SnpHub", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://guoweilong.github.io/SnpHub/" } \ No newline at end of file diff --git a/data/snpinfo/snpinfobioschemas.jsonld b/data/snpinfo/snpinfobioschemas.jsonld index b49a2406a6424..6a5f081abbfd4 100644 --- a/data/snpinfo/snpinfobioschemas.jsonld +++ b/data/snpinfo/snpinfobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SNPinfo", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://snpinfo.niehs.nih.gov/" } \ No newline at end of file diff --git a/data/snpitty/snpittybioschemas.jsonld b/data/snpitty/snpittybioschemas.jsonld index cc7460a3c948c..ce785ab870771 100644 --- a/data/snpitty/snpittybioschemas.jsonld +++ b/data/snpitty/snpittybioschemas.jsonld @@ -16,13 +16,13 @@ "sc:description": "Visualization tool for displaying loss-of-heterozygosity and/or allelic imbalance (LOH/AI) by making use of VCF files originating from primarily diagnostic panels, although it works on any input.", "sc:name": "SNPitty", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "Department of Urology, Erasmus University Medical Center, Rotterdam,", "Cancer Computational Biology Center", + "Department of Urology, Erasmus University Medical Center, Rotterdam,", "Erasmus MC" ], "sc:url": "https://ccbc.erasmusmc.nl/" diff --git a/data/snplice/snplicebioschemas.jsonld b/data/snplice/snplicebioschemas.jsonld index 535a0b00c672e..d63cf188ccdb8 100644 --- a/data/snplice/snplicebioschemas.jsonld +++ b/data/snplice/snplicebioschemas.jsonld @@ -14,10 +14,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4393518", { "@id": "https://doi.org/10.1093/bioinformatics/btu804" }, - "pmcid:PMC4393518", "pubmed:25481010" ], "sc:description": "A software tool to find and evaluate the co-occurrence of single-nucleotide-polymorphisms (SNP) and altered splicing in next-gen mRNA sequence reads.", diff --git a/data/snpls/snplsbioschemas.jsonld b/data/snpls/snplsbioschemas.jsonld index 141f9a11d6923..b007b18be6f88 100644 --- a/data/snpls/snplsbioschemas.jsonld +++ b/data/snpls/snplsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A package to integrate pairwise gene expression and drug response data as well as a gene interaction network for identifying joint gene-drug co-modules in a regression manner.", "sc:name": "SNPLS", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://page.amss.ac.cn/shihua.zhang/software.html" } \ No newline at end of file diff --git a/data/snpnexus/snpnexusbioschemas.jsonld b/data/snpnexus/snpnexusbioschemas.jsonld index 885346bfcbf5a..377c7d0b9eca0 100644 --- a/data/snpnexus/snpnexusbioschemas.jsonld +++ b/data/snpnexus/snpnexusbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Webserver allows for significance assessment of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models so to identify phenotypically important variants. Other variations have been included like insertions/deletions, block substitutions, etc.", "sc:name": "SNPnexus", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.snp-nexus.org" } \ No newline at end of file diff --git a/data/snprank/snprankbioschemas.jsonld b/data/snprank/snprankbioschemas.jsonld index 7881c4092b664..b5ed518b28584 100644 --- a/data/snprank/snprankbioschemas.jsonld +++ b/data/snprank/snprankbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SNPrank", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://insilico.utulsa.edu/snprank.php", "sc:version": "0.1.0" diff --git a/data/snprelate/snprelatebioschemas.jsonld b/data/snprelate/snprelatebioschemas.jsonld index 4c2bb03b1cb2a..23ff765b67728 100644 --- a/data/snprelate/snprelatebioschemas.jsonld +++ b/data/snprelate/snprelatebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-1390-0708", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/bioinformatics/bts606", "@type": "sc:CreativeWork" @@ -20,15 +24,15 @@ "@id": "http://orcid.org/0000-0002-1390-0708" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pmcid:PMC3519454", + "pubmed:23060615", { "@id": "https://doi.org/10.1093/bioinformatics/bts606" }, - "pubmed:23060615" + "pmcid:PMC3519454" ], "sc:description": "Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits.", "sc:featureList": [ @@ -42,16 +46,12 @@ "sc:license": "GPL-3.0", "sc:name": "SNPRelate", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SNPRelate.html", "sc:version": "1.8.0" - }, - { - "@id": "http://orcid.org/0000-0002-1390-0708", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/snps_and_go/snps_and_gobioschemas.jsonld b/data/snps_and_go/snps_and_gobioschemas.jsonld index b8ac89fc69598..9ac91e226e2c8 100644 --- a/data/snps_and_go/snps_and_gobioschemas.jsonld +++ b/data/snps_and_go/snps_and_gobioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/snps_and_go", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Pier Luigi Martelli", - "Rita Casadio" + "Rita Casadio", + "Pier Luigi Martelli" ], "sc:additionalType": "Web application", "sc:description": "A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans.s.", diff --git a/data/snpscan/snpscanbioschemas.jsonld b/data/snpscan/snpscanbioschemas.jsonld index 3f3fafd5b91cf..70d5064d8dbc6 100644 --- a/data/snpscan/snpscanbioschemas.jsonld +++ b/data/snpscan/snpscanbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A web-accessible tool for the analysis of single nucleotide polymorphism (SNP) array data.", "sc:name": "SNPscan", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://pevsnerlab.kennedykrieger.org/php/?q=node/101" diff --git a/data/snpspd/snpspdbioschemas.jsonld b/data/snpspd/snpspdbioschemas.jsonld index aa8943fb1af53..58cc43e74f12e 100644 --- a/data/snpspd/snpspdbioschemas.jsonld +++ b/data/snpspd/snpspdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A method of correcting for non-independence of SNPs in LD with each other.", "sc:name": "SNPSpD", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://neurogenetics.qimrberghofer.edu.au/SNPSpD/" } \ No newline at end of file diff --git a/data/snpstats/bioconda_snpstats.yaml b/data/snpstats/bioconda_snpstats.yaml index 7d86241674da8..53d1c8a92180a 100644 --- a/data/snpstats/bioconda_snpstats.yaml +++ b/data/snpstats/bioconda_snpstats.yaml @@ -4,7 +4,6 @@ description: Classes and statistical methods for large SNP association studies. home: https://bioconductor.org/packages/3.10/bioc/html/snpStats.html identifiers: - biotools:snpstats -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-snpstats diff --git a/data/snpstats/snpstatsbioschemas.jsonld b/data/snpstats/snpstatsbioschemas.jsonld index 1840d071667c2..573e91345ecf0 100644 --- a/data/snpstats/snpstatsbioschemas.jsonld +++ b/data/snpstats/snpstatsbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "David Clayton", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.", "sc:license": "GPL-3.0", diff --git a/data/snpsti/snpstibioschemas.jsonld b/data/snpsti/snpstibioschemas.jsonld index 783a6fdae5b04..8892bf2cb8221 100644 --- a/data/snpsti/snpstibioschemas.jsonld +++ b/data/snpsti/snpstibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SNPSTI", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/ubccr/SNPSTI" } \ No newline at end of file diff --git a/data/snpsyn/snpsynbioschemas.jsonld b/data/snpsyn/snpsynbioschemas.jsonld index d3a6b48157fc9..75e22be6068f3 100644 --- a/data/snpsyn/snpsynbioschemas.jsonld +++ b/data/snpsyn/snpsynbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The web server receives GWAS data submissions, invokes the interaction analysis and returns results. The user can explore details on identified SNP-SNP pairs, perform gene set enrichment analysis and interact with the constructed SNP synergy network.", "sc:name": "SNPsyn", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://snpsyn.biolab.si" } \ No newline at end of file diff --git a/data/snptest/snptestbioschemas.jsonld b/data/snptest/snptestbioschemas.jsonld index e527bde516189..679b51f2ef38e 100644 --- a/data/snptest/snptestbioschemas.jsonld +++ b/data/snptest/snptestbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "SNPTEST", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html" } \ No newline at end of file diff --git a/data/snptracker/snptrackerbioschemas.jsonld b/data/snptracker/snptrackerbioschemas.jsonld index b9aebc9e5a889..949b7cc7e5058 100644 --- a/data/snptracker/snptrackerbioschemas.jsonld +++ b/data/snptracker/snptrackerbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/snptracker", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:26585827", "sc:description": "A small tool to extract the latest version rsID and genomic coordinates of SNPs given any version of rs ID(s).", "sc:name": "SnpTracker", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://statgenpro.psychiatry.hku.hk/limx/snptracker/" } \ No newline at end of file diff --git a/data/snptree/snptreebioschemas.jsonld b/data/snptree/snptreebioschemas.jsonld index 4c92fab674209..bf566c6d16367 100644 --- a/data/snptree/snptreebioschemas.jsonld +++ b/data/snptree/snptreebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "snpTree", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cge.cbs.dtu.dk/services/snpTree/", diff --git a/data/snpversity/snpversitybioschemas.jsonld b/data/snpversity/snpversitybioschemas.jsonld index 55de1b46f12fe..b99c9c17061a1 100644 --- a/data/snpversity/snpversitybioschemas.jsonld +++ b/data/snpversity/snpversitybioschemas.jsonld @@ -17,8 +17,8 @@ "@id": "https://bio.tools/snpversity", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Taner Z Sen", - "Contact form" + "Contact form", + "Taner Z Sen" ], "sc:additionalType": "Web application", "sc:citation": [ @@ -34,8 +34,8 @@ }, "sc:name": "SNPversity", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://www.maizegdb.org/snpversity" diff --git a/data/snr/snrbioschemas.jsonld b/data/snr/snrbioschemas.jsonld index eeca8bf361450..4f2d3ec812f9b 100644 --- a/data/snr/snrbioschemas.jsonld +++ b/data/snr/snrbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "snr", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/snr-vis/" } \ No newline at end of file diff --git a/data/snsa/snsabioschemas.jsonld b/data/snsa/snsabioschemas.jsonld index e9f69bab6d2ef..71527a3839a65 100644 --- a/data/snsa/snsabioschemas.jsonld +++ b/data/snsa/snsabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A method to construct a supernetwork from partial trees based on simulated annealing.", "sc:name": "SNSA", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bs.ipm.ir/softwares/snsa/" } \ No newline at end of file diff --git a/data/snv-ppilp/snv-ppilpbioschemas.jsonld b/data/snv-ppilp/snv-ppilpbioschemas.jsonld index 883c74b05a6ec..60e0553a1809a 100644 --- a/data/snv-ppilp/snv-ppilpbioschemas.jsonld +++ b/data/snv-ppilp/snv-ppilpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A fast and easy to use tool for refining GATK’s Unified Genotyper SNV calls, for multiple samples assumed to form a phylogeny.", "sc:name": "SNV-PPILP", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.cs.helsinki.fi/en/gsa/snv-ppilp" } \ No newline at end of file diff --git a/data/snver/snverbioschemas.jsonld b/data/snver/snverbioschemas.jsonld index 46078ca9c5000..40e77b85b8ca8 100644 --- a/data/snver/snverbioschemas.jsonld +++ b/data/snver/snverbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for variant calling in pooled or individual sequence data.", "sc:name": "SNVer", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://snver.sourceforge.net/" diff --git a/data/soapdenovo/soapdenovobioschemas.jsonld b/data/soapdenovo/soapdenovobioschemas.jsonld index 405efafb97615..796ced68226eb 100644 --- a/data/soapdenovo/soapdenovobioschemas.jsonld +++ b/data/soapdenovo/soapdenovobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "SOAPdenovo", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://soap.genomics.org.cn/soapdenovo.html" } \ No newline at end of file diff --git a/data/soapindel/soapindelbioschemas.jsonld b/data/soapindel/soapindelbioschemas.jsonld index 864a37e197a34..7f1aee7d1ed20 100644 --- a/data/soapindel/soapindelbioschemas.jsonld +++ b/data/soapindel/soapindelbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1101/gr.132480.111", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/soapindel", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC3530679", + "pubmed:22972939", { "@id": "https://doi.org/10.1101/gr.132480.111" - }, - "pubmed:22972939", - "pmcid:PMC3530679" + } ], "sc:description": "Developed to find the insertion and deletion specially for re-sequence technology.", "sc:featureList": { @@ -28,10 +32,6 @@ "sc:name": "SOAPindel", "sc:operatingSystem": "Linux", "sc:url": "http://soap.genomics.org.cn/index.html" - }, - { - "@id": "https://doi.org/10.1101/gr.132480.111", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/soapsplice/soapsplicebioschemas.jsonld b/data/soapsplice/soapsplicebioschemas.jsonld index 3e31363bae6c2..084b91e24ddad 100644 --- a/data/soapsplice/soapsplicebioschemas.jsonld +++ b/data/soapsplice/soapsplicebioschemas.jsonld @@ -9,21 +9,25 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/nmeth.4106", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/soapsplice", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27941783", "pmcid:PMC5792058", + "pmcid:PMC3268599", + "pubmed:27941783", + "pubmed:22303342", { "@id": "https://doi.org/10.3389/fgene.2011.00046" }, { "@id": "https://doi.org/10.1038/nmeth.4106" - }, - "pmcid:PMC3268599", - "pubmed:22303342" + } ], "sc:description": "Designed to use RNA-Seq reads for genome-wide ab initio detection of splice junction sites and identification of alternative splicing (AS) events.", "sc:featureList": { @@ -34,10 +38,6 @@ "sc:operatingSystem": "Linux", "sc:url": "http://soap.genomics.org.cn/index.html" }, - { - "@id": "https://doi.org/10.1038/nmeth.4106", - "@type": "sc:CreativeWork" - }, { "@id": "https://doi.org/10.3389/fgene.2011.00046", "@type": "sc:CreativeWork" diff --git a/data/soba/sobabioschemas.jsonld b/data/soba/sobabioschemas.jsonld index cb6775fa60ad9..28cb1ca5fd72c 100644 --- a/data/soba/sobabioschemas.jsonld +++ b/data/soba/sobabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Provides a simple statistical and graphical summary of an annotated genome. To be used by annotators and for genome comparison.", "sc:name": "SOBA: Sequence Ontology Bioinformatics Analysis", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.sequenceontology.org/cgi-bin/soba.cgi" } \ No newline at end of file diff --git a/data/social_network/social_networkbioschemas.jsonld b/data/social_network/social_networkbioschemas.jsonld index 4fa5053d148f8..8ba49d104f8c8 100644 --- a/data/social_network/social_networkbioschemas.jsonld +++ b/data/social_network/social_networkbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.6804.3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/social_network", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Victor Kofia", "sc:additionalType": "Plug-in", "sc:citation": [ + "pmcid:PMC4760270", { "@id": "https://doi.org/10.12688/F1000RESEARCH.6804.3" }, - "pmcid:PMC4760270", "pubmed:26949516" ], "sc:description": "Creates visual summaries of individuals connected by co-authorship links in academia, created from bibliographic databases like PubMed, Scopus and InCites.", @@ -27,25 +31,21 @@ "@id": "edam:operation_0337" }, { - "@id": "edam:operation_3465" + "@id": "edam:operation_2497" }, { - "@id": "edam:operation_2497" + "@id": "edam:operation_3465" } ], "sc:license": "GPL-2.0", "sc:name": "Social Network", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://baderlab.org/Software/SocialNetworkApp", "sc:version": "1.3.0" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.6804.3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/socket/socketbioschemas.jsonld b/data/socket/socketbioschemas.jsonld index d0a1a0345b1da..00a072f4ee93a 100644 --- a/data/socket/socketbioschemas.jsonld +++ b/data/socket/socketbioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/socket", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:11292353", "sc:description": "The tool finds the Knobs-into-Holes mode of packing between alpha-helices which is characteristic of coiled coils. It unambiguously defines the beginning and end of coiled-coil motifs in protein structures and assigns a heptad register to the sequence, highlighting the core-residues with a RasMol script if required.", "sc:name": "SOCKET", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://coiledcoils.chm.bris.ac.uk/socket/" diff --git a/data/sockeye/sockeyebioschemas.jsonld b/data/sockeye/sockeyebioschemas.jsonld index 5f04686f9fea1..323df62656589 100644 --- a/data/sockeye/sockeyebioschemas.jsonld +++ b/data/sockeye/sockeyebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Sockeye is a visualization tool allowing one to assemble and analyze genomic information in a three dimensional workspace. It can be used to view features at various levels, ranging from SNPs to karyotypes. Sockeye displays genomic features along tracks, and links to the Ensembl database.", "sc:name": "Sockeye", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.bcgsc.ca/gc/bomge/sockeye/" diff --git a/data/soda-solubility/soda-solubilitybioschemas.jsonld b/data/soda-solubility/soda-solubilitybioschemas.jsonld index 7be2e28c5f091..e033ed6b26c65 100644 --- a/data/soda-solubility/soda-solubilitybioschemas.jsonld +++ b/data/soda-solubility/soda-solubilitybioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "CC-BY-NC-ND-4.0", "sc:name": "SODA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://protein.bio.unipd.it/soda/", "sc:version": "1.0" diff --git a/data/soda/sodabioschemas.jsonld b/data/soda/sodabioschemas.jsonld index 868bb020db101..a7335c6a0fc7b 100644 --- a/data/soda/sodabioschemas.jsonld +++ b/data/soda/sodabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SODa", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://babylone.ulb.ac.be/SODa/index3.php" } \ No newline at end of file diff --git a/data/sofi/sofibioschemas.jsonld b/data/sofi/sofibioschemas.jsonld index c700c169d31f0..b4e1b7f83c975 100644 --- a/data/sofi/sofibioschemas.jsonld +++ b/data/sofi/sofibioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0161602", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/sofi", "@type": "sc:SoftwareApplication", @@ -22,11 +18,11 @@ "Plug-in" ], "sc:citation": [ - "pubmed:27583365", { "@id": "https://doi.org/10.1371/journal.pone.0161602" }, - "pmcid:PMC5008722" + "pmcid:PMC5008722", + "pubmed:27583365" ], "sc:description": "A software tool for a simple qualitative comparison of super-resolution optical fluctuation imaging (SOFI) images under simulated conditions considering parameters of the microscope setup and essential properties of the biological sample.", "sc:featureList": { @@ -35,11 +31,15 @@ "sc:license": "GPL-1.0", "sc:name": "SOFI", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/lob-epfl/sofitool" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0161602", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/softpanel/softpanelbioschemas.jsonld b/data/softpanel/softpanelbioschemas.jsonld index de06e25de1a20..08e29ecb92d6a 100644 --- a/data/softpanel/softpanelbioschemas.jsonld +++ b/data/softpanel/softpanelbioschemas.jsonld @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "SoftPanel", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.isb.pku.edu.cn/SoftPanel/" }, diff --git a/data/soggi/bioconda_soggi.yaml b/data/soggi/bioconda_soggi.yaml index 547b3ef3e9c8f..85b39e4908d77 100644 --- a/data/soggi/bioconda_soggi.yaml +++ b/data/soggi/bioconda_soggi.yaml @@ -11,7 +11,6 @@ description: The soGGi package provides a toolset to create genomic interval agg home: https://bioconductor.org/packages/3.10/bioc/html/soGGi.html identifiers: - biotools:soggi -- doi:10.1038/nmeth.3252 license: GPL (>= 3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-soggi diff --git a/data/soggi/soggibioschemas.jsonld b/data/soggi/soggibioschemas.jsonld index af65a8c581141..dfd301b91d36d 100644 --- a/data/soggi/soggibioschemas.jsonld +++ b/data/soggi/soggibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "soGGi", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/soGGi.html", "sc:version": "1.6.0" diff --git a/data/soilgrids/soilgridsbioschemas.jsonld b/data/soilgrids/soilgridsbioschemas.jsonld index 18ae4c4fd7895..7d7536a3e5f24 100644 --- a/data/soilgrids/soilgridsbioschemas.jsonld +++ b/data/soilgrids/soilgridsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm).", "sc:name": "SoilGrids", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://soilgrids.org" diff --git a/data/soilgrids250m/soilgrids250mbioschemas.jsonld b/data/soilgrids250m/soilgrids250mbioschemas.jsonld index 6db216faa2eb6..78628a86736bb 100644 --- a/data/soilgrids250m/soilgrids250mbioschemas.jsonld +++ b/data/soilgrids250m/soilgrids250mbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm).", "sc:name": "SoilGrids250m", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://soilgrids.org" } \ No newline at end of file diff --git a/data/solar-eclipse/solar-eclipsebioschemas.jsonld b/data/solar-eclipse/solar-eclipsebioschemas.jsonld index c00b327b1dcb0..cffa07a031093 100644 --- a/data/solar-eclipse/solar-eclipsebioschemas.jsonld +++ b/data/solar-eclipse/solar-eclipsebioschemas.jsonld @@ -18,8 +18,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:25747917", "pmcid:PMC4387079", + "pubmed:25747917", { "@id": "https://doi.org/10.1016/j.neuroimage.2015.02.050" } @@ -32,8 +32,8 @@ "sc:name": "SOLAR-eclipse", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://solar-eclipse-genetics.org/" } diff --git a/data/solexaqa/solexaqabioschemas.jsonld b/data/solexaqa/solexaqabioschemas.jsonld index 50ff531b64947..d98b405aa1fcb 100644 --- a/data/solexaqa/solexaqabioschemas.jsonld +++ b/data/solexaqa/solexaqabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "SolexaQA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://solexaqa.sourceforge.net/" } \ No newline at end of file diff --git a/data/solgs/solgsbioschemas.jsonld b/data/solgs/solgsbioschemas.jsonld index d5b46140e91b0..ee8dd07950ecc 100644 --- a/data/solgs/solgsbioschemas.jsonld +++ b/data/solgs/solgsbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Contact form", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:25495537", "pmcid:PMC4269960", { "@id": "https://doi.org/10.1186/S12859-014-0398-7" - } + }, + "pubmed:25495537" ], "sc:description": "A web-based tool for genomic selection.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "solGS", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://cassavabase.org/solgs" } diff --git a/data/solid2fastq/solid2fastqbioschemas.jsonld b/data/solid2fastq/solid2fastqbioschemas.jsonld index 135f37336f704..16a1b356b5d0c 100644 --- a/data/solid2fastq/solid2fastqbioschemas.jsonld +++ b/data/solid2fastq/solid2fastqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "SOLiD output to fastq.", "sc:name": "solid2fastq", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", diff --git a/data/solid_qual_boxplot/solid_qual_boxplotbioschemas.jsonld b/data/solid_qual_boxplot/solid_qual_boxplotbioschemas.jsonld index f2cf17b6ba450..162ca90e4462e 100644 --- a/data/solid_qual_boxplot/solid_qual_boxplotbioschemas.jsonld +++ b/data/solid_qual_boxplot/solid_qual_boxplotbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "solid_qual_boxplot", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/galaxyproject/galaxy/tree/dev/tools", "sc:version": "1.0.0" diff --git a/data/solr-plant/solr-plantbioschemas.jsonld b/data/solr-plant/solr-plantbioschemas.jsonld index 9d8c0ebe2d9f3..eb9bb06cbd89c 100644 --- a/data/solr-plant/solr-plantbioschemas.jsonld +++ b/data/solr-plant/solr-plantbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://orcid.org/0000-0003-2054-7356", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1186/S12859-019-2874-6", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Solr-Plant", "@type": "sc:SoftwareApplication", @@ -25,32 +21,36 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6530169", "pubmed:31117932", { "@id": "https://doi.org/10.1186/S12859-019-2874-6" - } + }, + "pmcid:PMC6530169" ], "sc:description": "Identification and resolution of plant taxonomic names.", "sc:featureList": [ { - "@id": "edam:operation_2421" + "@id": "edam:operation_0495" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_2421" }, { - "@id": "edam:operation_0495" + "@id": "edam:operation_2422" } ], "sc:license": "MIT", "sc:name": "Solr-Plant", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bcbi.brown.edu/solrplant" + }, + { + "@id": "https://doi.org/10.1186/S12859-019-2874-6", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/solubis/solubisbioschemas.jsonld b/data/solubis/solubisbioschemas.jsonld index 8d3c82e8861b6..49eddcc0cda54 100644 --- a/data/solubis/solubisbioschemas.jsonld +++ b/data/solubis/solubisbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SolubiS", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://solubis.switchlab.org/" } \ No newline at end of file diff --git a/data/som/sombioschemas.jsonld b/data/som/sombioschemas.jsonld index a4e3642aa9a73..e962576d1971b 100644 --- a/data/som/sombioschemas.jsonld +++ b/data/som/sombioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "SOM", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/bougui505/SOM" } \ No newline at end of file diff --git a/data/somart/somartbioschemas.jsonld b/data/somart/somartbioschemas.jsonld index 8af926debb333..6648cb59c358d 100644 --- a/data/somart/somartbioschemas.jsonld +++ b/data/somart/somartbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SoMART", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bakerlab.berkeley.edu/somart-webserver-mirna-sirna-analysis" } \ No newline at end of file diff --git a/data/somaticsignatures/somaticsignaturesbioschemas.jsonld b/data/somaticsignatures/somaticsignaturesbioschemas.jsonld index 7dcd0d449a1ea..fbf3cec9e4e49 100644 --- a/data/somaticsignatures/somaticsignaturesbioschemas.jsonld +++ b/data/somaticsignatures/somaticsignaturesbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-0070-4975", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1093/bioinformatics/btv408", "@type": "sc:CreativeWork" @@ -24,11 +28,11 @@ "Library" ], "sc:citation": [ - "pubmed:26163694", + "pmcid:PMC4817139", { "@id": "https://doi.org/10.1093/bioinformatics/btv408" }, - "pmcid:PMC4817139" + "pubmed:26163694" ], "sc:description": "This package identifies mutational signatures of single nucleotide variants (SNVs).", "sc:featureList": { @@ -37,16 +41,12 @@ "sc:license": "MIT", "sc:name": "SomaticSignatures", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SomaticSignatures.html", "sc:version": "2.10.0" - }, - { - "@id": "http://orcid.org/0000-0003-0070-4975", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/sombrero/sombrerobioschemas.jsonld b/data/sombrero/sombrerobioschemas.jsonld index 9b660bef99253..14764090fc3f8 100644 --- a/data/sombrero/sombrerobioschemas.jsonld +++ b/data/sombrero/sombrerobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SOMBRERO", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinf.nuigalway.ie/sombrero/", "sc:version": "1.1" diff --git a/data/sominaclust/sominaclustbioschemas.jsonld b/data/sominaclust/sominaclustbioschemas.jsonld index f7f5f54535c66..109baa61b350d 100644 --- a/data/sominaclust/sominaclustbioschemas.jsonld +++ b/data/sominaclust/sominaclustbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Detection of cancer genes based on somatic mutation patterns of inactivation and clustering.", "sc:name": "SomInaClust", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/sominaclust", diff --git a/data/somvarius/somvariusbioschemas.jsonld b/data/somvarius/somvariusbioschemas.jsonld index c6c2a41a7fd57..bbce6d7117187 100644 --- a/data/somvarius/somvariusbioschemas.jsonld +++ b/data/somvarius/somvariusbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A computational method for detecting somatic variants using high throughput sequencing data from unpaired tissue samples.", "sc:name": "SomVarIUS", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/kylessmith/SomVarIUS" } \ No newline at end of file diff --git a/data/sonata/sonatabioschemas.jsonld b/data/sonata/sonatabioschemas.jsonld index b78859a44a347..db89ca50c4afb 100644 --- a/data/sonata/sonatabioschemas.jsonld +++ b/data/sonata/sonatabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "SONATA", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/AllenInstitute/sonata" diff --git a/data/sonicparanoid/sonicparanoidbioschemas.jsonld b/data/sonicparanoid/sonicparanoidbioschemas.jsonld index 45737ea8c7cc7..23c0a508b3b15 100644 --- a/data/sonicparanoid/sonicparanoidbioschemas.jsonld +++ b/data/sonicparanoid/sonicparanoidbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "SonicParanoid", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid/", "sc:version": "1.0.9" diff --git a/data/sopra/soprabioschemas.jsonld b/data/sopra/soprabioschemas.jsonld index 700deaab865a8..2bc9308da19b6 100644 --- a/data/sopra/soprabioschemas.jsonld +++ b/data/sopra/soprabioschemas.jsonld @@ -9,15 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-11-345", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/sopra", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC2909219", { "@id": "https://doi.org/10.1186/1471-2105-11-345" }, - "pmcid:PMC2909219", "pubmed:20576136" ], "sc:description": "Assembler for mate pair/paired-end reads from high throughput sequencing platforms, e.g. Illumina and SOLiD.", @@ -31,10 +35,6 @@ ], "sc:url": "http://www.physics.rutgers.edu/~anirvans/SOPRA/", "sc:version": "1.4.6" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-11-345", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sorfs/sorfsbioschemas.jsonld b/data/sorfs/sorfsbioschemas.jsonld index a215501ef0c5c..afa927ace19dd 100644 --- a/data/sorfs/sorfsbioschemas.jsonld +++ b/data/sorfs/sorfsbioschemas.jsonld @@ -17,18 +17,18 @@ "Database portal" ], "sc:citation": [ - "pmcid:PMC4702841", "pubmed:26527729", { "@id": "https://doi.org/10.1093/nar/gkv1175" - } + }, + "pmcid:PMC4702841" ], "sc:description": "Repository of small open reading frames identified by ribosome profiling in a database of over 3 million sORFs across 78 datasets from six species.", "sc:name": "sORFs", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.sorfs.org/" }, diff --git a/data/sort2/sort2bioschemas.jsonld b/data/sort2/sort2bioschemas.jsonld index ecf2015a25c8a..047b18d9c2918 100644 --- a/data/sort2/sort2bioschemas.jsonld +++ b/data/sort2/sort2bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SoRT2 is a web server that allows the user to perform genome rearrangement analysis involving reversals, generalized transpositions and translocation, and infer phylogenetic trees of genomes. Input is 2 genomes.", "sc:name": "SoRT2", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genome.cs.nthu.edu.tw/SORT2/" } \ No newline at end of file diff --git a/data/sortgff/sortgffbioschemas.jsonld b/data/sortgff/sortgffbioschemas.jsonld index fcbbc4d911344..17854e2e0a9cd 100644 --- a/data/sortgff/sortgffbioschemas.jsonld +++ b/data/sortgff/sortgffbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Sorts a gff file.", "sc:name": "sortgff", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/sortmerna/sortmernabioschemas.jsonld b/data/sortmerna/sortmernabioschemas.jsonld index 3b3ca74f45bac..36a1b81ef064e 100644 --- a/data/sortmerna/sortmernabioschemas.jsonld +++ b/data/sortmerna/sortmernabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:description": "Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.", "sc:name": "SortMeRna", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfo.lifl.fr/RNA/sortmerna/" } \ No newline at end of file diff --git a/data/sos/sosbioschemas.jsonld b/data/sos/sosbioschemas.jsonld index 8389a93e333a6..9f1f91fded387 100644 --- a/data/sos/sosbioschemas.jsonld +++ b/data/sos/sosbioschemas.jsonld @@ -22,29 +22,29 @@ "Workflow" ], "sc:citation": [ - "pubmed:30811390", { "@id": "https://doi.org/10.1371/journal.pcbi.1006843" }, + "pubmed:30811390", "pmcid:PMC6411228" ], "sc:description": "Script of Scripts (SoS) is a computational environment for the development and execution of scripts in multiple languages for daily computational research.", "sc:featureList": [ - { - "@id": "edam:operation_1812" - }, { "@id": "edam:operation_3196" }, { "@id": "edam:operation_3431" + }, + { + "@id": "edam:operation_1812" } ], "sc:license": "BSD-3-Clause", "sc:name": "SoS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://vatlab.github.io/sos-docs/" diff --git a/data/source/sourcebioschemas.jsonld b/data/source/sourcebioschemas.jsonld index ba0daf45014ed..8765cf24c95ba 100644 --- a/data/source/sourcebioschemas.jsonld +++ b/data/source/sourcebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Stanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat.", "sc:name": "SOURCE", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://source.stanford.edu" diff --git a/data/sourcer/sourcerbioschemas.jsonld b/data/sourcer/sourcerbioschemas.jsonld index 132b84903b611..5787af844366c 100644 --- a/data/sourcer/sourcerbioschemas.jsonld +++ b/data/sourcer/sourcerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "SourceR", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/sourceR/index.html" } \ No newline at end of file diff --git a/data/sourmash/sourmashbioschemas.jsonld b/data/sourmash/sourmashbioschemas.jsonld index c66501c7184fa..969e17ea1cbe2 100644 --- a/data/sourmash/sourmashbioschemas.jsonld +++ b/data/sourmash/sourmashbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "sourmash", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourmash.readthedocs.io/en/latest/", "sc:version": "2.0a8" diff --git a/data/soybase/soybasebioschemas.jsonld b/data/soybase/soybasebioschemas.jsonld index 05436ab83954a..e2dec5aec55a0 100644 --- a/data/soybase/soybasebioschemas.jsonld +++ b/data/soybase/soybasebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Soybean genetic database, is a comprehensive repository for curated genetics, genomics and related data resources for soybean. Contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase also contains the well-annotated ''Williams 82'' genomic sequence and associated data mining tools.", "sc:name": "SoyBase", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://soybase.org" diff --git a/data/soyfn/soyfnbioschemas.jsonld b/data/soyfn/soyfnbioschemas.jsonld index 36535a4df3d92..b5e2135c028aa 100644 --- a/data/soyfn/soyfnbioschemas.jsonld +++ b/data/soyfn/soyfnbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/database/bau019", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/soyfn", "@type": "sc:SoftwareApplication", @@ -30,16 +34,12 @@ }, "sc:name": "SoyFN", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://nclab.hit.edu.cn/SoyFN", "sc:version": "1.0" - }, - { - "@id": "https://doi.org/10.1093/database/bau019", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/spaced_radiology/spaced_radiologybioschemas.jsonld b/data/spaced_radiology/spaced_radiologybioschemas.jsonld index bda5b23f661e0..8b9817f656124 100644 --- a/data/spaced_radiology/spaced_radiologybioschemas.jsonld +++ b/data/spaced_radiology/spaced_radiologybioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1007/S00247-019-04415-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0003-1953-4486", "@type": "schema:Person" @@ -32,14 +36,10 @@ "sc:name": "Spaced Radiology", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.spacedradiology.com/" - }, - { - "@id": "https://doi.org/10.1007/S00247-019-04415-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/spaced_words/spaced_wordsbioschemas.jsonld b/data/spaced_words/spaced_wordsbioschemas.jsonld index 2702af407bb51..2842c226eef51 100644 --- a/data/spaced_words/spaced_wordsbioschemas.jsonld +++ b/data/spaced_words/spaced_wordsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/spaced_words", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "lhahn", - "Chris Leimeister" + "Chris Leimeister", + "lhahn" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:20494976", diff --git a/data/spacem3/spacem3bioschemas.jsonld b/data/spacem3/spacem3bioschemas.jsonld index a374b6fd92a66..9039ca10d6a3e 100644 --- a/data/spacem3/spacem3bioschemas.jsonld +++ b/data/spacem3/spacem3bioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The software is dedicated to Spatial Clustering with EM and Markov Models. It proposes a variety of algorithms for supervised and unsupervised classification of multidimensional and spatially-located data. The main techniques use the EM algorithm for soft clustering and Markov Random Fields (MRF) for spatial modelling.", "sc:name": "SpaCEM3", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://spacem3.gforge.inria.fr/" } \ No newline at end of file diff --git a/data/spacepac/spacepacbioschemas.jsonld b/data/spacepac/spacepacbioschemas.jsonld index c087766623cfa..c1c169e88ebdc 100644 --- a/data/spacepac/spacepacbioschemas.jsonld +++ b/data/spacepac/spacepacbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-1195-9607", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1186/1471-2105-15-231", "@type": "sc:CreativeWork" @@ -17,44 +21,40 @@ "@id": "https://bio.tools/spacepac", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Gregory Ryslik", { "@id": "https://orcid.org/0000-0003-1195-9607" - }, - "Gregory Ryslik" + } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pmcid:PMC4227039", + "pubmed:24990767", { "@id": "https://doi.org/10.1186/1471-2105-15-231" - }, - "pubmed:24990767", - "pmcid:PMC4227039" + } ], "sc:description": "Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein's tertiary structure.", "sc:featureList": [ { - "@id": "edam:operation_3432" + "@id": "edam:operation_2426" }, { - "@id": "edam:operation_2426" + "@id": "edam:operation_3432" } ], "sc:license": "GPL-2.0", "sc:name": "SpacePAC", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SpacePAC.html", "sc:version": "1.12.0" - }, - { - "@id": "https://orcid.org/0000-0003-1195-9607", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/spacer/spacerbioschemas.jsonld b/data/spacer/spacerbioschemas.jsonld index ccbb130ea33e6..56d827483170c 100644 --- a/data/spacer/spacerbioschemas.jsonld +++ b/data/spacer/spacerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/spacer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Igor Berezovsky", - "Alexander Goncearenco" + "Alexander Goncearenco", + "Igor Berezovsky" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:23737445", diff --git a/data/spades/spadesbioschemas.jsonld b/data/spades/spadesbioschemas.jsonld index a787eea83509e..0767f53b1b558 100644 --- a/data/spades/spadesbioschemas.jsonld +++ b/data/spades/spadesbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-2.0", "sc:name": "SPAdes", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cab.spbu.ru/software/spades/" } \ No newline at end of file diff --git a/data/spads/spadsbioschemas.jsonld b/data/spads/spadsbioschemas.jsonld index cbb2fcfb6d9c2..29d80eac46886 100644 --- a/data/spads/spadsbioschemas.jsonld +++ b/data/spads/spadsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A population genetics software computing several summary statistics from populations or groups of populations, and implementing two clustering algorithms to study the genetic structure of populations. It has been specifically developed for the analysis of DNA sequences. The first aim of SPADS is to compute, on real datasets, the summary statistics computed by PhyloGeoSim on each simulated datasets.", "sc:name": "SPADS", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://ebe.ulb.ac.be/ebe/SPADS.html" } \ No newline at end of file diff --git a/data/spang/spangbioschemas.jsonld b/data/spang/spangbioschemas.jsonld index f8fd099d485dd..da8088cecebcd 100644 --- a/data/spang/spangbioschemas.jsonld +++ b/data/spang/spangbioschemas.jsonld @@ -19,8 +19,8 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5299738", "pubmed:28178937", + "pmcid:PMC5299738", { "@id": "https://doi.org/10.1186/s12859-017-1531-1" } @@ -32,8 +32,8 @@ "sc:license": "MIT", "sc:name": "SPANG", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://spang.dbcls.jp/" } diff --git a/data/spaniel/spanielbioschemas.jsonld b/data/spaniel/spanielbioschemas.jsonld index 18501437a6ab4..7191e7bd63cd0 100644 --- a/data/spaniel/spanielbioschemas.jsonld +++ b/data/spaniel/spanielbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "Spaniel", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/RachelQueen1/Spaniel" diff --git a/data/spar/sparbioschemas.jsonld b/data/spar/sparbioschemas.jsonld index 85de4670f2bf7..20c68ce234c46 100644 --- a/data/spar/sparbioschemas.jsonld +++ b/data/spar/sparbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Small RNA-seq Portal for Analysis of sequencing expeRiments. interactive processing, analysis, annotation and visualization of small RNA sequencing data. Supports sequencing data generated from various experimental protocols, including smRNA-seq, short total RNA sequencing, microRNA-seq, and single-cell small RNA-seq.", "sc:name": "SPAR", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://www.lisanwanglab.org/SPAR/" } \ No newline at end of file diff --git a/data/sparc/sparcbioschemas.jsonld b/data/sparc/sparcbioschemas.jsonld index 8094cfdc4e9dc..1fc2e4867a4bc 100644 --- a/data/sparc/sparcbioschemas.jsonld +++ b/data/sparc/sparcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "SpaRC", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bitbucket.org/berkeleylab/jgi-sparc/" } \ No newline at end of file diff --git a/data/spark-cpvs/spark-cpvsbioschemas.jsonld b/data/spark-cpvs/spark-cpvsbioschemas.jsonld index 91f5468aa54e0..3e9d159d832f1 100644 --- a/data/spark-cpvs/spark-cpvsbioschemas.jsonld +++ b/data/spark-cpvs/spark-cpvsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Intelligent virtual screening with confidence based on conformal prediction.", "sc:name": "spark-cpvs", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/laeeq80/spark-cpvs" } \ No newline at end of file diff --git a/data/spark-msna/spark-msnabioschemas.jsonld b/data/spark-msna/spark-msnabioschemas.jsonld index 966f4876ccc3a..053785b9ae86f 100644 --- a/data/spark-msna/spark-msnabioschemas.jsonld +++ b/data/spark-msna/spark-msnabioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-6445-7833", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/SPARK-MSNA", "@type": "sc:SoftwareApplication", @@ -21,36 +17,40 @@ }, "sc:additionalType": "Script", "sc:citation": [ - "pubmed:31036850", { "@id": "https://doi.org/10.1038/S41598-019-42966-5" }, + "pubmed:31036850", "pmcid:PMC6488671" ], "sc:description": "Efficient algorithm on Apache Spark for aligning multiple similar DNA/RNA sequences with supervised learning.", "sc:featureList": [ - { - "@id": "edam:operation_0491" - }, { "@id": "edam:operation_0492" }, { "@id": "edam:operation_0323" + }, + { + "@id": "edam:operation_0491" } ], "sc:license": "Unlicense", "sc:name": "SPARK-MSNA", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/spark-msna/" }, { "@id": "https://doi.org/10.1038/S41598-019-42966-5", "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0001-6445-7833", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/spark-vs/spark-vsbioschemas.jsonld b/data/spark-vs/spark-vsbioschemas.jsonld index c1817c038ea35..0abee46714871 100644 --- a/data/spark-vs/spark-vsbioschemas.jsonld +++ b/data/spark-vs/spark-vsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "Spark-VS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/mcapuccini/spark-vs" diff --git a/data/sparse/sparsebioschemas.jsonld b/data/sparse/sparsebioschemas.jsonld index 49f6ef24808c1..5d1edf14d57c0 100644 --- a/data/sparse/sparsebioschemas.jsonld +++ b/data/sparse/sparsebioschemas.jsonld @@ -13,59 +13,51 @@ "@id": "http://orcid.org/0000-0001-8231-3323", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btv185", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-0173-3009", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/sparse", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Sebastian Will", { "@id": "http://orcid.org/0000-0001-8231-3323" - }, - "Sebastian Will" + } ], "edam:has_input": { "@id": "edam:data_3495" }, "edam:has_output": [ - { - "@id": "edam:data_0872" - }, { "@id": "edam:data_1465" }, { "@id": "edam:data_1916" + }, + { + "@id": "edam:data_0872" } ], "sc:additionalType": "Command-line tool", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0080" + "@id": "edam:topic_0097" }, { - "@id": "edam:topic_0097" + "@id": "edam:topic_0080" } ], "sc:author": [ - "Rolf Backofen", { "@id": "http://orcid.org/0000-0002-0173-3009" }, - "Sebastian Will" + "Sebastian Will", + "Rolf Backofen" ], "sc:citation": [ "pubmed:25838465", + "pmcid:PMC4514930", { "@id": "https://doi.org/10.1093/bioinformatics/btv185" - }, - "pmcid:PMC4514930" + } ], "sc:contributor": "Sebastian Will", "sc:description": "Very efficient structure-based alignment of RNAs.", @@ -80,14 +72,22 @@ "Linux" ], "sc:provider": [ - "rnateam", - "University Freiburg" + "University Freiburg", + "rnateam" ], "sc:softwareHelp": { "@id": "http://www.bioinf.uni-freiburg.de/Software/SPARSE/" }, "sc:url": "http://www.bioinf.uni-freiburg.de/Software/SPARSE", "sc:version": "1.8.9" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/btv185", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-0173-3009", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/sparsedossa/sparsedossabioschemas.jsonld b/data/sparsedossa/sparsedossabioschemas.jsonld index dc961d9a00c93..b07cff64854b6 100644 --- a/data/sparsedossa/sparsedossabioschemas.jsonld +++ b/data/sparsedossa/sparsedossabioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/sparsedossa", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Boyu Ren", "George Weingart", - "Emma Schwager" + "Emma Schwager", + "Boyu Ren" ], "sc:additionalType": "Library", "sc:description": "Sparse Data Observations for Simulating Synthetic Abundance. Provides a model based Bayesian method to characterize and simulate microbiome data. This model captures the marginal distribution of each microbial feature as a truncated, zero-inflated log-normal distribution, with parameters distributed as a parent log-normal distribution. The model can be effectively fit to reference microbial datasets in order to parameterize their microbes and communities, or to simulate synthetic datasets of similar population structure.", "sc:license": "MIT", "sc:name": "sparseDOSSA", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sparseDOSSA.html", "sc:version": "1.4.0" diff --git a/data/sparsesignatures/sparsesignaturesbioschemas.jsonld b/data/sparsesignatures/sparsesignaturesbioschemas.jsonld index 3e692a3db7fe0..b92f0b72df89c 100644 --- a/data/sparsesignatures/sparsesignaturesbioschemas.jsonld +++ b/data/sparsesignatures/sparsesignaturesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "SparseSignatures", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SparseSignatures.html", "sc:version": "1.0.0" diff --git a/data/sparta/spartabioschemas.jsonld b/data/sparta/spartabioschemas.jsonld index 20317814eb47e..180f3280d58e3 100644 --- a/data/sparta/spartabioschemas.jsonld +++ b/data/sparta/spartabioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-016-0923-y", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/sparta", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Robert B. Abramovitch", "Benjamin K. Johnson", + "Matthew B. Scholz", "Tracy K. Teal", - "Matthew B. Scholz" + "Robert B. Abramovitch" ], "sc:additionalType": "Workflow", "sc:citation": [ - "pubmed:6847232", - "pubmed:26847232", { "@id": "https://doi.org/10.1186/s12859-016-0923-y" }, - "pmcid:PMC4743240" + "pubmed:6847232", + "pmcid:PMC4743240", + "pubmed:26847232" ], "sc:description": "Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis. Analyze single-end Illumina RNA-seq data combining several tools: Trimmomatic (read trimming/adapter removal), FastQC (read quality analysis), Bowtie (mapping reads to the reference genome), HTSeq (transcript/gene feature abundance counting), and edgeR (differential gene expression analysis).", "sc:license": "CC-BY-4.0", "sc:name": "SPARTA", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://sparta.readthedocs.io/en/latest/", "sc:version": "1.0" - }, - { - "@id": "https://doi.org/10.1186/s12859-016-0923-y", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/spartaabc/spartaabcbioschemas.jsonld b/data/spartaabc/spartaabcbioschemas.jsonld index 517fa4637c309..ff7f9c2527a61 100644 --- a/data/spartaabc/spartaabcbioschemas.jsonld +++ b/data/spartaabc/spartaabcbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "GPL-2.0", "sc:name": "SpartaABC", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://spartaabc.tau.ac.il/webserver" } \ No newline at end of file diff --git a/data/spartan/spartanbioschemas.jsonld b/data/spartan/spartanbioschemas.jsonld index 57adecb83998d..f70073afed20f 100644 --- a/data/spartan/spartanbioschemas.jsonld +++ b/data/spartan/spartanbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-4411-1776", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/spartan", "@type": "sc:SoftwareApplication", @@ -24,12 +20,16 @@ "sc:license": "GPL-2.0", "sc:name": "SPARTAN", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.york.ac.uk/computational-immunology/software/spartan/", "sc:version": "3.0" + }, + { + "@id": "http://orcid.org/0000-0003-4411-1776", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/spatialde/spatialdebioschemas.jsonld b/data/spatialde/spatialdebioschemas.jsonld index c102f0b5d0a27..84df28fa7cffe 100644 --- a/data/spatialde/spatialdebioschemas.jsonld +++ b/data/spatialde/spatialdebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SpatialDE", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/Teichlab/SpatialDE" } \ No newline at end of file diff --git a/data/spatt/spattbioschemas.jsonld b/data/spatt/spattbioschemas.jsonld index bd42faf1535a2..2704e70efb768 100644 --- a/data/spatt/spattbioschemas.jsonld +++ b/data/spatt/spattbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Statistics for Patterns (SPatt) can compute the significance of a given DNA pattern in a genome sequence. This tool can be used to find patterns with unusual behaviour in DNA sequences.", "sc:name": "SPatt", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://nuel.perso.math.cnrs.fr/spatt/index.html" } \ No newline at end of file diff --git a/data/spatter/spatterbioschemas.jsonld b/data/spatter/spatterbioschemas.jsonld index 3c2be43ec6369..582c026757c50 100644 --- a/data/spatter/spatterbioschemas.jsonld +++ b/data/spatter/spatterbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Perform DNA microarray image analysis. It automatically quantitates two-color microarray images and performs gridding, segmentation, and data extraction in an efficient and fully-automated manner.", "sc:name": "Spatter", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.nongnu.org/spatter/", "sc:version": "0.5.3" diff --git a/data/spci/spcibioschemas.jsonld b/data/spci/spcibioschemas.jsonld index e14714df96881..17a096efa1be5 100644 --- a/data/spci/spcibioschemas.jsonld +++ b/data/spci/spcibioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-5088-8149", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/SPCI", "@type": "sc:SoftwareApplication", @@ -23,10 +19,14 @@ "sc:description": "Structural and physico-chemical interpretation of QSAR models", "sc:name": "SPCI", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://qsar4u.com/pages/sirms_qsar.php" + }, + { + "@id": "https://orcid.org/0000-0001-5088-8149", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/speaq/speaqbioschemas.jsonld b/data/speaq/speaqbioschemas.jsonld index 6d66d60c6ec8f..247c566d5e835 100644 --- a/data/speaq/speaqbioschemas.jsonld +++ b/data/speaq/speaqbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Apache-2.0", "sc:name": "speaq", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/speaq/index.html", "sc:version": "2.0" diff --git a/data/speci/specibioschemas.jsonld b/data/speci/specibioschemas.jsonld index 082f172701c86..588a0a42e5e2a 100644 --- a/data/speci/specibioschemas.jsonld +++ b/data/speci/specibioschemas.jsonld @@ -20,21 +20,21 @@ "@id": "http://orcid.org/0000-0003-1429-7485" }, "sc:additionalType": [ - "Web service", - "Command-line tool" + "Command-line tool", + "Web service" ], "sc:citation": "pubmed:23892899", "sc:description": "Species identification tool using genomic sequences to delineate prokaryotic species. It facilitates fast, accurate and automated taxonomic assignments of newly sequenced genomes based on comparisons of 40 universal, single-copy phylogenetic marker genes extracted from a comprehensive database of sequenced prokaryotic genomes.", "sc:license": "GPL-3.0", "sc:name": "SpecI", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": [ - "HD-HuB", - "European Molecular Biology Laboratory (EMBL)" + "European Molecular Biology Laboratory (EMBL)", + "HD-HuB" ], "sc:url": "http://vm-lux.embl.de/~mende/specI/", "sc:version": "1.0" diff --git a/data/specialize/specializebioschemas.jsonld b/data/specialize/specializebioschemas.jsonld index 57f7644eedc5c..56378028f9001 100644 --- a/data/specialize/specializebioschemas.jsonld +++ b/data/specialize/specializebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A novel approach to enable the expedited development of new algorithms for any types of PTM (post-translational modifications) peptide fragmentation.", "sc:name": "Specialize", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://proteomics.ucsd.edu/software-tools/specialize/" } \ No newline at end of file diff --git a/data/species_delimitation/species_delimitationbioschemas.jsonld b/data/species_delimitation/species_delimitationbioschemas.jsonld index cca65a145c146..053c0f23def01 100644 --- a/data/species_delimitation/species_delimitationbioschemas.jsonld +++ b/data/species_delimitation/species_delimitationbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This plugin for the Geneious bioinformatics software is an exploratory tool that allows users to assess putative species in phylogenetic trees.", "sc:name": "Species Delimitation", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.fos.auckland.ac.nz/~howardross/software.html" diff --git a/data/specl/speclbioschemas.jsonld b/data/specl/speclbioschemas.jsonld index 99f046e8d5c45..d8b20bb90b718 100644 --- a/data/specl/speclbioschemas.jsonld +++ b/data/specl/speclbioschemas.jsonld @@ -23,9 +23,9 @@ "sc:license": "GPL-3.0", "sc:name": "specL", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/specL.html", "sc:version": "1.8.0" diff --git a/data/specond/specondbioschemas.jsonld b/data/specond/specondbioschemas.jsonld index cc1ed6a510130..7cbc066b97fa6 100644 --- a/data/specond/specondbioschemas.jsonld +++ b/data/specond/specondbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Florence Cavalli", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression.", "sc:license": "GPL-2.0", diff --git a/data/spectrast/spectrastbioschemas.jsonld b/data/spectrast/spectrastbioschemas.jsonld index 91286c33e74f1..cc41ddaaedcdc 100644 --- a/data/spectrast/spectrastbioschemas.jsonld +++ b/data/spectrast/spectrastbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Matches peptide MS/MS spectra with library spectra.", "sc:name": "SpectraST", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.peptideatlas.org/spectrast/" } \ No newline at end of file diff --git a/data/spectre-phylogeny/spectre-phylogenybioschemas.jsonld b/data/spectre-phylogeny/spectre-phylogenybioschemas.jsonld index abea42f671087..0fc60f9582a51 100644 --- a/data/spectre-phylogeny/spectre-phylogenybioschemas.jsonld +++ b/data/spectre-phylogeny/spectre-phylogenybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "SPECTRE", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/maplesond/SPECTRE" } \ No newline at end of file diff --git a/data/spectre/spectrebioschemas.jsonld b/data/spectre/spectrebioschemas.jsonld index b65fb4b629d9c..daed350f3d3c0 100644 --- a/data/spectre/spectrebioschemas.jsonld +++ b/data/spectre/spectrebioschemas.jsonld @@ -17,15 +17,15 @@ "@id": "https://bio.tools/spectre", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Script", - "Command-line tool" + "Command-line tool", + "Script" ], "sc:citation": [ + "pubmed:27884106", + "pmcid:PMC5123373", { "@id": "https://doi.org/10.1186/s12859-016-1355-4" - }, - "pubmed:27884106", - "pmcid:PMC5123373" + } ], "sc:description": "Model the overall tri­nucleotide periodicity of ribosomal occupancy using a classifier based on spectral coherence. Examine the relationship of normalized ribosome profiling read coverage over a rolling series of windows along a transcript relative to an idealized reference signal without the matched requirement of mRNA-Seq.", "sc:featureList": { @@ -33,8 +33,8 @@ }, "sc:name": "SPECtre", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/mills-lab/spectre" } diff --git a/data/spectrum_similarity/spectrum_similaritybioschemas.jsonld b/data/spectrum_similarity/spectrum_similaritybioschemas.jsonld index ea74e8c39f0d2..75dd4252476e9 100644 --- a/data/spectrum_similarity/spectrum_similaritybioschemas.jsonld +++ b/data/spectrum_similarity/spectrum_similaritybioschemas.jsonld @@ -14,13 +14,13 @@ "sc:description": "A pipeline for differential proteomics in unsequenced species.", "sc:name": "Spectrum similarity", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "Ghent University", - "ugent.be" + "ugent.be", + "Ghent University" ], "sc:url": "https://github.com/compomics/spectrum_similarity", "sc:version": "1" diff --git a/data/spedre/spedrebioschemas.jsonld b/data/spedre/spedrebioschemas.jsonld index a78de52d5b1f9..dd1229c30d1bc 100644 --- a/data/spedre/spedrebioschemas.jsonld +++ b/data/spedre/spedrebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SPEDRE (Systematic Parameter Estimation in Data-Rich Environments) is a web server for estimating rate parameters of cell signalling dynamics in data-rich environments. SPEDRE estimates reaction rates for biochemical networks, taking as input the connectivity of the network and the concentrations of the molecular species at discrete time points.", "sc:name": "SPEDRE", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://LTKLab.org/SPEDRE" } \ No newline at end of file diff --git a/data/speer-server/speer-serverbioschemas.jsonld b/data/speer-server/speer-serverbioschemas.jsonld index 7a63b65f10ff9..c184e87185591 100644 --- a/data/speer-server/speer-serverbioschemas.jsonld +++ b/data/speer-server/speer-serverbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SPEER-SERVER", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.hpppi.iicb.res.in/ss/" } \ No newline at end of file diff --git a/data/spell/spellbioschemas.jsonld b/data/spell/spellbioschemas.jsonld index 9212749c4fcfb..193dc6a3c6737 100644 --- a/data/spell/spellbioschemas.jsonld +++ b/data/spell/spellbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Query-driven search engine for large gene expression microarray compendia. Given a small set of query genes, identifies which datasets are most informative for these genes, then within those datasets additional genes are identified with expression profiles most similar to the query set.", "sc:name": "SPELL", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://spell.princeton.edu/", "sc:version": "2.0.3" diff --git a/data/spem/spembioschemas.jsonld b/data/spem/spembioschemas.jsonld index 038939db50c21..8acf05ae16c15 100644 --- a/data/spem/spembioschemas.jsonld +++ b/data/spem/spembioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xinyi YANG", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package can optimize the parameter in S-system models given time series data.", "sc:license": "GPL-2.0", "sc:name": "SPEM", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SPEM.html", "sc:version": "1.14.0" diff --git a/data/speplip/speplipbioschemas.jsonld b/data/speplip/speplipbioschemas.jsonld index 6b04a76bdda67..2379170678535 100644 --- a/data/speplip/speplipbioschemas.jsonld +++ b/data/speplip/speplipbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SPEPLip", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://gpcr.biocomp.unibo.it/cgi/predictors/spep/pred_spepcgi.cgi" } \ No newline at end of file diff --git a/data/spex2/spex2bioschemas.jsonld b/data/spex2/spex2bioschemas.jsonld index d348663affac8..0efae12e19016 100644 --- a/data/spex2/spex2bioschemas.jsonld +++ b/data/spex2/spex2bioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/spex2", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Workflow", - "Command-line tool" + "Command-line tool", + "Workflow" ], "sc:citation": "pubmed:20529936", "sc:description": "An automatic system for embryonic ISH image processing, which can extract, transform, compare, classify and cluster spatial gene expression patterns in Drosophila embryos.", "sc:name": "SPEX2", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.sailing.cs.cmu.edu/main/?page_id=511" } \ No newline at end of file diff --git a/data/spharm-pdm/spharm-pdmbioschemas.jsonld b/data/spharm-pdm/spharm-pdmbioschemas.jsonld index de20ad2cd01bc..9dd0bf2d1e88f 100644 --- a/data/spharm-pdm/spharm-pdmbioschemas.jsonld +++ b/data/spharm-pdm/spharm-pdmbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Apache-2.0", "sc:name": "SPHARM-PDM", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://www.nitrc.org/projects/spharm-pdm/" diff --git a/data/spia/spiabioschemas.jsonld b/data/spia/spiabioschemas.jsonld index a7290075a2595..fd4e161113f4d 100644 --- a/data/spia/spiabioschemas.jsonld +++ b/data/spia/spiabioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Adi Laurentiu Tarca", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package implements the Signaling Pathway Impact Analysis which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.", "sc:name": "SPIA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SPIA.html", "sc:version": "2.26.0" diff --git a/data/spice-classify/spice-classifybioschemas.jsonld b/data/spice-classify/spice-classifybioschemas.jsonld index 61ed74d549410..b52b63cd1b98e 100644 --- a/data/spice-classify/spice-classifybioschemas.jsonld +++ b/data/spice-classify/spice-classifybioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "B. A. Vandenberg", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:24685258", { "@id": "https://doi.org/10.1186/1471-2105-15-93" }, - "pmcid:PMC4021553" + "pmcid:PMC4021553", + "pubmed:24685258" ], "sc:description": "Sequence-based protein classification and exploration.", "sc:featureList": { @@ -31,8 +31,8 @@ }, "sc:name": "SPiCE", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/basvandenberg/spice" } diff --git a/data/spider-barcoding/spider-barcodingbioschemas.jsonld b/data/spider-barcoding/spider-barcodingbioschemas.jsonld index 38d8411caede3..46992449861ca 100644 --- a/data/spider-barcoding/spider-barcodingbioschemas.jsonld +++ b/data/spider-barcoding/spider-barcodingbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A new R package implementing a number of useful analyses for DNA barcoding studies and associated research into species delimitation and speciation.", "sc:name": "SpideR", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://spider.r-forge.r-project.org/SpiderWebSite/spider.html" } \ No newline at end of file diff --git a/data/spidermass/spidermassbioschemas.jsonld b/data/spidermass/spidermassbioschemas.jsonld index be406fbbed745..9d66894c4633c 100644 --- a/data/spidermass/spidermassbioschemas.jsonld +++ b/data/spidermass/spidermassbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Semantic chemical database generation, metabolite identification and ''de novo'' formula generation.", "sc:name": "SpiderMass", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://lababi.bioprocess.org/index.php/lababi-software/80-spidermass" } \ No newline at end of file diff --git a/data/spidermir/spidermirbioschemas.jsonld b/data/spidermir/spidermirbioschemas.jsonld index 1981a0c8ef455..964ce4852e49e 100644 --- a/data/spidermir/spidermirbioschemas.jsonld +++ b/data/spidermir/spidermirbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Claudia Cava", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Aims: i) Facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data with appropriate gene nomenclature, iii) integration of miRNA data in a specific network, iv) provide different standard analyses and v) allow the user to visualize the results. In more detail, the package provides multiple methods for query, prepare and download network data, and the integration with validated and predicted miRNA data, the use of standard analysis and visualization methods.", "sc:license": "GPL-3.0", "sc:name": "SpidermiR", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SpidermiR.html", "sc:version": "1.4.4" diff --git a/data/spike/spikebioschemas.jsonld b/data/spike/spikebioschemas.jsonld index 76deb9242cf10..be24a415c938e 100644 --- a/data/spike/spikebioschemas.jsonld +++ b/data/spike/spikebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database for highly curated interactions for particular human pathways, along with literature-referenced information on the nature of each interaction. Pathways are laid out as maps that reflect the curator's understanding and make the utilization of the pathways easy. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways.", "sc:name": "SPIKE", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.cs.tau.ac.il/~spike/" } \ No newline at end of file diff --git a/data/spikeli/bioconda_spikeli.yaml b/data/spikeli/bioconda_spikeli.yaml index d17c694e98377..f0037c8f9096a 100644 --- a/data/spikeli/bioconda_spikeli.yaml +++ b/data/spikeli/bioconda_spikeli.yaml @@ -9,7 +9,6 @@ description: SpikeLI is a package that performs the analysis of the Affymetrix s home: https://bioconductor.org/packages/3.10/bioc/html/spikeLI.html identifiers: - biotools:spikeli -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-spikeli diff --git a/data/spikeli/spikelibioschemas.jsonld b/data/spikeli/spikelibioschemas.jsonld index bcda6b278a0e6..019395d32ee7e 100644 --- a/data/spikeli/spikelibioschemas.jsonld +++ b/data/spikeli/spikelibioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Enrico Carlon", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).", "sc:license": "GPL-2.0", "sc:name": "spikeLI", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/spikeLI.html", "sc:version": "2.34.0" diff --git a/data/spin/spinbioschemas.jsonld b/data/spin/spinbioschemas.jsonld index b202dfe7c10a7..281a4d0e1eebb 100644 --- a/data/spin/spinbioschemas.jsonld +++ b/data/spin/spinbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0002-1724-8358", - "@type": "schema:Person" + "@id": "https://doi.org/10.1186/1748-7188-7-33", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/spin", @@ -27,11 +27,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC3608327", { "@id": "https://doi.org/10.1186/1748-7188-7-33" }, - "pubmed:23190710", - "pmcid:PMC3608327" + "pubmed:23190710" ], "sc:description": "Model selection in phylogenetics based on algebraic invariants.", "sc:featureList": { @@ -44,8 +44,8 @@ "sc:version": "1" }, { - "@id": "https://doi.org/10.1186/1748-7188-7-33", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0002-1724-8358", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/spindel_workbench/spindel_workbenchbioschemas.jsonld b/data/spindel_workbench/spindel_workbenchbioschemas.jsonld index 64c8a98cfa252..2d943974a176c 100644 --- a/data/spindel_workbench/spindel_workbenchbioschemas.jsonld +++ b/data/spindel_workbench/spindel_workbenchbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/spindel_workbench", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Filipe Pereira", - "João Carneiro" + "João Carneiro", + "Filipe Pereira" ], "sc:additionalType": "Web application", "sc:description": "Method for species identification in all domains of life using multiplex analysis of variable-length sequences containing multiple insertion/deletion (indel) variants.", diff --git a/data/spindlep/spindlepbioschemas.jsonld b/data/spindlep/spindlepbioschemas.jsonld index 1af8b04f98332..2ddc3c0de4644 100644 --- a/data/spindlep/spindlepbioschemas.jsonld +++ b/data/spindlep/spindlepbioschemas.jsonld @@ -26,11 +26,11 @@ "@id": "edam:topic_0140" }, "sc:citation": [ - "pmcid:PMC3302876", + "pubmed:22427808", { "@id": "https://doi.org/10.1371/journal.pone.0031813" }, - "pubmed:22427808" + "pmcid:PMC3302876" ], "sc:description": "Neural networks prediction of whether a human gene is located at the meiotic spindle.", "sc:featureList": { @@ -39,9 +39,9 @@ "sc:license": "Other", "sc:name": "SpindleP", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/SpindleP/", diff --git a/data/spiral_genetics/spiral_geneticsbioschemas.jsonld b/data/spiral_genetics/spiral_geneticsbioschemas.jsonld index 9a5c14f2b1855..a97439f279619 100644 --- a/data/spiral_genetics/spiral_geneticsbioschemas.jsonld +++ b/data/spiral_genetics/spiral_geneticsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Novel aligner/variant caller, Anchored Assembly, which can detect large structural variations using short read NGS data with unmatched precision.", "sc:name": "Spiral Genetics", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.spiralgenetics.com" } \ No newline at end of file diff --git a/data/spirpro/spirprobioschemas.jsonld b/data/spirpro/spirprobioschemas.jsonld index 1117465ac8002..497177cf747ca 100644 --- a/data/spirpro/spirprobioschemas.jsonld +++ b/data/spirpro/spirprobioschemas.jsonld @@ -18,13 +18,13 @@ "sc:description": "A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.", "sc:name": "SpirPro", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ - "King Mongkut's University of Technology (Thonburi)", "National Center for Genetic Engineering and Biotechnology", + "King Mongkut's University of Technology (Thonburi)", "KMUTT" ], "sc:url": "http://spirpro.sbi.kmutt.ac.th" diff --git a/data/spktools/spktoolsbioschemas.jsonld b/data/spktools/spktoolsbioschemas.jsonld index 577516fd8dfc5..8f55eb1538a0a 100644 --- a/data/spktools/spktoolsbioschemas.jsonld +++ b/data/spktools/spktoolsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "spkTools", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/spkTools.html", "sc:version": "1.30.0" diff --git a/data/spladder/spladderbioschemas.jsonld b/data/spladder/spladderbioschemas.jsonld index a3bad3e98ec87..d3585ce6f49a7 100644 --- a/data/spladder/spladderbioschemas.jsonld +++ b/data/spladder/spladderbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SplAdder", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://raetschlab.org/suppl/spladder" } \ No newline at end of file diff --git a/data/splatche3/splatche3bioschemas.jsonld b/data/splatche3/splatche3bioschemas.jsonld index 68a4ac05b1f0e..612d85d199127 100644 --- a/data/splatche3/splatche3bioschemas.jsonld +++ b/data/splatche3/splatche3bioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mathias Currat", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:citation": "pubmed:31077292", "sc:description": "Simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.", "sc:license": "Unlicense", "sc:name": "SPLATCHE3", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.splatche.com/splatche3" } \ No newline at end of file diff --git a/data/splatter/splatterbioschemas.jsonld b/data/splatter/splatterbioschemas.jsonld index 2baf42c0e64d8..205672f7d4f61 100644 --- a/data/splatter/splatterbioschemas.jsonld +++ b/data/splatter/splatterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "splatter", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/splatter.html", "sc:version": "1.4.1" diff --git a/data/spliceaid-f/spliceaid-fbioschemas.jsonld b/data/spliceaid-f/spliceaid-fbioschemas.jsonld index c4bda589d4a7d..7d0beb9bca25c 100644 --- a/data/spliceaid-f/spliceaid-fbioschemas.jsonld +++ b/data/spliceaid-f/spliceaid-fbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "SpliceAid-F", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "ELIXIR-ITA-CNR", "sc:url": "http://srv00.recas.ba.infn.it/SpliceAidF/" diff --git a/data/spliceaid/spliceaidbioschemas.jsonld b/data/spliceaid/spliceaidbioschemas.jsonld index 56500aab8efe3..55062e882f6d5 100644 --- a/data/spliceaid/spliceaidbioschemas.jsonld +++ b/data/spliceaid/spliceaidbioschemas.jsonld @@ -24,9 +24,9 @@ "sc:description": "Experimental RNA target motifs bound by splicing proteins in humans.", "sc:name": "SpliceAid", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.introni.it/splicing.html" } diff --git a/data/splicedisease_db/splicedisease_dbbioschemas.jsonld b/data/splicedisease_db/splicedisease_dbbioschemas.jsonld index 3ca855b198678..4978b52ee8cf8 100644 --- a/data/splicedisease_db/splicedisease_dbbioschemas.jsonld +++ b/data/splicedisease_db/splicedisease_dbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Linking RNA splicing and disease. Database that collects and curates data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease.", "sc:name": "SpliceDisease DB", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://202.38.126.151:8080/SDisease/" } \ No newline at end of file diff --git a/data/splicegear/bioconda_splicegear.yaml b/data/splicegear/bioconda_splicegear.yaml index bed53ca0ab719..2a13c8ccea49e 100644 --- a/data/splicegear/bioconda_splicegear.yaml +++ b/data/splicegear/bioconda_splicegear.yaml @@ -3,7 +3,6 @@ description: A set of tools to work with alternative splicing home: https://bioconductor.org/packages/3.10/bioc/html/splicegear.html identifiers: - biotools:splicegear -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-splicegear diff --git a/data/splicegear/splicegearbioschemas.jsonld b/data/splicegear/splicegearbioschemas.jsonld index befffd7ec2263..0606ba8bd38d3 100644 --- a/data/splicegear/splicegearbioschemas.jsonld +++ b/data/splicegear/splicegearbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laurent Gautier", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A set of tools to work with alternative splicing.", "sc:license": "GPL-3.0", "sc:name": "splicegear", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/splicegear.html", "sc:version": "1.46.0" diff --git a/data/splicegrapher/splicegrapherbioschemas.jsonld b/data/splicegrapher/splicegrapherbioschemas.jsonld index c2d1ad96d7874..65d95a6fa1c09 100644 --- a/data/splicegrapher/splicegrapherbioschemas.jsonld +++ b/data/splicegrapher/splicegrapherbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "SpliceGrapher is a package for creating splice graphs from RNA-Seq data, guided by gene models and EST data (when available).", "sc:name": "SpliceGrapher", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://splicegrapher.sourceforge.net/" } \ No newline at end of file diff --git a/data/splicemachine/splicemachinebioschemas.jsonld b/data/splicemachine/splicemachinebioschemas.jsonld index f6ab5f59a5598..1d19347275fa3 100644 --- a/data/splicemachine/splicemachinebioschemas.jsonld +++ b/data/splicemachine/splicemachinebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Splice site prediction.", "sc:name": "SpliceMachine", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/SpliceMachine", diff --git a/data/spliceogen/spliceogenbioschemas.jsonld b/data/spliceogen/spliceogenbioschemas.jsonld index 525cd4747638e..71d1a1948b116 100644 --- a/data/spliceogen/spliceogenbioschemas.jsonld +++ b/data/spliceogen/spliceogenbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "Spliceogen", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/VCCRI/Spliceogen" } \ No newline at end of file diff --git a/data/spliceplot/spliceplotbioschemas.jsonld b/data/spliceplot/spliceplotbioschemas.jsonld index c3b4d1bc8ebaa..440b75687b02d 100644 --- a/data/spliceplot/spliceplotbioschemas.jsonld +++ b/data/spliceplot/spliceplotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SplicePlot is a simple command line utility that produces intuitive visualization of alternative splicing and splicing quantitative trait loci (sQTL) and their effects", "sc:name": "SplicePlot", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://montgomerylab.stanford.edu/spliceplot/index.html" } \ No newline at end of file diff --git a/data/spliceport/spliceportbioschemas.jsonld b/data/spliceport/spliceportbioschemas.jsonld index 50d5040d946af..28ba8ffceddb1 100644 --- a/data/spliceport/spliceportbioschemas.jsonld +++ b/data/spliceport/spliceportbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SplicePort makes splice-site predictions for submitted sequences, and allows browsing of the motifs used in the prediction. Feature selection is optimized for human splice sites.", "sc:name": "SplicePort", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://spliceport.cbcb.umd.edu/" diff --git a/data/splicer/splicerbioschemas.jsonld b/data/splicer/splicerbioschemas.jsonld index 52f54216d5f37..7d943c03dad66 100644 --- a/data/splicer/splicerbioschemas.jsonld +++ b/data/splicer/splicerbioschemas.jsonld @@ -11,20 +11,20 @@ "@id": "https://bio.tools/splicer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kristoffer Vitting-Seerup", - "Johannes Waage" + "Johannes Waage", + "Kristoffer Vitting-Seerup" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.", "sc:license": "GPL-2.0", "sc:name": "spliceR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/spliceR.html", "sc:version": "1.16.0" diff --git a/data/splicev/splicevbioschemas.jsonld b/data/splicev/splicevbioschemas.jsonld index 8806915ed6346..1b0248f70df2c 100644 --- a/data/splicev/splicevbioschemas.jsonld +++ b/data/splicev/splicevbioschemas.jsonld @@ -9,32 +9,28 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-019-2865-7", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/SpliceV", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Erik Flemington", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC6507234", { "@id": "https://doi.org/10.1186/S12859-019-2865-7" }, + "pmcid:PMC6507234", "pubmed:31068132" ], "sc:description": "Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.", "sc:featureList": [ { - "@id": "edam:operation_0433" + "@id": "edam:operation_0264" }, { "@id": "edam:operation_0446" }, { - "@id": "edam:operation_0264" + "@id": "edam:operation_0433" } ], "sc:license": "GPL-3.0", @@ -44,6 +40,10 @@ "Mac" ], "sc:url": "https://github.com/flemingtonlab/SpliceV" + }, + { + "@id": "https://doi.org/10.1186/S12859-019-2865-7", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/splicing_express/splicing_expressbioschemas.jsonld b/data/splicing_express/splicing_expressbioschemas.jsonld index 237579f27b690..328e3087e0e0e 100644 --- a/data/splicing_express/splicing_expressbioschemas.jsonld +++ b/data/splicing_express/splicing_expressbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/splicing_express", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Suite", - "Command-line tool" + "Command-line tool", + "Suite" ], "sc:citation": "pubmed:26618088", "sc:description": "A software suite for alternative splicing analysis using next-generation sequencing data.", diff --git a/data/splicinggraphs/splicinggraphsbioschemas.jsonld b/data/splicinggraphs/splicinggraphsbioschemas.jsonld index bd1225a2667f4..b12bb1938f4ab 100644 --- a/data/splicinggraphs/splicinggraphsbioschemas.jsonld +++ b/data/splicinggraphs/splicinggraphsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "H. Pagès", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.", "sc:license": "Artistic-2.0", "sc:name": "SplicingGraphs", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SplicingGraphs.html", "sc:version": "1.14.0" diff --git a/data/splicingtypesanno/splicingtypesannobioschemas.jsonld b/data/splicingtypesanno/splicingtypesannobioschemas.jsonld index 64b2a05f0e201..29979335bf085 100644 --- a/data/splicingtypesanno/splicingtypesannobioschemas.jsonld +++ b/data/splicingtypesanno/splicingtypesannobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Annotates four major splicing types by RNA-Seq data, including intron retention, exon skipping, alternative donor site, and alternative acceptor site. As a post-processing tool for alignment files, it annotates the alternative splicing types with details at the intron or exon level.", "sc:name": "SplicingTypesAnno", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sourceforge.net/projects/splicingtypes/" } \ No newline at end of file diff --git a/data/splicingviewer/splicingviewerbioschemas.jsonld b/data/splicingviewer/splicingviewerbioschemas.jsonld index 08e3bb636d094..f42ddd62a281e 100644 --- a/data/splicingviewer/splicingviewerbioschemas.jsonld +++ b/data/splicingviewer/splicingviewerbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/splicingviewer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Linglin Zhou", - "Huabin Hou", "SplicingViewer team", - "Qi Liu" + "Qi Liu", + "Huabin Hou", + "Linglin Zhou" ], "sc:additionalType": "Desktop application", "sc:description": "SplicingViewer is an integrated tool developed to enable users to detect the splice junctions, annotate alternative splicing events, and visualization of the patterns of alternative splicing events.", "sc:license": "BSD-3-Clause", "sc:name": "SplicingViewer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinformatics.zj.cn/splicingviewer/" } \ No newline at end of file diff --git a/data/splinetimer/splinetimerbioschemas.jsonld b/data/splinetimer/splinetimerbioschemas.jsonld index 46c775b546445..25077b3fc5e4a 100644 --- a/data/splinetimer/splinetimerbioschemas.jsonld +++ b/data/splinetimer/splinetimerbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Herbert Braselmann", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks.", "sc:license": "GPL-3.0", "sc:name": "splineTimeR", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/splineTimeR.html", diff --git a/data/splinter/bioconda_splinter.yaml b/data/splinter/bioconda_splinter.yaml index 2674152247232..4298ae6195c17 100644 --- a/data/splinter/bioconda_splinter.yaml +++ b/data/splinter/bioconda_splinter.yaml @@ -5,7 +5,6 @@ description: Provides tools to analyze alternative splicing sites, interpret out home: https://bioconductor.org/packages/3.10/bioc/html/SPLINTER.html identifiers: - biotools:splinter -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-splinter diff --git a/data/splinter/splinterbioschemas.jsonld b/data/splinter/splinterbioschemas.jsonld index 9562a3321b129..deb11b053a2b0 100644 --- a/data/splinter/splinterbioschemas.jsonld +++ b/data/splinter/splinterbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "SPLINTER", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SPLINTER.html", "sc:version": "1.0.0" diff --git a/data/split-gal4/split-gal4bioschemas.jsonld b/data/split-gal4/split-gal4bioschemas.jsonld index cabeeb8c33ab8..837ab2517d006 100644 --- a/data/split-gal4/split-gal4bioschemas.jsonld +++ b/data/split-gal4/split-gal4bioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.7554/ELIFE.43079", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0002-0587-9355", - "@type": "schema:Person" - }, { "@id": "https://orcid.org/0000-0001-8762-8703", "@type": "schema:Person" @@ -57,6 +49,14 @@ "Mac" ], "sc:url": "http://www.janelia.org/split-gal4" + }, + { + "@id": "https://doi.org/10.7554/ELIFE.43079", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0002-0587-9355", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/splitpocket/splitpocketbioschemas.jsonld b/data/splitpocket/splitpocketbioschemas.jsonld index 93febf20e2512..bb4e5ec1940ad 100644 --- a/data/splitpocket/splitpocketbioschemas.jsonld +++ b/data/splitpocket/splitpocketbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding ligand. >,26,000 structures in PDB have been found to have split pockets.", "sc:name": "SplitPocket", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://pocket.med.wayne.edu/patch/" } \ No newline at end of file diff --git a/data/splitsource/splitsourcebioschemas.jsonld b/data/splitsource/splitsourcebioschemas.jsonld index 3f176cd2a1ab1..38764fc8ca8e0 100644 --- a/data/splitsource/splitsourcebioschemas.jsonld +++ b/data/splitsource/splitsourcebioschemas.jsonld @@ -13,9 +13,9 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", + "Wellcome Trust", "EMBOSS Contributors", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:description": "Split sequence(s) into original source sequences.", "sc:funder": [ @@ -27,12 +27,12 @@ "sc:name": "splitsource", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/splitsource.html", "sc:version": "r6" diff --git a/data/splitter/splitterbioschemas.jsonld b/data/splitter/splitterbioschemas.jsonld index bb8f76e7c7d66..8eedf785b3152 100644 --- a/data/splitter/splitterbioschemas.jsonld +++ b/data/splitter/splitterbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "Wellcome Trust", "UK MRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Split sequence(s) into smaller sequences.", "sc:funder": [ - "Wellcome Trust", "UK MRC", + "Wellcome Trust", "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "splitter", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/splitter.html", "sc:version": "r6" diff --git a/data/splots/bioconda_splots.yaml b/data/splots/bioconda_splots.yaml index 95dd44869ead2..21866965dad99 100644 --- a/data/splots/bioconda_splots.yaml +++ b/data/splots/bioconda_splots.yaml @@ -4,7 +4,6 @@ description: The splots package provides the plotScreen function for visualising home: https://bioconductor.org/packages/3.10/bioc/html/splots.html identifiers: - biotools:splots -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-splots diff --git a/data/splots/splotsbioschemas.jsonld b/data/splots/splotsbioschemas.jsonld index 1d2b35cabb4e3..a9f3f57e512ce 100644 --- a/data/splots/splotsbioschemas.jsonld +++ b/data/splots/splotsbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "splots", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/splots.html", "sc:version": "1.40.0" diff --git a/data/spm/spmbioschemas.jsonld b/data/spm/spmbioschemas.jsonld index ce09edfa66e32..60f6386f10686 100644 --- a/data/spm/spmbioschemas.jsonld +++ b/data/spm/spmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "SPM", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://www.fil.ion.ucl.ac.uk/spm/" } \ No newline at end of file diff --git a/data/spmm/spmmbioschemas.jsonld b/data/spmm/spmmbioschemas.jsonld index 3f8d5a36af64c..ecf51c9f963b6 100644 --- a/data/spmm/spmmbioschemas.jsonld +++ b/data/spmm/spmmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool estimates the infection duration of a single variant or multi-variant HIV infections based on the characteristics of HIV transmission and early evolution.", "sc:name": "SPMM", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://p512.usc.edu/" } \ No newline at end of file diff --git a/data/spnconverter/spnconverterbioschemas.jsonld b/data/spnconverter/spnconverterbioschemas.jsonld index b0734c46f05a6..af0bb61a0f728 100644 --- a/data/spnconverter/spnconverterbioschemas.jsonld +++ b/data/spnconverter/spnconverterbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language (SBML) to Graphml format.", "sc:name": "SPNConverter", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.picb.ac.cn/ClinicalGenomicNTW/SPNConverter.html", diff --git a/data/sponge/spongebioschemas.jsonld b/data/sponge/spongebioschemas.jsonld index 381626dca9c6d..9521a3d71f0f8 100644 --- a/data/sponge/spongebioschemas.jsonld +++ b/data/sponge/spongebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SPONGE", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SPONGE.html", "sc:version": "1.2.0" diff --git a/data/spongescan/spongescanbioschemas.jsonld b/data/spongescan/spongescanbioschemas.jsonld index 06ea6b3f53724..cdc3e8fbf4da6 100644 --- a/data/spongescan/spongescanbioschemas.jsonld +++ b/data/spongescan/spongescanbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "spongeScan", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://spongescan.rc.ufl.edu/" } \ No newline at end of file diff --git a/data/spot-seq-rna/spot-seq-rnabioschemas.jsonld b/data/spot-seq-rna/spot-seq-rnabioschemas.jsonld index 908bb8481b6ae..717301f09575f 100644 --- a/data/spot-seq-rna/spot-seq-rnabioschemas.jsonld +++ b/data/spot-seq-rna/spot-seq-rnabioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1007/978-1-4939-0366-5_9", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/spot-seq-rna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yaoqi Zhou", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:24573478", - "pmcid:PMC3937850", { "@id": "https://doi.org/10.1007/978-1-4939-0366-5_9" - } + }, + "pubmed:24573478", + "pmcid:PMC3937850" ], "sc:description": "Predicting Protein–RNA Complex Structure and RNA-Binding Function by Fold Recognition and Binding Affinity Prediction.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "SPOT-Seq-RNA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://sparks-lab.org/server/SPOT-Seq-RNA/" + }, + { + "@id": "https://doi.org/10.1007/978-1-4939-0366-5_9", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/spot-struct-dna/spot-struct-dnabioschemas.jsonld b/data/spot-struct-dna/spot-struct-dnabioschemas.jsonld index 18b5bb5a8a41c..84c8fc40a4351 100644 --- a/data/spot-struct-dna/spot-struct-dnabioschemas.jsonld +++ b/data/spot-struct-dna/spot-struct-dnabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "SPOT-Struct-DNA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sparks-lab.org/yueyang/server/SPOT-Struct-DNA" } \ No newline at end of file diff --git a/data/spot/spotbioschemas.jsonld b/data/spot/spotbioschemas.jsonld index eab919232a1c7..d2a6d51fd3c17 100644 --- a/data/spot/spotbioschemas.jsonld +++ b/data/spot/spotbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A web‐based program that prioritizes the results of a genetic association study using genomic annotation data.Given a collection that are to receive higher priority when selecting SNPs for further study after an initial genetic association study, SPOT offers a systematic way of doing this while taking into a account a variety range of additional biological information.", "sc:name": "SPOT", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://spot.cgsmd.isi.edu" } \ No newline at end of file diff --git a/data/spotcaliper/spotcaliperbioschemas.jsonld b/data/spotcaliper/spotcaliperbioschemas.jsonld index 446f9a5a730fb..d55a5077363f9 100644 --- a/data/spotcaliper/spotcaliperbioschemas.jsonld +++ b/data/spotcaliper/spotcaliperbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A novel wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size.", "sc:name": "SpotCaliper", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bigwww.epfl.ch/algorithms/spotcaliper/" diff --git a/data/spotlight/spotlightbioschemas.jsonld b/data/spotlight/spotlightbioschemas.jsonld index 12be129ecd202..534a50133347f 100644 --- a/data/spotlight/spotlightbioschemas.jsonld +++ b/data/spotlight/spotlightbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The tool is designed to detect community structures in a network. Community, in which vertices are joined tightly together, between which there are only looser edges, exists in many real networks.", "sc:name": "Spotlight", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://hub.iis.sinica.edu.tw/spotlight/" } \ No newline at end of file diff --git a/data/spotlite/spotlitebioschemas.jsonld b/data/spotlite/spotlitebioschemas.jsonld index 97f4c24a722d3..a2f5a6ba438c6 100644 --- a/data/spotlite/spotlitebioschemas.jsonld +++ b/data/spotlite/spotlitebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A user-friendly web application for predicting complex co-membership from affinity purification – mass spectrometry data. This web application employs a logistic regression classifier that integrates existing, proven APMS scoring approaches (SAINT, CompPASS, and HGSCore), gene co-expression patterns, functional annotations, domain-domain binding affinity, and homologous interactions, which we have shown outperforms existing APMS scoring methods.", "sc:name": "Spotlite", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://cancer.unc.edu/majorlab/software.php" diff --git a/data/spotpy/spotpybioschemas.jsonld b/data/spotpy/spotpybioschemas.jsonld index ce6669e75d9a1..beec891bbb1d2 100644 --- a/data/spotpy/spotpybioschemas.jsonld +++ b/data/spotpy/spotpybioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0145180", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0001-7780-2376", "@type": "schema:Person" @@ -21,8 +25,8 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4682995", "pubmed:26680783", + "pmcid:PMC4682995", { "@id": "https://doi.org/10.1371/journal.pone.0145180" } @@ -39,10 +43,6 @@ "Windows" ], "sc:url": "https://pypi.org/project/spotpy/" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0145180", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/spotsegmentation/spotsegmentationbioschemas.jsonld b/data/spotsegmentation/spotsegmentationbioschemas.jsonld index e88bf38b9a512..966d5f06452f4 100644 --- a/data/spotsegmentation/spotsegmentationbioschemas.jsonld +++ b/data/spotsegmentation/spotsegmentationbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chris Fraley", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Spot segmentation via model-based clustering and gridding for blocks within microarray slides, as described in Li et al, Robust Model-Based Segmentation of Microarray Images, Technical Report no. 473, Department of Statistics, University of Washington.", "sc:license": "GPL-2.0", "sc:name": "spotSegmentation", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/spotSegmentation.html", diff --git a/data/spotyping/spotypingbioschemas.jsonld b/data/spotyping/spotypingbioschemas.jsonld index a9f10d638f141..4fdc09a53e4e5 100644 --- a/data/spotyping/spotypingbioschemas.jsonld +++ b/data/spotyping/spotypingbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S13073-016-0270-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/spotyping", "@type": "sc:SoftwareApplication", @@ -32,10 +36,6 @@ ], "sc:url": "https://github.com/xiaeryu/SpoTyping-v2.0", "sc:version": "2.0" - }, - { - "@id": "https://doi.org/10.1186/S13073-016-0270-7", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sppg/sppgbioschemas.jsonld b/data/sppg/sppgbioschemas.jsonld index 6ee15176d1f75..4d2993ce48609 100644 --- a/data/sppg/sppgbioschemas.jsonld +++ b/data/sppg/sppgbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Sequence Platform for the phylogenetic analysis of Plant Genes.", "sc:name": "SPPG", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "ugent.be", diff --git a/data/sppider/sppiderbioschemas.jsonld b/data/sppider/sppiderbioschemas.jsonld index 6564427785c59..a5c1565d2f55b 100644 --- a/data/sppider/sppiderbioschemas.jsonld +++ b/data/sppider/sppiderbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The server can be used to: (1) predict residues to be at the putative protein interface(s) by considering single protein chain with resolved 3D structure; (2) analyse protein-protein complex with given 3D structural information and identify residues that are being in interchain contact.", "sc:name": "SPPIDER", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sppider.cchmc.org/" } \ No newline at end of file diff --git a/data/spring/springbioschemas.jsonld b/data/spring/springbioschemas.jsonld index eb7b028bd0373..65bd8e9e50317 100644 --- a/data/spring/springbioschemas.jsonld +++ b/data/spring/springbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Chuan Yi Tang", - "Ying Chih Lin", - "Chin Lung Lu" + "Chin Lung Lu", + "Ying Chih Lin" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:15814563", "sc:description": "A tool for the analysis of genome rearrangements. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges for transforming one chromosome into another. Phylogenetic trees based on the rearrangement analysis are also shown as part of the results.", "sc:name": "SPRING", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://algorithm.cs.nthu.edu.tw/tools/SPRING" } \ No newline at end of file diff --git a/data/sprint-rna/sprint-rnabioschemas.jsonld b/data/sprint-rna/sprint-rnabioschemas.jsonld index 2c1457ee13dbb..ecd9087c22f52 100644 --- a/data/sprint-rna/sprint-rnabioschemas.jsonld +++ b/data/sprint-rna/sprint-rnabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "SNP-free toolkit for identifying RNA editing sites.", "sc:name": "SPRINT", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sprint.tianlab.cn/" } \ No newline at end of file diff --git a/data/sprite/spritebioschemas.jsonld b/data/sprite/spritebioschemas.jsonld index e419b9ff44431..4a728027df19a 100644 --- a/data/sprite/spritebioschemas.jsonld +++ b/data/sprite/spritebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SPRITE is a protein structural motif database searching program. Users can upload a PDB file of a query protein structure, and SPRITE compares the input coordinates to a database of 3D side chain arrangements of sites and motifs using a graph theoretical approach.", "sc:name": "SPRITE", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://mfrlab.org/grafss/sprite" } \ No newline at end of file diff --git a/data/spritz/spritzbioschemas.jsonld b/data/spritz/spritzbioschemas.jsonld index 2321d5673e6a1..b4a3522f6ede8 100644 --- a/data/spritz/spritzbioschemas.jsonld +++ b/data/spritz/spritzbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Spritz", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://distill.ucd.ie/spritz/" } \ No newline at end of file diff --git a/data/spurio/spuriobioschemas.jsonld b/data/spurio/spuriobioschemas.jsonld index 37197bcc36668..dfa8ac651bb1b 100644 --- a/data/spurio/spuriobioschemas.jsonld +++ b/data/spurio/spuriobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/f1000research.14050.1", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/spurio", "@type": "sc:SoftwareApplication", @@ -16,10 +20,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5897793", + "pubmed:29721311", { "@id": "https://doi.org/10.12688/f1000research.14050.1" - }, - "pubmed:29721311" + } ], "sc:description": "Identify spurious protein predictions in prokaryotes. It searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequences. Features of the matches are used to score the query sequences' likelihood to be a spurious protein prediction using a Gaussian process model.", "sc:featureList": { @@ -29,10 +33,6 @@ "sc:name": "Spurio", "sc:operatingSystem": "Linux", "sc:url": "https://bitbucket.org/bateman-group/spurio" - }, - { - "@id": "https://doi.org/10.12688/f1000research.14050.1", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sputnik/sputnikbioschemas.jsonld b/data/sputnik/sputnikbioschemas.jsonld index 9dbbb097997bb..8456f0e173ffc 100644 --- a/data/sputnik/sputnikbioschemas.jsonld +++ b/data/sputnik/sputnikbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Paolo Inglese", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC6298046", + "pubmed:30010780", { "@id": "https://doi.org/10.1093/bioinformatics/bty622" - }, - "pubmed:30010780", - "pmcid:PMC6298046" + } ], "sc:description": "R package for filtering of spatially related peaks in mass spectrometry imaging data.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:license": "GPL-3.0", "sc:name": "SPUTNIK", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/paoloinglese/SPUTNIK" diff --git a/data/sqtlseeker/sqtlseekerbioschemas.jsonld b/data/sqtlseeker/sqtlseekerbioschemas.jsonld index 9937c0d708855..bab77aec15e3d 100644 --- a/data/sqtlseeker/sqtlseekerbioschemas.jsonld +++ b/data/sqtlseeker/sqtlseekerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "sQTLseekeR", "sc:operatingSystem": "Linux", "sc:provider": [ - "R.Guigo Group: Computational Biology of RNA processing @ CRG, Barcelona.", - "crg.eu" + "crg.eu", + "R.Guigo Group: Computational Biology of RNA processing @ CRG, Barcelona." ], "sc:url": "https://github.com/guigolab/sQTLseekeR", "sc:version": "2.0" diff --git a/data/squadd/bioconda_squadd.yaml b/data/squadd/bioconda_squadd.yaml index 7d9ee059dd244..403638cdd8010 100644 --- a/data/squadd/bioconda_squadd.yaml +++ b/data/squadd/bioconda_squadd.yaml @@ -4,7 +4,6 @@ description: This package SQUADD is a SQUAD add-on. It permits to generate SQUAD home: https://bioconductor.org/packages/3.10/bioc/html/SQUADD.html identifiers: - biotools:squadd -- doi:10.1038/nmeth.3252 license: GPL (>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-squadd diff --git a/data/squadd/squaddbioschemas.jsonld b/data/squadd/squaddbioschemas.jsonld index 4b9868533b320..40066c959444d 100644 --- a/data/squadd/squaddbioschemas.jsonld +++ b/data/squadd/squaddbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "SQUADD", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SQUADD.html", "sc:version": "1.24.0" diff --git a/data/squiggle/squigglebioschemas.jsonld b/data/squiggle/squigglebioschemas.jsonld index 1e0cdc278324e..e43ca4ba0d540 100644 --- a/data/squiggle/squigglebioschemas.jsonld +++ b/data/squiggle/squigglebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "Squiggle", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/Lab41/squiggle" } \ No newline at end of file diff --git a/data/sr-tesseler/sr-tesselerbioschemas.jsonld b/data/sr-tesseler/sr-tesselerbioschemas.jsonld index c86249e67eaa3..82db16cf4c726 100644 --- a/data/sr-tesseler/sr-tesselerbioschemas.jsonld +++ b/data/sr-tesseler/sr-tesselerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool is an open-source segmentation software using Voronoi tessellation constructed from the coordinates of localized molecules. It allows precise, robust and automatic quantification of protein organization at different scales, from the cellular level down to clusters of a few fluorescent markers. It is insensitive to cell shape, molecular organization, background and noise, allowing comparing efficiently different biological conditions in a non-biased manner.", "sc:name": "SR-Tesseler", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.iins.u-bordeaux.fr/team-sibarita-sr-tesseler", "sc:version": "1.0" diff --git a/data/sra/srabioschemas.jsonld b/data/sra/srabioschemas.jsonld index a3d22efee7b1c..7e6e2a764a3de 100644 --- a/data/sra/srabioschemas.jsonld +++ b/data/sra/srabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "SRA", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/Traces/sra" } \ No newline at end of file diff --git a/data/sradb/sradbbioschemas.jsonld b/data/sradb/sradbbioschemas.jsonld index 121c7399c24d4..b99db3ba7760f 100644 --- a/data/sradb/sradbbioschemas.jsonld +++ b/data/sradb/sradbbioschemas.jsonld @@ -14,8 +14,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jack Zhu", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ { diff --git a/data/sramp/srampbioschemas.jsonld b/data/sramp/srampbioschemas.jsonld index bc87314a4b549..e74102e20b7a6 100644 --- a/data/sramp/srampbioschemas.jsonld +++ b/data/sramp/srampbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "A useful tool to predict m6A modification sites on the RNA sequences", "sc:name": "SRAMP", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.cuilab.cn/sramp" } \ No newline at end of file diff --git a/data/srap/srapbioschemas.jsonld b/data/srap/srapbioschemas.jsonld index 402e342129a43..ee9cea1a1a89c 100644 --- a/data/srap/srapbioschemas.jsonld +++ b/data/srap/srapbioschemas.jsonld @@ -30,22 +30,22 @@ ], "sc:description": "This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.", "sc:featureList": [ - { - "@id": "edam:operation_0571" - }, { "@id": "edam:operation_3223" }, { "@id": "edam:operation_2495" + }, + { + "@id": "edam:operation_0571" } ], "sc:license": "GPL-3.0", "sc:name": "sRAP", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sRAP.html", "sc:version": "1.14.0" diff --git a/data/srcpred/srcpredbioschemas.jsonld b/data/srcpred/srcpredbioschemas.jsonld index 1ad447c7dfb64..26641f6025c37 100644 --- a/data/srcpred/srcpredbioschemas.jsonld +++ b/data/srcpred/srcpredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SRCPred predicts the RNA dinucleotide contacts in protein using evolutionary information in the form of PSSM using Neural Networks.", "sc:name": "SRCPred", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://mizuguchilab.org/netasa/srcpred/" diff --git a/data/srd/srdbioschemas.jsonld b/data/srd/srdbioschemas.jsonld index 45e6ef385e206..38db097307521 100644 --- a/data/srd/srdbioschemas.jsonld +++ b/data/srd/srdbioschemas.jsonld @@ -9,39 +9,27 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-0527-1171", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1261/rna.049346.114", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-6816-5931", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/srd", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Olivier Collin", "sc:additionalType": "Database portal", "sc:author": [ - { - "@id": "http://orcid.org/0000-0002-6816-5931" - }, - "Ivain L.", { "@id": "http://orcid.org/0000-0002-0527-1171" }, "Hallier M.", "Felden B.", + "Ivain L.", "Chabelskaya S.", + { + "@id": "http://orcid.org/0000-0002-6816-5931" + }, "Mauro T." ], "sc:citation": [ - "pubmed:25805861", "pmcid:PMC4408781", + "pubmed:25805861", { "@id": "https://doi.org/10.1261/rna.049346.114" } @@ -52,15 +40,27 @@ }, "sc:name": "Staphylococcus regulatory RNA database (SRD)", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "irisa.fr", "Université Rennes 1" ], "sc:url": "http://srd.genouest.org/" + }, + { + "@id": "https://doi.org/10.1261/rna.049346.114", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-0527-1171", + "@type": "schema:Person" + }, + { + "@id": "http://orcid.org/0000-0002-6816-5931", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/srda/srdabioschemas.jsonld b/data/srda/srdabioschemas.jsonld index 406f0b4f24a81..2eb18cfab4fb9 100644 --- a/data/srda/srdabioschemas.jsonld +++ b/data/srda/srdabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "sRDA", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/sRDA/index.html", "sc:version": "1.0.0" diff --git a/data/srfim/srfimbioschemas.jsonld b/data/srfim/srfimbioschemas.jsonld index f36dd6858bdcd..83361dbfed313 100644 --- a/data/srfim/srfimbioschemas.jsonld +++ b/data/srfim/srfimbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Srfim does model-based quality assessment and base-calling for Illumina GA second-generation sequencing data.", "sc:name": "Srfim", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.cbcb.umd.edu/~hcorrada/secgen/", "sc:version": "0.0-95" diff --git a/data/srgnet/srgnetbioschemas.jsonld b/data/srgnet/srgnetbioschemas.jsonld index 5cd466c3de6a2..c7cdfdaf4ae79 100644 --- a/data/srgnet/srgnetbioschemas.jsonld +++ b/data/srgnet/srgnetbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "SRGnet", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SRGnet.html", "sc:version": "1.0.0" diff --git a/data/sride/sridebioschemas.jsonld b/data/sride/sridebioschemas.jsonld index 4cc728da9a889..49aa0b00fce66 100644 --- a/data/sride/sridebioschemas.jsonld +++ b/data/sride/sridebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "A server for identifying stabilizing residues in proteins.", "sc:name": "SRide", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://sride.enzim.hu/" diff --git a/data/srinversion/srinversionbioschemas.jsonld b/data/srinversion/srinversionbioschemas.jsonld index 851fb9ed3910e..4fde0081993c9 100644 --- a/data/srinversion/srinversionbioschemas.jsonld +++ b/data/srinversion/srinversionbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A framework to analyze poorly mapped or unmapped reads by splitting and re-aligning them for the purpose of inversion detection.", "sc:name": "SRinversion", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://paed.hku.hk/genome/software/SRinversion/index.html" } \ No newline at end of file diff --git a/data/srmstats/srmstatsbioschemas.jsonld b/data/srmstats/srmstatsbioschemas.jsonld index c039a97342f15..61c0dafbb6696 100644 --- a/data/srmstats/srmstatsbioschemas.jsonld +++ b/data/srmstats/srmstatsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A statistical framework for protein quantification in SRM experiments based on a family of linear mixed-effects models.", "sc:name": "SRMstats", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.stat.purdue.edu/~chang54/SRMstats/Home.html" } \ No newline at end of file diff --git a/data/srna_plant_portal/srna_plant_portalbioschemas.jsonld b/data/srna_plant_portal/srna_plant_portalbioschemas.jsonld index c7f199f512c7f..a8b2e0be6ab06 100644 --- a/data/srna_plant_portal/srna_plant_portalbioschemas.jsonld +++ b/data/srna_plant_portal/srna_plant_portalbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "sRNA plant portal", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://srna-portal.biodata.pt/" } \ No newline at end of file diff --git a/data/srnabench/srnabenchbioschemas.jsonld b/data/srnabench/srnabenchbioschemas.jsonld index 2375a56cbc796..ee82449a417b4 100644 --- a/data/srnabench/srnabenchbioschemas.jsonld +++ b/data/srnabench/srnabenchbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKZ415", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/sRNAbench", "@type": "sc:SoftwareApplication", @@ -20,18 +16,18 @@ "sc:additionalType": "Web application", "sc:citation": [ "pmcid:PMC6602500", - "pubmed:31114926", { "@id": "https://doi.org/10.1093/NAR/GKZ415" - } + }, + "pubmed:31114926" ], "sc:description": "Web-server tool and standalone application for processing small-RNA data obtained from next generation sequencing platforms such as Illumina or SOLiD.", "sc:featureList": [ { - "@id": "edam:operation_0463" + "@id": "edam:operation_3792" }, { - "@id": "edam:operation_3792" + "@id": "edam:operation_0463" }, { "@id": "edam:operation_3431" @@ -40,11 +36,15 @@ "sc:license": "Unlicense", "sc:name": "sRNAbench", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://bioinfo5.ugr.es/srnatoolbox/srnabench/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ415", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/srnadiff/srnadiffbioschemas.jsonld b/data/srnadiff/srnadiffbioschemas.jsonld index 0f67d14c1a13f..9a57c2385647b 100644 --- a/data/srnadiff/srnadiffbioschemas.jsonld +++ b/data/srnadiff/srnadiffbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "srnadiff", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/srnadiff.html", "sc:version": "1.0.0" diff --git a/data/srnatoolbox/srnatoolboxbioschemas.jsonld b/data/srnatoolbox/srnatoolboxbioschemas.jsonld index 60dc9ad14371d..0bdc505d64998 100644 --- a/data/srnatoolbox/srnatoolboxbioschemas.jsonld +++ b/data/srnatoolbox/srnatoolboxbioschemas.jsonld @@ -14,23 +14,23 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Michael Hackenberg", "sc:additionalType": [ - "Suite", - "Web application" + "Web application", + "Suite" ], "sc:citation": [ - "pubmed:31114926", { "@id": "https://doi.org/10.1093/NAR/GKZ415" }, - "pmcid:PMC6602500" + "pmcid:PMC6602500", + "pubmed:31114926" ], "sc:description": "Intuitive fast small RNA profiling and differential expression.", "sc:featureList": [ { - "@id": "edam:operation_3792" + "@id": "edam:operation_0463" }, { - "@id": "edam:operation_0463" + "@id": "edam:operation_3792" }, { "@id": "edam:operation_3431" @@ -39,9 +39,9 @@ "sc:license": "Unlicense", "sc:name": "sRNAtoolbox", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://arn.ugr.es/srnatoolbox/" }, diff --git a/data/sroogle/srooglebioschemas.jsonld b/data/sroogle/srooglebioschemas.jsonld index 971dc02093d0e..72f96d2492cec 100644 --- a/data/sroogle/srooglebioschemas.jsonld +++ b/data/sroogle/srooglebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SROOGLE is a webserver that makes splicing signal sequence and scoring data available to the biologist in an integrated, visual and user friendly format.", "sc:name": "SROOGLE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://sroogle.tau.ac.il" } \ No newline at end of file diff --git a/data/ssa/ssabioschemas.jsonld b/data/ssa/ssabioschemas.jsonld index 3ce00be4cda6f..ca2634fc27c8a 100644 --- a/data/ssa/ssabioschemas.jsonld +++ b/data/ssa/ssabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "SSA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://ccg.vital-it.ch/ssa/" } \ No newline at end of file diff --git a/data/ssaha/ssahabioschemas.jsonld b/data/ssaha/ssahabioschemas.jsonld index 9ff69970e8ca5..04ceed47087c3 100644 --- a/data/ssaha/ssahabioschemas.jsonld +++ b/data/ssaha/ssahabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:description": "Sequence Search and Alignment by Hashing Algorithm is an algorithm for very fast matching and alignment of DNA sequences.", "sc:name": "SSAHA", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.sanger.ac.uk/science/tools/ssaha2-0" } \ No newline at end of file diff --git a/data/ssaha2/ssaha2bioschemas.jsonld b/data/ssaha2/ssaha2bioschemas.jsonld index d1a630a35300f..8cdd6104a5836 100644 --- a/data/ssaha2/ssaha2bioschemas.jsonld +++ b/data/ssaha2/ssaha2bioschemas.jsonld @@ -21,30 +21,30 @@ "@id": "https://bio.tools/ssaha2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Adam Spargo", "Zemin Ning", - "Hannes Ponstingl" + "Hannes Ponstingl", + "Adam Spargo" ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:24708189", + "pmcid:PMC4051166", { "@id": "https://doi.org/10.1101/gr.194201" }, "pmcid:PMC311141", - "pubmed:11591649", - "pmcid:PMC4051166", { "@id": "https://doi.org/10.1186/1471-2164-15-264" - } + }, + "pubmed:11591649", + "pubmed:24708189" ], "sc:description": "Pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.", "sc:license": "GPL-3.0", "sc:name": "SSAHA2", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://www.sanger.ac.uk/science/tools/ssaha2-0" } diff --git a/data/ssahasnp/ssahasnpbioschemas.jsonld b/data/ssahasnp/ssahasnpbioschemas.jsonld index 0ae9db1491970..1029f807d989a 100644 --- a/data/ssahasnp/ssahasnpbioschemas.jsonld +++ b/data/ssahasnp/ssahasnpbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "SsahaSNP", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.sanger.ac.uk/science/tools/ssahasnp" } \ No newline at end of file diff --git a/data/ssbio/ssbiobioschemas.jsonld b/data/ssbio/ssbiobioschemas.jsonld index 3ed26579ce8ff..e4e7c95a18870 100644 --- a/data/ssbio/ssbiobioschemas.jsonld +++ b/data/ssbio/ssbiobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "ssbio", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/SBRG/ssbio" } \ No newline at end of file diff --git a/data/sscore/sscorebioschemas.jsonld b/data/sscore/sscorebioschemas.jsonld index 826f21ac3df47..2e1754acd47bb 100644 --- a/data/sscore/sscorebioschemas.jsonld +++ b/data/sscore/sscorebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "sscore", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sscore.html", "sc:version": "1.46.0" diff --git a/data/sscu/bioconda_sscu.yaml b/data/sscu/bioconda_sscu.yaml index 65062dbc91853..13fa80fa2c462 100644 --- a/data/sscu/bioconda_sscu.yaml +++ b/data/sscu/bioconda_sscu.yaml @@ -20,7 +20,6 @@ description: The package calculates the indexes for selective stength in codon u home: https://bioconductor.org/packages/3.10/bioc/html/sscu.html identifiers: - biotools:sscu -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-sscu diff --git a/data/sscu/sscubioschemas.jsonld b/data/sscu/sscubioschemas.jsonld index 1da17c8a6a213..ab96387e72452 100644 --- a/data/sscu/sscubioschemas.jsonld +++ b/data/sscu/sscubioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yu Sun", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package can calculate the indexes for selective stength in codon usage in bacteria species. (1) Calculate the strength of selected codon usage bias based on Paul Sharp's method (comparable among different species). (2) Translational accuracy selection can be inferred from Akashi's test. (3) Optimal codon lists can be calculated by either op_highly function, or op_corre_CodonW/op_corre_NCprime function.", "sc:license": "GPL-2.0", diff --git a/data/ssea/sseabioschemas.jsonld b/data/ssea/sseabioschemas.jsonld index a09dd7f00b811..1712346174024 100644 --- a/data/ssea/sseabioschemas.jsonld +++ b/data/ssea/sseabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "New SNP-based pathway analysis software for GWAS studies. SSEA consists of two main steps: selecting representative SNPs for each gene, and performing pathway enrichment analysis using all selected SNPs.", "sc:name": "SSEA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://cbcl.ics.uci.edu/SSEA/", diff --git a/data/sseq/sseqbioschemas.jsonld b/data/sseq/sseqbioschemas.jsonld index f3a440d44602a..722eeed0b590d 100644 --- a/data/sseq/sseqbioschemas.jsonld +++ b/data/sseq/sseqbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Danni Yu", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation.", "sc:license": "GPL-3.0", "sc:name": "sSeq", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sSeq.html", "sc:version": "1.12.0" diff --git a/data/ssize/bioconda_ssize.yaml b/data/ssize/bioconda_ssize.yaml index c335d17a1d3e6..6f7535b27678f 100644 --- a/data/ssize/bioconda_ssize.yaml +++ b/data/ssize/bioconda_ssize.yaml @@ -4,7 +4,6 @@ description: Functions for computing and displaying sample size information for home: https://bioconductor.org/packages/3.10/bioc/html/ssize.html identifiers: - biotools:ssize -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-ssize diff --git a/data/ssize/ssizebioschemas.jsonld b/data/ssize/ssizebioschemas.jsonld index 30dc1b09956a5..6abec20f456bf 100644 --- a/data/ssize/ssizebioschemas.jsonld +++ b/data/ssize/ssizebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Gregory R. Warnes", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Functions for computing and displaying sample size information for gene expression arrays.", "sc:license": "GPL-3.0", "sc:name": "ssize", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ssize.html", "sc:version": "1.48.0" diff --git a/data/sspa/sspabioschemas.jsonld b/data/sspa/sspabioschemas.jsonld index 75d949cf227ba..97099d3933b1c 100644 --- a/data/sspa/sspabioschemas.jsonld +++ b/data/sspa/sspabioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Maarten van Iterson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": "pubmed:23934609", "sc:description": "General Sample size and power analysis for microarray and next-generation sequencing data.", @@ -21,8 +21,8 @@ "sc:name": "SSPA", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SSPA.html", "sc:version": "2.14.0" diff --git a/data/sspred/sspredbioschemas.jsonld b/data/sspred/sspredbioschemas.jsonld index a85fd4c467764..6da2a6643f470 100644 --- a/data/sspred/sspredbioschemas.jsonld +++ b/data/sspred/sspredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A prediction server for the identification & classification of proteins involved in bacterial secretion systems.", "sc:name": "SSPred", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.bioinformatics.org/sspred/html/sspred.html" } \ No newline at end of file diff --git a/data/sspro/ssprobioschemas.jsonld b/data/sspro/ssprobioschemas.jsonld index caba422184650..f744216e06799 100644 --- a/data/sspro/ssprobioschemas.jsonld +++ b/data/sspro/ssprobioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/sspro", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:24860169", "sc:description": "The first hybrid approach of combining neural network (ab initio) and homology analysis to improve the prediction of secondary structure and solvent accessibility.", "sc:name": "SSpro", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://scratch.proteomics.ics.uci.edu/" } \ No newline at end of file diff --git a/data/ssrcalc/ssrcalcbioschemas.jsonld b/data/ssrcalc/ssrcalcbioschemas.jsonld index ae1fb7f19b226..effddcb6f53f4 100644 --- a/data/ssrcalc/ssrcalcbioschemas.jsonld +++ b/data/ssrcalc/ssrcalcbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Sequence-specific retention time calculator.", "sc:name": "SSRCalc", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://hs2.proteome.ca/SSRCalc/SSRCalc.html" } \ No newline at end of file diff --git a/data/sst/sstbioschemas.jsonld b/data/sst/sstbioschemas.jsonld index d5261fc72ce7f..2dc3fcb8441cb 100644 --- a/data/sst/sstbioschemas.jsonld +++ b/data/sst/sstbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/bioinformatics/bts223", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/sst", "@type": "sc:SoftwareApplication", @@ -22,10 +18,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC3371855", + "pubmed:22689785", { "@id": "https://doi.org/10.1093/bioinformatics/bts223" - }, - "pubmed:22689785" + } ], "sc:description": "Assign secondary structures to protein coordinate data using the Bayesian method of Minimum Message Length (MML) inference.", "sc:featureList": { @@ -39,6 +35,10 @@ ], "sc:url": "http://lcb.infotech.monash.edu.au/sstweb/Submission_page.html" }, + { + "@id": "https://doi.org/10.1093/bioinformatics/bts223", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0002-9020-3164", "@type": "schema:Person" diff --git a/data/sstack/sstackbioschemas.jsonld b/data/sstack/sstackbioschemas.jsonld index e71ebafe9ade9..f2ed048911bec 100644 --- a/data/sstack/sstackbioschemas.jsonld +++ b/data/sstack/sstackbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "Sstack", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/Sstack/index.html", "sc:version": "1.0.1" diff --git a/data/sstructview/sstructviewbioschemas.jsonld b/data/sstructview/sstructviewbioschemas.jsonld index c8e503b6c097d..bcc9af076f983 100644 --- a/data/sstructview/sstructviewbioschemas.jsonld +++ b/data/sstructview/sstructviewbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "RNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends.", "sc:name": "SStructView", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://www.ctu.edu.vn/~dvxe/Bioinformatic/Software/BIT%20Software/home.html" } \ No newline at end of file diff --git a/data/ssviz/bioconda_ssviz.yaml b/data/ssviz/bioconda_ssviz.yaml index 6064ce615f664..8e85f19a69b53 100644 --- a/data/ssviz/bioconda_ssviz.yaml +++ b/data/ssviz/bioconda_ssviz.yaml @@ -3,7 +3,6 @@ description: Small RNA sequencing viewer home: https://bioconductor.org/packages/3.10/bioc/html/ssviz.html identifiers: - biotools:ssviz -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-ssviz diff --git a/data/ssviz/ssvizbioschemas.jsonld b/data/ssviz/ssvizbioschemas.jsonld index 6cc98c08bc28e..33707e95555a0 100644 --- a/data/ssviz/ssvizbioschemas.jsonld +++ b/data/ssviz/ssvizbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "ssviz", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ssviz.html", "sc:version": "1.8.0" diff --git a/data/st_viewer/st_viewerbioschemas.jsonld b/data/st_viewer/st_viewerbioschemas.jsonld index 9a55a94016c65..78d1829561ebb 100644 --- a/data/st_viewer/st_viewerbioschemas.jsonld +++ b/data/st_viewer/st_viewerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "ST viewer", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/SpatialTranscriptomicsResearch/st_viewer" } \ No newline at end of file diff --git a/data/stabs/stabsbioschemas.jsonld b/data/stabs/stabsbioschemas.jsonld index 5969d50accc5a..1243e3f29dafc 100644 --- a/data/stabs/stabsbioschemas.jsonld +++ b/data/stabs/stabsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An R package for Stability selection. Resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting.", "sc:name": "stabs", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://cran.r-project.org/web/packages/stabs/index.html" } \ No newline at end of file diff --git a/data/stac/stacbioschemas.jsonld b/data/stac/stacbioschemas.jsonld index 365bc663a78e2..6429a5c6d6e31 100644 --- a/data/stac/stacbioschemas.jsonld +++ b/data/stac/stacbioschemas.jsonld @@ -9,15 +9,19 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1101/gr.5076506", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/stac", "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:16899652", { "@id": "https://doi.org/10.1101/gr.5076506" }, + "pubmed:16899652", "pmcid:PMC1557772" ], "sc:description": "Method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. It utilizes two complementary statistics in combination with a novel search strategy. The significance of both statistics is assessed, and P-values are assigned to each location on the genome by using a multiple testing corrected permutation approach.", @@ -32,10 +36,6 @@ ], "sc:url": "http://www.cbil.upenn.edu/STAC/", "sc:version": "1.2" - }, - { - "@id": "https://doi.org/10.1101/gr.5076506", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/stacks/stacksbioschemas.jsonld b/data/stacks/stacksbioschemas.jsonld index 7f6bb37c1397a..e281bd211cd67 100644 --- a/data/stacks/stacksbioschemas.jsonld +++ b/data/stacks/stacksbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "Stacks", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://catchenlab.life.illinois.edu/stacks/" } \ No newline at end of file diff --git a/data/staden_io_lib/staden_io_libbioschemas.jsonld b/data/staden_io_lib/staden_io_libbioschemas.jsonld index 6eed736bd37d9..dd4a5371ed234 100644 --- a/data/staden_io_lib/staden_io_libbioschemas.jsonld +++ b/data/staden_io_lib/staden_io_libbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface.", "sc:name": "Staden io_lib", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://staden.sourceforge.net/" } \ No newline at end of file diff --git a/data/staden_package/staden_packagebioschemas.jsonld b/data/staden_package/staden_packagebioschemas.jsonld index 80b271638c5ac..debe15c8e9ec6 100644 --- a/data/staden_package/staden_packagebioschemas.jsonld +++ b/data/staden_package/staden_packagebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Staden Package", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://staden.sourceforge.net/" } \ No newline at end of file diff --git a/data/stager/stagerbioschemas.jsonld b/data/stager/stagerbioschemas.jsonld index 3c20f6c856e90..49d056cf7956e 100644 --- a/data/stager/stagerbioschemas.jsonld +++ b/data/stager/stagerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "stageR", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/stageR.html", "sc:version": "1.2.22" diff --git a/data/stamp-3d/stamp-3dbioschemas.jsonld b/data/stamp-3d/stamp-3dbioschemas.jsonld index eb2d3eff16bd1..6666943bdad7a 100644 --- a/data/stamp-3d/stamp-3dbioschemas.jsonld +++ b/data/stamp-3d/stamp-3dbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A package for the alignment of protein sequences based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit’ superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments.", "sc:name": "STAMP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.compbio.dundee.ac.uk/software.html#3Dstructure" } \ No newline at end of file diff --git a/data/stamp-metagenomic/stamp-metagenomicbioschemas.jsonld b/data/stamp-metagenomic/stamp-metagenomicbioschemas.jsonld index 748e3c619ce24..e31d6b1d4be8a 100644 --- a/data/stamp-metagenomic/stamp-metagenomicbioschemas.jsonld +++ b/data/stamp-metagenomic/stamp-metagenomicbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A software package for analyzing metagenomic profiles (e.g., a taxonomic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance.", "sc:name": "STAMP", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://kiwi.cs.dal.ca/Software/index.php/STAMP" } \ No newline at end of file diff --git a/data/stamp/stampbioschemas.jsonld b/data/stamp/stampbioschemas.jsonld index 7a1e17276e4c3..bb99b54ca8535 100644 --- a/data/stamp/stampbioschemas.jsonld +++ b/data/stamp/stampbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.", "sc:name": "STAMP", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.benoslab.pitt.edu/stamp/" diff --git a/data/stampy/stampybioschemas.jsonld b/data/stampy/stampybioschemas.jsonld index 57fa68e1f3021..5e5ad58d5774f 100644 --- a/data/stampy/stampybioschemas.jsonld +++ b/data/stampy/stampybioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1101/gr.111120.110", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0002-3798-2058", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/stampy", "@type": "sc:SoftwareApplication", @@ -25,17 +21,21 @@ }, "sc:additionalType": "Script", "sc:citation": [ - "pmcid:PMC3106326", "pubmed:20980556", + "pubmed:28286147", + "pmcid:PMC3106326", { "@id": "https://doi.org/10.1101/gr.111120.110" - }, - "pubmed:28286147" + } ], "sc:description": "a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation.", "sc:name": "Stampy", "sc:operatingSystem": "Linux", "sc:url": "http://www.well.ox.ac.uk/project-stampy" + }, + { + "@id": "http://orcid.org/0000-0002-3798-2058", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/stampy_mapper/stampy_mapperbioschemas.jsonld b/data/stampy_mapper/stampy_mapperbioschemas.jsonld index 38748d028392f..da09d5dd66ce4 100644 --- a/data/stampy_mapper/stampy_mapperbioschemas.jsonld +++ b/data/stampy_mapper/stampy_mapperbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Mapper for divergent genomes.", "sc:name": "stampy_mapper", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/stampy_mapper/stampy_mapper/1.0.20", diff --git a/data/stan/stanbioschemas.jsonld b/data/stan/stanbioschemas.jsonld index 7e5ee7183915d..ed5f75264f8b6 100644 --- a/data/stan/stanbioschemas.jsonld +++ b/data/stan/stanbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.15252/msb.20145654", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/stan", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Benedikt Zacher", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ "pmcid:PMC4300491", - "pubmed:25527639", { "@id": "https://doi.org/10.15252/msb.20145654" - } + }, + "pubmed:25527639" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-8924-8365" @@ -35,8 +39,8 @@ "sc:name": "STAN", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/STAN.html", "sc:version": "2.2.0" @@ -44,10 +48,6 @@ { "@id": "http://orcid.org/0000-0002-8924-8365", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.15252/msb.20145654", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/standardized_velvet_assembly_report/standardized_velvet_assembly_reportbioschemas.jsonld b/data/standardized_velvet_assembly_report/standardized_velvet_assembly_reportbioschemas.jsonld index 03155e3e18180..207a0779c8143 100644 --- a/data/standardized_velvet_assembly_report/standardized_velvet_assembly_reportbioschemas.jsonld +++ b/data/standardized_velvet_assembly_report/standardized_velvet_assembly_reportbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Standardized Velvet Assembly Report", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://code.google.com/archive/p/standardized-velvet-assembly-report/" } \ No newline at end of file diff --git a/data/stanex1/stanex1bioschemas.jsonld b/data/stanex1/stanex1bioschemas.jsonld index 3cc2c7ee729f1..25c40b6eeff50 100644 --- a/data/stanex1/stanex1bioschemas.jsonld +++ b/data/stanex1/stanex1bioschemas.jsonld @@ -17,8 +17,8 @@ "@id": "https://bio.tools/StanEx1", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Seung K. Kim", - "Lutfi Huq" + "Lutfi Huq", + "Seung K. Kim" ], "sc:additionalType": "Web application", "sc:citation": [ @@ -35,9 +35,9 @@ "sc:license": "Unlicense", "sc:name": "StanEx1", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://stanex.stanford.edu/about/" } diff --git a/data/stanfordmicroarraydb/stanfordmicroarraydbbioschemas.jsonld b/data/stanfordmicroarraydb/stanfordmicroarraydbbioschemas.jsonld index df87c5a32ae57..cec35dc4ad477 100644 --- a/data/stanfordmicroarraydb/stanfordmicroarraydbbioschemas.jsonld +++ b/data/stanfordmicroarraydb/stanfordmicroarraydbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Stanford Microarray Database (SMD)", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genome-www5.stanford.edu/" } \ No newline at end of file diff --git a/data/stap/stapbioschemas.jsonld b/data/stap/stapbioschemas.jsonld index c7f4b9323868a..47c712fae7ac2 100644 --- a/data/stap/stapbioschemas.jsonld +++ b/data/stap/stapbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "STAP", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://psb.kobic.re.kr/STAP/refinement/" } \ No newline at end of file diff --git a/data/star-genome-browser/star-genome-browserbioschemas.jsonld b/data/star-genome-browser/star-genome-browserbioschemas.jsonld index 636f87145e5f9..7eb6c6f459cc5 100644 --- a/data/star-genome-browser/star-genome-browserbioschemas.jsonld +++ b/data/star-genome-browser/star-genome-browserbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Wei Wang", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC3842760", + "pubmed:24078702", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTT558" - }, - "pmcid:PMC3842760", - "pubmed:24078702" + } ], "sc:description": "An integrated solution to management and visualization of sequencing data.", "sc:featureList": { diff --git a/data/star/starbioschemas.jsonld b/data/star/starbioschemas.jsonld index fad105b0342ba..bb2857986e664 100644 --- a/data/star/starbioschemas.jsonld +++ b/data/star/starbioschemas.jsonld @@ -13,36 +13,36 @@ "@id": "https://doi.org/10.1038/nmeth.4106", "@type": "sc:CreativeWork" }, - { - "@id": "https://doi.org/10.1093/bioinformatics/bts635", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/star", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "rna-styar team", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27941783", - "pubmed:24626854", - "pubmed:23104886", { "@id": "https://doi.org/10.1038/nmeth.4106" }, + "pmcid:PMC3530905", { "@id": "https://doi.org/10.1093/bioinformatics/bts635" }, - "pmcid:PMC3530905", - "pmcid:PMC5792058" + "pubmed:27941783", + "pubmed:24626854", + "pmcid:PMC5792058", + "pubmed:23104886" ], "sc:description": "Ultrafast universal RNA-seq aligner", "sc:license": "GPL-3.0", "sc:name": "STAR", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://code.google.com/p/rna-star/" + }, + { + "@id": "https://doi.org/10.1093/bioinformatics/bts635", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/starank/starankbioschemas.jsonld b/data/starank/starankbioschemas.jsonld index 5b6c44d838c9e..e55ec2c43e7ea 100644 --- a/data/starank/starankbioschemas.jsonld +++ b/data/starank/starankbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Juliane Siebourg", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Detecting all relevant variables from a data set is challenging, especially when only few samples are available and data is noisy. Stability ranking provides improved variable rankings of increased robustness using resampling or subsampling.", "sc:license": "GPL-3.0", "sc:name": "staRank", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/staRank.html", "sc:version": "1.16.0" diff --git a/data/starbiotrek/starbiotrekbioschemas.jsonld b/data/starbiotrek/starbiotrekbioschemas.jsonld index cfcf5fc256ad4..fbc050a7c6eeb 100644 --- a/data/starbiotrek/starbiotrekbioschemas.jsonld +++ b/data/starbiotrek/starbiotrekbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Claudia Cava", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This tool presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.", "sc:license": "GPL-3.0", diff --git a/data/starmir/starmirbioschemas.jsonld b/data/starmir/starmirbioschemas.jsonld index 03fa89c40d907..947ac9ecff0e3 100644 --- a/data/starmir/starmirbioschemas.jsonld +++ b/data/starmir/starmirbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "STarMir is a web server for prediction of microRNA binding sites.", "sc:name": "STarMir", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://sfold.wadsworth.org/starmir.html" } \ No newline at end of file diff --git a/data/starpdb/starpdbbioschemas.jsonld b/data/starpdb/starpdbbioschemas.jsonld index f9dd902582db6..ea3d5dc5425bb 100644 --- a/data/starpdb/starpdbbioschemas.jsonld +++ b/data/starpdb/starpdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "StarPDB", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://crdd.osdd.net/raghava/starpdb/index.php" } \ No newline at end of file diff --git a/data/starr/starrbioschemas.jsonld b/data/starr/starrbioschemas.jsonld index 5de4d67412346..dfdff29734562 100644 --- a/data/starr/starrbioschemas.jsonld +++ b/data/starr/starrbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Benedikt Zacher", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This tool facilitates the analysis of ChIP-data, in particular the output of Affymetrix tiling arrays. It provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles.", "sc:license": "Artistic-2.0", "sc:name": "Starr", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Starr.html", diff --git a/data/startscan/startscanbioschemas.jsonld b/data/startscan/startscanbioschemas.jsonld index ab7298ff7c5ca..431203619f98f 100644 --- a/data/startscan/startscanbioschemas.jsonld +++ b/data/startscan/startscanbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A tool to detect translation initiation sites in genomic sequences.", "sc:name": "StartScan", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/StartScan", diff --git a/data/statalign/statalignbioschemas.jsonld b/data/statalign/statalignbioschemas.jsonld index a6ae2415f443b..0c23cbeb3c2f9 100644 --- a/data/statalign/statalignbioschemas.jsonld +++ b/data/statalign/statalignbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/molbev/msu184", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/StatAlign", "@type": "sc:SoftwareApplication", @@ -23,8 +19,8 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pmcid:PMC4137710", - "pubmed:24899668", "pubmed:30298398", + "pubmed:24899668", { "@id": "https://doi.org/10.1093/molbev/msu184" } @@ -33,11 +29,15 @@ "sc:license": "GPL-3.0", "sc:name": "StatAlign", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://statalign.github.io/" + }, + { + "@id": "https://doi.org/10.1093/molbev/msu184", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/stategra/stategrabioschemas.jsonld b/data/stategra/stategrabioschemas.jsonld index 80740e358ee95..9c080a864bc91 100644 --- a/data/stategra/stategrabioschemas.jsonld +++ b/data/stategra/stategrabioschemas.jsonld @@ -23,9 +23,9 @@ "sc:license": "GPL-2.0", "sc:name": "STATegRa", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/STATegRa.html", "sc:version": "1.8.0" diff --git a/data/stattarget/stattargetbioschemas.jsonld b/data/stattarget/stattargetbioschemas.jsonld index 7a0d96e70fda5..bb982954a9e20 100644 --- a/data/stattarget/stattargetbioschemas.jsonld +++ b/data/stattarget/stattargetbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hemi Luan", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "An easy to use tool provide a graphical user interface for quality control based shift signal correction, integration of metabolomic data from multi-batch experiments, and the comprehensive statistic analysis in non-targeted or targeted metabolomics.", "sc:license": "GPL-2.0", "sc:name": "statTarget", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/statTarget.html", "sc:version": "1.4.7" diff --git a/data/stavrox/stavroxbioschemas.jsonld b/data/stavrox/stavroxbioschemas.jsonld index 6fba2db88c44b..4440f81bd16f3 100644 --- a/data/stavrox/stavroxbioschemas.jsonld +++ b/data/stavrox/stavroxbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-4001-2324", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/stavrox", "@type": "sc:SoftwareApplication", @@ -26,6 +22,10 @@ "sc:name": "StavroX", "sc:operatingSystem": "Windows", "sc:url": "http://www.stavrox.com/" + }, + { + "@id": "https://orcid.org/0000-0003-4001-2324", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/steak/steakbioschemas.jsonld b/data/steak/steakbioschemas.jsonld index 8a21b3ee8bbbc..fb03a7a5600ea 100644 --- a/data/steak/steakbioschemas.jsonld +++ b/data/steak/steakbioschemas.jsonld @@ -17,16 +17,16 @@ "@id": "https://bio.tools/steak", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Philippe Gambron", - "Cindy Santander" + "Cindy Santander", + "Philippe Gambron" ], "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5597868", - "pubmed:28948042", { "@id": "https://doi.org/10.1093/ve/vex023" - } + }, + "pubmed:28948042" ], "sc:description": "Specific Transposable Element Aligner (HERV-K).", "sc:featureList": { @@ -34,8 +34,8 @@ }, "sc:name": "STEAK", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/applevir/STEAK" } diff --git a/data/stego/stegobioschemas.jsonld b/data/stego/stegobioschemas.jsonld index 04c3c9454237b..ef689b51a6a71 100644 --- a/data/stego/stegobioschemas.jsonld +++ b/data/stego/stegobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Identification of genetic outliers due to sub-structure and cryptic relationships.", "sc:name": "STEGO", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/dschlauch/stego" diff --git a/data/stellar/stellarbioschemas.jsonld b/data/stellar/stellarbioschemas.jsonld index cc495dbdb1cce..2b9e4969953a6 100644 --- a/data/stellar/stellarbioschemas.jsonld +++ b/data/stellar/stellarbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A local pairwise aligner that has full sensitivity, i.e. guarantees to report all matches of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. For filtering it applies the SWIFT algorithm, for which we have developed a new, exact verification strategy.", "sc:name": "Stellar", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.seqan.de/projects/stellar/", "sc:version": "1.4" diff --git a/data/stells/stellsbioschemas.jsonld b/data/stells/stellsbioschemas.jsonld index ecdd4ac6334b9..e9dae139e26b5 100644 --- a/data/stells/stellsbioschemas.jsonld +++ b/data/stells/stellsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A program for finding the maximum likelihood estimate of the species tree for the given gene trees, which undergo incomplete lineage sorting.", "sc:name": "STELLS", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.engr.uconn.edu/~ywu/STELLS.html" } \ No newline at end of file diff --git a/data/stemcellnet/stemcellnetbioschemas.jsonld b/data/stemcellnet/stemcellnetbioschemas.jsonld index 4d431ec407c62..e6938136a9fb6 100644 --- a/data/stemcellnet/stemcellnetbioschemas.jsonld +++ b/data/stemcellnet/stemcellnetbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gku455", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/stemcellnet", "@type": "sc:SoftwareApplication", @@ -31,10 +35,10 @@ } ], "sc:citation": [ - "pubmed:24852251", { "@id": "https://doi.org/10.1093/nar/gku455" }, + "pubmed:24852251", "pmcid:PMC4086070" ], "sc:description": "Web-server that allows users to interactively query, visualize and interrogate molecular networks in the context of stem cell biology. It includes a comprehensive set of physical and regulatory interactions for both human and mouse. Any retrieved network can be readily examined for the presence of genes linked to stemness.", @@ -44,9 +48,9 @@ "sc:isAccessibleForFree": true, "sc:name": "StemCellNet", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:softwareHelp": { "@id": "http://193.136.227.181:8080/stemcellnet/help.jsf" @@ -57,10 +61,6 @@ { "@id": "http://orcid.org/0000-0002-6245-8071", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/nar/gku455", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/stemchecker/stemcheckerbioschemas.jsonld b/data/stemchecker/stemcheckerbioschemas.jsonld index 3d3943b56214b..ee1ce5202e0dd 100644 --- a/data/stemchecker/stemcheckerbioschemas.jsonld +++ b/data/stemchecker/stemcheckerbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkv529", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-6245-8071", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/stemchecker", "@type": "sc:SoftwareApplication", @@ -29,28 +21,36 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:26007653", - "pmcid:PMC4489266", { "@id": "https://doi.org/10.1093/nar/gkv529" - } + }, + "pmcid:PMC4489266" ], "sc:description": "Web-server that enables researchers to rapidly check whether a given list of genes can be associated with stemness. It compares the genes uploaded by the user with those in curated stemness signatures, and evaluates the statistical significance of the overlap. The results are then displayed in alternative formats showing the overall association of the whole set of input genes with stemness, as well as the occurrence of individual genes in the curated stemness signatures.", "sc:featureList": [ { - "@id": "edam:operation_0315" + "@id": "edam:operation_0314" }, { - "@id": "edam:operation_0314" + "@id": "edam:operation_0315" } ], "sc:name": "StemChecker", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://193.136.227.168:8080/stemchecker/stemsethome.jsf", "sc:version": "1.2.1" + }, + { + "@id": "https://doi.org/10.1093/nar/gkv529", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-6245-8071", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/steps/stepsbioschemas.jsonld b/data/steps/stepsbioschemas.jsonld index 215eb61bc6e4a..c820ff065f5ee 100644 --- a/data/steps/stepsbioschemas.jsonld +++ b/data/steps/stepsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "STEPS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://steps.sourceforge.net/STEPS/default.php" diff --git a/data/stepwisecm/stepwisecmbioschemas.jsonld b/data/stepwisecm/stepwisecmbioschemas.jsonld index 8132a6658feb6..4ef272067861a 100644 --- a/data/stepwisecm/stepwisecmbioschemas.jsonld +++ b/data/stepwisecm/stepwisecmbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Askar Obulkasim", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package implements a cancer samples classification strategy using multiple data sets. It uses the data type for which full measurements are available at the first stage, and the data type for which only partial measurements are available at the second stage. For incoming new samples, it quantifies how much improvement will be obtained if covariates of new samples for the data types at the second stage are measured.", "sc:license": "GPL-2.0", "sc:name": "stepwiseCM", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://bioconductor.riken.jp/packages/3.1/bioc/html/stepwiseCM.html", "sc:version": "1.20.0" diff --git a/data/stereogene/stereogenebioschemas.jsonld b/data/stereogene/stereogenebioschemas.jsonld index 3d4bb7bfca756..de5f10a4a294c 100644 --- a/data/stereogene/stereogenebioschemas.jsonld +++ b/data/stereogene/stereogenebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Rapid estimation of genome-wide correlation of continuous or interval feature data.", "sc:name": "StereoGene", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://stereogene.bioinf.fbb.msu.ru/" } \ No newline at end of file diff --git a/data/stereomate/stereomatebioschemas.jsonld b/data/stereomate/stereomatebioschemas.jsonld index 2b12f8d5492ef..06431a2ff70a3 100644 --- a/data/stereomate/stereomatebioschemas.jsonld +++ b/data/stereomate/stereomatebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/StereoMate", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Steven J. West", - "David L. Bennett" + "David L. Bennett", + "Steven J. West" ], "sc:additionalType": "Suite", "sc:description": "Stereological and Automated Analysis Platform for Assessing Histological Labelling in Cleared Tissue Specimens.", diff --git a/data/sti-gmas/sti-gmasbioschemas.jsonld b/data/sti-gmas/sti-gmasbioschemas.jsonld index 3626fb3e7b49c..0e19c127a072a 100644 --- a/data/sti-gmas/sti-gmasbioschemas.jsonld +++ b/data/sti-gmas/sti-gmasbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "STI-GMaS", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.sti-gmas.org/" } \ No newline at end of file diff --git a/data/sting_millenium/sting_milleniumbioschemas.jsonld b/data/sting_millenium/sting_milleniumbioschemas.jsonld index 95f04f2d297b0..68be8c7afc79b 100644 --- a/data/sting_millenium/sting_milleniumbioschemas.jsonld +++ b/data/sting_millenium/sting_milleniumbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.", "sc:name": "STING Millenium", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/" } \ No newline at end of file diff --git a/data/stingray/stingraybioschemas.jsonld b/data/stingray/stingraybioschemas.jsonld index 337bfd8613ea5..d166d7654f805 100644 --- a/data/stingray/stingraybioschemas.jsonld +++ b/data/stingray/stingraybioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Alberto MR Dávila", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:24606808", - "pmcid:PMC4015962", { "@id": "https://doi.org/10.1186/1756-0500-7-132" - } + }, + "pmcid:PMC4015962", + "pubmed:24606808" ], "sc:description": "System for integrated genomic resources and analysis.", "sc:featureList": [ @@ -37,9 +37,9 @@ "sc:license": "GPL-2.0", "sc:name": "STINGRAY", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://stingray.biowebdb.org/" } diff --git a/data/stitch/stitchbioschemas.jsonld b/data/stitch/stitchbioschemas.jsonld index 341ef1821039b..d1fd1bb156171 100644 --- a/data/stitch/stitchbioschemas.jsonld +++ b/data/stitch/stitchbioschemas.jsonld @@ -15,42 +15,42 @@ "biotools:primaryContact": "Michael Kuhn", "sc:additionalType": [ "Web application", - "Database portal", - "Command-line tool" + "Command-line tool", + "Database portal" ], "sc:author": "Michael Kuhn", "sc:citation": [ - "pubmed:19897548", "pubmed:18084021", + "pmcid:PMC2238848", + "pubmed:19897548", { "@id": "https://doi.org/10.1093/nar/gkm795" - }, - "pmcid:PMC2238848" + } ], "sc:contributor": [ - "EMBO", - "SUND-KU", + "EC FP6", + "TUD", "CPR", "BMBF", "EMBL", - "TUD", - "EC FP6" + "SUND-KU", + "EMBO" ], "sc:description": "Resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.", "sc:funder": [ - "EMBO", - "TUD", - "EC FP6", "EMBL", + "SUND-KU", + "EMBO", "CPR", + "TUD", "BMBF", - "SUND-KU" + "EC FP6" ], "sc:name": "STITCH", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "HD-HuB", "sc:url": "http://stitch.embl.de/" diff --git a/data/stitchprofiles/stitchprofilesbioschemas.jsonld b/data/stitchprofiles/stitchprofilesbioschemas.jsonld index c4f9232905b99..00c957e78b426 100644 --- a/data/stitchprofiles/stitchprofilesbioschemas.jsonld +++ b/data/stitchprofiles/stitchprofilesbioschemas.jsonld @@ -13,23 +13,23 @@ "biotools:primaryContact": "Eivind Hovig", "sc:additionalType": "Web application", "sc:author": [ - "Eivind Hovig", + "Geir Ivar Jerstad", "Eivind Tøstesen", - "Geir Ivar Jerstad" + "Eivind Hovig" ], "sc:contributor": "The Research Council of Norway", "sc:description": "Web-based computations on DNA melting, thus predicting the localized separation of the two strands for sequences provided by the users.", "sc:funder": "The Research Council of Norway", "sc:name": "Stitchprofiles", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ "UiO", - "University of Oslo", - "The Norwegian Radium Hospital" + "The Norwegian Radium Hospital", + "University of Oslo" ], "sc:url": "http://stitchprofiles.uio.no/", "sc:version": "1" diff --git a/data/stochdecomp/stochdecompbioschemas.jsonld b/data/stochdecomp/stochdecompbioschemas.jsonld index 129b0aa013d0e..fa232d5a1557f 100644 --- a/data/stochdecomp/stochdecompbioschemas.jsonld +++ b/data/stochdecomp/stochdecompbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "StochDecomp", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://sourceforge.net/p/stochdecomp/wiki/Home/" } \ No newline at end of file diff --git a/data/ston/stonbioschemas.jsonld b/data/ston/stonbioschemas.jsonld index 686ee078d6231..cb3e1962d72e1 100644 --- a/data/ston/stonbioschemas.jsonld +++ b/data/ston/stonbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A new algorithm to find aligned residues in two proteins with desired rmsd value.", "sc:name": "STON", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bs.ipm.ir/softwares/ston/" } \ No newline at end of file diff --git a/data/stpm/stpmbioschemas.jsonld b/data/stpm/stpmbioschemas.jsonld index d8f67b6909a1e..1f6463494f0b0 100644 --- a/data/stpm/stpmbioschemas.jsonld +++ b/data/stpm/stpmbioschemas.jsonld @@ -15,8 +15,8 @@ "biotools:primaryContact": "Ilya Y. Zhbannikov", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:28231764", "pmcid:PMC5324240", + "pubmed:28231764", { "@id": "https://doi.org/10.1186/s12859-017-1538-7" } @@ -28,9 +28,9 @@ "sc:license": "GPL-3.0", "sc:name": "stpm", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/stpm/index.html", "sc:version": "1.7.5" diff --git a/data/stradwin/stradwinbioschemas.jsonld b/data/stradwin/stradwinbioschemas.jsonld index 8b54dc8ea6969..efc4989f8465d 100644 --- a/data/stradwin/stradwinbioschemas.jsonld +++ b/data/stradwin/stradwinbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13014-017-0880-2", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/stradwin", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "D. Thurtle", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:28854948", { "@id": "https://doi.org/10.1186/s13014-017-0880-2" }, - "pmcid:PMC5577835" + "pmcid:PMC5577835", + "pubmed:28854948" ], "sc:description": "Experimental, cross-platform tool primarily for freehand 3D ultrasound acquisition, visualisation and elastography. It can also be used with 3D medical data of any sort: its segmentation and surface extraction facilities are particularly powerful. It can load most types of DICOM image files and has unique facilities to measure bone cortical thickness from CT data.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "Stradwin", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mi.eng.cam.ac.uk/~rwp/stradwin/", "sc:version": "5.3" - }, - { - "@id": "https://doi.org/10.1186/s13014-017-0880-2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/straininfo/straininfobioschemas.jsonld b/data/straininfo/straininfobioschemas.jsonld index 3a89b42306e18..5a61a01569edb 100644 --- a/data/straininfo/straininfobioschemas.jsonld +++ b/data/straininfo/straininfobioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The largest integrated microbial knowledge base.", "sc:name": "StrainInfo", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://www.straininfo.net/" diff --git a/data/strand_ngs/strand_ngsbioschemas.jsonld b/data/strand_ngs/strand_ngsbioschemas.jsonld index 42be10030e03e..04ddaf2a69f0f 100644 --- a/data/strand_ngs/strand_ngsbioschemas.jsonld +++ b/data/strand_ngs/strand_ngsbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/strand_ngs", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Contact Form", - "Strand NGS Support" + "Strand NGS Support", + "Contact Form" ], "sc:additionalType": "Suite", "sc:description": "Software platform for alignment, analysis, visualization, and management of data generated by NGS platforms. It supports workflows for RNA-Seq, DNA-Seq, small RNA-Seq, ChIP-seq, and Methyl-Seq data analysis.", "sc:name": "Strand NGS", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.strand-ngs.com/" } \ No newline at end of file diff --git a/data/strap/strapbioschemas.jsonld b/data/strap/strapbioschemas.jsonld index 082d8f9c5c57b..348579d566c2a 100644 --- a/data/strap/strapbioschemas.jsonld +++ b/data/strap/strapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The Structural Alignment Program for Proteins (STRAP) is a java-based program that can be run over the web using a Java Web Start enabled browser or downloaded and run as a stand-alone application. Alignments can be done using one of several methods, including ClustalW, JAligner and T_coffee. STRAP is also able to incorporate structure information and interfaces with programs such as Pymol and Rasmol. There is also a tutorial included.", "sc:name": "STRAP", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.bioinformatics.org/strap/" diff --git a/data/straw/strawbioschemas.jsonld b/data/straw/strawbioschemas.jsonld index fc8a814eb2174..3c28f1f4e4cf2 100644 --- a/data/straw/strawbioschemas.jsonld +++ b/data/straw/strawbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "STRAW", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/" } \ No newline at end of file diff --git a/data/stream/streambioschemas.jsonld b/data/stream/streambioschemas.jsonld index 5f84ec65f8b1a..f0e54d63f305d 100644 --- a/data/stream/streambioschemas.jsonld +++ b/data/stream/streambioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Bioinformatics application for researchers, who want to model the transcriptional regulation of a specific gene and predict its transcriptional output in different situations.", "sc:name": "STREAM", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://stream.imb.uq.edu.au/" } \ No newline at end of file diff --git a/data/streamer/bioconda_streamer.yaml b/data/streamer/bioconda_streamer.yaml index e63efe1055e0d..876ae08e052a2 100644 --- a/data/streamer/bioconda_streamer.yaml +++ b/data/streamer/bioconda_streamer.yaml @@ -8,7 +8,6 @@ description: Large data files can be difficult to work with in R, where data gen home: https://bioconductor.org/packages/3.10/bioc/html/Streamer.html identifiers: - biotools:streamer -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-streamer summary: Enabling stream processing of large files diff --git a/data/streamer/streamerbioschemas.jsonld b/data/streamer/streamerbioschemas.jsonld index 780c69213ac24..d70eb06749065 100644 --- a/data/streamer/streamerbioschemas.jsonld +++ b/data/streamer/streamerbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "Streamer", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Streamer.html", "sc:version": "1.20.0" diff --git a/data/stretcher-api-ebi/stretcher-api-ebibioschemas.jsonld b/data/stretcher-api-ebi/stretcher-api-ebibioschemas.jsonld index c62e29fa5f71f..aefb5823fc57a 100644 --- a/data/stretcher-api-ebi/stretcher-api-ebibioschemas.jsonld +++ b/data/stretcher-api-ebi/stretcher-api-ebibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Pairwise sequence alignment of DNA or protein sequences using Myers and Miller global alignment.", "sc:name": "stretcher-api (EBI)", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/psa/emboss_stretcher_rest", "sc:version": "1" diff --git a/data/stretcher-ebi/stretcher-ebibioschemas.jsonld b/data/stretcher-ebi/stretcher-ebibioschemas.jsonld index 2951820f1ccf5..73c988316ba65 100644 --- a/data/stretcher-ebi/stretcher-ebibioschemas.jsonld +++ b/data/stretcher-ebi/stretcher-ebibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Improved version of the Needleman-Wunsch algorithm that allows rapid global alignment of two larger sequences.", "sc:name": "stretcher (EBI)", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/psa/emboss_stretcher/", diff --git a/data/stretcher/stretcherbioschemas.jsonld b/data/stretcher/stretcherbioschemas.jsonld index c8c64a5f6e241..fed53e4fb0f85 100644 --- a/data/stretcher/stretcherbioschemas.jsonld +++ b/data/stretcher/stretcherbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "Wellcome Trust", "UK MRC", - "UK BBSRC" + "Wellcome Trust", + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Needleman-Wunsch rapid global alignment of two sequences.", "sc:funder": [ @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "stretcher", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/stretcher.html", "sc:version": "r6" diff --git a/data/stretching_dna/stretching_dnabioschemas.jsonld b/data/stretching_dna/stretching_dnabioschemas.jsonld index f757540b518bd..c9c2e69e616c2 100644 --- a/data/stretching_dna/stretching_dnabioschemas.jsonld +++ b/data/stretching_dna/stretching_dnabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The program explores stretching just a single strand of DNA using optical tweezers or fluid flow. Experiment with the forces involved and measure the relationship between the stretched DNA length and the force required to keep it stretched.", "sc:name": "Stretching DNA", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://phet.colorado.edu/en/simulation/stretching-dna" } \ No newline at end of file diff --git a/data/strictlyincludegff/strictlyincludegffbioschemas.jsonld b/data/strictlyincludegff/strictlyincludegffbioschemas.jsonld index 9438a869408ec..144e42296ab1b 100644 --- a/data/strictlyincludegff/strictlyincludegffbioschemas.jsonld +++ b/data/strictlyincludegff/strictlyincludegffbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Prints the elements which are strictly included in the template.", "sc:name": "strictlyincludegff", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", diff --git a/data/stride/stridebioschemas.jsonld b/data/stride/stridebioschemas.jsonld index dfb40002fb7cc..a6c5a533c83b0 100644 --- a/data/stride/stridebioschemas.jsonld +++ b/data/stride/stridebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map.", "sc:name": "STRIDE", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://webclu.bio.wzw.tum.de/stride/" } \ No newline at end of file diff --git a/data/string/stringbioschemas.jsonld b/data/string/stringbioschemas.jsonld index 153dda6191cd8..69c6e9310386c 100644 --- a/data/string/stringbioschemas.jsonld +++ b/data/string/stringbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. STRING is regularly updated and gives a comprehensive view on protein-protein interactions currently available.", "sc:name": "STRING", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", diff --git a/data/stringapp/stringappbioschemas.jsonld b/data/stringapp/stringappbioschemas.jsonld index d5bd45b5b5ffa..2a7f35e4fd548 100644 --- a/data/stringapp/stringappbioschemas.jsonld +++ b/data/stringapp/stringappbioschemas.jsonld @@ -9,48 +9,48 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkw937", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/stringapp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lars Juhl Jensen", { "@id": "http://orcid.org/0000-0003-0290-7979" - } + }, + "Lars Juhl Jensen" ], "sc:additionalType": "Plug-in", "sc:citation": [ { "@id": "https://doi.org/10.1093/nar/gkw937" }, - "pubmed:27924014", - "pmcid:PMC5210637" + "pmcid:PMC5210637", + "pubmed:27924014" ], "sc:description": "Imports protein-protein and protein-chemical interaction data from STRING and STITCH databases into Cytoscape.", "sc:featureList": [ - { - "@id": "edam:operation_2422" - }, { "@id": "edam:operation_3083" }, { "@id": "edam:operation_2497" + }, + { + "@id": "edam:operation_2422" } ], "sc:name": "stringApp", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://apps.cytoscape.org/apps/stringapp", "sc:version": "1.1.0" }, - { - "@id": "https://doi.org/10.1093/nar/gkw937", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-0290-7979", "@type": "schema:Person" diff --git a/data/stringdb/stringdbbioschemas.jsonld b/data/stringdb/stringdbbioschemas.jsonld index 360ea595d00eb..947a30494e333 100644 --- a/data/stringdb/stringdbbioschemas.jsonld +++ b/data/stringdb/stringdbbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alexander Roth", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC3531103", - "pubmed:23203871", { "@id": "https://doi.org/10.1093/nar/gks1094" - } + }, + "pubmed:23203871", + "pmcid:PMC3531103" ], "sc:description": "This package provides a R interface to the STRING protein-protein interactions database.", "sc:featureList": { diff --git a/data/stringgaussnet/stringgaussnetbioschemas.jsonld b/data/stringgaussnet/stringgaussnetbioschemas.jsonld index 3ba1d14977833..6252524a58fee 100644 --- a/data/stringgaussnet/stringgaussnetbioschemas.jsonld +++ b/data/stringgaussnet/stringgaussnetbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A toolbox for a construction of protein-protein interaction networks through the ‘STRING’ application programming interface, and an inference of Gaussian networks through ‘SIMoNe’ and ‘WGCNA’ approach, from DE genes analysis results and expression data. Additional functions are provided to import automatically networks into an active ‘Cytoscape’ session.", "sc:name": "stringgaussnet", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/stringgaussnet/" } \ No newline at end of file diff --git a/data/strmix/strmixbioschemas.jsonld b/data/strmix/strmixbioschemas.jsonld index 7a064d0484402..1555213e6adf2 100644 --- a/data/strmix/strmixbioschemas.jsonld +++ b/data/strmix/strmixbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Other", "sc:name": "STRmix", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://www.strmix.com/" } \ No newline at end of file diff --git a/data/strms/strmsbioschemas.jsonld b/data/strms/strmsbioschemas.jsonld index f11967d4c1298..215d2d7536d8c 100644 --- a/data/strms/strmsbioschemas.jsonld +++ b/data/strms/strmsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Structural RNA motif search that takes as input the secondary structure of the query and a target sequence database, and reports all occurrences of the query in the target. The search is based on subtree homeomorphism for ordered, rooted trees (which we use to represent the RNA structures) .", "sc:name": "STRMS", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://www.cs.bgu.ac.il/~vaksler/STRMS.htm", "sc:version": "0.5.2" diff --git a/data/struct2net/struct2netbioschemas.jsonld b/data/struct2net/struct2netbioschemas.jsonld index 5ac634ee643f3..43de5317428b1 100644 --- a/data/struct2net/struct2netbioschemas.jsonld +++ b/data/struct2net/struct2netbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure based approach.", "sc:name": "Struct2Net", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://struct2net.csail.mit.edu" } \ No newline at end of file diff --git a/data/structalign/structalignbioschemas.jsonld b/data/structalign/structalignbioschemas.jsonld index a58df680a9317..81cf6f696f59f 100644 --- a/data/structalign/structalignbioschemas.jsonld +++ b/data/structalign/structalignbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "StructAlign", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://mouse.genebee.msu.ru/tools/StructAlign.html" } \ No newline at end of file diff --git a/data/structator/structatorbioschemas.jsonld b/data/structator/structatorbioschemas.jsonld index 72c39277989c8..97e5ff9788238 100644 --- a/data/structator/structatorbioschemas.jsonld +++ b/data/structator/structatorbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "A complete and robust open-source software solution for index-based search of RNA sequence-structure patterns.", "sc:name": "Structator", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.zbh.uni-hamburg.de/?id=271", "sc:version": "1.1" diff --git a/data/structuprint/structuprintbioschemas.jsonld b/data/structuprint/structuprintbioschemas.jsonld index 12193e4ac27c0..519d65e217096 100644 --- a/data/structuprint/structuprintbioschemas.jsonld +++ b/data/structuprint/structuprintbioschemas.jsonld @@ -24,15 +24,15 @@ "@id": "http://orcid.org/0000-0002-5082-1929" }, "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:citation": [ - "pmcid:PMC4765231", - "pubmed:26911476", { "@id": "https://doi.org/10.1186/s12900-016-0055-7" - } + }, + "pubmed:26911476", + "pmcid:PMC4765231" ], "sc:description": "Scalable and extensible tool for two-dimensional representation of protein surfaces.", "sc:featureList": { @@ -41,9 +41,9 @@ "sc:license": "GPL-3.0", "sc:name": "Structuprint", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://dgkontopoulos.io/Structuprint/" } diff --git a/data/structure-ppi/structure-ppibioschemas.jsonld b/data/structure-ppi/structure-ppibioschemas.jsonld index affefdae9bd58..77dbcdddd4c81 100644 --- a/data/structure-ppi/structure-ppibioschemas.jsonld +++ b/data/structure-ppi/structure-ppibioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTV142", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/structure-ppi", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Miguel Vazquez", - "Support" + "Support", + "Miguel Vazquez" ], "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:25765346", - "pmcid:PMC4495296", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTV142" - } + }, + "pmcid:PMC4495296", + "pubmed:25765346" ], "sc:description": "Module for the annotation of cancer-related single-nucleotide variants at protein–protein interfaces.", "sc:featureList": { @@ -38,6 +34,10 @@ "Mac" ], "sc:url": "http://structureppi.bioinfo.cnio.es/Structure" + }, + { + "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTV142", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/structure/structurebioschemas.jsonld b/data/structure/structurebioschemas.jsonld index 77479c70cff2a..7c81e63faac61 100644 --- a/data/structure/structurebioschemas.jsonld +++ b/data/structure/structurebioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC1461096", - "pubmed:10835412" + "pubmed:10835412", + "pmcid:PMC1461096" ], "sc:description": "The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.", "sc:license": "Not licensed", diff --git a/data/structure_threader/structure_threaderbioschemas.jsonld b/data/structure_threader/structure_threaderbioschemas.jsonld index be4b53b0388a9..73c86852bed69 100644 --- a/data/structure_threader/structure_threaderbioschemas.jsonld +++ b/data/structure_threader/structure_threaderbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Structure_threader", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/StuntsPT/Structure_threader", "sc:version": "1.0.2" diff --git a/data/structureprofiler/structureprofilerbioschemas.jsonld b/data/structureprofiler/structureprofilerbioschemas.jsonld index 832e16155a619..8e0c0f111efd3 100644 --- a/data/structureprofiler/structureprofilerbioschemas.jsonld +++ b/data/structureprofiler/structureprofilerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Other", "sc:name": "StructureProfiler", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://www.zbh.uni-hamburg.de/forschung/amd/software/structureprofiler.html" } \ No newline at end of file diff --git a/data/strum/strumbioschemas.jsonld b/data/strum/strumbioschemas.jsonld index e80629061028a..f730a22481da9 100644 --- a/data/strum/strumbioschemas.jsonld +++ b/data/strum/strumbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12863-015-0190-3", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0001-7989-5764", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/strum", "@type": "sc:SoftwareApplication", @@ -38,12 +30,20 @@ "sc:license": "GPL-3.0", "sc:name": "strum", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/web/packages/strum/index.html", "sc:version": "0.6.2" + }, + { + "@id": "http://orcid.org/0000-0001-7989-5764", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/s12863-015-0190-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/stse/stsebioschemas.jsonld b/data/stse/stsebioschemas.jsonld index 52b2f02e46121..a287fb78a10e9 100644 --- a/data/stse/stsebioschemas.jsonld +++ b/data/stse/stsebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images.", "sc:name": "STSE", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.stse-software.org/" diff --git a/data/stsnp/stsnpbioschemas.jsonld b/data/stsnp/stsnpbioschemas.jsonld index 6aea8f09123ee..e35869e81cfce 100644 --- a/data/stsnp/stsnpbioschemas.jsonld +++ b/data/stsnp/stsnpbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "StSNP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://ilyinlab.org/StSNP/" } \ No newline at end of file diff --git a/data/stssearch/stssearchbioschemas.jsonld b/data/stssearch/stssearchbioschemas.jsonld index 5890d63fbc70b..1031ac6bc1e81 100644 --- a/data/stssearch/stssearchbioschemas.jsonld +++ b/data/stssearch/stssearchbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "EMBOSS Contributors", "UK MRC", - "Wellcome Trust" + "UK BBSRC", + "Wellcome Trust", + "EMBOSS Contributors" ], "sc:description": "Search a DNA database for matches with a set of STS primers.", "sc:funder": [ "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "stssearch", @@ -31,8 +31,8 @@ "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/stssearch.html", "sc:version": "r6" diff --git a/data/sub-gse/sub-gsebioschemas.jsonld b/data/sub-gse/sub-gsebioschemas.jsonld index 65c0d11d6ad21..3e1ce8a75c2cc 100644 --- a/data/sub-gse/sub-gsebioschemas.jsonld +++ b/data/sub-gse/sub-gsebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "It is developed for gene set enrichment analysis.The primary objective of this program is to measure the enrichment of differentially expressed or phenotype associated genes in given gene sets.The input for the program includes the gene expression data of several samples with corresponding phenotypic data and several given gene sets.The program will assess the significance of the enrichment of genes, whose gene expression profiles are associated with the phenotypic data, in each given gene set.", "sc:name": "Sub-GSE", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www-rcf.usc.edu/~fsun/Programs/SubGSEWebPages/SubGSEMain.html" } \ No newline at end of file diff --git a/data/suba3/suba3bioschemas.jsonld b/data/suba3/suba3bioschemas.jsonld index a58047ca09fc5..18848be50d857 100644 --- a/data/suba3/suba3bioschemas.jsonld +++ b/data/suba3/suba3bioschemas.jsonld @@ -17,22 +17,22 @@ ], "sc:additionalType": "Database portal", "sc:contributor": [ - "Harvey Millar", + "Sandra Tanz", "Cornelia Hooper", - "Ian Castleden", - "Sandra Tanz" + "Harvey Millar", + "Ian Castleden" ], "sc:description": "A subcellular localisation database for Arabidopsis proteins, with online search interface.", "sc:name": "SUBA3", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "ARC Centre of Excellence in Plant Energy Biology", - "University of Western Australia", - "unimelb.edu.au" + "unimelb.edu.au", + "University of Western Australia" ], "sc:url": "http://suba3.plantenergy.uwa.edu.au/" } \ No newline at end of file diff --git a/data/subacon/subaconbioschemas.jsonld b/data/subacon/subaconbioschemas.jsonld index e23194d70e109..1f58f7127d016 100644 --- a/data/subacon/subaconbioschemas.jsonld +++ b/data/subacon/subaconbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A naive Bayes classifier that integrates 22 computational prediction algorithms, experimental GFP and MS localizations, protein-protein interaction and co-expression data to derive a consensus call and probability.", "sc:name": "SUBAcon", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://subacon.plantenergy.uwa.edu.au//SUBAcon.html" } \ No newline at end of file diff --git a/data/subchlo/subchlobioschemas.jsonld b/data/subchlo/subchlobioschemas.jsonld index a80d3caddfcb7..bb42050eccc20 100644 --- a/data/subchlo/subchlobioschemas.jsonld +++ b/data/subchlo/subchlobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "SubChlo", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinfo.au.tsinghua.edu.cn/software/subchlo/" } \ No newline at end of file diff --git a/data/subdyquency/subdyquencybioschemas.jsonld b/data/subdyquency/subdyquencybioschemas.jsonld index e62b6c6707dea..cd0905674e4fc 100644 --- a/data/subdyquency/subdyquencybioschemas.jsonld +++ b/data/subdyquency/subdyquencybioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://orcid.org/0000-0002-9572-951X", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/S12859-019-2847-9", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Subdyquency", "@type": "sc:SoftwareApplication", @@ -21,11 +25,11 @@ }, "sc:additionalType": "Script", "sc:citation": [ + "pubmed:31088372", + "pmcid:PMC6518800", { "@id": "https://doi.org/10.1186/S12859-019-2847-9" - }, - "pubmed:31088372", - "pmcid:PMC6518800" + } ], "sc:description": "Random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph.", "sc:featureList": { @@ -35,14 +39,10 @@ "sc:name": "Subdyquency", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/weiba/Subdyquency" - }, - { - "@id": "https://doi.org/10.1186/S12859-019-2847-9", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/subjunc/subjuncbioschemas.jsonld b/data/subjunc/subjuncbioschemas.jsonld index ed993161c818b..b6d9bc29d4369 100644 --- a/data/subjunc/subjuncbioschemas.jsonld +++ b/data/subjunc/subjuncbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called \"seed-and-vote\" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-exon junctions from RNA-seq data.", "sc:name": "Subjunc", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://subread.sourceforge.net" } \ No newline at end of file diff --git a/data/subliminal_toolbox/subliminal_toolboxbioschemas.jsonld b/data/subliminal_toolbox/subliminal_toolboxbioschemas.jsonld index fd319f8d350a5..1f66e60ea4586 100644 --- a/data/subliminal_toolbox/subliminal_toolboxbioschemas.jsonld +++ b/data/subliminal_toolbox/subliminal_toolboxbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The software comprises of a number of independent tools that can be used to automate steps in the development of genome-scale metabolic reconstructions.", "sc:name": "SuBliMinaL Toolbox", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.mcisb.org/resources/subliminal/" } \ No newline at end of file diff --git a/data/subpatcnv/subpatcnvbioschemas.jsonld b/data/subpatcnv/subpatcnvbioschemas.jsonld index 7285452a1c115..ad1ef2d7fb769 100644 --- a/data/subpatcnv/subpatcnvbioschemas.jsonld +++ b/data/subpatcnv/subpatcnvbioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12859-014-0426-7", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/subpatcnv", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Kuang R.", - "Johnson N." + "Johnson N.", + "Kuang R." ], "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:25591662", + "pmcid:PMC4305219", { "@id": "https://doi.org/10.1186/S12859-014-0426-7" - }, - "pubmed:25591662", - "pmcid:PMC4305219" + } ], "sc:description": "Approximate subspace pattern mining for mapping copy-number variations.", "sc:featureList": { @@ -38,6 +34,10 @@ "Mac" ], "sc:url": "https://sourceforge.net/projects/subpatcnv/" + }, + { + "@id": "https://doi.org/10.1186/S12859-014-0426-7", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/subphospred/subphospredbioschemas.jsonld b/data/subphospred/subphospredbioschemas.jsonld index 7024abb0d2b80..d5b9a73f3255e 100644 --- a/data/subphospred/subphospredbioschemas.jsonld +++ b/data/subphospred/subphospredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SubPhosPred", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioinfo.ncu.edu.cn/SubPhosPred.aspx" } \ No newline at end of file diff --git a/data/subread/subreadbioschemas.jsonld b/data/subread/subreadbioschemas.jsonld index 6501efbf9c5cc..66e10fc0579e5 100644 --- a/data/subread/subreadbioschemas.jsonld +++ b/data/subread/subreadbioschemas.jsonld @@ -13,26 +13,22 @@ "@id": "https://doi.org/10.1038/nmeth.4106", "@type": "sc:CreativeWork" }, - { - "@id": "https://doi.org/10.1093/nar/gkt214", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/subread", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr Wei Shi", "sc:additionalType": "Suite", "sc:citation": [ - "pubmed:27941783", + "pubmed:23558742", + "pmcid:PMC3664803", "pmcid:PMC5792058", + "pubmed:27941783", { "@id": "https://doi.org/10.1093/nar/gkt214" }, { "@id": "https://doi.org/10.1038/nmeth.4106" - }, - "pmcid:PMC3664803", - "pubmed:23558742" + } ], "sc:description": "Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called \"seed-and-vote\" to achieve fast, accurate and scalable read mapping. It automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports indel detection and can map reads with both fixed and variable lengths.", "sc:featureList": { @@ -45,6 +41,10 @@ "Mac" ], "sc:url": "http://subread.sourceforge.net/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkt214", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/subseq/subseqbioschemas.jsonld b/data/subseq/subseqbioschemas.jsonld index 72ea57e850317..af1e7ea330fe0 100644 --- a/data/subseq/subseqbioschemas.jsonld +++ b/data/subseq/subseqbioschemas.jsonld @@ -11,12 +11,12 @@ "@id": "https://bio.tools/subseq", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "John D. Storey", - "Andrew J. Bass" + "Andrew J. Bass", + "John D. Storey" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Subsampling of high throughput sequencing count data for use in experiment design and analysis.", "sc:license": "MIT", diff --git a/data/subseqer/subseqerbioschemas.jsonld b/data/subseqer/subseqerbioschemas.jsonld index 6417d8b5ab402..4c5c8e8ea05f5 100644 --- a/data/subseqer/subseqerbioschemas.jsonld +++ b/data/subseqer/subseqerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool to find sequence motifs in low complexity protein sequences. It uses the application of a unique graph based approach.", "sc:name": "SubSeqer", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.compsysbio.org/subseqer/" diff --git a/data/subvis/subvisbioschemas.jsonld b/data/subvis/subvisbioschemas.jsonld index bc0737800d11c..d355cdba0c0d3 100644 --- a/data/subvis/subvisbioschemas.jsonld +++ b/data/subvis/subvisbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.7717/peerj.3492", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/subvis", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Scott Barlowe", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5490468", { "@id": "https://doi.org/10.7717/peerj.3492" }, - "pubmed:28674656", - "pmcid:PMC5490468" + "pubmed:28674656" ], "sc:description": "Visual Exploration of Protein Alignments Resulting from Multiple Substitution Matrices.", "sc:featureList": { @@ -33,10 +37,6 @@ "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/SubVis/" - }, - { - "@id": "https://doi.org/10.7717/peerj.3492", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/succfind/succfindbioschemas.jsonld b/data/succfind/succfindbioschemas.jsonld index 0361408ddc7fe..6d2221b4be2aa 100644 --- a/data/succfind/succfindbioschemas.jsonld +++ b/data/succfind/succfindbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Novel succinylation site online prediction tool which is constructed to predict the lysine succinylation sites based on two major categories of characteristics: sequence-derived features and evolutionary-derived information of sequence and via an enhanced feature strategy for further optimizations.", "sc:name": "SuccFind", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioinfo.ncu.edu.cn/SuccFind.aspx" } \ No newline at end of file diff --git a/data/sucos/sucosbioschemas.jsonld b/data/sucos/sucosbioschemas.jsonld index f17c4917ebffb..30a87b7637b45 100644 --- a/data/sucos/sucosbioschemas.jsonld +++ b/data/sucos/sucosbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "SuCOS", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/susanhleung/SuCOS" } \ No newline at end of file diff --git a/data/sugarbind/sugarbindbioschemas.jsonld b/data/sugarbind/sugarbindbioschemas.jsonld index 5e778d2657e3e..3356645ef2cda 100644 --- a/data/sugarbind/sugarbindbioschemas.jsonld +++ b/data/sugarbind/sugarbindbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:description": "Database portal of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals. The data were compiled through an exhaustive search of literature published over the past 30 years by glycobiologists, microbiologists, and medical histologists.", "sc:name": "SugarBind", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "https://sugarbind.expasy.org" diff --git a/data/sugarsketcher/sugarsketcherbioschemas.jsonld b/data/sugarsketcher/sugarsketcherbioschemas.jsonld index 148bb241cd524..5d6850e3db4b1 100644 --- a/data/sugarsketcher/sugarsketcherbioschemas.jsonld +++ b/data/sugarsketcher/sugarsketcherbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SugarSketcher", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://glycoproteome.expasy.org/sugarsketcher/" } \ No newline at end of file diff --git a/data/suitemsa/suitemsabioschemas.jsonld b/data/suitemsa/suitemsabioschemas.jsonld index 9698c41430a03..a7e7a56620ad8 100644 --- a/data/suitemsa/suitemsabioschemas.jsonld +++ b/data/suitemsa/suitemsabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent) or disagree (are inconsistent).", "sc:name": "SuiteMSA", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfolab.unl.edu/~canderson/SuiteMSA/" } \ No newline at end of file diff --git a/data/sumer/sumerbioschemas.jsonld b/data/sumer/sumerbioschemas.jsonld index 549dd147728bb..e54f47fbda3c8 100644 --- a/data/sumer/sumerbioschemas.jsonld +++ b/data/sumer/sumerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Sumer", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://github.com/bzhanglab/sumer" diff --git a/data/sumher/sumherbioschemas.jsonld b/data/sumher/sumherbioschemas.jsonld index 6b583e756cd63..8f85641c9bc5b 100644 --- a/data/sumher/sumherbioschemas.jsonld +++ b/data/sumher/sumherbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "SumHer", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://dougspeed.com/sumher/" } \ No newline at end of file diff --git a/data/summarizedbenchmark/summarizedbenchmarkbioschemas.jsonld b/data/summarizedbenchmark/summarizedbenchmarkbioschemas.jsonld index ceea41d6f59d3..91ee63c3771b3 100644 --- a/data/summarizedbenchmark/summarizedbenchmarkbioschemas.jsonld +++ b/data/summarizedbenchmark/summarizedbenchmarkbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/summarizedbenchmark", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Patrick Kimes", - "Alejandro Reyes" + "Alejandro Reyes", + "Patrick Kimes" ], "sc:additionalType": "Library", "sc:description": "This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. The SummarizedBenchmark class extends the RangedSummarizedExperiment object, and is designed to provide infrastructure to store and compare the results of applying different methods to a shared data set.", @@ -20,8 +20,8 @@ "sc:name": "SummarizedBenchmark", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SummarizedBenchmark.html", "sc:version": "1.0.3" diff --git a/data/summarizedexperiment/bioconda_summarizedexperiment.yaml b/data/summarizedexperiment/bioconda_summarizedexperiment.yaml index 5626946b8cd4f..17d9db08efdcc 100644 --- a/data/summarizedexperiment/bioconda_summarizedexperiment.yaml +++ b/data/summarizedexperiment/bioconda_summarizedexperiment.yaml @@ -5,7 +5,6 @@ description: The SummarizedExperiment container contains one or more assays, eac home: https://bioconductor.org/packages/3.10/bioc/html/SummarizedExperiment.html identifiers: - biotools:summarizedexperiment -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-summarizedexperiment summary: SummarizedExperiment container diff --git a/data/summarizedexperiment/summarizedexperimentbioschemas.jsonld b/data/summarizedexperiment/summarizedexperimentbioschemas.jsonld index 86971acbc03cf..d0afcd346a8ce 100644 --- a/data/summarizedexperiment/summarizedexperimentbioschemas.jsonld +++ b/data/summarizedexperiment/summarizedexperimentbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "SummarizedExperiment", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html", "sc:version": "1.4.0" diff --git a/data/summaryauc/summaryaucbioschemas.jsonld b/data/summaryauc/summaryaucbioschemas.jsonld index 40ee73fcbe129..ecc2b959c2347 100644 --- a/data/summaryauc/summaryaucbioschemas.jsonld +++ b/data/summaryauc/summaryaucbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "SummaryAUC", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/lsncibb/SummaryAUC" diff --git a/data/sumoamvr/sumoamvrbioschemas.jsonld b/data/sumoamvr/sumoamvrbioschemas.jsonld index dfc62ee6e59da..d83daffbe7ff6 100644 --- a/data/sumoamvr/sumoamvrbioschemas.jsonld +++ b/data/sumoamvr/sumoamvrbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for prediction of sumoylation related amino acid variations that affect sumoylation sites or enzymes involved in the process of connectivity.", "sc:name": "SUMOAMVR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfo.ncu.edu.cn/SUMOAMVR_Home.aspx" } \ No newline at end of file diff --git a/data/sumstat/sumstatbioschemas.jsonld b/data/sumstat/sumstatbioschemas.jsonld index 62a0dc5ecc409..7ce4ded8bc865 100644 --- a/data/sumstat/sumstatbioschemas.jsonld +++ b/data/sumstat/sumstatbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool considers a number of marker loci in the genome. At each marker, genotypes are available for two types of observations.", "sc:name": "SUMSTAT", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.jurgott.org/linkage/sumstat.html" } \ No newline at end of file diff --git a/data/super-delta/super-deltabioschemas.jsonld b/data/super-delta/super-deltabioschemas.jsonld index 9ee30ebad8129..c2d59a005b7f9 100644 --- a/data/super-delta/super-deltabioschemas.jsonld +++ b/data/super-delta/super-deltabioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/super-delta", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Xing Qiu", - "Jinfeng Zhang" + "Jinfeng Zhang", + "Xing Qiu" ], "sc:additionalType": "Library", "sc:description": "Robust gene expression data normalization and differential expression analysis pipeline.", "sc:name": "Super-delta", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/fhlsjs/Super-delta" } \ No newline at end of file diff --git a/data/super/superbioschemas.jsonld b/data/super/superbioschemas.jsonld index 3ac82dad9e049..36fa220947cec 100644 --- a/data/super/superbioschemas.jsonld +++ b/data/super/superbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Super is a webserver for rapidly screening the PDB to identify all oligopeptide fragments that superpose with a query under a pre-specified threshold of root mean-square deviation.", "sc:name": "Super", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://lcb.infotech.monash.edu.au/super" diff --git a/data/supercyp/supercypbioschemas.jsonld b/data/supercyp/supercypbioschemas.jsonld index 0ca7c736edbc7..a1f3c332d9329 100644 --- a/data/supercyp/supercypbioschemas.jsonld +++ b/data/supercyp/supercypbioschemas.jsonld @@ -11,19 +11,19 @@ "@id": "https://bio.tools/supercyp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mathias Dunkel", "Katharina Kroll", - "Daniel Kuzmann", + "Saskia Preissner", "Stefan Guenther", - "Saskia Preissner" + "Mathias Dunkel", + "Daniel Kuzmann" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:19934256", "sc:description": "The database contains about drugs, Cytochrome-Drug interactions and 1,200 alleles. SNPs and mutations are also listed and ordered according to their effect on expression and/or activity. It is a comprehensive resource focused on CYPs and drug metabolism. Homology-modeled structures of the CYPs can be downloaded in PDB format and related drugs are available as MOL-files.", "sc:name": "SuperCYP", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioinformatics.charite.de/supercyp" diff --git a/data/superfamily/superfamilybioschemas.jsonld b/data/superfamily/superfamilybioschemas.jsonld index 08550041f20ae..e126a34861abd 100644 --- a/data/superfamily/superfamilybioschemas.jsonld +++ b/data/superfamily/superfamilybioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "It provides protein domain assignments at the structural classification of protein superfamily level for completely sequenced genomes, metagenomes and other gene collections such as UniProt. Our scoring component now uses HMMER3. A cloud-based pipeline was implemented and is publicly available. The SUPERFAMILY reference tree of life has been improved allowing the user to highlight a chosen superfamily, family or domain architecture on the tree of life.", "sc:name": "SUPERFAMILY", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://supfam.org" } \ No newline at end of file diff --git a/data/superlooper/superlooperbioschemas.jsonld b/data/superlooper/superlooperbioschemas.jsonld index 202108fb868f0..5fbf80c295c73 100644 --- a/data/superlooper/superlooperbioschemas.jsonld +++ b/data/superlooper/superlooperbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SuperLooper is a web tool for the modeling of loops in globular and membrane proteins.", "sc:name": "SuperLooper", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioinf-applied.charite.de/superlooper/" diff --git a/data/supermatcher/supermatcherbioschemas.jsonld b/data/supermatcher/supermatcherbioschemas.jsonld index 8106c9492b101..f923901d8858d 100644 --- a/data/supermatcher/supermatcherbioschemas.jsonld +++ b/data/supermatcher/supermatcherbioschemas.jsonld @@ -20,15 +20,15 @@ "sc:description": "Calculate approximate local pair-wise alignments of larger sequences.", "sc:funder": [ "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "supermatcher", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/superpc/superpcbioschemas.jsonld b/data/superpc/superpcbioschemas.jsonld index 11566be53e20b..61460bb563dcd 100644 --- a/data/superpc/superpcbioschemas.jsonld +++ b/data/superpc/superpcbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This tool does prediction for a censored survival outcome, or a regression outcome, using the “supervised principal component” approach. It is especially useful when the number of features p is >> n, the number of samples, for example in microarray studies.", "sc:name": "SuperPC", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www-stat.stanford.edu/~tibs/superpc/" } \ No newline at end of file diff --git a/data/superphy/superphybioschemas.jsonld b/data/superphy/superphybioschemas.jsonld index ddecd170c0ca5..a60b2ab2c560c 100644 --- a/data/superphy/superphybioschemas.jsonld +++ b/data/superphy/superphybioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4828761", - "pubmed:27067409", { "@id": "https://doi.org/10.1186/S12866-016-0680-0" - } + }, + "pmcid:PMC4828761", + "pubmed:27067409" ], "sc:description": "Predictive genomics for the bacterial pathogen Escherichia coli.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "SuperPhy", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://lfz.corefacility.ca/superphy/" } diff --git a/data/superpose/superposebioschemas.jsonld b/data/superpose/superposebioschemas.jsonld index e75fd13288560..bb2748a9c311f 100644 --- a/data/superpose/superposebioschemas.jsonld +++ b/data/superpose/superposebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molecules.", "sc:name": "SuperPose", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://wishart.biology.ualberta.ca/SuperPose/" diff --git a/data/superpose3d/superpose3dbioschemas.jsonld b/data/superpose3d/superpose3dbioschemas.jsonld index aa782f4efaf34..585aae82de49a 100644 --- a/data/superpose3d/superpose3dbioschemas.jsonld +++ b/data/superpose3d/superpose3dbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A Local Structural Comparison Program That Allows for User-Defined Structure Representations.", "sc:name": "Superpose3D", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "ELIXIR-ITA-TORVERGATA", "sc:url": "http://cbm.bio.uniroma2.it/superpose3D", diff --git a/data/superpred/superpredbioschemas.jsonld b/data/superpred/superpredbioschemas.jsonld index 4d7ec0799fc8f..fe9cccc03b940 100644 --- a/data/superpred/superpredbioschemas.jsonld +++ b/data/superpred/superpredbioschemas.jsonld @@ -13,18 +13,18 @@ "biotools:primaryContact": [ "Janette Nickel", "Mathias Dunke", - "Priyanka Banerjee", "Bjoern-Oliver Gohlke", - "Jevgeni Ehreman" + "Jevgeni Ehreman", + "Priyanka Banerjee" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:18499712", "sc:description": "The SuperPred web server compares the structural fingerprint of an input molecule to a database of drugs connected to their drug targets and affected pathways. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. Such information can be useful in drug classification and target prediction.", "sc:name": "SuperPred", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinformatics.charite.de/superpred" } \ No newline at end of file diff --git a/data/superq/superqbioschemas.jsonld b/data/superq/superqbioschemas.jsonld index 749f10b70b4ed..0dcd6c45d0d45 100644 --- a/data/superq/superqbioschemas.jsonld +++ b/data/superq/superqbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees.", "sc:name": "SuperQ", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.uea.ac.uk/computing/superq" diff --git a/data/superquantnode/superquantnodebioschemas.jsonld b/data/superquantnode/superquantnodebioschemas.jsonld index 03e821fbdb23c..e40d0e263ed10 100644 --- a/data/superquantnode/superquantnodebioschemas.jsonld +++ b/data/superquantnode/superquantnodebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-0170-5785", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/superquantnode", "@type": "sc:SoftwareApplication", @@ -23,10 +27,6 @@ "sc:operatingSystem": "Windows", "sc:url": "https://github.com/caetera/SuperQuantNode", "sc:version": "1.0" - }, - { - "@id": "http://orcid.org/0000-0003-0170-5785", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/supertarget/supertargetbioschemas.jsonld b/data/supertarget/supertargetbioschemas.jsonld index 009474702272c..630654869d7b2 100644 --- a/data/supertarget/supertargetbioschemas.jsonld +++ b/data/supertarget/supertargetbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web resource for analyzing drug-target interactions. Integrates drug-related info associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins.", "sc:name": "SuperTarget", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioinformatics.charite.de/supertarget/" } \ No newline at end of file diff --git a/data/supertree/supertreebioschemas.jsonld b/data/supertree/supertreebioschemas.jsonld index 2b3c6db4485fc..78a5a9abdeaa0 100644 --- a/data/supertree/supertreebioschemas.jsonld +++ b/data/supertree/supertreebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "SuperTree is a software to assemble phylogenetic trees into a more comprehensive one, called supertree, using specific algorithms", "sc:name": "SuperTree", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www2.unil.ch/phylo/bioinformatics/supertree.html" } \ No newline at end of file diff --git a/data/suppa/suppabioschemas.jsonld b/data/suppa/suppabioschemas.jsonld index d79ab4e2f33a3..08eb43051e71d 100644 --- a/data/suppa/suppabioschemas.jsonld +++ b/data/suppa/suppabioschemas.jsonld @@ -13,22 +13,22 @@ "biotools:primaryContact": "SUPPA Users group", "sc:additionalType": "Command-line tool", "sc:author": [ - "Gael P. Alamancos", + "Amadí­s Pagès", "Miha Skalic", "JC Entizne", - "Amadí­s Pagès" + "Gael P. Alamancos" ], "sc:description": "This tool generates Alternative Splicing (AS) events from an annotation and calculates the PSI (\"Percentage Spliced In\") value for each event exploiting fast quantification of transcript abundances from multiple samples.", "sc:license": "MIT", "sc:name": "SUPPA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ - "upf.edu", - "Pompeu Fabra University" + "Pompeu Fabra University", + "upf.edu" ], "sc:url": "https://bitbucket.org/regulatorygenomicsupf/suppa/", "sc:version": "1" diff --git a/data/suprahex/suprahexbioschemas.jsonld b/data/suprahex/suprahexbioschemas.jsonld index 62e4a469280e8..786d901f97708 100644 --- a/data/suprahex/suprahexbioschemas.jsonld +++ b/data/suprahex/suprahexbioschemas.jsonld @@ -9,6 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-3961-8572", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1016/j.bbrc.2013.11.103", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/suprahex", "@type": "sc:SoftwareApplication", @@ -21,37 +29,29 @@ ], "sc:citation": [ "pubmed:24309102", + "pmcid:PMC3905187", { "@id": "https://doi.org/10.1016/j.bbrc.2013.11.103" - }, - "pmcid:PMC3905187" + } ], "sc:description": "This tool carries out gene clustering, sample correlation and intuitive visualisations to facilitate exploratory analysis with high-dimensional omics input data. More importantly, it allows for overlaying additional data onto the trained map to explore relations between input and additional data. Some newly added utilities are advanced heatmap visualisation and tree-based analysis of sample relationships.", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_3432" }, { - "@id": "edam:operation_3432" + "@id": "edam:operation_0337" } ], "sc:license": "GPL-2.0", "sc:name": "supraHex", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/supraHex.html", "sc:version": "1.12.0" - }, - { - "@id": "https://doi.org/10.1016/j.bbrc.2013.11.103", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-3961-8572", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/suretypesc/suretypescbioschemas.jsonld b/data/suretypesc/suretypescbioschemas.jsonld index 8b0143e051694..0595ca3dae601 100644 --- a/data/suretypesc/suretypescbioschemas.jsonld +++ b/data/suretypesc/suretypescbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-3.0", "sc:name": "SureTypeSC", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/puko818/SureTypeSC" } \ No newline at end of file diff --git a/data/surfcut/surfcutbioschemas.jsonld b/data/surfcut/surfcutbioschemas.jsonld index fa673063482b6..76a32323517b3 100644 --- a/data/surfcut/surfcutbioschemas.jsonld +++ b/data/surfcut/surfcutbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-3643-3978", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1186/S12915-019-0657-1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/SurfCut", "@type": "sc:SoftwareApplication", @@ -26,10 +18,10 @@ "sc:additionalType": "Desktop application", "sc:citation": [ "pmcid:PMC6509810", - "pubmed:31072374", { "@id": "https://doi.org/10.1186/S12915-019-0657-1" - } + }, + "pubmed:31072374" ], "sc:description": "Pipeline for high-throughput extraction of cell contours from 3D image stacks.", "sc:featureList": [ @@ -43,11 +35,19 @@ "sc:license": "CECILL-C", "sc:name": "SurfCut", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://github.com/sverger/SurfCut" + }, + { + "@id": "https://orcid.org/0000-0003-3643-3978", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/S12915-019-0657-1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/surfy/surfybioschemas.jsonld b/data/surfy/surfybioschemas.jsonld index 7ed19b363bd14..5e3dbada37acb 100644 --- a/data/surfy/surfybioschemas.jsonld +++ b/data/surfy/surfybioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Visualize the human surface proteome (surfaceome) and load your own expression data to inspect and uncover cellular phenotypes and new surfaceome markers.", "sc:name": "SURFY", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://wlab.ethz.ch/surfaceome/" } \ No newline at end of file diff --git a/data/surpresi/surpresibioschemas.jsonld b/data/surpresi/surpresibioschemas.jsonld index 65704508faa04..e3e82516dd154 100644 --- a/data/surpresi/surpresibioschemas.jsonld +++ b/data/surpresi/surpresibioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Method for finding binding sites in proteins based on the probabilitic analysis of global radial distributions of atoms.", "sc:name": "SurpResi", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://pmbm.ippt.gov.pl/services/surpresi/cgi-bin/prediction.py", "sc:version": "201108" diff --git a/data/survcomp/survcompbioschemas.jsonld b/data/survcomp/survcompbioschemas.jsonld index ccdf9f98e7c6a..754b5e6f4461a 100644 --- a/data/survcomp/survcompbioschemas.jsonld +++ b/data/survcomp/survcompbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btn374", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/survcomp", "@type": "sc:SoftwareApplication", @@ -24,11 +28,11 @@ "Library" ], "sc:citation": [ - "pmcid:PMC2553442", "pubmed:18635567", { "@id": "https://doi.org/10.1093/bioinformatics/btn374" - } + }, + "pmcid:PMC2553442" ], "sc:description": "R package providing functions to assess and to compare the performance of risk prediction (survival) models.", "sc:featureList": { @@ -47,10 +51,6 @@ { "@id": "http://orcid.org/0000-0002-7684-0079", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btn374", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/survcurve/survcurvebioschemas.jsonld b/data/survcurve/survcurvebioschemas.jsonld index 5985b15d1372b..32294be9be947 100644 --- a/data/survcurve/survcurvebioschemas.jsonld +++ b/data/survcurve/survcurvebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SurvCurve", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "https://www.ebi.ac.uk/thornton-srv/databases/SurvCurv/analyse.php", diff --git a/data/survgenesinterim/survgenesinterimbioschemas.jsonld b/data/survgenesinterim/survgenesinterimbioschemas.jsonld index e5bd9654f7bee..f544824beee36 100644 --- a/data/survgenesinterim/survgenesinterimbioschemas.jsonld +++ b/data/survgenesinterim/survgenesinterimbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "survGenesInterim is an R package for simulation of survival studies based on simulated gene expression level and patient data. Includes functions to generate such data. Resulting error and power rate can be visualized.", "sc:name": "survGenesInterim", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.ams.med.uni-goettingen.de/software-en.shtml", "sc:version": "1.0" diff --git a/data/survival_kit/survival_kitbioschemas.jsonld b/data/survival_kit/survival_kitbioschemas.jsonld index 7ccd8814cb59c..bf572406642b8 100644 --- a/data/survival_kit/survival_kitbioschemas.jsonld +++ b/data/survival_kit/survival_kitbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/survival_kit", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Survival analysis methods were first developed in the biomedical field, which generally involves smaller file sizes and lower levels of effects than agronomic applications. The relative theory of random effects in survival analysis (\"fragile\" models) is not as advanced as with linear models and no freeware is available to use such models. The survival kit analyses large populations with complex models.", "sc:license": "Not licensed", diff --git a/data/survivalgwas_power/survivalgwas_powerbioschemas.jsonld b/data/survivalgwas_power/survivalgwas_powerbioschemas.jsonld index cc3321be9b84c..f2794dff51210 100644 --- a/data/survivalgwas_power/survivalgwas_powerbioschemas.jsonld +++ b/data/survivalgwas_power/survivalgwas_powerbioschemas.jsonld @@ -21,11 +21,11 @@ }, "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:27931206", "pmcid:PMC5146816", { "@id": "https://doi.org/10.1186/s12859-016-1407-9" - } + }, + "pubmed:27931206" ], "sc:description": "SurvivalGWAS_Power performs power calculations for time to event outcomes over a range of study designs and different analytical approaches. The software calculates the power to detect single nucleotide polymorphism association with a time to event outcome over a range of study design scenarios.", "sc:featureList": { diff --git a/data/survivalgwas_sv/survivalgwas_svbioschemas.jsonld b/data/survivalgwas_sv/survivalgwas_svbioschemas.jsonld index 522127840d9b0..c0112a3c7c3c7 100644 --- a/data/survivalgwas_sv/survivalgwas_svbioschemas.jsonld +++ b/data/survivalgwas_sv/survivalgwas_svbioschemas.jsonld @@ -19,8 +19,8 @@ "biotools:primaryContact": "Hamzah Syed", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:28525968", "pmcid:PMC5438515", + "pubmed:28525968", { "@id": "https://doi.org/10.1186/s12859-017-1683-z" } @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "SurvivalGWAS_SV", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.liverpool.ac.uk/translational-medicine/research/statistical-genetics/survival-gwas-sv/" } diff --git a/data/survmicro/survmicrobioschemas.jsonld b/data/survmicro/survmicrobioschemas.jsonld index 084df0f3355eb..b784413d0bffc 100644 --- a/data/survmicro/survmicrobioschemas.jsonld +++ b/data/survmicro/survmicrobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "SurvMicro", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinformatica.mty.itesm.mx:8080/Biomatec/Survmicro.jsp" } \ No newline at end of file diff --git a/data/survnet/survnetbioschemas.jsonld b/data/survnet/survnetbioschemas.jsonld index 4059fc877dc8f..1ccc88c787365 100644 --- a/data/survnet/survnetbioschemas.jsonld +++ b/data/survnet/survnetbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SurvNet is a webserver for identifying network-based biomarkers that most correlate with patient survival data. Users provide a biological network file, a molecular profiling file from high-throughput experiment and a patient survival data file. Returned is a list of network biomarkers that best correlate with the observed patient survival data.", "sc:name": "SurvNet", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioinformatics.mdanderson.org/main/SurvNet" } \ No newline at end of file diff --git a/data/sushi/sushibioschemas.jsonld b/data/sushi/sushibioschemas.jsonld index d75e800f226dd..bc64d7a83f483 100644 --- a/data/sushi/sushibioschemas.jsonld +++ b/data/sushi/sushibioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "Sushi", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Sushi.html", "sc:version": "1.12.0" diff --git a/data/suspect-bdq/suspect-bdqbioschemas.jsonld b/data/suspect-bdq/suspect-bdqbioschemas.jsonld index fc67a6020fc32..4acae593eca4e 100644 --- a/data/suspect-bdq/suspect-bdqbioschemas.jsonld +++ b/data/suspect-bdq/suspect-bdqbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "SUSPECT-BDQ", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://biosig.unimelb.edu.au/suspect_bdq/" } \ No newline at end of file diff --git a/data/sv-callers/sv-callersbioschemas.jsonld b/data/sv-callers/sv-callersbioschemas.jsonld index 2f2a675c87355..24cc5c6a25543 100644 --- a/data/sv-callers/sv-callersbioschemas.jsonld +++ b/data/sv-callers/sv-callersbioschemas.jsonld @@ -17,17 +17,17 @@ "@id": "https://bio.tools/sv-callers", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Workflow", - "Command-line tool" + "Command-line tool", + "Workflow" ], "sc:author": "Arnold Kuzniar", "sc:contributor": [ - "Carl Shneider", "Stefan Verhoeven", { "@id": "https://orcid.org/0000-0001-8784-2507" }, - "Jason Maassen" + "Jason Maassen", + "Carl Shneider" ], "sc:description": "A highly portable HPC workflow for detecting structural variants in whole genome sequencing data.", "sc:license": "Apache-2.0", @@ -35,9 +35,9 @@ "sc:operatingSystem": "Linux", "sc:url": "https://github.com/GooglingTheCancerGenome/sv-callers", "sc:version": [ - "1.0.0", "1.1.0", - "1.1.1" + "1.1.1", + "1.0.0" ] } ] diff --git a/data/sva/svabioschemas.jsonld b/data/sva/svabioschemas.jsonld index 20781f31b9995..cd4e59f3acb5a 100644 --- a/data/sva/svabioschemas.jsonld +++ b/data/sva/svabioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/sva", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "W. Evan Johnson", + "John D. Storey", "Jeffrey T. Leek", - "John D. Storey" + "W. Evan Johnson" ], "sc:additionalType": [ "Library", @@ -24,8 +24,8 @@ "sc:name": "sva", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/sva.html", "sc:version": "3.22.0" diff --git a/data/svamp/svampbioschemas.jsonld b/data/svamp/svampbioschemas.jsonld index 66863bf1fbac7..38cb6cf6a4465 100644 --- a/data/svamp/svampbioschemas.jsonld +++ b/data/svamp/svampbioschemas.jsonld @@ -9,30 +9,22 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-1734-1007", - "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU176", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/svamp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Lailatul Hidayah", { "@id": "http://orcid.org/0000-0003-1734-1007" - }, - "Lailatul Hidayah" + } ], "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC4103593", - "pubmed:24700318", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU176" - } + }, + "pmcid:PMC4103593", + "pubmed:24700318" ], "sc:description": "Standalone desktop application to visualise variants (SNPs and indels) and peform realtime analysis on selected regions of a genome on specific samples.", "sc:featureList": { @@ -41,10 +33,18 @@ "sc:name": "SVAMP", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.cbrc.kaust.edu.sa/svamp/" + }, + { + "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTU176", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-1734-1007", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/svapls/svaplsbioschemas.jsonld b/data/svapls/svaplsbioschemas.jsonld index 0b58ff6098c69..ccffc46ae4b79 100644 --- a/data/svapls/svaplsbioschemas.jsonld +++ b/data/svapls/svaplsbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Sutirtha Chakraborty", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:23883280", { "@id": "https://doi.org/10.1186/1471-2105-14-236" }, - "pubmed:23883280", "pmcid:PMC3733742" ], "sc:description": "Accurate identification of genes that are truly differentially expressed over two sample\nvarieties, after adjusting for hidden subject-specific effects of residual heterogeneity.", @@ -28,8 +28,8 @@ "sc:name": "svapls", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/svapls/index.html" }, diff --git a/data/svaplsseq/svaplsseqbioschemas.jsonld b/data/svaplsseq/svaplsseqbioschemas.jsonld index 8f00de3589f4f..23dcf7fe4533c 100644 --- a/data/svaplsseq/svaplsseqbioschemas.jsonld +++ b/data/svaplsseq/svaplsseqbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sutirtha Chakraborty", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package contains functions that are intended for the identification of differentially expressed genes between two groups of samples from RNAseq data after adjusting for various hidden biological and technical factors of variability.", "sc:license": "GPL-3.0", "sc:name": "SVAPLSseq", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SVAPLSseq.html", "sc:version": "1.0.0" diff --git a/data/svd-phy/svd-phybioschemas.jsonld b/data/svd-phy/svd-phybioschemas.jsonld index b9c53f1f3e1b1..afc064f7f612d 100644 --- a/data/svd-phy/svd-phybioschemas.jsonld +++ b/data/svd-phy/svd-phybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A phylogenetic profiling algorithm which uses truncated singular value decomposition to address the problem of uninformative profiles giving rise to false positive predictions.", "sc:name": "SVD-Phy", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://bitbucket.org/andrea/svd-phy" } \ No newline at end of file diff --git a/data/svdetect_bam_preprocessing_pairs/svdetect_bam_preprocessing_pairsbioschemas.jsonld b/data/svdetect_bam_preprocessing_pairs/svdetect_bam_preprocessing_pairsbioschemas.jsonld index e8015e3b26e2f..07c8f229dc98f 100644 --- a/data/svdetect_bam_preprocessing_pairs/svdetect_bam_preprocessing_pairsbioschemas.jsonld +++ b/data/svdetect_bam_preprocessing_pairs/svdetect_bam_preprocessing_pairsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "BAM preprocessing to get abnormal pairs.", "sc:name": "svdetect_bam_preprocessing_pairs", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://svdetect.sourceforge.net/Site/Home.html", "sc:version": "1.0.0" diff --git a/data/svdetect_compare_step/svdetect_compare_stepbioschemas.jsonld b/data/svdetect_compare_step/svdetect_compare_stepbioschemas.jsonld index 3de1e2f531861..ea468babfd141 100644 --- a/data/svdetect_compare_step/svdetect_compare_stepbioschemas.jsonld +++ b/data/svdetect_compare_step/svdetect_compare_stepbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "svdetect_compare_step", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://svdetect.sourceforge.net/Site/Home.html", "sc:version": "1.0.0" diff --git a/data/svdetect_run_parallel_step/svdetect_run_parallel_stepbioschemas.jsonld b/data/svdetect_run_parallel_step/svdetect_run_parallel_stepbioschemas.jsonld index c6c64e87ea9d0..51b01112fb0d7 100644 --- a/data/svdetect_run_parallel_step/svdetect_run_parallel_stepbioschemas.jsonld +++ b/data/svdetect_run_parallel_step/svdetect_run_parallel_stepbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Detect clusters of anomalously mapped pairs and identify structural variants.", "sc:name": "svdetect_run_parallel_step", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://svdetect.sourceforge.net/Site/Home.html", diff --git a/data/svist4get/svist4getbioschemas.jsonld b/data/svist4get/svist4getbioschemas.jsonld index 2d068bacb3e6d..91a8c72b0e7bc 100644 --- a/data/svist4get/svist4getbioschemas.jsonld +++ b/data/svist4get/svist4getbioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-019-2706-8", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/svist4get", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Artyom Egorov", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC6404320", { "@id": "https://doi.org/10.1186/s12859-019-2706-8" }, - "pmcid:PMC6404320", "pubmed:30841857" ], "sc:description": "Simple visualization tool for genomic tracks from sequencing experiments.", "sc:featureList": [ { - "@id": "edam:operation_3680" + "@id": "edam:operation_3436" }, { "@id": "edam:operation_3208" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_3680" } ], "sc:license": "WTFPL", "sc:name": "svist4get", "sc:operatingSystem": "Linux", "sc:url": "https://bitbucket.org/artegorov/svist4get/" - }, - { - "@id": "https://doi.org/10.1186/s12859-019-2706-8", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/svm-prot/svm-protbioschemas.jsonld b/data/svm-prot/svm-protbioschemas.jsonld index ecfbe393badeb..b8680c73ecfc7 100644 --- a/data/svm-prot/svm-protbioschemas.jsonld +++ b/data/svm-prot/svm-protbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.", "sc:name": "SVM-PROT", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bidd2.nus.edu.sg/cgi-bin/svm-prot/svmprot.cgi" } \ No newline at end of file diff --git a/data/svm-rne/svm-rnebioschemas.jsonld b/data/svm-rne/svm-rnebioschemas.jsonld index a69a6d2990fa1..4bdced9b8e61c 100644 --- a/data/svm-rne/svm-rnebioschemas.jsonld +++ b/data/svm-rne/svm-rnebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Classification and biomarker identification using gene network modules and support vector machines. Uses the Gene Expression Network Analysis Tool (GXNA) as clustering method to identify correlated gene clusters, and Support Vector Machines to identify and (rank) those gene networks (clusters) for accuracy of classification.", "sc:name": "SVM-RNE", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://web.macam.ac.il/~myousef/MyTools/SVM-RNE.htm" } \ No newline at end of file diff --git a/data/svm2/svm2bioschemas.jsonld b/data/svm2/svm2bioschemas.jsonld index 30df0f0060781..65c2eb38ba92c 100644 --- a/data/svm2/svm2bioschemas.jsonld +++ b/data/svm2/svm2bioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/svm2", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "David Horner", - "Matteo Chiara" + "Matteo Chiara", + "David Horner" ], "sc:additionalType": "Command-line tool", "sc:description": "Detection and characterization of genomic structural variation (SV) from ultra high-throughput genome resequencing data.", diff --git a/data/svm2crm/svm2crmbioschemas.jsonld b/data/svm2crm/svm2crmbioschemas.jsonld index 0618dd678d799..25b91e99836f9 100644 --- a/data/svm2crm/svm2crmbioschemas.jsonld +++ b/data/svm2crm/svm2crmbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "SVM2CRM", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SVM2CRM.html", diff --git a/data/svmtm/svmtmbioschemas.jsonld b/data/svmtm/svmtmbioschemas.jsonld index 98c38caaa51eb..416d812b14edb 100644 --- a/data/svmtm/svmtmbioschemas.jsonld +++ b/data/svmtm/svmtmbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Support Vector Machine Transmembrane (SVMtm) predicts transmembrane helices when given protein sequences in FASTA format.", "sc:name": "SVMtm", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://ccb.imb.uq.edu.au/svmtm/svmtm_predictor.shtml" } \ No newline at end of file diff --git a/data/svn/svnbioschemas.jsonld b/data/svn/svnbioschemas.jsonld index 16d5d505066cf..0fc4294609238 100644 --- a/data/svn/svnbioschemas.jsonld +++ b/data/svn/svnbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A program for removing systematic variation in microarray gene expression data. Based on an analysis of how systematic variation contributes to variability in microarray data sets, this procedure includes background subtraction determined from the distribution of pixel intensity values and log conversion, linear or non-linear regression, restoration or transformation, and multiarray normalization.", "sc:name": "SVN", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.niehs.nih.gov/research/resources/software/biostatistics/svn/index.cfm" } \ No newline at end of file diff --git a/data/swakk/swakkbioschemas.jsonld b/data/swakk/swakkbioschemas.jsonld index b19fa3efc2b57..8b03aa5bf9c00 100644 --- a/data/swakk/swakkbioschemas.jsonld +++ b/data/swakk/swakkbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.", "sc:name": "SWAKK", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://oxytricha.princeton.edu/SWAKK/" } \ No newline at end of file diff --git a/data/swarmdock/swarmdockbioschemas.jsonld b/data/swarmdock/swarmdockbioschemas.jsonld index 698a64f8c6d58..dc9d93d552347 100644 --- a/data/swarmdock/swarmdockbioschemas.jsonld +++ b/data/swarmdock/swarmdockbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Generating 3D structures of protein-protein complexes. Allows flexible modelling of protein-protein complexes using the SwarmDock algorithm which incorporates a normal modes approach.", "sc:name": "SwarmDock", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bmm.cancerresearchuk.org/~SwarmDock/index.html" } \ No newline at end of file diff --git a/data/swath2stats/swath2statsbioschemas.jsonld b/data/swath2stats/swath2statsbioschemas.jsonld index 76e78d99a6d71..31522304fe287 100644 --- a/data/swath2stats/swath2statsbioschemas.jsonld +++ b/data/swath2stats/swath2statsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0153160", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/swath2stats", "@type": "sc:SoftwareApplication", @@ -22,18 +26,18 @@ "@id": "edam:data_3111" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": { "@id": "edam:topic_3520" }, "sc:citation": [ "pmcid:PMC4824525", + "pubmed:27054327", { "@id": "https://doi.org/10.1371/journal.pone.0153160" - }, - "pubmed:27054327" + } ], "sc:description": "This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.", "sc:featureList": { @@ -43,8 +47,8 @@ "sc:name": "SWATH2stats", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SWATH2stats.html", "sc:version": "1.4.1" @@ -52,10 +56,6 @@ { "@id": "http://orcid.org/0000-0001-9105-6381", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0153160", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/swathxtend/swathxtendbioschemas.jsonld b/data/swathxtend/swathxtendbioschemas.jsonld index d023092bc142b..f160006fd66e0 100644 --- a/data/swathxtend/swathxtendbioschemas.jsonld +++ b/data/swathxtend/swathxtendbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "SwathXtend", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/SwathXtend.html", "sc:version": "1.2.0" diff --git a/data/swdmr/swdmrbioschemas.jsonld b/data/swdmr/swdmrbioschemas.jsonld index 44121fc5c8174..1d1e54117444f 100644 --- a/data/swdmr/swdmrbioschemas.jsonld +++ b/data/swdmr/swdmrbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/swdmr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "BingYu Chen", - "Dongsheng Huang" + "Dongsheng Huang", + "BingYu Chen" ], "sc:additionalType": "Command-line tool", "sc:description": "swDMR: a sliding window approach to identify differentially methylated regions based on bisulfite sequencing", diff --git a/data/sweblast/sweblastbioschemas.jsonld b/data/sweblast/sweblastbioschemas.jsonld index 67136ac3d591c..7bf446d08f2bb 100644 --- a/data/sweblast/sweblastbioschemas.jsonld +++ b/data/sweblast/sweblastbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A perl program that looks for recombinations in non-aligned sequences using BLAST.", "sc:name": "SWeBLAST", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioinformatics.org/sweblast/wiki/" } \ No newline at end of file diff --git a/data/sweed/sweedbioschemas.jsonld b/data/sweed/sweedbioschemas.jsonld index 9652d9c23e585..40f25c614a720 100644 --- a/data/sweed/sweedbioschemas.jsonld +++ b/data/sweed/sweedbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:16251466", { "@id": "https://doi.org/10.1101/gr.4252305" }, - "pmcid:PMC1310644", - "pubmed:16251466" + "pmcid:PMC1310644" ], "sc:description": "Parallel and checkpointable tool implementing a composite ratio test for detecting selective sweeps. SweeD is based on the SweepFinder algorithm. SweeD can calculate the theoretical SFS of a give demographic model (stepwise changes or with an exponential growth phase + stepwise changes) using the method of Zickovic and Stephan (2011).", "sc:featureList": { diff --git a/data/swepep/swepepbioschemas.jsonld b/data/swepep/swepepbioschemas.jsonld index 444ed4d4fb705..e2825b8432752 100644 --- a/data/swepep/swepepbioschemas.jsonld +++ b/data/swepep/swepepbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "An endogenous peptide database.", "sc:name": "SwePep", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "bils.se", "sc:url": "http://www.swepep.se/" diff --git a/data/swfdr/swfdrbioschemas.jsonld b/data/swfdr/swfdrbioschemas.jsonld index 3c4c708753a6e..c173cbdd3b4e7 100644 --- a/data/swfdr/swfdrbioschemas.jsonld +++ b/data/swfdr/swfdrbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/swfdr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jeffrey T. Leek", - "Simina M. Boca" + "Simina M. Boca", + "Jeffrey T. Leek" ], "sc:additionalType": "Library", "sc:description": "This package allows users to estimate the science-wise false discovery rate from Jager and Leek, \"Empirical estimates suggest most published medical research is true,\" 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the proportion of true null hypotheses in the presence of covariates, using a regression framework.", "sc:license": "GPL-3.0", "sc:name": "swfdr", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/swfdr.html", "sc:version": "1.6.0" diff --git a/data/swicz/swiczbioschemas.jsonld b/data/swicz/swiczbioschemas.jsonld index d2a0c592a951f..673d9441b5864 100644 --- a/data/swicz/swiczbioschemas.jsonld +++ b/data/swicz/swiczbioschemas.jsonld @@ -17,9 +17,9 @@ ], "sc:contributor": [ "Marek Basler", - "Jan Bobek", - "Karel Mikulik", "Urs Jenal", + "Karel Mikulik", + "Jan Bobek", "Bjorn Grunenfelder" ], "sc:description": "A proteomics web database.", diff --git a/data/swift/swiftbioschemas.jsonld b/data/swift/swiftbioschemas.jsonld index 71c588f6a503a..8fe468cf09fae 100644 --- a/data/swift/swiftbioschemas.jsonld +++ b/data/swift/swiftbioschemas.jsonld @@ -19,9 +19,9 @@ "Mac" ], "sc:provider": [ - "CeBiTec", + "Bielefeld University", "BiBiServ", - "Bielefeld University" + "CeBiTec" ], "sc:url": "https://bibiserv.cebitec.uni-bielefeld.de/swift", "sc:version": "1" diff --git a/data/swiss-2dpage/swiss-2dpagebioschemas.jsonld b/data/swiss-2dpage/swiss-2dpagebioschemas.jsonld index c62f8667fdd25..e9fc0789b1b69 100644 --- a/data/swiss-2dpage/swiss-2dpagebioschemas.jsonld +++ b/data/swiss-2dpage/swiss-2dpagebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps.", "sc:name": "SWISS-2DPAGE", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.expasy.org/ch2d/" } \ No newline at end of file diff --git a/data/swiss-model_repository/swiss-model_repositorybioschemas.jsonld b/data/swiss-model_repository/swiss-model_repositorybioschemas.jsonld index 02cc9fdc9d30a..c9e8e7387be68 100644 --- a/data/swiss-model_repository/swiss-model_repositorybioschemas.jsonld +++ b/data/swiss-model_repository/swiss-model_repositorybioschemas.jsonld @@ -11,15 +11,15 @@ "@id": "https://bio.tools/swiss-model_repository", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Workbench", - "Database portal" + "Database portal", + "Workbench" ], "sc:description": "Database of protein structure homology models generated by the fully automated SWISS-MODEL modeling pipeline.", "sc:name": "SWISS-MODEL Repository", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "https://swissmodel.expasy.org/repository/", diff --git a/data/swiss-model_workspace/swiss-model_workspacebioschemas.jsonld b/data/swiss-model_workspace/swiss-model_workspacebioschemas.jsonld index 08abe55eaf7f0..4d883d1d89e81 100644 --- a/data/swiss-model_workspace/swiss-model_workspacebioschemas.jsonld +++ b/data/swiss-model_workspace/swiss-model_workspacebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gku340", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/swiss-model_workspace", "@type": "sc:SoftwareApplication", @@ -21,14 +17,14 @@ { "@id": "edam:data_1384" }, - { - "@id": "edam:data_2974" - }, { "@id": "edam:data_2291" }, { "@id": "edam:data_3021" + }, + { + "@id": "edam:data_2974" } ], "edam:has_output": { @@ -39,14 +35,14 @@ { "@id": "edam:topic_0081" }, - { - "@id": "edam:topic_0082" - }, { "@id": "edam:topic_2275" }, { "@id": "edam:topic_3306" + }, + { + "@id": "edam:topic_0082" } ], "sc:citation": [ @@ -62,13 +58,17 @@ }, "sc:name": "SWISS-MODEL Workspace", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "https://swissmodel.expasy.org/", "sc:version": "1" + }, + { + "@id": "https://doi.org/10.1093/nar/gku340", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/swiss-pdbviewer/swiss-pdbviewerbioschemas.jsonld b/data/swiss-pdbviewer/swiss-pdbviewerbioschemas.jsonld index 5b142d1fb5700..ad0814259306a 100644 --- a/data/swiss-pdbviewer/swiss-pdbviewerbioschemas.jsonld +++ b/data/swiss-pdbviewer/swiss-pdbviewerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Excellent tool for comparing, colouring, annotating, mutating 3-D structures; a.k.a. Deep View; tutorial *Molecular Modeling for Beginners* is a must (listed on this page).", "sc:name": "Swiss-PdbViewer", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://spdbv.vital-it.ch/" } \ No newline at end of file diff --git a/data/swiss_embnet/swiss_embnetbioschemas.jsonld b/data/swiss_embnet/swiss_embnetbioschemas.jsonld index a2e3326c009ea..8eb2a79f965b9 100644 --- a/data/swiss_embnet/swiss_embnetbioschemas.jsonld +++ b/data/swiss_embnet/swiss_embnetbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Swiss EMBnet", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.ch.embnet.org/" } \ No newline at end of file diff --git a/data/swiss_mass_abacus/swiss_mass_abacusbioschemas.jsonld b/data/swiss_mass_abacus/swiss_mass_abacusbioschemas.jsonld index 7b27d85cf9e3f..414992801771c 100644 --- a/data/swiss_mass_abacus/swiss_mass_abacusbioschemas.jsonld +++ b/data/swiss_mass_abacus/swiss_mass_abacusbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Swiss Mass Abacus", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://glycoproteome.expasy.org/swiss-mass-abacus/" } \ No newline at end of file diff --git a/data/swiss_model/swiss_modelbioschemas.jsonld b/data/swiss_model/swiss_modelbioschemas.jsonld index e9c093f5d839a..2e2c91c443a46 100644 --- a/data/swiss_model/swiss_modelbioschemas.jsonld +++ b/data/swiss_model/swiss_modelbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide.", "sc:name": "SWISS-MODEL", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "https://swissmodel.expasy.org/" } \ No newline at end of file diff --git a/data/swissadme/swissadmebioschemas.jsonld b/data/swissadme/swissadmebioschemas.jsonld index c0d6effccd122..42cec0a4cfd5f 100644 --- a/data/swissadme/swissadmebioschemas.jsonld +++ b/data/swissadme/swissadmebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Gives free access to a number of parameters and predictive models in order to compute the physicochemistry and estimate the pharmacokinetics, druglikeness and medicinal chemistry friendliness of one or several small molecules.", "sc:name": "SwissADME", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://www.swissadme.ch/index.php", diff --git a/data/swissbioisostere/swissbioisosterebioschemas.jsonld b/data/swissbioisostere/swissbioisosterebioschemas.jsonld index 60658079a42bd..87d064f1037d5 100644 --- a/data/swissbioisostere/swissbioisosterebioschemas.jsonld +++ b/data/swissbioisostere/swissbioisosterebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "SwissBioisostere is a database containing information on millions of molecular replacements and their performance in biochemical assays. It is meant to provide researchers in drug discovery projects with ideas for bioisosteric modifications of their current lead molecule, and to give access to the details on particular molecular replacements.", "sc:name": "SwissBioIsostere", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.swissbioisostere.ch/" } \ No newline at end of file diff --git a/data/swissdock/swissdockbioschemas.jsonld b/data/swissdock/swissdockbioschemas.jsonld index 8a37a1f49658a..1f6ad2d018fce 100644 --- a/data/swissdock/swissdockbioschemas.jsonld +++ b/data/swissdock/swissdockbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Protein ligand docking server, accessible via the ExPASy web server, and based on EADock DSS. The purpose of this server is to make protein-ligand docking accessible to a wide scientific community worldwide.", "sc:name": "SwissDock", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://www.swissdock.ch/", diff --git a/data/swissregulon/swissregulonbioschemas.jsonld b/data/swissregulon/swissregulonbioschemas.jsonld index aa3c4bcc80ee6..3534cb820b5c2 100644 --- a/data/swissregulon/swissregulonbioschemas.jsonld +++ b/data/swissregulon/swissregulonbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "SwissRegulon is a database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a clear and comprehensible graphical form.", "sc:name": "SwissRegulon", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://swissregulon.unibas.ch/sr/" diff --git a/data/swisssimilarity/swisssimilaritybioschemas.jsonld b/data/swisssimilarity/swisssimilaritybioschemas.jsonld index 8ae5eb84cb5a7..4a4848415496a 100644 --- a/data/swisssimilarity/swisssimilaritybioschemas.jsonld +++ b/data/swisssimilarity/swisssimilaritybioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Allows the rapid screening of small to very large-scale libraries of drugs, bioactive small molecules, commercially available compounds, and an ultra-large library of virtual compounds readily synthesizable from commercially available reagents. The virtual screening can be performed using molecular fingerprints, as well as superpositional or fast non-superpositional 3D shape similarity approaches.", "sc:name": "SwissSimilarity", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://www.swisssimilarity.ch/", diff --git a/data/swisstargetprediction/swisstargetpredictionbioschemas.jsonld b/data/swisstargetprediction/swisstargetpredictionbioschemas.jsonld index 99271750bd9ae..cc66fff1f6d84 100644 --- a/data/swisstargetprediction/swisstargetpredictionbioschemas.jsonld +++ b/data/swisstargetprediction/swisstargetpredictionbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "SwissTargetPrediction is a web server for target prediction of bioactive small molecules. This website allows you to predict the targets of a small molecule. Using a combination of 2D and 3D similarity measures, it compares the query molecule to a library of 280 000 compounds active on more than 2000 targets of 5 different organisms.", "sc:name": "SwissTargetPrediction", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.swisstargetprediction.ch" } \ No newline at end of file diff --git a/data/swisstree/swisstreebioschemas.jsonld b/data/swisstree/swisstreebioschemas.jsonld index 9f29dc2eacc36..914a76cd9b4d1 100644 --- a/data/swisstree/swisstreebioschemas.jsonld +++ b/data/swisstree/swisstreebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Aims to provide a collection of 100 Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. SwissTree is used for benchmarking at the Orthology Benchmarking web service.", "sc:name": "SwissTree", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://swisstree.vital-it.ch/" } \ No newline at end of file diff --git a/data/swissvar/swissvarbioschemas.jsonld b/data/swissvar/swissvarbioschemas.jsonld index 4ac0b9b90b7ab..aaadda29a73e1 100644 --- a/data/swissvar/swissvarbioschemas.jsonld +++ b/data/swissvar/swissvarbioschemas.jsonld @@ -20,29 +20,29 @@ { "@id": "edam:data_1150" }, + { + "@id": "edam:data_1009" + }, { "@id": "edam:data_2291" }, { - "@id": "edam:data_2299" + "@id": "edam:data_3021" }, { - "@id": "edam:data_3498" + "@id": "edam:data_1177" }, { "@id": "edam:data_1153" }, { - "@id": "edam:data_3021" + "@id": "edam:data_3498" }, { - "@id": "edam:data_1177" + "@id": "edam:data_2299" }, { "@id": "edam:data_2099" - }, - { - "@id": "edam:data_1009" } ], "edam:has_output": { @@ -50,19 +50,19 @@ }, "sc:additionalType": "Database portal", "sc:applicationSubCategory": [ - { - "@id": "edam:topic_0634" - }, { "@id": "edam:topic_3120" }, { "@id": "edam:topic_0625" + }, + { + "@id": "edam:topic_0634" } ], "sc:citation": [ - "pubmed:20106818", "pmcid:PMC2832822", + "pubmed:20106818", { "@id": "https://doi.org/10.1093/bioinformatics/btq028" } @@ -78,9 +78,9 @@ ], "sc:name": "SwissVar", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://swissvar.expasy.org/" diff --git a/data/switchbox/switchboxbioschemas.jsonld b/data/switchbox/switchboxbioschemas.jsonld index 3849d7554e604..14cf97e88cab1 100644 --- a/data/switchbox/switchboxbioschemas.jsonld +++ b/data/switchbox/switchboxbioschemas.jsonld @@ -13,19 +13,15 @@ "@id": "https://doi.org/10.1186/1471-2164-14-336", "@type": "sc:CreativeWork" }, - { - "@id": "http://orcid.org/0000-0002-7336-8071", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/switchbox", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Wikum Dinalankara", { "@id": "http://orcid.org/0000-0002-7336-8071" }, - "Bahman Afsari", - "Wikum Dinalankara" + "Bahman Afsari" ], "edam:has_input": { "@id": "edam:data_2603" @@ -34,23 +30,23 @@ "@id": "edam:data_1772" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3365" + "@id": "edam:topic_0203" }, { - "@id": "edam:topic_0203" + "@id": "edam:topic_3365" } ], "sc:citation": [ + "pmcid:PMC3662649", { "@id": "https://doi.org/10.1186/1471-2164-14-336" }, - "pubmed:23682826", - "pmcid:PMC3662649" + "pubmed:23682826" ], "sc:description": "The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle).", "sc:featureList": { @@ -65,6 +61,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/switchBox.html", "sc:version": "1.10.0" + }, + { + "@id": "http://orcid.org/0000-0002-7336-8071", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/switchde/switchdebioschemas.jsonld b/data/switchde/switchdebioschemas.jsonld index a5b3530482a2f..324e420de184b 100644 --- a/data/switchde/switchdebioschemas.jsonld +++ b/data/switchde/switchdebioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Kieran Campbell", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.", "sc:license": "GPL-2.0", "sc:name": "switchde", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/switchde.html", "sc:version": "1.0.0" diff --git a/data/switchdna/switchdnabioschemas.jsonld b/data/switchdna/switchdnabioschemas.jsonld index 5077e32b5c545..efc4f71d02e84 100644 --- a/data/switchdna/switchdnabioschemas.jsonld +++ b/data/switchdna/switchdnabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A software to identify regions of Copy Number Aberrations based on intensity data generated from copy number platforms. This method performs identification of transition points followed by significance testing of defined segments.", "sc:name": "SWITCHdna", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://genome.unc.edu/pubsup/SWITCHdna/" } \ No newline at end of file diff --git a/data/sxoligosearch/sxoligosearchbioschemas.jsonld b/data/sxoligosearch/sxoligosearchbioschemas.jsonld index 5a05c970d3d61..981398f439275 100644 --- a/data/sxoligosearch/sxoligosearchbioschemas.jsonld +++ b/data/sxoligosearch/sxoligosearchbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Commercial platform offered by the Malaysian based Synamatix that aligns Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms.", "sc:name": "SXOligoSearch", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.synamatix.com/secondGenSoftware.html" } \ No newline at end of file diff --git a/data/syapse/syapsebioschemas.jsonld b/data/syapse/syapsebioschemas.jsonld index 101bb5dd85288..8981beba5f4c8 100644 --- a/data/syapse/syapsebioschemas.jsonld +++ b/data/syapse/syapsebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Platform and application suite for bringing together omics and clinical data.", "sc:name": "Syapse", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.Syapse.com" } \ No newline at end of file diff --git a/data/sybil-metabolic/sybil-metabolicbioschemas.jsonld b/data/sybil-metabolic/sybil-metabolicbioschemas.jsonld index 391a2f4455bf3..c86bda684dc1a 100644 --- a/data/sybil-metabolic/sybil-metabolicbioschemas.jsonld +++ b/data/sybil-metabolic/sybil-metabolicbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "sybil", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/sybil/index.html" } \ No newline at end of file diff --git a/data/syco/sycobioschemas.jsonld b/data/syco/sycobioschemas.jsonld index 9acad25c0b487..fdc25f07b0b3e 100644 --- a/data/syco/sycobioschemas.jsonld +++ b/data/syco/sycobioschemas.jsonld @@ -19,16 +19,16 @@ ], "sc:description": "Draw synonymous codon usage statistic plot for a nucleotide sequence.", "sc:funder": [ - "UK MRC", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "syco", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/sydseq/sydseqbioschemas.jsonld b/data/sydseq/sydseqbioschemas.jsonld index 5b3aa1e5c180e..8cf08b91b21f1 100644 --- a/data/sydseq/sydseqbioschemas.jsonld +++ b/data/sydseq/sydseqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An R package containing the functions exClust, TshrinkPlus and pMim.", "sc:name": "sydSeq", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.ellispatrick.com/r-packages/" } \ No newline at end of file diff --git a/data/syfpeithi/syfpeithibioschemas.jsonld b/data/syfpeithi/syfpeithibioschemas.jsonld index 7781a8b41a75f..ef182f4bc48fa 100644 --- a/data/syfpeithi/syfpeithibioschemas.jsonld +++ b/data/syfpeithi/syfpeithibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. The database can be used to predict the immunogenicity of given peptide sequences.", "sc:name": "SYFPEITHI", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.syfpeithi.de/" } \ No newline at end of file diff --git a/data/sylamer/sylamerbioschemas.jsonld b/data/sylamer/sylamerbioschemas.jsonld index 0f906cb565f23..6f39e595dbf71 100644 --- a/data/sylamer/sylamerbioschemas.jsonld +++ b/data/sylamer/sylamerbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "System for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist.", "sc:name": "Sylamer", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www-test.ebi.ac.uk/enright/sylamer/", "sc:version": "1.0" diff --git a/data/sylarray/sylarraybioschemas.jsonld b/data/sylarray/sylarraybioschemas.jsonld index c544492838d6e..a9fc479b7be5d 100644 --- a/data/sylarray/sylarraybioschemas.jsonld +++ b/data/sylarray/sylarraybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Examine influence of small RNAs on expression profiles.", "sc:name": "Sylarray", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "EMBL-EBI", diff --git a/data/sylvx/sylvxbioschemas.jsonld b/data/sylvx/sylvxbioschemas.jsonld index 95c67ee1f04fe..44ac6d24b0892 100644 --- a/data/sylvx/sylvxbioschemas.jsonld +++ b/data/sylvx/sylvxbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking sub-reconciliations).", "sc:name": "SylvX", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.sylvx.org/" } \ No newline at end of file diff --git a/data/symbiogbr/symbiogbrbioschemas.jsonld b/data/symbiogbr/symbiogbrbioschemas.jsonld index 33201bd587d48..3c52a0b2b0c16 100644 --- a/data/symbiogbr/symbiogbrbioschemas.jsonld +++ b/data/symbiogbr/symbiogbrbioschemas.jsonld @@ -13,15 +13,15 @@ "@id": "https://bio.tools/symbiogbr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Pim Bongaerts", - "Linda Tonk" + "Linda Tonk", + "Pim Bongaerts" ], "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:23497177", { "@id": "https://doi.org/10.1186/1472-6785-13-7" }, - "pubmed:23497177", "pmcid:PMC3616961" ], "sc:description": "Database of all currently available Symbiodinium sequences and associated host information of data collected from the Great Barrier Reef into a single relational database.", @@ -30,9 +30,9 @@ }, "sc:name": "SymbioGBR", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.symbiogbr.org" }, diff --git a/data/symbiogenomesdb/symbiogenomesdbbioschemas.jsonld b/data/symbiogenomesdb/symbiogenomesdbbioschemas.jsonld index 32e7fbdf23d28..7d7f548721c78 100644 --- a/data/symbiogenomesdb/symbiogenomesdbbioschemas.jsonld +++ b/data/symbiogenomesdb/symbiogenomesdbbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/DATABASE/BAV109", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/symbiogenomesdb", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact form", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:26607947", "pmcid:PMC4659445", { "@id": "https://doi.org/10.1093/DATABASE/BAV109" - } + }, + "pubmed:26607947" ], "sc:description": "A database for the integration and access to knowledge on host-symbiont relationships.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "SymbioGenomesDB", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://symbiogenomesdb.uv.es/" + }, + { + "@id": "https://doi.org/10.1093/DATABASE/BAV109", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/symcurv/symcurvbioschemas.jsonld b/data/symcurv/symcurvbioschemas.jsonld index 428faf34ec327..2b48414a6cf36 100644 --- a/data/symcurv/symcurvbioschemas.jsonld +++ b/data/symcurv/symcurvbioschemas.jsonld @@ -13,8 +13,8 @@ "biotools:primaryContact": "Sonja Althammer", "sc:additionalType": "Command-line tool", "sc:author": [ - "Sonja Althammer", - "Christoforos Nikolau" + "Christoforos Nikolau", + "Sonja Althammer" ], "sc:description": "SymCurv is a computational ab initio method for nucleosome positioning prediction. It is based on the structural property of natural nucleosome forming sequences, to be symmetrically curved around a local minimum of curvature.", "sc:name": "SymCurv", @@ -23,8 +23,8 @@ "Mac" ], "sc:provider": [ - "crg.eu", - "Lab Roderic Guigo Group" + "Lab Roderic Guigo Group", + "crg.eu" ], "sc:url": "http://genome.crg.es/cgi-bin/SymCurv/SymCurv.pl", "sc:version": "1" diff --git a/data/symmdock/symmdockbioschemas.jsonld b/data/symmdock/symmdockbioschemas.jsonld index 2eabcd0f5292a..72798618009ef 100644 --- a/data/symmdock/symmdockbioschemas.jsonld +++ b/data/symmdock/symmdockbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "SymmDock is an server for prediction of complexes with cyclically symmetry by geometry based molecular docking.", "sc:name": "SymmDock", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioinfo3d.cs.tau.ac.il/SymmDock/" } \ No newline at end of file diff --git a/data/synapter/synapterbioschemas.jsonld b/data/synapter/synapterbioschemas.jsonld index 75c4bbb8b8805..810f57cfde185 100644 --- a/data/synapter/synapterbioschemas.jsonld +++ b/data/synapter/synapterbioschemas.jsonld @@ -9,34 +9,34 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-1520-2268", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/synapter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Sebastian Gibb", { "@id": "http://orcid.org/0000-0002-1520-2268" - }, - "Sebastian Gibb" + } ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:23514362", "sc:description": "This package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.", "sc:license": "GPL-2.0", "sc:name": "synapter", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/synapter.html", "sc:version": "1.16.0" + }, + { + "@id": "http://orcid.org/0000-0002-1520-2268", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/synbadm/synbadmbioschemas.jsonld b/data/synbadm/synbadmbioschemas.jsonld index 368de6d30beaa..bae955cf0e0ed 100644 --- a/data/synbadm/synbadmbioschemas.jsonld +++ b/data/synbadm/synbadmbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A Matlab-based toolbox for the automatic design of gene circuits with targeted functions from libraries of components.", "sc:name": "SYNBADm", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://sites.google.com/site/synbadm/" diff --git a/data/syncx_ct_aligner/syncx_ct_alignerbioschemas.jsonld b/data/syncx_ct_aligner/syncx_ct_alignerbioschemas.jsonld index 1ce467e7fd4ef..b2d237013e2c1 100644 --- a/data/syncx_ct_aligner/syncx_ct_alignerbioschemas.jsonld +++ b/data/syncx_ct_aligner/syncx_ct_alignerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "SyncX CT Aligner is a computer method to compensate for the vibration of the rotational holder by aligning neighboring X-ray images.", "sc:name": "SyncX CT Aligner", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://people.cs.nctu.edu.tw/~chengchc/SCTA/", "sc:version": "1.0" diff --git a/data/synergizer/synergizerbioschemas.jsonld b/data/synergizer/synergizerbioschemas.jsonld index f1236deced0f9..034e85614e2c3 100644 --- a/data/synergizer/synergizerbioschemas.jsonld +++ b/data/synergizer/synergizerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a “namespace”) to another.", "sc:name": "Synergizer", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://llama.mshri.on.ca/synergizer/doc/" } \ No newline at end of file diff --git a/data/synergyfinder/synergyfinderbioschemas.jsonld b/data/synergyfinder/synergyfinderbioschemas.jsonld index 1a519acc29909..5f070f36c610d 100644 --- a/data/synergyfinder/synergyfinderbioschemas.jsonld +++ b/data/synergyfinder/synergyfinderbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "synergyfinder", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/synergyfinder.html", "sc:version": "1.0.0" diff --git a/data/synfind/synfindbioschemas.jsonld b/data/synfind/synfindbioschemas.jsonld index 7b74ceddf9311..f1be03d9f0a05 100644 --- a/data/synfind/synfindbioschemas.jsonld +++ b/data/synfind/synfindbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/GBE/EVV219", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/synfind", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:26560340", - "pmcid:PMC4700967", { "@id": "https://doi.org/10.1093/GBE/EVV219" - } + }, + "pmcid:PMC4700967", + "pubmed:26560340" ], "sc:description": "Compiling Syntenic Regions across Any Set of Genomes on Demand.", "sc:featureList": { @@ -27,15 +31,11 @@ }, "sc:name": "SynFind", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://genomevolution.org/CoGe/SynFind.pl" - }, - { - "@id": "https://doi.org/10.1093/GBE/EVV219", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/synima/synimabioschemas.jsonld b/data/synima/synimabioschemas.jsonld index 705253913b5db..5ba1a1b2275bd 100644 --- a/data/synima/synimabioschemas.jsonld +++ b/data/synima/synimabioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Rhys A. Farrer", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5697234", "pubmed:29162056", { "@id": "https://doi.org/10.1186/s12859-017-1939-7" - }, - "pmcid:PMC5697234" + } ], "sc:description": "Synteny imaging tool for annotated genome assemblies.", "sc:featureList": { diff --git a/data/synlet/synletbioschemas.jsonld b/data/synlet/synletbioschemas.jsonld index 53b9e8005a8b0..1a082e708062c 100644 --- a/data/synlet/synletbioschemas.jsonld +++ b/data/synlet/synletbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Chunxuan Shao", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Select hits from synthetic lethal RNAi screen data. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA, implementing quality control and various visualisation tools. Four different algorithms could be used to pick up the interesting hits.", "sc:license": "GPL-3.0", diff --git a/data/synlinker/synlinkerbioschemas.jsonld b/data/synlinker/synlinkerbioschemas.jsonld index 82cff3d6ad4e0..639fac2142d4a 100644 --- a/data/synlinker/synlinkerbioschemas.jsonld +++ b/data/synlinker/synlinkerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An integrated system to provide suitable linker candidates for novel recombinant fusion proteins.", "sc:name": "SynLinker", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://synlinker.syncti.org/" } \ No newline at end of file diff --git a/data/synor/synorbioschemas.jsonld b/data/synor/synorbioschemas.jsonld index 6e371de124bd3..4ade68da825fb 100644 --- a/data/synor/synorbioschemas.jsonld +++ b/data/synor/synorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "SynoR searches vertebrate genomes for synonymous regulatory elements.", "sc:name": "SynoR", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://synor.dcode.org/" diff --git a/data/syntarget/syntargetbioschemas.jsonld b/data/syntarget/syntargetbioschemas.jsonld index f5d7f88f56719..6bf0f0fe845b6 100644 --- a/data/syntarget/syntargetbioschemas.jsonld +++ b/data/syntarget/syntargetbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An online tool to test the synergetic effect of genes on survival outcome in cancer.", "sc:name": "SynTarget", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.chemoprofiling.org/cgi-bin/GEO/cancertarget/web_run_CT.EXAMPLES.pl" diff --git a/data/synteny_portal/synteny_portalbioschemas.jsonld b/data/synteny_portal/synteny_portalbioschemas.jsonld index fed1046636b66..c02edde10f227 100644 --- a/data/synteny_portal/synteny_portalbioschemas.jsonld +++ b/data/synteny_portal/synteny_portalbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:27154270", "pmcid:PMC4987893", { "@id": "https://doi.org/10.1093/NAR/GKW310" - } + }, + "pubmed:27154270" ], "sc:description": "Portal for synteny block analysis.", "sc:featureList": { @@ -31,9 +31,9 @@ }, "sc:name": "Synteny Portal", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioinfo.konkuk.ac.kr/synteny_portal/" } diff --git a/data/syntren/syntrenbioschemas.jsonld b/data/syntren/syntrenbioschemas.jsonld index b278fc74eb48a..1c121c503b739 100644 --- a/data/syntren/syntrenbioschemas.jsonld +++ b/data/syntren/syntrenbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Synthetic transcriptional regulatory networks. A generator of synthetic gene expression data for design and analysis of structure learning algorithms.", "sc:name": "SynTReN", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/kmarchal/SynTReN/index.html", diff --git a/data/synttax/synttaxbioschemas.jsonld b/data/synttax/synttaxbioschemas.jsonld index 4d0f870c872b9..9360ff181ff39 100644 --- a/data/synttax/synttaxbioschemas.jsonld +++ b/data/synttax/synttaxbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1471-2105-14-4", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/synttax", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jacques Oberto", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC3571937", "pubmed:23323735", { "@id": "https://doi.org/10.1186/1471-2105-14-4" - } + }, + "pmcid:PMC3571937" ], "sc:description": "A web server linking synteny to prokaryotic taxonomy.", "sc:featureList": { @@ -32,10 +36,6 @@ "Linux" ], "sc:url": "http://archaea.u-psud.fr/SyntTax/" - }, - { - "@id": "https://doi.org/10.1186/1471-2105-14-4", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/syntview/syntviewbioschemas.jsonld b/data/syntview/syntviewbioschemas.jsonld index f1798bfe1b281..1f99d64f0a4c7 100644 --- a/data/syntview/syntviewbioschemas.jsonld +++ b/data/syntview/syntviewbioschemas.jsonld @@ -9,30 +9,26 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-14-277", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/syntview", "@type": "sc:SoftwareApplication", "edam:has_input": [ { - "@id": "edam:data_3498" + "@id": "edam:data_3002" }, { "@id": "edam:data_0872" }, { - "@id": "edam:data_3002" + "@id": "edam:data_3498" } ], "edam:has_output": { "@id": "edam:data_2884" }, "sc:additionalType": [ - "Web application", - "Desktop application" + "Desktop application", + "Web application" ], "sc:applicationSubCategory": [ { @@ -43,11 +39,11 @@ } ], "sc:citation": [ - "pubmed:24053737", { "@id": "https://doi.org/10.1186/1471-2105-14-277" }, - "pmcid:PMC3849071" + "pmcid:PMC3849071", + "pubmed:24053737" ], "sc:description": "Comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic genome browser with sub-maps holding information about genomic objects. The software is characterized by the presentation of syntenic organisations of microbial genomes and the visualization of polymorphism data along these genomes; these features are accessible to the user in an integrated way.", "sc:featureList": [ @@ -62,8 +58,8 @@ "sc:license": "LGPL-3.0", "sc:name": "SynTView", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:softwareHelp": { @@ -71,6 +67,10 @@ }, "sc:url": "http://genopole.pasteur.fr/SynTView/", "sc:version": "1" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-14-277", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/sysbio_modelica_library/sysbio_modelica_librarybioschemas.jsonld b/data/sysbio_modelica_library/sysbio_modelica_librarybioschemas.jsonld index 9fedb9d3d3b80..c93301aecb194 100644 --- a/data/sysbio_modelica_library/sysbio_modelica_librarybioschemas.jsonld +++ b/data/sysbio_modelica_library/sysbio_modelica_librarybioschemas.jsonld @@ -13,10 +13,10 @@ "biotools:primaryContact": "Miha Moškon", "sc:additionalType": "Library", "sc:author": [ + "Miha Moškon", "Miha Mraz", "Damjana Rozman", - "Tanja Cvitanović", - "Miha Moškon" + "Tanja Cvitanović" ], "sc:contributor": [ "Adviti Naik", @@ -25,13 +25,13 @@ "sc:description": "Library which implements basic systems biology objects within the modelica environment.", "sc:name": "SysBio modelica library", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "Faculty of Computer and Information Science, University of Ljubljana", - "ELIXIR-SI-hackathon" + "ELIXIR-SI-hackathon", + "Faculty of Computer and Information Science, University of Ljubljana" ], "sc:url": "http://lrss.fri.uni-lj.si/bio/sysbio", "sc:version": "1" diff --git a/data/systempiper/systempiperbioschemas.jsonld b/data/systempiper/systempiperbioschemas.jsonld index 62f793dd38240..148dbc5383efb 100644 --- a/data/systempiper/systempiperbioschemas.jsonld +++ b/data/systempiper/systempiperbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-0710-3777", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-016-1241-0", "@type": "sc:CreativeWork" }, + { + "@id": "http://orcid.org/0000-0003-0710-3777", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/systempiper", "@type": "sc:SoftwareApplication", @@ -30,8 +30,8 @@ "@id": "edam:data_1383" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { @@ -60,9 +60,9 @@ "sc:license": "Artistic-2.0", "sc:name": "systemPipeR", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/systemPipeR.html", "sc:version": "1.8.1" diff --git a/data/szn_zoological_collection_database/szn_zoological_collection_databasebioschemas.jsonld b/data/szn_zoological_collection_database/szn_zoological_collection_databasebioschemas.jsonld index 4c342421deb9e..e8f86726888ac 100644 --- a/data/szn_zoological_collection_database/szn_zoological_collection_databasebioschemas.jsonld +++ b/data/szn_zoological_collection_database/szn_zoological_collection_databasebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/SZN_Zoological_Collection_Database", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:description": "Database containing 4.373 video, 18.212 still images and 7.771 labels concerning sampled that were prepared and stored from 1910 at the “Stazione Zoologica Anton Dohrn di Napoli (SZN)”. Moreover, the digitised version of 38 documents (totalling 8406 pages) with important information about taxonomy, ecology and phylogenetic is also included.", "sc:license": "Unlicense", "sc:name": "SZN Zoological Collection Database", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://szn.i.hosei.ac.jp/HTML/index.php" } \ No newline at end of file diff --git a/data/t-lex2/t-lex2bioschemas.jsonld b/data/t-lex2/t-lex2bioschemas.jsonld index 8355be2295a0d..ca9653fa34901 100644 --- a/data/t-lex2/t-lex2bioschemas.jsonld +++ b/data/t-lex2/t-lex2bioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Anna-Sophie Fiston-Lavier", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:25510498", "pmcid:PMC4344482", { "@id": "https://doi.org/10.1093/nar/gku1250" - } + }, + "pubmed:25510498" ], "sc:description": "Software that allows routine, automatic and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing data.", "sc:featureList": { diff --git a/data/t-profiler/t-profilerbioschemas.jsonld b/data/t-profiler/t-profilerbioschemas.jsonld index ef0fc2af4da11..d49bf450b4e83 100644 --- a/data/t-profiler/t-profilerbioschemas.jsonld +++ b/data/t-profiler/t-profilerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "T-profiler", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.t-profiler.org/" } \ No newline at end of file diff --git a/data/t-reg_comparator/t-reg_comparatorbioschemas.jsonld b/data/t-reg_comparator/t-reg_comparatorbioschemas.jsonld index 0bfc3fc1091a3..9dbd3552b6ea1 100644 --- a/data/t-reg_comparator/t-reg_comparatorbioschemas.jsonld +++ b/data/t-reg_comparator/t-reg_comparatorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar).", "sc:name": "T-Reg Comparator", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://treg.molgen.mpg.de/" diff --git a/data/t-rex/t-rexbioschemas.jsonld b/data/t-rex/t-rexbioschemas.jsonld index 96949b49627e8..9b08ccf5407f4 100644 --- a/data/t-rex/t-rexbioschemas.jsonld +++ b/data/t-rex/t-rexbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tree and Reticulogram REconstruction (T-REX) is a web server for the reconstruction of phylogenetic trees, reticulation networks and the inference of horizontal gene transfer events.", "sc:name": "T-REX", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.trex.uqam.ca" diff --git a/data/t1dbase/t1dbasebioschemas.jsonld b/data/t1dbase/t1dbasebioschemas.jsonld index c9773a302ddcb..3b765e9f0d9d6 100644 --- a/data/t1dbase/t1dbasebioschemas.jsonld +++ b/data/t1dbase/t1dbasebioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "Database for type 1 diabetes (T1D). It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. New data sets include curated summary data from four genome-wide association studies relevant to T1D, HaemAtlas-a data set and tool to query gene expression levels in haematopoietic cells and a manually curated table of human T1D susceptibility loci.", "sc:name": "T1DBase", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.t1dbase.org" diff --git a/data/t346hunter/t346hunterbioschemas.jsonld b/data/t346hunter/t346hunterbioschemas.jsonld index fdbdaa4271f7d..ac3cfdb294299 100644 --- a/data/t346hunter/t346hunterbioschemas.jsonld +++ b/data/t346hunter/t346hunterbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/t346hunter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Cayo Ramos Rodríguez", + "Pedro M. Martínez García", "Pablo Rodríguez-Palenzuela", - "Pedro M. Martínez García" + "Cayo Ramos Rodríguez" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:25867189", @@ -21,8 +21,8 @@ "sc:name": "T346Hunter", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bacterial-virulence-factors.cbgp.upm.es/T346Hunter" } \ No newline at end of file diff --git a/data/t3_mm/t3_mmbioschemas.jsonld b/data/t3_mm/t3_mmbioschemas.jsonld index 12224519376ff..a236b1fc6c375 100644 --- a/data/t3_mm/t3_mmbioschemas.jsonld +++ b/data/t3_mm/t3_mmbioschemas.jsonld @@ -27,9 +27,9 @@ }, "sc:name": "T3_MM", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://biocomputer.bio.cuhk.edu.hk/T3DB/T3_MM.php" }, diff --git a/data/t3db/t3dbbioschemas.jsonld b/data/t3db/t3dbbioschemas.jsonld index c8c3b51ff54ae..2c9de9700c550 100644 --- a/data/t3db/t3dbbioschemas.jsonld +++ b/data/t3db/t3dbbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Unique bioinformatics resource that compiles comprehensive information about common or ubiquitous toxins and their toxin-targets. Each record (ToxCard) contains over 80 data fields providing detailed information on chemical properties and descriptors, toxicity values, protein and gene sequences (for both targets and toxins), molecular and cellular interaction data, toxicological data, mechanistic information and references.", "sc:name": "T3DB", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.t3db.org" } \ No newline at end of file diff --git a/data/t7/t7bioschemas.jsonld b/data/t7/t7bioschemas.jsonld index 7a826b2c75733..3a1e5c0d620f7 100644 --- a/data/t7/t7bioschemas.jsonld +++ b/data/t7/t7bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A simulator for the intracellular infection kinetics of phage T7.", "sc:name": "T7", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.genome.duke.edu/labs/YouLab/software/index.php" } \ No newline at end of file diff --git a/data/ta-si_prediction/ta-si_predictionbioschemas.jsonld b/data/ta-si_prediction/ta-si_predictionbioschemas.jsonld index b026c81c290a1..b6f8bccf5a049 100644 --- a/data/ta-si_prediction/ta-si_predictionbioschemas.jsonld +++ b/data/ta-si_prediction/ta-si_predictionbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "ta-siRNA (trans-acting short interfering RNA): prediction of phased ta-siRNAs in plant sRNA datasets.", "sc:name": "Ta-si prediction", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://srna-workbench.cmp.uea.ac.uk" } \ No newline at end of file diff --git a/data/tableannotator/tableannotatorbioschemas.jsonld b/data/tableannotator/tableannotatorbioschemas.jsonld index 2592d96214a8d..66f3b1d7300f5 100644 --- a/data/tableannotator/tableannotatorbioschemas.jsonld +++ b/data/tableannotator/tableannotatorbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "TableAnnotator", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": "manchester.ac.uk", "sc:url": "https://github.com/nikolamilosevic86/TableAnnotator", diff --git a/data/tableparser/tableparserbioschemas.jsonld b/data/tableparser/tableparserbioschemas.jsonld index bbe93c57a6cd9..c4175aaf7d69c 100644 --- a/data/tableparser/tableparserbioschemas.jsonld +++ b/data/tableparser/tableparserbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Extract sequences from tab-delimited assembly alignment files (e.g. SimAssembly and AceParser output). Parse out contigs, singletons, and assembled reads into separate files.", "sc:name": "TableParser", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.personal.psu.edu/jhm10/Vera/SoftwareC.html" diff --git a/data/tacs/tacsbioschemas.jsonld b/data/tacs/tacsbioschemas.jsonld index fea9d9a1cf135..2a56d127ac8dc 100644 --- a/data/tacs/tacsbioschemas.jsonld +++ b/data/tacs/tacsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "tacs", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://github.com/takenakayoichi/tacs", diff --git a/data/tactics/tacticsbioschemas.jsonld b/data/tactics/tacticsbioschemas.jsonld index a5572f332669d..cc5b26e0a2642 100644 --- a/data/tactics/tacticsbioschemas.jsonld +++ b/data/tactics/tacticsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A versatile MATLAB toolbox for High Content Analysis (HCA) of microscopy data. TATICS has been developed for image cytometry of non-adherent cells such as hematopoietic cells.", "sc:name": "TACTICS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.tactics-toolbox.com/" } \ No newline at end of file diff --git a/data/tadb/tadbbioschemas.jsonld b/data/tadb/tadbbioschemas.jsonld index 055769b7a7839..d86cc5f240db3 100644 --- a/data/tadb/tadbbioschemas.jsonld +++ b/data/tadb/tadbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "TADB is an integrated database that provides comprehensive information about Type 2 toxin-antitoxin (TA) loci. TADB offers both predicted and experimentally supported Type 2 TA loci-relevant data. A broad range of similarity search, sequence alignment, genome context browser and phylogenetic tools are readily accessible via TADB.", "sc:name": "TADB", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioinfo-mml.sjtu.edu.cn/TADB/" diff --git a/data/tadtree/tadtreebioschemas.jsonld b/data/tadtree/tadtreebioschemas.jsonld index 55eb3497900b7..89ba89825df9b 100644 --- a/data/tadtree/tadtreebioschemas.jsonld +++ b/data/tadtree/tadtreebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An algorithm the identification of hierarchical topological domains in Hi-C data.", "sc:name": "TADtree", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://compbio.cs.brown.edu/projects/tadtree/" } \ No newline at end of file diff --git a/data/taec/taecbioschemas.jsonld b/data/taec/taecbioschemas.jsonld index 0ad10d783bb0b..1232c6693a376 100644 --- a/data/taec/taecbioschemas.jsonld +++ b/data/taec/taecbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A new homology-based approach for taxonomic analysis, utilizes the similarity in the genomic sequence in addition to the result of an alignment tool.", "sc:name": "TAEC", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://cals.arizona.edu/~anling/software.htm" } \ No newline at end of file diff --git a/data/taf/tafbioschemas.jsonld b/data/taf/tafbioschemas.jsonld index 601fe483308d9..9beac8a10129c 100644 --- a/data/taf/tafbioschemas.jsonld +++ b/data/taf/tafbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "Unlicense", "sc:name": "TaF", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://taf.genome-report.com/" diff --git a/data/tag-db/tag-dbbioschemas.jsonld b/data/tag-db/tag-dbbioschemas.jsonld index 308f51b7d5388..9a82ae84bff11 100644 --- a/data/tag-db/tag-dbbioschemas.jsonld +++ b/data/tag-db/tag-dbbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Provides a user-friendly, lightweight and open-source graphical user interface for running the de novo sequencing algorithm PepNovo+ and also holds the possibiliy to search derived short amino acid sequences (so-called tags) against a protein database in order to retrieve peptide and protein identifications.", "sc:name": "Tag-DB", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://code.google.com/p/tag-db/", "sc:version": "0.4.0" diff --git a/data/tagcleaner/tagcleanerbioschemas.jsonld b/data/tagcleaner/tagcleanerbioschemas.jsonld index d175306b40a91..60e9554718d45 100644 --- a/data/tagcleaner/tagcleanerbioschemas.jsonld +++ b/data/tagcleaner/tagcleanerbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "TagCleaner", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://tagcleaner.sourceforge.net/index.html" diff --git a/data/tagcna/tagcnabioschemas.jsonld b/data/tagcna/tagcnabioschemas.jsonld index 6982d828dbe3f..f88e47c3712c3 100644 --- a/data/tagcna/tagcnabioschemas.jsonld +++ b/data/tagcna/tagcnabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "TAGCNA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://sourceforge.net/projects/tagcna/" } \ No newline at end of file diff --git a/data/taggd/taggdbioschemas.jsonld b/data/taggd/taggdbioschemas.jsonld index 200392529885f..1807c30746930 100644 --- a/data/taggd/taggdbioschemas.jsonld +++ b/data/taggd/taggdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy.", "sc:name": "TagGD", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/pelinakan/UBD.git" } \ No newline at end of file diff --git a/data/taggraph/taggraphbioschemas.jsonld b/data/taggraph/taggraphbioschemas.jsonld index 1ad4417c82d43..0a452c1f8d99a 100644 --- a/data/taggraph/taggraphbioschemas.jsonld +++ b/data/taggraph/taggraphbioschemas.jsonld @@ -9,35 +9,35 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/s41587-019-0067-5", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/TagGraph", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web service", "sc:citation": [ - "pubmed:30936560", { "@id": "https://doi.org/10.1038/s41587-019-0067-5" }, - "pmcid:PMC6447449" + "pmcid:PMC6447449", + "pubmed:30936560" ], "sc:description": "Computational tool that reveals vast protein modification landscapes from large tandem mass spectrometry datasets.", "sc:featureList": [ { - "@id": "edam:operation_3649" + "@id": "edam:operation_0417" }, { - "@id": "edam:operation_3645" + "@id": "edam:operation_3649" }, { - "@id": "edam:operation_0417" + "@id": "edam:operation_3645" } ], "sc:name": "TagGraph", "sc:url": "http://kronos.stanford.edu/TAG_GRAPH/" - }, - { - "@id": "https://doi.org/10.1038/s41587-019-0067-5", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tagident/tagidentbioschemas.jsonld b/data/tagident/tagidentbioschemas.jsonld index 84256070f320c..c23c1a2d837d5 100644 --- a/data/tagident/tagidentbioschemas.jsonld +++ b/data/tagident/tagidentbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw.", "sc:name": "TagIdent", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://web.expasy.org/tagident/" diff --git a/data/tagoos/tagoosbioschemas.jsonld b/data/tagoos/tagoosbioschemas.jsonld index 01af9ace93058..e95fa64718a46 100644 --- a/data/tagoos/tagoosbioschemas.jsonld +++ b/data/tagoos/tagoosbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "TAGOOS", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/aitgon/tagoos" diff --git a/data/tagtog/tagtogbioschemas.jsonld b/data/tagtog/tagtogbioschemas.jsonld index 3c88e1651a0ea..02110e2534701 100644 --- a/data/tagtog/tagtogbioschemas.jsonld +++ b/data/tagtog/tagtogbioschemas.jsonld @@ -16,15 +16,15 @@ "Web application" ], "sc:author": [ - "Jorge Campos", - "Juan Miguel Cejuela" + "Juan Miguel Cejuela", + "Jorge Campos" ], "sc:description": "Automatic, manual, and search annotation tool.", "sc:name": "tagtog", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "tagtog.net", "sc:url": "https://www.tagtog.net", diff --git a/data/taipan/taipanbioschemas.jsonld b/data/taipan/taipanbioschemas.jsonld index 505c4b4bd2a2e..03292b0f33171 100644 --- a/data/taipan/taipanbioschemas.jsonld +++ b/data/taipan/taipanbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make better decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources.", "sc:name": "Taipan", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/taipan/" } \ No newline at end of file diff --git a/data/tair/tairbioschemas.jsonld b/data/tair/tairbioschemas.jsonld index d16fcbb2ae3f9..53719399cc55d 100644 --- a/data/tair/tairbioschemas.jsonld +++ b/data/tair/tairbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:description": "The Arabidopsis Information Resource (TAIR): genome database for Arabidopsis thaliana. Central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation.", "sc:name": "The Arabidopsis information resource (TAIR)", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://arabidopsis.org/" diff --git a/data/takeabreak/takeabreakbioschemas.jsonld b/data/takeabreak/takeabreakbioschemas.jsonld index 868899021aa4e..98c0ac95c4a29 100644 --- a/data/takeabreak/takeabreakbioschemas.jsonld +++ b/data/takeabreak/takeabreakbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A tool that can detect inversion breakpoints directly from raw NGS reads.", "sc:name": "TakeABreak", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "GenOuest", diff --git a/data/tale-nt/tale-ntbioschemas.jsonld b/data/tale-nt/tale-ntbioschemas.jsonld index 11038d32c6134..0736976248f66 100644 --- a/data/tale-nt/tale-ntbioschemas.jsonld +++ b/data/tale-nt/tale-ntbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Transcription activator-like (TAL) Effector-Nucleotide Targeter 2.0 (TALE-NT) is a suite of web-based tools that allows for custom design of TAL effector repeat arrays for desired targets and prediction of TAL effector binding sites.", "sc:name": "TALE-NT", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://boglab.plp.iastate.edu/" } \ No newline at end of file diff --git a/data/talenoffer/talenofferbioschemas.jsonld b/data/talenoffer/talenofferbioschemas.jsonld index dc5ab678b8f17..b0b56adc846d5 100644 --- a/data/talenoffer/talenofferbioschemas.jsonld +++ b/data/talenoffer/talenofferbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "TALENoffer", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.jstacs.de/index.php/TALENoffer" } \ No newline at end of file diff --git a/data/tally/tallybioschemas.jsonld b/data/tally/tallybioschemas.jsonld index 78b7b6f58a4da..1ff6aa28a7ceb 100644 --- a/data/tally/tallybioschemas.jsonld +++ b/data/tally/tallybioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/tally", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Christian LE PEUCH", "Andrey V. KAJAVA", - "Julien JORDA", - "Christian LE PEUCH" + "Julien JORDA" ], "sc:additionalType": "Web application", "sc:description": "Tally is a program for deduplicating sequence fragments for both single and paired end input. Single reads, paired-end reads.", diff --git a/data/tammicol/tammicolbioschemas.jsonld b/data/tammicol/tammicolbioschemas.jsonld index 6091844e807ba..d0aff4b38a60a 100644 --- a/data/tammicol/tammicolbioschemas.jsonld +++ b/data/tammicol/tammicolbioschemas.jsonld @@ -18,33 +18,33 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "H. Tronnolone", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": [ - "pubmed:30507938", - "pmcid:PMC6292648", { "@id": "https://doi.org/10.1371/journal.pcbi.1006629" - } + }, + "pubmed:30507938", + "pmcid:PMC6292648" ], "sc:description": "Tool for analysis of the morphology of microbial colonies.", "sc:featureList": [ { - "@id": "edam:operation_3443" + "@id": "edam:operation_0417" }, { - "@id": "edam:operation_3799" + "@id": "edam:operation_3443" }, { - "@id": "edam:operation_0417" + "@id": "edam:operation_3799" } ], "sc:license": "GPL-3.0", "sc:name": "TAMMiCol", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/HaydenTronnolone/TAMMiCol" } diff --git a/data/tango-nuclear/tango-nuclearbioschemas.jsonld b/data/tango-nuclear/tango-nuclearbioschemas.jsonld index 5764261233da0..b0ca2db9c2ae8 100644 --- a/data/tango-nuclear/tango-nuclearbioschemas.jsonld +++ b/data/tango-nuclear/tango-nuclearbioschemas.jsonld @@ -17,20 +17,20 @@ "@id": "https://bio.tools/tango-nuclear", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jean Ollion", + "Thomas Boudier", "Julien Cochennec", - "Thomas Boudier" + "Jean Ollion" ], "sc:additionalType": [ "Library", "Plug-in" ], "sc:citation": [ + "pmcid:PMC3702251", "pubmed:23681123", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTT276" - }, - "pmcid:PMC3702251" + } ], "sc:description": "Generic tool for high-throughput 3D image analysis for studying nuclear organization.", "sc:featureList": { @@ -40,8 +40,8 @@ "sc:name": "TANGO", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://biophysique.mnhn.fr/tango/HomePage" } diff --git a/data/tanric/tanricbioschemas.jsonld b/data/tanric/tanricbioschemas.jsonld index 160f8ff216bc6..ba2ce9b2b05b7 100644 --- a/data/tanric/tanricbioschemas.jsonld +++ b/data/tanric/tanricbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1158/0008-5472.CAN-15-0273", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/tanric", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dr. Han Liang", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:26208906", { "@id": "https://doi.org/10.1158/0008-5472.CAN-15-0273" }, - "pmcid:PMC4573884", - "pubmed:26208906" + "pmcid:PMC4573884" ], "sc:description": "An interactive open platform to explore the function of lncRNAs in cancer.", "sc:featureList": { @@ -36,6 +32,10 @@ "Windows" ], "sc:url": "http://bioinformatics.mdanderson.org/main/TANRIC:Overview" + }, + { + "@id": "https://doi.org/10.1158/0008-5472.CAN-15-0273", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tapir/tapirbioschemas.jsonld b/data/tapir/tapirbioschemas.jsonld index af69d68cf6527..050a04082432a 100644 --- a/data/tapir/tapirbioschemas.jsonld +++ b/data/tapir/tapirbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A web server for the prediction of plant microRNA targets, including target mimics.", "sc:name": "TAPIR", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "PSB", "sc:url": "http://bioinformatics.psb.ugent.be/webtools/tapir/", diff --git a/data/tapir_cbs/tapir_cbsbioschemas.jsonld b/data/tapir_cbs/tapir_cbsbioschemas.jsonld index a20957e5a0aec..bd7527861d943 100644 --- a/data/tapir_cbs/tapir_cbsbioschemas.jsonld +++ b/data/tapir_cbs/tapir_cbsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "This service is like a DNA search engine.", "sc:name": "Tapir", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": "CBS", diff --git a/data/tappred/tappredbioschemas.jsonld b/data/tappred/tappredbioschemas.jsonld index e9cf422cd50e9..21bb470f6775e 100644 --- a/data/tappred/tappredbioschemas.jsonld +++ b/data/tappred/tappredbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "On-line service for predicting binding affinity of peptides toward the TAP transporter. The Prediction is based on cascade SVM, using sequence and properties of the the amino acids.", "sc:name": "TAPPred", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.imtech.res.in/raghava/tappred/" diff --git a/data/tapyr/tapyrbioschemas.jsonld b/data/tapyr/tapyrbioschemas.jsonld index e5ba40451c346..e1160dea3e9d5 100644 --- a/data/tapyr/tapyrbioschemas.jsonld +++ b/data/tapyr/tapyrbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "TAPyR", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.tapyr.net" diff --git a/data/tara_blast_service/tara_blast_servicebioschemas.jsonld b/data/tara_blast_service/tara_blast_servicebioschemas.jsonld index ca392a2a7bf54..a2cef5f6f3a13 100644 --- a/data/tara_blast_service/tara_blast_servicebioschemas.jsonld +++ b/data/tara_blast_service/tara_blast_servicebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "TARA BLAST Service", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioinfo.szn.it/tara-oceans-data-blast-service/" diff --git a/data/tarbase/tarbasebioschemas.jsonld b/data/tarbase/tarbasebioschemas.jsonld index 009e31dcbcb0e..30ed179d95553 100644 --- a/data/tarbase/tarbasebioschemas.jsonld +++ b/data/tarbase/tarbasebioschemas.jsonld @@ -13,25 +13,21 @@ "@id": "https://doi.org/10.1093/nar/gkx1141", "@type": "sc:CreativeWork" }, - { - "@id": "https://doi.org/10.1093/nar/gkr1161", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/tarbase", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact Form", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC5753203", - "pubmed:22135297", "pubmed:29156006", + "pubmed:22135297", "pmcid:PMC3245116", { - "@id": "https://doi.org/10.1093/nar/gkr1161" + "@id": "https://doi.org/10.1093/nar/gkx1141" }, + "pmcid:PMC5753203", { - "@id": "https://doi.org/10.1093/nar/gkx1141" + "@id": "https://doi.org/10.1093/nar/gkr1161" } ], "sc:description": "Reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Comprehensive cataloging of the miRNA interactome that enables the browsing of interactions through different filtering combinations.", @@ -46,20 +42,24 @@ "@id": "edam:operation_2423" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_2436" }, { - "@id": "edam:operation_2436" + "@id": "edam:operation_3431" } ], "sc:name": "TarBase v8", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.microrna.gr/tarbase", "sc:version": "8" + }, + { + "@id": "https://doi.org/10.1093/nar/gkr1161", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/target_explorer/target_explorerbioschemas.jsonld b/data/target_explorer/target_explorerbioschemas.jsonld index f580bf8d83518..b14ff217a6737 100644 --- a/data/target_explorer/target_explorerbioschemas.jsonld +++ b/data/target_explorer/target_explorerbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "Target Explorer", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://luna.bioc.columbia.edu/Target_Explorer/" } \ No newline at end of file diff --git a/data/targetatpsite/targetatpsitebioschemas.jsonld b/data/targetatpsite/targetatpsitebioschemas.jsonld index 27dcd2c6b960d..801bd690cdc38 100644 --- a/data/targetatpsite/targetatpsitebioschemas.jsonld +++ b/data/targetatpsite/targetatpsitebioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/targetatpsite", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Jun Hu", - "Dong-Jun Yu" + "Dong-Jun Yu", + "Jun Hu" ], "sc:additionalType": "Desktop application", "sc:citation": "pubmed:23288787", "sc:description": "Full-featured GUI application for targeting protein-ATP binding residues in protein sequences, consisting of two parts of local client and remote server.", "sc:name": "TargetATPsite", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.csbio.sjtu.edu.cn/bioinf/targetATP/" } \ No newline at end of file diff --git a/data/targetedretrieval/targetedretrievalbioschemas.jsonld b/data/targetedretrieval/targetedretrievalbioschemas.jsonld index 64e8cca499be6..d9941eda8ba2b 100644 --- a/data/targetedretrieval/targetedretrievalbioschemas.jsonld +++ b/data/targetedretrieval/targetedretrievalbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "targetedRetrieval", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://research.ics.aalto.fi/mi/software/rex12/", "sc:version": "120705" diff --git a/data/targethub/targethubbioschemas.jsonld b/data/targethub/targethubbioschemas.jsonld index 13ba81b4fee76..68bc5f690a121 100644 --- a/data/targethub/targethubbioschemas.jsonld +++ b/data/targethub/targethubbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "CouchDB database of miRNA-gene interactions.", "sc:name": "targetHub", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://app1.bioinformatics.mdanderson.org/tarhub/_design/basic/docs.html", "sc:version": "1" diff --git a/data/targetidentifier/targetidentifierbioschemas.jsonld b/data/targetidentifier/targetidentifierbioschemas.jsonld index dcdb5fd6aa6eb..7baae6c3b73f5 100644 --- a/data/targetidentifier/targetidentifierbioschemas.jsonld +++ b/data/targetidentifier/targetidentifierbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "TargetIdentifier is designed for identifying full-length EST cDNAs and functionally annotating EST cDNAs.", "sc:name": "TargetIdentifier", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinformatics.ysu.edu/tools/TargetIdentifier.html" } \ No newline at end of file diff --git a/data/targetmine/targetminebioschemas.jsonld b/data/targetmine/targetminebioschemas.jsonld index df523df70429b..ff57af329335e 100644 --- a/data/targetmine/targetminebioschemas.jsonld +++ b/data/targetmine/targetminebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "TargetMine", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://targetmine.mizuguchilab.org/", "sc:version": "20150831" diff --git a/data/targetp/targetpbioschemas.jsonld b/data/targetp/targetpbioschemas.jsonld index 3b747b0d4120a..8fad4164f1a71 100644 --- a/data/targetp/targetpbioschemas.jsonld +++ b/data/targetp/targetpbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-9412-9643", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/targetp", "@type": "sc:SoftwareApplication", @@ -20,9 +16,9 @@ "@id": "http://orcid.org/0000-0002-9412-9643" }, "sc:additionalType": [ + "Web service", "Command-line tool", - "Web application", - "Web service" + "Web application" ], "sc:citation": "pubmed:10891285", "sc:description": "Prediction of the subcellular location of eukaryotic proteins.", @@ -32,6 +28,10 @@ "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/TargetP/", "sc:version": "1.1" + }, + { + "@id": "http://orcid.org/0000-0002-9412-9643", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/targetrna/targetrnabioschemas.jsonld b/data/targetrna/targetrnabioschemas.jsonld index 1f1530cb3545f..94522f7f689be 100644 --- a/data/targetrna/targetrnabioschemas.jsonld +++ b/data/targetrna/targetrnabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "TargetRNA is a web based tool for identifying mRNA targets of small non-coding RNAs in bacterial species.", "sc:name": "TargetRNA", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://cs.wellesley.edu/~btjaden/TargetRNA2/" } \ No newline at end of file diff --git a/data/targets-mirna/targets-mirnabioschemas.jsonld b/data/targets-mirna/targets-mirnabioschemas.jsonld index c4cfad865265d..82a6fe5361f76 100644 --- a/data/targets-mirna/targets-mirnabioschemas.jsonld +++ b/data/targets-mirna/targets-mirnabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A novel computational approach for predicting miRNA targets with the target sites located along entire gene sequences, which permits finding additional targets that are not located in the 3′ un-translated regions.", "sc:name": "TargetS", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://liubioinfolab.org/targetS/mirna.html" } \ No newline at end of file diff --git a/data/targets/targetsbioschemas.jsonld b/data/targets/targetsbioschemas.jsonld index a85ec1218c902..705cd48a8d6e0 100644 --- a/data/targets/targetsbioschemas.jsonld +++ b/data/targets/targetsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Nnew ligand-specific template-free predictor for targeting protein-ligand binding sites from primary sequences.", "sc:name": "TargetS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.csbio.sjtu.edu.cn:8080/TargetS/" } \ No newline at end of file diff --git a/data/targetscore/targetscorebioschemas.jsonld b/data/targetscore/targetscorebioschemas.jsonld index 989b954bd9659..57bb641de7a11 100644 --- a/data/targetscore/targetscorebioschemas.jsonld +++ b/data/targetscore/targetscorebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yue Li", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Infers the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variational Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final score is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.", "sc:license": "GPL-2.0", "sc:name": "TargetScore", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TargetScore.html", diff --git a/data/targetsearch/targetsearchbioschemas.jsonld b/data/targetsearch/targetsearchbioschemas.jsonld index b3f8be9831a56..1fd9d3f8af158 100644 --- a/data/targetsearch/targetsearchbioschemas.jsonld +++ b/data/targetsearch/targetsearchbioschemas.jsonld @@ -18,14 +18,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alvaro Cuadros-Inostroza", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:20015393", { "@id": "https://doi.org/10.1186/1471-2105-10-428" }, + "pubmed:20015393", "pmcid:PMC3087348" ], "sc:description": "This packages provides a targeted pre-processing method for GC-MS data.", @@ -35,8 +35,8 @@ "sc:license": "GPL-2.0", "sc:name": "TargetSearch", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TargetSearch.html", diff --git a/data/targetseqview/targetseqviewbioschemas.jsonld b/data/targetseqview/targetseqviewbioschemas.jsonld index 19e1c868f3449..6ed59a047e83c 100644 --- a/data/targetseqview/targetseqviewbioschemas.jsonld +++ b/data/targetseqview/targetseqviewbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A probability-based score and visualization method to aid in distinguishing true structural variants from alignment artifacts.", "sc:name": "targetSeqView", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/Eitan177/targetSeqView" diff --git a/data/tarsvm/tarsvmbioschemas.jsonld b/data/tarsvm/tarsvmbioschemas.jsonld index b04fe4a0517ee..05e6cb6222722 100644 --- a/data/tarsvm/tarsvmbioschemas.jsonld +++ b/data/tarsvm/tarsvmbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Sampson MG", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4902911", + "pubmed:27287006", { "@id": "https://doi.org/10.1186/S12859-016-1108-4" - }, - "pmcid:PMC4902911", - "pubmed:27287006" + } ], "sc:description": "This increases the accuracy of variant calling when using microfluidic PCR based targeted sequencing approaches.", "sc:featureList": { diff --git a/data/tarv/tarvbioschemas.jsonld b/data/tarv/tarvbioschemas.jsonld index 605631ccfd753..1aa73df609624 100644 --- a/data/tarv/tarvbioschemas.jsonld +++ b/data/tarv/tarvbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "TARV", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://c2s2.yale.edu/software/TARV/" } \ No newline at end of file diff --git a/data/tase/tasebioschemas.jsonld b/data/tase/tasebioschemas.jsonld index 4153b1d74e91f..39703594e9149 100644 --- a/data/tase/tasebioschemas.jsonld +++ b/data/tase/tasebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Rapid tag-counting and annotation software tool specifically designed for Illumina CASAVA sequencing datasets.", "sc:name": "TASE", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/tase/" } \ No newline at end of file diff --git a/data/tassel/tasselbioschemas.jsonld b/data/tassel/tasselbioschemas.jsonld index 070a766751eb6..89757fe977ed7 100644 --- a/data/tassel/tasselbioschemas.jsonld +++ b/data/tassel/tasselbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/tassel", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Desktop application", - "Command-line tool" + "Command-line tool", + "Desktop application" ], "sc:description": "Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.", "sc:license": "LGPL-2.1", "sc:name": "TASSEL", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.maizegenetics.net/tassel" } \ No newline at end of file diff --git a/data/tasuke/tasukebioschemas.jsonld b/data/tasuke/tasukebioschemas.jsonld index 9585aa3341196..c15cbbd49d4da 100644 --- a/data/tasuke/tasukebioschemas.jsonld +++ b/data/tasuke/tasukebioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTT295", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/tasuke", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Takeshi Itoh", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC3702261", + "pubmed:23749962", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTT295" - }, - "pmcid:PMC3702261", - "pubmed:23749962" + } ], "sc:description": "Web-based genome browser that visualizes large-scale resequencing data generated by next-generation sequencing technologies. The variation and read depth of multiple genomes, as well as annotations, can be shown simultaneously at various scales. The frequency of variants and depth of coverage are shown by gradational colors in a block whose size is variable from 1bp to 100kb.", "sc:featureList": { @@ -36,6 +32,10 @@ "Linux" ], "sc:url": "http://tasuke.dna.affrc.go.jp/" + }, + { + "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTT295", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tatp/tatpbioschemas.jsonld b/data/tatp/tatpbioschemas.jsonld index ffa01b3bf14a5..3a8ee56162707 100644 --- a/data/tatp/tatpbioschemas.jsonld +++ b/data/tatp/tatpbioschemas.jsonld @@ -38,10 +38,10 @@ "sc:description": "Prediction of the presence and location of Twin-arginine signal peptide cleavage sites in bacteria.", "sc:featureList": [ { - "@id": "edam:operation_0422" + "@id": "edam:operation_0418" }, { - "@id": "edam:operation_0418" + "@id": "edam:operation_0422" } ], "sc:isAccessibleForFree": true, @@ -55,13 +55,13 @@ "sc:url": "http://cbs.dtu.dk/services/TatP/", "sc:version": "1.0" }, - { - "@id": "http://orcid.org/0000-0002-9412-9643", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/1471-2105-6-167", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-9412-9643", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/taverna/tavernabioschemas.jsonld b/data/taverna/tavernabioschemas.jsonld index fa94d121af291..911e344b1a4a8 100644 --- a/data/taverna/tavernabioschemas.jsonld +++ b/data/taverna/tavernabioschemas.jsonld @@ -18,8 +18,8 @@ "sc:description": "An open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation.", "sc:name": "Taverna", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://taverna.incubator.apache.org/", diff --git a/data/taverna_compbio/taverna_compbiobioschemas.jsonld b/data/taverna_compbio/taverna_compbiobioschemas.jsonld index 8d1764d878aca..e4e10d4640bc1 100644 --- a/data/taverna_compbio/taverna_compbiobioschemas.jsonld +++ b/data/taverna_compbio/taverna_compbiobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.", "sc:name": "taveRNA", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://compbio.cs.sfu.ca/taverna/" diff --git a/data/tax2tree/tax2treebioschemas.jsonld b/data/tax2tree/tax2treebioschemas.jsonld index af0652f9e2d3c..74a12e4a68b33 100644 --- a/data/tax2tree/tax2treebioschemas.jsonld +++ b/data/tax2tree/tax2treebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Tool for automatically decorating taxonomy onto a phylogenetic tree. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.", "sc:name": "tax2tree", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://knightlab.ucsd.edu/wordpress/?p=194", "sc:version": "1.0" diff --git a/data/tax4fun/tax4funbioschemas.jsonld b/data/tax4fun/tax4funbioschemas.jsonld index 875d7507375aa..ed51d5da2fefb 100644 --- a/data/tax4fun/tax4funbioschemas.jsonld +++ b/data/tax4fun/tax4funbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An open-source R package that predicts the functional capabilities of microbial communities based on 16S datasets.", "sc:name": "Tax4Fun", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://tax4fun.gobics.de/" } \ No newline at end of file diff --git a/data/taxa/taxabioschemas.jsonld b/data/taxa/taxabioschemas.jsonld index 79f100e7b7da3..ee36aa0f38dfb 100644 --- a/data/taxa/taxabioschemas.jsonld +++ b/data/taxa/taxabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "Taxa", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/ropensci/taxa", "sc:version": "0.3.1" diff --git a/data/taxget/taxgetbioschemas.jsonld b/data/taxget/taxgetbioschemas.jsonld index 1bd4ea82121fc..550cf929dd4e7 100644 --- a/data/taxget/taxgetbioschemas.jsonld +++ b/data/taxget/taxgetbioschemas.jsonld @@ -19,20 +19,20 @@ ], "sc:description": "Get taxon(s).", "sc:funder": [ - "UK MRC", "UK BBSRC", + "UK MRC", "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "taxget", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/taxget.html", "sc:version": "r6" diff --git a/data/taxgetdown/taxgetdownbioschemas.jsonld b/data/taxgetdown/taxgetdownbioschemas.jsonld index b377a7da76083..bb4c7fad2674e 100644 --- a/data/taxgetdown/taxgetdownbioschemas.jsonld +++ b/data/taxgetdown/taxgetdownbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK BBSRC", "EMBOSS Contributors", - "UK MRC" + "Wellcome Trust", + "UK MRC", + "UK BBSRC" ], "sc:description": "Get descendants of taxon(s).", "sc:funder": [ "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "taxgetdown", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/taxgetrank/taxgetrankbioschemas.jsonld b/data/taxgetrank/taxgetrankbioschemas.jsonld index fa527b3cd03d5..2e8329a66d95f 100644 --- a/data/taxgetrank/taxgetrankbioschemas.jsonld +++ b/data/taxgetrank/taxgetrankbioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "Wellcome Trust", "UK MRC", "UK BBSRC", - "Wellcome Trust", "EMBOSS Contributors" ], "sc:description": "Get parents of taxon(s).", @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "taxgetrank", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/taxgetrank.html", "sc:version": "r6" diff --git a/data/taxgetspecies/taxgetspeciesbioschemas.jsonld b/data/taxgetspecies/taxgetspeciesbioschemas.jsonld index ddc2cc70c8307..e64f274fb06fe 100644 --- a/data/taxgetspecies/taxgetspeciesbioschemas.jsonld +++ b/data/taxgetspecies/taxgetspeciesbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK MRC", + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Get all species under taxon(s).", "sc:funder": [ "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "taxgetspecies", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/taxgetup/taxgetupbioschemas.jsonld b/data/taxgetup/taxgetupbioschemas.jsonld index 8261ba5d357b4..4bd8dba9807dd 100644 --- a/data/taxgetup/taxgetupbioschemas.jsonld +++ b/data/taxgetup/taxgetupbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK BBSRC", "UK MRC", + "UK BBSRC", + "EMBOSS Contributors", "Wellcome Trust" ], "sc:description": "Get parents of taxon(s).", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "taxgetup", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/taxgetup.html", "sc:version": "r6" diff --git a/data/taxize/taxizebioschemas.jsonld b/data/taxize/taxizebioschemas.jsonld index 5d0b865d52b63..ed75071be40e1 100644 --- a/data/taxize/taxizebioschemas.jsonld +++ b/data/taxize/taxizebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.2-191.V2", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0003-1444-9135", "@type": "schema:Person" @@ -21,37 +25,33 @@ }, "sc:additionalType": "Library", "sc:citation": [ - "pubmed:24555091", "pmcid:PMC3901538", { "@id": "https://doi.org/10.12688/F1000RESEARCH.2-191.V2" - } + }, + "pubmed:24555091" ], "sc:description": "Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.", "sc:featureList": [ { - "@id": "edam:operation_3460" + "@id": "edam:operation_2422" }, { "@id": "edam:operation_2421" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_3460" } ], "sc:license": "MIT", "sc:name": "taxize", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/ropensci/taxize", "sc:version": "0.9.4" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.2-191.V2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/taxman/taxmanbioschemas.jsonld b/data/taxman/taxmanbioschemas.jsonld index 12575f76a15e2..acec8d9a244b7 100644 --- a/data/taxman/taxmanbioschemas.jsonld +++ b/data/taxman/taxmanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Trims rRNA reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa.", "sc:name": "TaxMan", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.ibi.vu.nl/programs/taxmanwww/" } \ No newline at end of file diff --git a/data/taxmapper/taxmapperbioschemas.jsonld b/data/taxmapper/taxmapperbioschemas.jsonld index a05bc92eaec5e..5777816dc64a5 100644 --- a/data/taxmapper/taxmapperbioschemas.jsonld +++ b/data/taxmapper/taxmapperbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12864-017-4168-6", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/taxmapper", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Daniela Beisser", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:29037173", { "@id": "https://doi.org/10.1186/s12864-017-4168-6" }, - "pmcid:PMC5644092", - "pubmed:29037173" + "pmcid:PMC5644092" ], "sc:description": "Analysis tool for a reliable mapping to a provided microeukaryotic reference database and part of a comprehensive Snakemake workflow. It is used to assign taxonomic information to each NGS read by mapping to the database and filtering low quality assignments.", "sc:featureList": { @@ -27,14 +31,10 @@ }, "sc:name": "TaxMapper", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bitbucket.org/dbeisser/taxmapper" - }, - { - "@id": "https://doi.org/10.1186/s12864-017-4168-6", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/taxonomic_metagenome_tool/taxonomic_metagenome_toolbioschemas.jsonld b/data/taxonomic_metagenome_tool/taxonomic_metagenome_toolbioschemas.jsonld index 87dbc12988ca6..d5e9e7f01ee95 100644 --- a/data/taxonomic_metagenome_tool/taxonomic_metagenome_toolbioschemas.jsonld +++ b/data/taxonomic_metagenome_tool/taxonomic_metagenome_toolbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Taxonomic classification of shotgun metagenomic sequences.", "sc:name": "Taxonomic metagenome tool", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "ELIXIR-NO", diff --git a/data/taxonomy_krona_chart/taxonomy_krona_chartbioschemas.jsonld b/data/taxonomy_krona_chart/taxonomy_krona_chartbioschemas.jsonld index 63026a4c746ad..29b49ba2661e5 100644 --- a/data/taxonomy_krona_chart/taxonomy_krona_chartbioschemas.jsonld +++ b/data/taxonomy_krona_chart/taxonomy_krona_chartbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Krona pie chart from taxonomic profile.", "sc:name": "taxonomy_krona_chart", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/kronatools/taxonomy_krona_chart/2.0.0", "sc:version": "2.0.0" diff --git a/data/taxonomy_summary/taxonomy_summarybioschemas.jsonld b/data/taxonomy_summary/taxonomy_summarybioschemas.jsonld index 5fe5aefedf0ed..c74bb3f03c245 100644 --- a/data/taxonomy_summary/taxonomy_summarybioschemas.jsonld +++ b/data/taxonomy_summary/taxonomy_summarybioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Count the redundancy from a taxonomy file.", "sc:name": "taxonomy_summary", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/Taxonomy_summary/0.1%20beta", "sc:version": "0.1 beta" diff --git a/data/taxoptimizer/taxoptimizerbioschemas.jsonld b/data/taxoptimizer/taxoptimizerbioschemas.jsonld index 5c7afb9fc24b5..bbd6190c409b3 100644 --- a/data/taxoptimizer/taxoptimizerbioschemas.jsonld +++ b/data/taxoptimizer/taxoptimizerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Retrieves taxonomy using tabulated BLAST results.", "sc:name": "taxoptimizer", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/C3BI-pasteur-fr/taxo_pack", "sc:version": "0.0.2" diff --git a/data/tbi/tbibioschemas.jsonld b/data/tbi/tbibioschemas.jsonld index 3c75fbad16e99..a7bb6a474ef1d 100644 --- a/data/tbi/tbibioschemas.jsonld +++ b/data/tbi/tbibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "TBI (Tightly Bound Ion Model ) predicts the electrostatic free energy, the different free energy components, the average binding fraction of ions, and the most probable ion binding modes for a given RNA structure (provided in the PDB format) in a salt solution of given ion concentrations.", "sc:name": "TBI", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://rna.physics.missouri.edu/MCTBI/" } \ No newline at end of file diff --git a/data/tbl2knowngene/tbl2knowngenebioschemas.jsonld b/data/tbl2knowngene/tbl2knowngenebioschemas.jsonld index aeec3f69890f4..54b3b977affaa 100644 --- a/data/tbl2knowngene/tbl2knowngenebioschemas.jsonld +++ b/data/tbl2knowngene/tbl2knowngenebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A wrapper tool that parses the contents of a NCBI .tbl annotation table and produces a UCSC Known Genes annotation table.", "sc:name": "Tbl2KnownGene", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://isu.indstate.edu/ybai2/Tbl2KnownGene/index.html" } \ No newline at end of file diff --git a/data/tcc/tccbioschemas.jsonld b/data/tcc/tccbioschemas.jsonld index 187da5cea1e6f..4e959800a24b4 100644 --- a/data/tcc/tccbioschemas.jsonld +++ b/data/tcc/tccbioschemas.jsonld @@ -15,16 +15,16 @@ "Tomoaki Nishiyama" ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization. A major characteristic of the tool is to provide the robust normalization methods for several kinds of count data using combinations of functions in depended packages.", "sc:license": "GPL-2.0", "sc:name": "TCC", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TCC.html", "sc:version": "1.14.0" diff --git a/data/tcdb/tcdbbioschemas.jsonld b/data/tcdb/tcdbbioschemas.jsonld index 5b299d3e154a0..6b25beed4e6c6 100644 --- a/data/tcdb/tcdbbioschemas.jsonld +++ b/data/tcdb/tcdbbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkt1097", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/tcdb", "@type": "sc:SoftwareApplication", @@ -29,11 +33,11 @@ } ], "sc:citation": [ + "pmcid:PMC3964967", "pubmed:24225317", { "@id": "https://doi.org/10.1093/nar/gkt1097" - }, - "pmcid:PMC3964967" + } ], "sc:description": "A comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.", "sc:featureList": { @@ -46,10 +50,6 @@ "Linux" ], "sc:url": "http://www.tcdb.org/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkt1097", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tcga-assembler/tcga-assemblerbioschemas.jsonld b/data/tcga-assembler/tcga-assemblerbioschemas.jsonld index bb5c6f1ab5f17..09d01166aad6f 100644 --- a/data/tcga-assembler/tcga-assemblerbioschemas.jsonld +++ b/data/tcga-assembler/tcga-assemblerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An open-source, freely available tool that automatically downloads, assembles, and processes public The Cancer Genome Atlas (TCGA) data, to facilitate downstream data analysis by relieving investigators from the burdens of data preparation.", "sc:name": "TCGA-Assembler", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.compgenome.org/TCGA-Assembler/" diff --git a/data/tcga-assembler_2/tcga-assembler_2bioschemas.jsonld b/data/tcga-assembler_2/tcga-assembler_2bioschemas.jsonld index 6aa5a4b34892f..93e2258ff0872 100644 --- a/data/tcga-assembler_2/tcga-assembler_2bioschemas.jsonld +++ b/data/tcga-assembler_2/tcga-assembler_2bioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "TCGA-Assembler 2", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.compgenome.org/TCGA-Assembler/" } \ No newline at end of file diff --git a/data/tcga2stat/tcga2statbioschemas.jsonld b/data/tcga2stat/tcga2statbioschemas.jsonld index a43b4cc83bec0..3a9f41f9635cc 100644 --- a/data/tcga2stat/tcga2statbioschemas.jsonld +++ b/data/tcga2stat/tcga2statbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment.", "sc:name": "TCGA2STAT", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.liuzlab.org/TCGA2STAT/" diff --git a/data/tcga_api/tcga_apibioschemas.jsonld b/data/tcga_api/tcga_apibioschemas.jsonld index 5f538596cb7e1..73afbc8f3ba83 100644 --- a/data/tcga_api/tcga_apibioschemas.jsonld +++ b/data/tcga_api/tcga_apibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "The Cancer Genome Atlas API", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://wiki.nci.nih.gov/display/TCGA/TCGA+DCC+Web+Service+User's+Guide", "sc:version": "1" diff --git a/data/tcgabiolinks/tcgabiolinksbioschemas.jsonld b/data/tcgabiolinks/tcgabiolinksbioschemas.jsonld index 049b3acb830e9..164d8278640d9 100644 --- a/data/tcgabiolinks/tcgabiolinksbioschemas.jsonld +++ b/data/tcgabiolinks/tcgabiolinksbioschemas.jsonld @@ -23,8 +23,8 @@ "sc:name": "TCGAbiolinks", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html", "sc:version": "2.2.6" diff --git a/data/tcgabiolinksgui/tcgabiolinksguibioschemas.jsonld b/data/tcgabiolinksgui/tcgabiolinksguibioschemas.jsonld index c2e6d055384c9..5fe41711b81d9 100644 --- a/data/tcgabiolinksgui/tcgabiolinksguibioschemas.jsonld +++ b/data/tcgabiolinksgui/tcgabiolinksguibioschemas.jsonld @@ -20,19 +20,19 @@ "sc:additionalType": "Library", "sc:citation": [ "pubmed:26704973", + "pmcid:PMC4856967", { "@id": "https://doi.org/10.1093/nar/gkv1507" - }, - "pmcid:PMC4856967" + } ], "sc:contributor": "Gianluca Bontempi", "sc:description": "A Graphical User Interface to analyze cancer molecular and clinical data.", "sc:license": "GPL-3.0", "sc:name": "TCGAbiolinksGUI", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TCGAbiolinksGUI.html", "sc:version": "1.6.0" diff --git a/data/tcgautils/tcgautilsbioschemas.jsonld b/data/tcgautils/tcgautilsbioschemas.jsonld index ae417b3071ab2..c1ec97681b81d 100644 --- a/data/tcgautils/tcgautilsbioschemas.jsonld +++ b/data/tcgautils/tcgautilsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "TCGAutils", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TCGAutils.html", "sc:version": "1.0.1" diff --git a/data/tcode/tcodebioschemas.jsonld b/data/tcode/tcodebioschemas.jsonld index c14b0e4486729..bfa081096af2c 100644 --- a/data/tcode/tcodebioschemas.jsonld +++ b/data/tcode/tcodebioschemas.jsonld @@ -14,14 +14,14 @@ "sc:contributor": [ "UK MRC", "Wellcome Trust", - "EMBOSS Contributors", - "UK BBSRC" + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Identify protein-coding regions using Fickett TESTCODE statistic.", "sc:funder": [ - "UK MRC", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "tcode", @@ -31,8 +31,8 @@ "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/tcode.html", "sc:version": "r6" diff --git a/data/tcof-db/tcof-dbbioschemas.jsonld b/data/tcof-db/tcof-dbbioschemas.jsonld index b37e7181bc1af..d88c2a1eda981 100644 --- a/data/tcof-db/tcof-dbbioschemas.jsonld +++ b/data/tcof-db/tcof-dbbioschemas.jsonld @@ -11,18 +11,18 @@ "@id": "https://bio.tools/tcof-db", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sebastian Schmeier", "Vladimir B. Bajic", - "Ulf Schaefer" + "Ulf Schaefer", + "Sebastian Schmeier" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:20965969", "sc:description": "TcoF is a database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors). Proteins can be searched by a variety of identifiers or predefined sets of proteins can be viewed.", "sc:name": "TcoF-DB", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cbrc.kaust.edu.sa/tcof/" } \ No newline at end of file diff --git a/data/tcoffee/tcoffeebioschemas.jsonld b/data/tcoffee/tcoffeebioschemas.jsonld index 49be6a866efeb..959dcdf838b47 100644 --- a/data/tcoffee/tcoffeebioschemas.jsonld +++ b/data/tcoffee/tcoffeebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "T-Coffee", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.tcoffee.org/Projects/tcoffee/", "sc:version": "1" diff --git a/data/tcoffee_ebi/tcoffee_ebibioschemas.jsonld b/data/tcoffee_ebi/tcoffee_ebibioschemas.jsonld index 0846cb6b91f86..f7d238893093c 100644 --- a/data/tcoffee_ebi/tcoffee_ebibioschemas.jsonld +++ b/data/tcoffee_ebi/tcoffee_ebibioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Web Production", "sc:additionalType": "Web application", "sc:author": [ - "Cedric Notredame", - "Web Production" + "Web Production", + "Cedric Notredame" ], "sc:description": "Multiple sequence alignment that combines several alignment methods.", "sc:name": "T-Coffee EBI", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "EMBL-EBI", diff --git a/data/tcoffee_sib/tcoffee_sibbioschemas.jsonld b/data/tcoffee_sib/tcoffee_sibbioschemas.jsonld index 7ca2119365e74..4b0dc3260fcb0 100644 --- a/data/tcoffee_sib/tcoffee_sibbioschemas.jsonld +++ b/data/tcoffee_sib/tcoffee_sibbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0003-1461-0988", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/TCoffee_SIB", "@type": "sc:SoftwareApplication", @@ -22,42 +26,42 @@ "@id": "edam:data_0863" }, "sc:additionalType": [ - "Suite", - "Web application" + "Web application", + "Suite" ], "sc:applicationSubCategory": [ { "@id": "edam:topic_0622" }, { - "@id": "edam:topic_0080" + "@id": "edam:topic_0121" }, { - "@id": "edam:topic_0121" + "@id": "edam:topic_0080" } ], "sc:citation": [ - "pmcid:PMC3125728", - "pubmed:21558174", { "@id": "https://doi.org/10.1093/nar/gkr245" - } + }, + "pubmed:21558174", + "pmcid:PMC3125728" ], "sc:description": "A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures. Includes M-Coffee, R-Coffee, Expresso, PSI-Coffee, iRMSD-APDB.", "sc:featureList": [ { - "@id": "edam:operation_0492" + "@id": "edam:operation_2403" }, { - "@id": "edam:operation_2403" + "@id": "edam:operation_0492" } ], "sc:isAccessibleForFree": true, "sc:name": "T-Coffee (SIB)", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:softwareHelp": { "@id": "http://www.tcoffee.org/Projects/tcoffee/" @@ -67,10 +71,6 @@ { "@id": "https://doi.org/10.1093/nar/gkr245", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0003-1461-0988", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/tcr/tcrbioschemas.jsonld b/data/tcr/tcrbioschemas.jsonld index eb9f9fb0d833c..23986b0c2587d 100644 --- a/data/tcr/tcrbioschemas.jsonld +++ b/data/tcr/tcrbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0003-3659-2709", - "@type": "schema:Person" + "@id": "https://doi.org/10.1186/s12859-015-0613-1", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/tcr", @@ -20,14 +20,14 @@ "@id": "http://orcid.org/0000-0003-3659-2709" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC4445501", { "@id": "https://doi.org/10.1186/s12859-015-0613-1" }, + "pmcid:PMC4445501", "pubmed:26017500" ], "sc:description": "TCR repertoire data analysis after preprocessing data with CDR3 extraction and gene alignment software tools such as MiTCR, ImmunoSEQ and MiGEC.", @@ -40,8 +40,8 @@ "sc:version": "2.2.1.7" }, { - "@id": "https://doi.org/10.1186/s12859-015-0613-1", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0003-3659-2709", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/tcre/tcrebioschemas.jsonld b/data/tcre/tcrebioschemas.jsonld index 3057ee4396619..89b8f591cabc0 100644 --- a/data/tcre/tcrebioschemas.jsonld +++ b/data/tcre/tcrebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "TCRE", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/hammerlab/t-cell-relation-extraction" } \ No newline at end of file diff --git a/data/tcs-msa/tcs-msabioschemas.jsonld b/data/tcs-msa/tcs-msabioschemas.jsonld index d38bae0249663..16b9ea4f2f2ef 100644 --- a/data/tcs-msa/tcs-msabioschemas.jsonld +++ b/data/tcs-msa/tcs-msabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "TCS", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://tcoffee.crg.cat/apps/tcoffee/do:core" } \ No newline at end of file diff --git a/data/tcs/tcsbioschemas.jsonld b/data/tcs/tcsbioschemas.jsonld index 37509adb039a4..9191e55bdf355 100644 --- a/data/tcs/tcsbioschemas.jsonld +++ b/data/tcs/tcsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks). The network estimation implemented is also known as Statistical Parsimony. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data.", "sc:name": "TCS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://darwin.uvigo.es/software/tcs.html" } \ No newline at end of file diff --git a/data/tcsbu/tcsbubioschemas.jsonld b/data/tcsbu/tcsbubioschemas.jsonld index 4c1683b337600..eb0e9ffc53ce8 100644 --- a/data/tcsbu/tcsbubioschemas.jsonld +++ b/data/tcsbu/tcsbubioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web-based program that extends the capabilities of TCS, by implementing haplotype classification into an arbitrary user-defined scheme, which is displayed as pie-chart like graphs embedded into the network.", "sc:name": "tcsBU", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://cibio.up.pt/software/tcsBU/" } \ No newline at end of file diff --git a/data/tcseq/tcseqbioschemas.jsonld b/data/tcseq/tcseqbioschemas.jsonld index ebf11f28b7cef..d0a848976e199 100644 --- a/data/tcseq/tcseqbioschemas.jsonld +++ b/data/tcseq/tcseqbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "TCseq", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TCseq.html", "sc:version": "1.4.0" diff --git a/data/tdr_targets/tdr_targetsbioschemas.jsonld b/data/tdr_targets/tdr_targetsbioschemas.jsonld index 77690688075b0..8f0d3173ab3d5 100644 --- a/data/tdr_targets/tdr_targetsbioschemas.jsonld +++ b/data/tdr_targets/tdr_targetsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Tropical Disease Research (TDR) Database: Designed and developed to facilitate the rapid identification and prioritization of molecular targets for drug development, focusing on pathogens responsible for neglected human diseases. The database integrates pathogen specific genomic information with functional data for genes collected from various sources, including literature curation. Information can be browsed and queried.", "sc:name": "TDR Targets", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://tdrtargets.org/" diff --git a/data/teak/teakbioschemas.jsonld b/data/teak/teakbioschemas.jsonld index 3e1e811b79ce3..472d374f77103 100644 --- a/data/teak/teakbioschemas.jsonld +++ b/data/teak/teakbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An open source GUI software consisting of two modules: Topology Enrichment Analysis frameworK and Query Structure Enrichment Analysis. TEAK is used to find biologically activated KEGG subpathways given molecular profiling data whereas QSEA is used to perform hierarchical querying of the KEGG pathways.", "sc:name": "TEAK", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://code.google.com/p/teak/" } \ No newline at end of file diff --git a/data/team/teambioschemas.jsonld b/data/team/teambioschemas.jsonld index 2653482ba962a..fc39ef9952360 100644 --- a/data/team/teambioschemas.jsonld +++ b/data/team/teambioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "TEAM", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://team.babelomics.org" } \ No newline at end of file diff --git a/data/tebacten/tebactenbioschemas.jsonld b/data/tebacten/tebactenbioschemas.jsonld index c7d15f0a0652c..5a3a533062d90 100644 --- a/data/tebacten/tebactenbioschemas.jsonld +++ b/data/tebacten/tebactenbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "A tool designed to facilitate the retrieval, extraction and annotation of bacterial enzymatic reactions and pathways from the literature.", "sc:name": "TeBactEn", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "cnio.es", "sc:url": "http://tebacten.bioinfo.cnio.es/", diff --git a/data/tegs/tegsbioschemas.jsonld b/data/tegs/tegsbioschemas.jsonld index 7595fccc41d1e..947389a5bb4dd 100644 --- a/data/tegs/tegsbioschemas.jsonld +++ b/data/tegs/tegsbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "TEGS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/wzhangwhu/TEGS" } \ No newline at end of file diff --git a/data/teiser/teiserbioschemas.jsonld b/data/teiser/teiserbioschemas.jsonld index 17a0994302931..43d141b50d8cb 100644 --- a/data/teiser/teiserbioschemas.jsonld +++ b/data/teiser/teiserbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Robust and powerful framework for discovering post-transcriptional regulatory elemenets.", "sc:name": "TEISER", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://tavazoielab.c2b2.columbia.edu/TEISER/", "sc:version": "1.0" diff --git a/data/telomerehunter/telomerehunterbioschemas.jsonld b/data/telomerehunter/telomerehunterbioschemas.jsonld index 09ac633cdba66..1dd93701dfc77 100644 --- a/data/telomerehunter/telomerehunterbioschemas.jsonld +++ b/data/telomerehunter/telomerehunterbioschemas.jsonld @@ -9,38 +9,38 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2851-0", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/TelomereHunter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lina Sieverling", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:31138115", - "pmcid:PMC6540518", { "@id": "https://doi.org/10.1186/s12859-019-2851-0" - } + }, + "pubmed:31138115", + "pmcid:PMC6540518" ], "sc:description": "In silico estimation of telomere content and composition from cancer genomes.", "sc:featureList": [ - { - "@id": "edam:operation_3799" - }, { "@id": "edam:operation_3798" }, { "@id": "edam:operation_3435" + }, + { + "@id": "edam:operation_3799" } ], "sc:license": "GPL-3.0", "sc:name": "TelomereHunter", "sc:operatingSystem": "Linux", "sc:url": "https://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2851-0", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/telometric/telometricbioschemas.jsonld b/data/telometric/telometricbioschemas.jsonld index 525f2b03d032e..fc407bf5fba4f 100644 --- a/data/telometric/telometricbioschemas.jsonld +++ b/data/telometric/telometricbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Telometric", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioinformatics.fccc.edu/software/OpenSource/telometric/telometric.shtml" } \ No newline at end of file diff --git a/data/tenet/tenetbioschemas.jsonld b/data/tenet/tenetbioschemas.jsonld index 88829c0e69cd5..4de882e88a9d0 100644 --- a/data/tenet/tenetbioschemas.jsonld +++ b/data/tenet/tenetbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool first computes a set of topological features and then leverages a SVM-based approach to identify predictive topological features that characterizes known targets.", "sc:name": "TENET", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://sites.google.com/site/cosbyntu/softwares/tenet" diff --git a/data/tenxplore/tenxplorebioschemas.jsonld b/data/tenxplore/tenxplorebioschemas.jsonld index 957f8f13d4b8b..5608d507c4bf8 100644 --- a/data/tenxplore/tenxplorebioschemas.jsonld +++ b/data/tenxplore/tenxplorebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "tenXplore", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/tenXplore.html", "sc:version": "1.2.0" diff --git a/data/tepitool/tepitoolbioschemas.jsonld b/data/tepitool/tepitoolbioschemas.jsonld index d8766bcb53017..57c26ae0c90fb 100644 --- a/data/tepitool/tepitoolbioschemas.jsonld +++ b/data/tepitool/tepitoolbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool provides prediction of peptides binding to MHC class I and class II molecules.", "sc:name": "TepiTool", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://tools.iedb.org/tepitool/" diff --git a/data/teqc/teqcbioschemas.jsonld b/data/teqc/teqcbioschemas.jsonld index d0e4c894470ad..00053c2a92cf2 100644 --- a/data/teqc/teqcbioschemas.jsonld +++ b/data/teqc/teqcbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "TEQC", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TEQC.html", "sc:version": "3.14.0" diff --git a/data/terapca/terapcabioschemas.jsonld b/data/terapca/terapcabioschemas.jsonld index 54334d44b7167..6a322763f5c02 100644 --- a/data/terapca/terapcabioschemas.jsonld +++ b/data/terapca/terapcabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "TeraPCA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://github.com/aritra90/TeraPCA" } \ No newline at end of file diff --git a/data/terastitcher/terastitcherbioschemas.jsonld b/data/terastitcher/terastitcherbioschemas.jsonld index 3177edc0167df..9e31316f75326 100644 --- a/data/terastitcher/terastitcherbioschemas.jsonld +++ b/data/terastitcher/terastitcherbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (< 8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently retrieved and processed.", "sc:name": "TeraStitcher", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://abria.github.io/TeraStitcher/", diff --git a/data/termine/terminebioschemas.jsonld b/data/termine/terminebioschemas.jsonld index 99a52324259c8..29e044d589f52 100644 --- a/data/termine/terminebioschemas.jsonld +++ b/data/termine/terminebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Input some source text and retrieve a list of terms discovered, ranked by their importance within the text.", "sc:name": "termine", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.nactem.ac.uk/software/termine", diff --git a/data/terminus/terminusbioschemas.jsonld b/data/terminus/terminusbioschemas.jsonld index 8885456d82d19..c16efe39b7e00 100644 --- a/data/terminus/terminusbioschemas.jsonld +++ b/data/terminus/terminusbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/terminus", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:description": "N-Terminal Acetylation and initial methionine predictor based on patterns discovery and decision trees. The proposed algorithm builds a decision tree, by coupling the C4.5 algorithm with genetic algorithms, producing high-performance white box classifiers. Our method was tested on the initiator methionine cleavage (IMC) and Nα-terminal acetylation (N-Ac), two of the most common PTMs.", "sc:name": "Terminus", diff --git a/data/ternarynet/ternarynetbioschemas.jsonld b/data/ternarynet/ternarynetbioschemas.jsonld index 9eaa017d57b2b..1c7f8317c6554 100644 --- a/data/ternarynet/ternarynetbioschemas.jsonld +++ b/data/ternarynet/ternarynetbioschemas.jsonld @@ -9,28 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.2202/1544-6115.1727", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ternarynet", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Matthew N. McCall", "edam:has_input": [ { - "@id": "edam:data_3108" + "@id": "edam:data_3112" }, { - "@id": "edam:data_3112" + "@id": "edam:data_3108" } ], "edam:has_output": { "@id": "edam:data_0951" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { @@ -44,11 +40,11 @@ } ], "sc:citation": [ - "pubmed:23089817", - "pmcid:PMC3215431", { "@id": "https://doi.org/10.2202/1544-6115.1727" - } + }, + "pubmed:23089817", + "pmcid:PMC3215431" ], "sc:description": "A computational Bayesian approach to ternary gene regulatory network estimation from gene perturbation experiments.", "sc:featureList": { @@ -63,6 +59,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ternarynet.html", "sc:version": "1.18.0" + }, + { + "@id": "https://doi.org/10.2202/1544-6115.1727", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tesla/teslabioschemas.jsonld b/data/tesla/teslabioschemas.jsonld index eed7e29c22270..55d90aa65f1f5 100644 --- a/data/tesla/teslabioschemas.jsonld +++ b/data/tesla/teslabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A software for estimating time-varying network from time-series of nodal attributes. It stems from the acronym TESLLOR, which stands for TEmporally Smoothed 11-regularized Logistic Regression. It represents a novel extension of the well-known lasso-style sparse structure recovery technique.", "sc:name": "TESLA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.sailing.cs.cmu.edu/main/?page_id=444" diff --git a/data/tess/tessbioschemas.jsonld b/data/tess/tessbioschemas.jsonld index 1fc63a4953cd8..e21fd60462a59 100644 --- a/data/tess/tessbioschemas.jsonld +++ b/data/tess/tessbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An R-package for simulation of reconstructed phylogenetic trees under global, time-dependent birth-death processes. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.", "sc:name": "TESS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://cran.r-project.org/web/packages/TESS/" diff --git a/data/testdose/testdosebioschemas.jsonld b/data/testdose/testdosebioschemas.jsonld index fdc2a8ce7a975..1fb4ba52ca3a6 100644 --- a/data/testdose/testdosebioschemas.jsonld +++ b/data/testdose/testdosebioschemas.jsonld @@ -20,9 +20,9 @@ "sc:description": "Nuclear medicine software based on Monte Carlo modeling for generating gamma camera acquisitions and dosimetry.", "sc:name": "TestDose", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.dositest.com/" } \ No newline at end of file diff --git a/data/teststorm/teststormbioschemas.jsonld b/data/teststorm/teststormbioschemas.jsonld index 39353a77f1028..93a3debff4adf 100644 --- a/data/teststorm/teststormbioschemas.jsonld +++ b/data/teststorm/teststormbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "CC-BY-SA-4.0", "sc:name": "TestSTORM", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://titan.physx.u-szeged.hu/~adoptim/?page_id=183" } \ No newline at end of file diff --git a/data/tetramito/tetramitobioschemas.jsonld b/data/tetramito/tetramitobioschemas.jsonld index b82e1b3f74093..6d3a159c7db83 100644 --- a/data/tetramito/tetramitobioschemas.jsonld +++ b/data/tetramito/tetramitobioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/tetramito", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Hao Lin", - "Lin Ding Group" + "Lin Ding Group", + "Hao Lin" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:23475502", "sc:description": "Sequence-based predictor for identifying submitochondria location of proteins.", "sc:name": "TetraMito", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://lin.uestc.edu.cn/server/TetraMito" } \ No newline at end of file diff --git a/data/texmed/texmedbioschemas.jsonld b/data/texmed/texmedbioschemas.jsonld index a0e05dc85bc77..86036ebfb3c42 100644 --- a/data/texmed/texmedbioschemas.jsonld +++ b/data/texmed/texmedbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Query PubMed and store references in BibTeX format.", "sc:name": "TeXMed", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.bioinformatics.org/texmed/", "sc:version": "2.0.7" diff --git a/data/textget/textgetbioschemas.jsonld b/data/textget/textgetbioschemas.jsonld index 92bed5847e0c1..b6b098407cacf 100644 --- a/data/textget/textgetbioschemas.jsonld +++ b/data/textget/textgetbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "EMBOSS Contributors", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Get text data entries.", "sc:funder": [ + "UK BBSRC", "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "textget", @@ -31,8 +31,8 @@ "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/textget.html", "sc:version": "r6" diff --git a/data/textsearch/textsearchbioschemas.jsonld b/data/textsearch/textsearchbioschemas.jsonld index 4fa19bf2e09ec..8639381ea32d0 100644 --- a/data/textsearch/textsearchbioschemas.jsonld +++ b/data/textsearch/textsearchbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "UK MRC", + "UK BBSRC", "EMBOSS Contributors", "Wellcome Trust" ], @@ -27,8 +27,8 @@ "sc:name": "textsearch", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/tfarm/tfarmbioschemas.jsonld b/data/tfarm/tfarmbioschemas.jsonld index 7a979928f56ef..2444831845cb4 100644 --- a/data/tfarm/tfarmbioschemas.jsonld +++ b/data/tfarm/tfarmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "TFARM", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TFARM.html", "sc:version": "1.2.0" diff --git a/data/tfbind/tfbindbioschemas.jsonld b/data/tfbind/tfbindbioschemas.jsonld index fb71c01b7b2ce..e23d2a59fe062 100644 --- a/data/tfbind/tfbindbioschemas.jsonld +++ b/data/tfbind/tfbindbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "TFBIND", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://tfbind.hgc.jp/" } \ No newline at end of file diff --git a/data/tfbscluster/tfbsclusterbioschemas.jsonld b/data/tfbscluster/tfbsclusterbioschemas.jsonld index 2853bf06ee7d9..40d2c38ebfdd8 100644 --- a/data/tfbscluster/tfbsclusterbioschemas.jsonld +++ b/data/tfbscluster/tfbsclusterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.", "sc:name": "TFBScluster", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.html" } \ No newline at end of file diff --git a/data/tfbstools/tfbstoolsbioschemas.jsonld b/data/tfbstools/tfbstoolsbioschemas.jsonld index 7e853bc6a700b..9dc9c7e0fff19 100644 --- a/data/tfbstools/tfbstoolsbioschemas.jsonld +++ b/data/tfbstools/tfbstoolsbioschemas.jsonld @@ -34,29 +34,29 @@ }, "sc:citation": [ "pmcid:PMC4866524", - "pubmed:26794315", { "@id": "https://doi.org/10.1093/bioinformatics/btw024" - } + }, + "pubmed:26794315" ], "sc:description": "Package for the analysis and manipulation of transcription factor binding sites. It includes a matrix conversion system between Position Frequency Matrix (PFM), Position Weight Matrix (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query the JASPAR database and provide a wrapper of de novo motif discovery software.", "sc:featureList": [ { - "@id": "edam:operation_0445" + "@id": "edam:operation_0239" }, { - "@id": "edam:operation_0438" + "@id": "edam:operation_0445" }, { - "@id": "edam:operation_0239" + "@id": "edam:operation_0438" } ], "sc:license": "GPL-2.0", "sc:name": "TFBSTools", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TFBSTools.html", "sc:version": "1.12.1" diff --git a/data/tfcheckpoint/tfcheckpointbioschemas.jsonld b/data/tfcheckpoint/tfcheckpointbioschemas.jsonld index ae9d163c9a6f6..5d480ded0020d 100644 --- a/data/tfcheckpoint/tfcheckpointbioschemas.jsonld +++ b/data/tfcheckpoint/tfcheckpointbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "TFcheckpoint", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.tfcheckpoint.org/" } \ No newline at end of file diff --git a/data/tfextract/tfextractbioschemas.jsonld b/data/tfextract/tfextractbioschemas.jsonld index 3345f18992c12..4088de13a2265 100644 --- a/data/tfextract/tfextractbioschemas.jsonld +++ b/data/tfextract/tfextractbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK MRC", "UK BBSRC", "Wellcome Trust", - "UK MRC", "EMBOSS Contributors" ], "sc:description": "Process TRANSFAC transcription factor database for use by tfscan.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "tfextract", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/tfgd/tfgdbioschemas.jsonld b/data/tfgd/tfgdbioschemas.jsonld index 13782f7c5b7f0..42a14129cfd7e 100644 --- a/data/tfgd/tfgdbioschemas.jsonld +++ b/data/tfgd/tfgdbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Tomato Functional Genomics Database (TFGD)", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://ted.bti.cornell.edu" } \ No newline at end of file diff --git a/data/tfhaz/tfhazbioschemas.jsonld b/data/tfhaz/tfhazbioschemas.jsonld index a49d9b8703b67..ef4dfcc5f2d1f 100644 --- a/data/tfhaz/tfhazbioschemas.jsonld +++ b/data/tfhaz/tfhazbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "TFHAZ", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TFHAZ.html", "sc:version": "1.2.0" diff --git a/data/tfm-explorer/tfm-explorerbioschemas.jsonld b/data/tfm-explorer/tfm-explorerbioschemas.jsonld index 277570cc2938b..9089be671d44d 100644 --- a/data/tfm-explorer/tfm-explorerbioschemas.jsonld +++ b/data/tfm-explorer/tfm-explorerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.", "sc:name": "TFM-Explorer", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://bioinfo.lifl.fr/TFM" } \ No newline at end of file diff --git a/data/tfm/tfmbioschemas.jsonld b/data/tfm/tfmbioschemas.jsonld index 2b10af10c9857..8bf43b3b20397 100644 --- a/data/tfm/tfmbioschemas.jsonld +++ b/data/tfm/tfmbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "Wellcome Trust", "UK BBSRC", + "UK MRC", "EMBOSS Contributors" ], "sc:description": "Display full documentation for an application.", "sc:funder": [ "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "tfm", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/tfmodeller/tfmodellerbioschemas.jsonld b/data/tfmodeller/tfmodellerbioschemas.jsonld index 6df8284d1e6e7..8c53a9e191e59 100644 --- a/data/tfmodeller/tfmodellerbioschemas.jsonld +++ b/data/tfmodeller/tfmodellerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "TFmodellerServiceService", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://maya.ccg.unam.mx/~tfmodell/tutorial.html", "sc:version": "1" diff --git a/data/tfold/tfoldbioschemas.jsonld b/data/tfold/tfoldbioschemas.jsonld index c102c8d9cc09b..1ee6884fc85be 100644 --- a/data/tfold/tfoldbioschemas.jsonld +++ b/data/tfold/tfoldbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "An algorithm for predicting non-coding RNA secondary structures.", "sc:name": "TFold", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://evryrna.ibisc.univ-evry.fr/evryrna/tfold" } \ No newline at end of file diff --git a/data/tfpredict/tfpredictbioschemas.jsonld b/data/tfpredict/tfpredictbioschemas.jsonld index cebbf63532900..da0d6c1593e1a 100644 --- a/data/tfpredict/tfpredictbioschemas.jsonld +++ b/data/tfpredict/tfpredictbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Transcription Factor predict. Combines sequence similarity searching with supervised machine learning methods for the identification of TFs and the prediction of their structural superclass.", "sc:name": "TFpredict", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.ra.cs.uni-tuebingen.de/software/TFpredict/welcome_e.html", diff --git a/data/tfscan/tfscanbioschemas.jsonld b/data/tfscan/tfscanbioschemas.jsonld index 63decc32c3bc0..3bed8079c4b0e 100644 --- a/data/tfscan/tfscanbioschemas.jsonld +++ b/data/tfscan/tfscanbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "EMBOSS Contributors", - "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC", + "UK MRC" ], "sc:description": "Identify transcription factor binding sites in DNA sequences.", "sc:funder": [ + "UK MRC", "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "tfscan", diff --git a/data/tfutils/tfutilsbioschemas.jsonld b/data/tfutils/tfutilsbioschemas.jsonld index 3efefd17f4123..4648640cdcf3a 100644 --- a/data/tfutils/tfutilsbioschemas.jsonld +++ b/data/tfutils/tfutilsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Artistic-2.0", "sc:name": "TFutils", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TFutils.html", "sc:version": "1.0.0" diff --git a/data/tgge-star/tgge-starbioschemas.jsonld b/data/tgge-star/tgge-starbioschemas.jsonld index 97ca8b993ab3a..575941c0344de 100644 --- a/data/tgge-star/tgge-starbioschemas.jsonld +++ b/data/tgge-star/tgge-starbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "TGGE-STAR assists in the design of PCR primers for temperature gradient gel electrophoresis. It also incorporates the concept of bipolar clamping.", "sc:name": "TGGE-STAR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.charite.de/bioinf/tgge/" } \ No newline at end of file diff --git a/data/tgnet/tgnetbioschemas.jsonld b/data/tgnet/tgnetbioschemas.jsonld index 35449827a73ae..b97ffcaa5f2c3 100644 --- a/data/tgnet/tgnetbioschemas.jsonld +++ b/data/tgnet/tgnetbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Cytoscape-based tool for visualization and quality assessment of de novo genome assemblies. Specifically it facilitates rapid detection of inconsistencies between a genome assembly and an independently derived transcriptome assembly.", "sc:name": "TGNet", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/ksanao/TGNet", "sc:version": "1.0.0" diff --git a/data/tgs-tb/tgs-tbbioschemas.jsonld b/data/tgs-tb/tgs-tbbioschemas.jsonld index 845e8e4a59b11..6f3231cbc5624 100644 --- a/data/tgs-tb/tgs-tbbioschemas.jsonld +++ b/data/tgs-tb/tgs-tbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An all-in-one web-based tool for genotyping Mtb to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenies with core genomic SNVs, IS6110 insertion sites, and 43 customized loci for variable number tandem repeat (VNTR) through a user-friendly, simple click interface.", "sc:name": "TGS-TB", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://gph.niid.go.jp/tgs-tb/" } \ No newline at end of file diff --git a/data/the_ark/the_arkbioschemas.jsonld b/data/the_ark/the_arkbioschemas.jsonld index ad5bee6f5e46e..8b302d248b617 100644 --- a/data/the_ark/the_arkbioschemas.jsonld +++ b/data/the_ark/the_arkbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "The Ark", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sphinx.org.au/the-ark/" } \ No newline at end of file diff --git a/data/the_autophagy_database/the_autophagy_databasebioschemas.jsonld b/data/the_autophagy_database/the_autophagy_databasebioschemas.jsonld index f3a4e23ab185d..8712ac2f50a54 100644 --- a/data/the_autophagy_database/the_autophagy_databasebioschemas.jsonld +++ b/data/the_autophagy_database/the_autophagy_databasebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "The Autophagy Database", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.tanpaku.org/autophagy/" } \ No newline at end of file diff --git a/data/the_chickpea_portal/the_chickpea_portalbioschemas.jsonld b/data/the_chickpea_portal/the_chickpea_portalbioschemas.jsonld index 00b3721d46944..c89815674cc4e 100644 --- a/data/the_chickpea_portal/the_chickpea_portalbioschemas.jsonld +++ b/data/the_chickpea_portal/the_chickpea_portalbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A collaborative chickpea genomics program comprising advanced pre-breeding tools for the discovery and validation of novel genes and traits leading to development of abiotic stress tolerant chickpea. This is a project for an abiotic stress tolerant chickpea, and contains: Chickpea GBrowse Viewer; Sequence Similarity Search Tools; Raw data download.", "sc:name": "The Chickpea Portal", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "unimelb.edu.au", diff --git a/data/the_flux_capacitor/the_flux_capacitorbioschemas.jsonld b/data/the_flux_capacitor/the_flux_capacitorbioschemas.jsonld index 8cd854ebbfd69..23736c82acba1 100644 --- a/data/the_flux_capacitor/the_flux_capacitorbioschemas.jsonld +++ b/data/the_flux_capacitor/the_flux_capacitorbioschemas.jsonld @@ -17,12 +17,12 @@ "sc:license": "BSD-3-Clause", "sc:name": "The Flux Capacitor", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "Lab Roderic Guigo Group", - "crg.eu" + "crg.eu", + "Lab Roderic Guigo Group" ], "sc:url": "http://sammeth.net/confluence/display/FLUX/Home", "sc:version": "1.6.1" diff --git a/data/the_genetic_map_comparator/the_genetic_map_comparatorbioschemas.jsonld b/data/the_genetic_map_comparator/the_genetic_map_comparatorbioschemas.jsonld index 7702ab3dedfc8..e7b11ffb439b3 100644 --- a/data/the_genetic_map_comparator/the_genetic_map_comparatorbioschemas.jsonld +++ b/data/the_genetic_map_comparator/the_genetic_map_comparatorbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/the_genetic_map_comparator", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Yan Holtz", - "Vincent Ranwez" + "Vincent Ranwez", + "Yan Holtz" ], "sc:additionalType": "Web service", "sc:description": "A user-friendly application to display and compare genetic maps.", "sc:name": "The Genetic Map Comparator", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioweb.supagro.inra.fr/geneticMapComparator/" } \ No newline at end of file diff --git a/data/the_grid/the_gridbioschemas.jsonld b/data/the_grid/the_gridbioschemas.jsonld index 41b5029906a8d..3fc7ff9c7d075 100644 --- a/data/the_grid/the_gridbioschemas.jsonld +++ b/data/the_grid/the_gridbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of genetic and physical interactions; contains interaction data from several genome/proteome wide-studies, the MIPS database, and BIND; provides a powerful visualization system for looking at interactions graphically.", "sc:name": "The GRID", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.thebiogrid.org/" } \ No newline at end of file diff --git a/data/the_interactorium/the_interactoriumbioschemas.jsonld b/data/the_interactorium/the_interactoriumbioschemas.jsonld index 8e58ed5c4752a..0cab2e3ed7f7d 100644 --- a/data/the_interactorium/the_interactoriumbioschemas.jsonld +++ b/data/the_interactorium/the_interactoriumbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Platform built to visualise very large interactome datasets. It functions as an atlas of known protein-protein interactions.", "sc:name": "The Interactorium", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "unimelb.edu.au", "sc:url": "http://www.systemsbiology.org.au/the-interactorium/", diff --git a/data/the_ithanet_portal/the_ithanet_portalbioschemas.jsonld b/data/the_ithanet_portal/the_ithanet_portalbioschemas.jsonld index 8df7528dfc001..265dcded1372e 100644 --- a/data/the_ithanet_portal/the_ithanet_portalbioschemas.jsonld +++ b/data/the_ithanet_portal/the_ithanet_portalbioschemas.jsonld @@ -9,28 +9,28 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0103020", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0003-2681-4355", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1371/journal.pone.0103020", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/the_ithanet_portal", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ "pmcid:PMC4109966", - "pubmed:25058394", + "pubmed:19657830", { "@id": "https://doi.org/10.1371/journal.pone.0103020" }, - "pubmed:19657830" + "pubmed:25058394" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-2681-4355" @@ -38,8 +38,8 @@ "sc:description": "The portal integrates information on news, events, clinical trials and thalassaemia-related organisations, research projects and other scientific networks, wiki-based content of protocols, clinical guidelines and educational articles. Most importantly, disease-specific databases are developed and maintained on the portal, such as databases of haemoglobin variations (IthaGenes), epidemiology (IthaMaps) and HbF inducers (IthaDrugs).", "sc:name": "ITHANET", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "cing.ac.cy", diff --git a/data/the_mendel_site/the_mendel_sitebioschemas.jsonld b/data/the_mendel_site/the_mendel_sitebioschemas.jsonld index 98d44a35311d4..d611115e4d965 100644 --- a/data/the_mendel_site/the_mendel_sitebioschemas.jsonld +++ b/data/the_mendel_site/the_mendel_sitebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.", "sc:name": "The Mendel Site", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://mendel.imp.ac.at/" } \ No newline at end of file diff --git a/data/theme/themebioschemas.jsonld b/data/theme/themebioschemas.jsonld index e3a8b3b2a70a7..31275b7654b79 100644 --- a/data/theme/themebioschemas.jsonld +++ b/data/theme/themebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "THEME", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://metadb.bmes.nthu.edu.tw/theme/home.php" } \ No newline at end of file diff --git a/data/theorchromo/theorchromobioschemas.jsonld b/data/theorchromo/theorchromobioschemas.jsonld index 62bfc8c00ca1e..38b3dbd8dff47 100644 --- a/data/theorchromo/theorchromobioschemas.jsonld +++ b/data/theorchromo/theorchromobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An online tool for peptide and protein retention time prediction in liquid chromatography. It implements the BioLCCC model for the most popular case of linear gradient chromatography.", "sc:name": "TheorChromo", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.theorchromo.ru/" } \ No newline at end of file diff --git a/data/theorets/theoretsbioschemas.jsonld b/data/theorets/theoretsbioschemas.jsonld index 4743d7548b708..e456e0610e038 100644 --- a/data/theorets/theoretsbioschemas.jsonld +++ b/data/theorets/theoretsbioschemas.jsonld @@ -21,9 +21,9 @@ "sc:license": "Unlicense", "sc:name": "TheoReTS", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://theorets.univ-reims.fr" } \ No newline at end of file diff --git a/data/theospec/theospecbioschemas.jsonld b/data/theospec/theospecbioschemas.jsonld index a49d0e4c4980d..6e6503e42e85a 100644 --- a/data/theospec/theospecbioschemas.jsonld +++ b/data/theospec/theospecbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Command line tool for predicting MS/MS spectra.", "sc:name": "theospec", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://sourceforge.net/projects/protms/files/theospec/" diff --git a/data/thermo_msf_parser/thermo_msf_parserbioschemas.jsonld b/data/thermo_msf_parser/thermo_msf_parserbioschemas.jsonld index f0c1675ffc264..05828e849a337 100644 --- a/data/thermo_msf_parser/thermo_msf_parserbioschemas.jsonld +++ b/data/thermo_msf_parser/thermo_msf_parserbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Parser and viewer for thermo msf files.", "sc:name": "Thermo MSF Parser", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "ugent.be", diff --git a/data/theseed/theseedbioschemas.jsonld b/data/theseed/theseedbioschemas.jsonld index 04f1e7f95f858..eca6044c9fc18 100644 --- a/data/theseed/theseedbioschemas.jsonld +++ b/data/theseed/theseedbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Environment for comparative genome analysis.", "sc:name": "The SEED genome comparison environment", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.theseed.org/" } \ No newline at end of file diff --git a/data/thread_mapper_studio/thread_mapper_studiobioschemas.jsonld b/data/thread_mapper_studio/thread_mapper_studiobioschemas.jsonld index c58594c029740..56fdfd018235d 100644 --- a/data/thread_mapper_studio/thread_mapper_studiobioschemas.jsonld +++ b/data/thread_mapper_studio/thread_mapper_studiobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "THREaD Mapper Studio is a web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers.", "sc:name": "THREaD Mapper Studio", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://cbr.jic.ac.uk/threadmapper" } \ No newline at end of file diff --git a/data/threadna/threadnabioschemas.jsonld b/data/threadna/threadnabioschemas.jsonld index 7bf45d4e417e5..d7c3d2533adf2 100644 --- a/data/threadna/threadnabioschemas.jsonld +++ b/data/threadna/threadnabioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sam Meyer", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Predicting DNA mechanics’ contribution to sequence selectivity of proteins along whole genomes.", "sc:name": "ThreaDNA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioinfo.insa-lyon.fr/prod.php" } \ No newline at end of file diff --git a/data/threadom/threadombioschemas.jsonld b/data/threadom/threadombioschemas.jsonld index 423dceffeb53f..afcff7c7ab70a 100644 --- a/data/threadom/threadombioschemas.jsonld +++ b/data/threadom/threadombioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A template-based algorithm for protein domain boundary prediction. Given a protein sequence, ThreaDom first threads the target through the PDB library to identify protein template that have similar structure fold. A domain conservation score (DCS) will be calculated for each residue which combines information from template domain structure, terminal and internal gaps and insertions. Finally, the domain boundary information is derived from the DCS profile distributions.", "sc:name": "ThreaDom", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://zhanglab.ccmb.med.umich.edu/ThreaDom/" } \ No newline at end of file diff --git a/data/threadom_ex/threadom_exbioschemas.jsonld b/data/threadom_ex/threadom_exbioschemas.jsonld index 0775823a03489..c0201c1cb0052 100644 --- a/data/threadom_ex/threadom_exbioschemas.jsonld +++ b/data/threadom_ex/threadom_exbioschemas.jsonld @@ -17,8 +17,8 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28498994", "pmcid:PMC5793814", + "pubmed:28498994", { "@id": "https://doi.org/10.1093/nar/gkx410" } @@ -29,10 +29,10 @@ "@id": "edam:operation_2479" }, { - "@id": "edam:operation_0267" + "@id": "edam:operation_0246" }, { - "@id": "edam:operation_0246" + "@id": "edam:operation_0267" } ], "sc:name": "ThreaDomEx", diff --git a/data/three_to_one/three_to_onebioschemas.jsonld b/data/three_to_one/three_to_onebioschemas.jsonld index 19f3eddcde6f7..c845a158cb141 100644 --- a/data/three_to_one/three_to_onebioschemas.jsonld +++ b/data/three_to_one/three_to_onebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Three to One converts three letter translations to single letter translations", "sc:name": "Three to One", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioinformatics.org/sms2/three_to_one.html" } \ No newline at end of file diff --git a/data/threshold-seq/threshold-seqbioschemas.jsonld b/data/threshold-seq/threshold-seqbioschemas.jsonld index db72ada90cb6e..42325553ee57b 100644 --- a/data/threshold-seq/threshold-seqbioschemas.jsonld +++ b/data/threshold-seq/threshold-seqbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Threshold-seq", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://cm.jefferson.edu/threshold-seq/" } \ No newline at end of file diff --git a/data/thunderstorm/thunderstormbioschemas.jsonld b/data/thunderstorm/thunderstormbioschemas.jsonld index 6d5bb8ad5a5a3..4e6a811d9b623 100644 --- a/data/thunderstorm/thunderstormbioschemas.jsonld +++ b/data/thunderstorm/thunderstormbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy.", "sc:name": "ThunderSTORM", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://zitmen.github.io/thunderstorm/" } \ No newline at end of file diff --git a/data/thyme/thymebioschemas.jsonld b/data/thyme/thymebioschemas.jsonld index a67f9b5ab9fb7..69fb3cdac90e2 100644 --- a/data/thyme/thymebioschemas.jsonld +++ b/data/thyme/thymebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "This database has amino acid sequences and 3D (tertiary) structures of all the enzymes constituting the fatty acid synthesis and polyketide synthesis cycles.", "sc:name": "ThYme", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.enzyme.cbirc.iastate.edu" } \ No newline at end of file diff --git a/data/tiara/tiarabioschemas.jsonld b/data/tiara/tiarabioschemas.jsonld index 5c5aca945bd45..74d16b979744b 100644 --- a/data/tiara/tiarabioschemas.jsonld +++ b/data/tiara/tiarabioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "TIARA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://tiara.gmi.ac.kr" } \ No newline at end of file diff --git a/data/tibanna/tibannabioschemas.jsonld b/data/tibanna/tibannabioschemas.jsonld index 5c172eb5d1659..d585f29de5cbd 100644 --- a/data/tibanna/tibannabioschemas.jsonld +++ b/data/tibanna/tibannabioschemas.jsonld @@ -15,16 +15,16 @@ "Peter J. Park" ], "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Software for scalable execution of portable pipelines on the cloud.", "sc:license": "MIT", "sc:name": "Tibanna", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/4dn-dcic/tibanna" } \ No newline at end of file diff --git a/data/tiddit/tidditbioschemas.jsonld b/data/tiddit/tidditbioschemas.jsonld index c320f17df0ed2..17bc53020b93a 100644 --- a/data/tiddit/tidditbioschemas.jsonld +++ b/data/tiddit/tidditbioschemas.jsonld @@ -15,8 +15,8 @@ "Francesco Vezzi" ], "sc:additionalType": [ - "Script", - "Command-line tool" + "Command-line tool", + "Script" ], "sc:description": "Efficient and comprehensive structural variant caller for massive parallel sequencing data. Identify chromosomal rearrangements using Mate Pair or Paired End sequencing data. It allows identification of intra and inter-chromosomal translocations, deletions, tandem-duplications and inversions, using supplementary alignments as well as discordant pairs.", "sc:license": "GPL-3.0", diff --git a/data/tiger/tigerbioschemas.jsonld b/data/tiger/tigerbioschemas.jsonld index 7ae1864da60de..e1fa07f2bf707 100644 --- a/data/tiger/tigerbioschemas.jsonld +++ b/data/tiger/tigerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A software platform for building and analyzing genome-scale models of metabolism. TIGER provides methods for combining gene-protein-reaction associations, transcriptional regulation, and other biological constraints into a single mixed-integer linear programming (MILP) framework.", "sc:name": "TIGER", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.bme.virginia.edu/csbl/Downloads1-tiger.html" } \ No newline at end of file diff --git a/data/tigr_gene_indices/tigr_gene_indicesbioschemas.jsonld b/data/tigr_gene_indices/tigr_gene_indicesbioschemas.jsonld index c8783b9823b4a..aab796eaf34f0 100644 --- a/data/tigr_gene_indices/tigr_gene_indicesbioschemas.jsonld +++ b/data/tigr_gene_indices/tigr_gene_indicesbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An analysis of a set of unique, highly accurate virtual transcripts that are represented in the worlds public EST data; can perform a BLAST search against the TIGR unique Gene Indices.", "sc:name": "TIGR Gene Indices", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://compbio.dfci.harvard.edu/tgi/" } \ No newline at end of file diff --git a/data/tigre/tigrebioschemas.jsonld b/data/tigre/tigrebioschemas.jsonld index a6175126d5068..523eb7747a890 100644 --- a/data/tigre/tigrebioschemas.jsonld +++ b/data/tigre/tigrebioschemas.jsonld @@ -18,8 +18,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Antti Honkela", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:18689843", "sc:contributor": { @@ -29,9 +29,9 @@ "sc:license": "GPL-3.0", "sc:name": "tigre", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/tigre.html", "sc:version": "1.28.0" diff --git a/data/tigrfams/tigrfamsbioschemas.jsonld b/data/tigrfams/tigrfamsbioschemas.jsonld index 97101f05e2d05..b29f8a711bf0a 100644 --- a/data/tigrfams/tigrfamsbioschemas.jsonld +++ b/data/tigrfams/tigrfamsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gks1234", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/tigrfams", "@type": "sc:SoftwareApplication", @@ -32,11 +28,11 @@ } ], "sc:citation": [ - "pubmed:23197656", + "pmcid:PMC3531188", { "@id": "https://doi.org/10.1093/nar/gks1234" }, - "pmcid:PMC3531188" + "pubmed:23197656" ], "sc:description": "Protein families based on hidden Markov models (HMMs).", "sc:featureList": { @@ -44,12 +40,16 @@ }, "sc:name": "TIGRFAMS protein family database", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "J Craig Venter Institute", "sc:url": "http://www.tigr.org/TIGRFAMs/" + }, + { + "@id": "https://doi.org/10.1093/nar/gks1234", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tilehmm/tilehmmbioschemas.jsonld b/data/tilehmm/tilehmmbioschemas.jsonld index bd8df086d2ba6..cd66f2be89994 100644 --- a/data/tilehmm/tilehmmbioschemas.jsonld +++ b/data/tilehmm/tilehmmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "TileHMM", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.bioinformatics.csiro.au/tilehmm/", "sc:version": "1.0-6" diff --git a/data/tilingarray/tilingarraybioschemas.jsonld b/data/tilingarray/tilingarraybioschemas.jsonld index dba4ef6a427a5..63a90c3ffeeaa 100644 --- a/data/tilingarray/tilingarraybioschemas.jsonld +++ b/data/tilingarray/tilingarraybioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "tilingArray", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/tilingArray.html", diff --git a/data/tilingscan/tilingscanbioschemas.jsonld b/data/tilingscan/tilingscanbioschemas.jsonld index 1e5e04d177fe1..e54a7e7cc0dd5 100644 --- a/data/tilingscan/tilingscanbioschemas.jsonld +++ b/data/tilingscan/tilingscanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An application for the identification of differentially expressed DNA regions in Tiling Microarray data.", "sc:name": "TilingScan", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://tilingscan.uv.es/" } \ No newline at end of file diff --git a/data/timeclip/timeclipbioschemas.jsonld b/data/timeclip/timeclipbioschemas.jsonld index 7bbfb1a68d7cc..5e83e391997c2 100644 --- a/data/timeclip/timeclipbioschemas.jsonld +++ b/data/timeclip/timeclipbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Chiara Romualdi", "sc:additionalType": "Library", "sc:citation": [ - "pubmed:25077979", - "pmcid:PMC4095003", { "@id": "https://doi.org/10.1186/1471-2105-15-S5-S3" - } + }, + "pubmed:25077979", + "pmcid:PMC4095003" ], "sc:description": "Topology based pathway analysis specifically tailored to long time series without replicates. It combines dimension reduction techniques and graph decomposition theory to explore and identify the portion of pathways that is most time-dependent. In the first step, it selects the time-dependent pathways; in the second step, the most time dependent portions of these pathways are highlighted.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:license": "AGPL-3.0", "sc:name": "timeClip", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", diff --git a/data/timecourse/bioconda_timecourse.yaml b/data/timecourse/bioconda_timecourse.yaml index c2e607b271642..16252ad1f18cb 100644 --- a/data/timecourse/bioconda_timecourse.yaml +++ b/data/timecourse/bioconda_timecourse.yaml @@ -4,7 +4,6 @@ description: Functions for data analysis and graphical displays for developmenta home: https://bioconductor.org/packages/3.10/bioc/html/timecourse.html identifiers: - biotools:timecourse -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-timecourse diff --git a/data/timecourse/timecoursebioschemas.jsonld b/data/timecourse/timecoursebioschemas.jsonld index ce445093937aa..6266e5946d7a4 100644 --- a/data/timecourse/timecoursebioschemas.jsonld +++ b/data/timecourse/timecoursebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yu Chuan Tai", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Functions for data analysis and graphical displays for developmental microarray time course data.", "sc:license": "GPL-3.0", "sc:name": "timecourse", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/timecourse.html", diff --git a/data/timescape/timescapebioschemas.jsonld b/data/timescape/timescapebioschemas.jsonld index b23c4d6749876..12aa72f4acf95 100644 --- a/data/timescape/timescapebioschemas.jsonld +++ b/data/timescape/timescapebioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Maia Smith", "sc:additionalType": [ - "Plug-in", - "Library" + "Library", + "Plug-in" ], "sc:description": "a tool from E-scape suite for visualizing clonal dynamics over time.", "sc:license": "GPL-3.0", "sc:name": "TimeScape", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://bioconductor.org/packages/release/bioc/html/timescape.html", diff --git a/data/timexnet_web/timexnet_webbioschemas.jsonld b/data/timexnet_web/timexnet_webbioschemas.jsonld index 02954540cbd7a..54937acb4ad77 100644 --- a/data/timexnet_web/timexnet_webbioschemas.jsonld +++ b/data/timexnet_web/timexnet_webbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Identifying cellular response networks from diverse omics time-course data.", "sc:name": "TimeXNet Web", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://txnet.hgc.jp/" } \ No newline at end of file diff --git a/data/tin/tinbioschemas.jsonld b/data/tin/tinbioschemas.jsonld index a72e582ba7ce4..930dfae517ac4 100644 --- a/data/tin/tinbioschemas.jsonld +++ b/data/tin/tinbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "TIN", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TIN.html", "sc:version": "1.6.0" diff --git a/data/tipmt/tipmtbioschemas.jsonld b/data/tipmt/tipmtbioschemas.jsonld index 5b500178022cf..222f14f41b4f2 100644 --- a/data/tipmt/tipmtbioschemas.jsonld +++ b/data/tipmt/tipmtbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0003-3838-1008", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/tipmt", "@type": "sc:SoftwareApplication", @@ -25,8 +21,8 @@ ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28187714", "pmcid:PMC5303226", + "pubmed:28187714", { "@id": "https://doi.org/10.1186/S12859-017-1485-3" } @@ -34,20 +30,24 @@ "sc:description": "Web tool to search and design primers for genotyping based on genomic data. The tool identifies and targets Single Sequence Repeat (SSR) or ortholog sequences for large-scale identification and design of taxon-specific primers.", "sc:featureList": [ { - "@id": "edam:operation_3196" + "@id": "edam:operation_2419" }, { - "@id": "edam:operation_2419" + "@id": "edam:operation_3196" } ], "sc:name": "TipMT", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://200.131.37.155/tipMT/" }, + { + "@id": "http://orcid.org/0000-0003-3838-1008", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1186/S12859-017-1485-3", "@type": "sc:CreativeWork" diff --git a/data/tipp/tippbioschemas.jsonld b/data/tipp/tippbioschemas.jsonld index 6f09178d3438e..b39f4a6f170d3 100644 --- a/data/tipp/tippbioschemas.jsonld +++ b/data/tipp/tippbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A new marker-based method developed for abundance profiling of metagenomic data.  It uses a collection of 30 universal marker genes and bins the fragments to the marker genes.  For each set of fragments binned to a marker gene, this classifies the fragments by inserting the fragments into the taxonomic tree estimated on the marker gene.", "sc:name": "TIPP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.cs.utexas.edu/users/phylo/software/sepp/tipp-submission/" } \ No newline at end of file diff --git a/data/tips/tipsbioschemas.jsonld b/data/tips/tipsbioschemas.jsonld index fc0856998d6d0..b1bb4c1d2ecd4 100644 --- a/data/tips/tipsbioschemas.jsonld +++ b/data/tips/tipsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "This database collects predicted drug targets in 150 pathogen species. The structural details of the drug mode of binding are also provided. Predictions are made using the information coming from drug-target three-dimensional complexes and by exploiting the homology relationships of known drug targets with pathogen proteins. Predicted pathogen targets are further annotated with sequence, structural and functional information.", "sc:name": "TiPs", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "ELIXIR-ITA-SAPIENZA", diff --git a/data/tiquant/tiquantbioschemas.jsonld b/data/tiquant/tiquantbioschemas.jsonld index 5c5dbe151fae9..459cd3f822936 100644 --- a/data/tiquant/tiquantbioschemas.jsonld +++ b/data/tiquant/tiquantbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A modular software tool for efficient quantification of biological tissues based on volume data obtained by biomedical image modalities. It includes a number of versatile image and volume processing chains tailored to the analysis of different tissue types which have been experimentally verified.", "sc:name": "TiQuant", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.msysbio.com/tiquant" } \ No newline at end of file diff --git a/data/tisan/tisanbioschemas.jsonld b/data/tisan/tisanbioschemas.jsonld index 87336e6a7066a..42e60ba3573a9 100644 --- a/data/tisan/tisanbioschemas.jsonld +++ b/data/tisan/tisanbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Estimating tissue-specific effects of coding and non-coding variants.", "sc:name": "TiSAn", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/kevinVervier/TiSAn" } \ No newline at end of file diff --git a/data/tissueenrich/tissueenrichbioschemas.jsonld b/data/tissueenrich/tissueenrichbioschemas.jsonld index 03c4c878f774c..ebcd6daa651f9 100644 --- a/data/tissueenrich/tissueenrichbioschemas.jsonld +++ b/data/tissueenrich/tissueenrichbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "TissueEnrich", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TissueEnrich.html", "sc:version": "1.0.0" diff --git a/data/tissues/tissuesbioschemas.jsonld b/data/tissues/tissuesbioschemas.jsonld index 0417dd5810251..9b42ac473c1b0 100644 --- a/data/tissues/tissuesbioschemas.jsonld +++ b/data/tissues/tissuesbioschemas.jsonld @@ -39,8 +39,8 @@ } ], "sc:citation": [ - "pmcid:PMC4493645", "pubmed:26157623", + "pmcid:PMC4493645", { "@id": "https://doi.org/10.7717/peerj.1054" } @@ -53,9 +53,9 @@ "sc:license": "CC-BY-4.0", "sc:name": "TISSUES", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://tissues.jensenlab.org/" } diff --git a/data/titancna/titancnabioschemas.jsonld b/data/titancna/titancnabioschemas.jsonld index 93a21d43da628..d896d142dc73c 100644 --- a/data/titancna/titancnabioschemas.jsonld +++ b/data/titancna/titancnabioschemas.jsonld @@ -9,52 +9,52 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1101/gr.180281.114", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/titancna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sohrab P Shah", { "@id": "http://orcid.org/0000-0001-7578-7272" - } + }, + "Sohrab P Shah" ], "sc:additionalType": [ "Command-line tool", "Library" ], "sc:citation": [ + "pmcid:PMC4216928", { "@id": "https://doi.org/10.1101/gr.180281.114" }, - "pubmed:25060187", - "pmcid:PMC4216928" + "pubmed:25060187" ], "sc:description": "Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalenece of clonal clusters in tumour whole genome sequencing data.", "sc:featureList": [ { - "@id": "edam:operation_3202" + "@id": "edam:operation_2403" }, { - "@id": "edam:operation_3228" + "@id": "edam:operation_3202" }, { - "@id": "edam:operation_2403" + "@id": "edam:operation_3228" } ], "sc:license": "GPL-3.0", "sc:name": "TitanCNA", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TitanCNA.html", "sc:version": "1.16.0" }, - { - "@id": "https://doi.org/10.1101/gr.180281.114", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0001-7578-7272", "@type": "schema:Person" diff --git a/data/titindb/titindbbioschemas.jsonld b/data/titindb/titindbbioschemas.jsonld index bec0cf57cfc27..1932597484223 100644 --- a/data/titindb/titindbbioschemas.jsonld +++ b/data/titindb/titindbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "TITINdb", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://fraternalilab.kcl.ac.uk/TITINdb/" } \ No newline at end of file diff --git a/data/tlinkage/tlinkagebioschemas.jsonld b/data/tlinkage/tlinkagebioschemas.jsonld index 79ef9a0a21c78..f8373415ee74d 100644 --- a/data/tlinkage/tlinkagebioschemas.jsonld +++ b/data/tlinkage/tlinkagebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The programs described here are an extension of the general LINKAGE programs for genetic linkage analysis. The extension consists of allowing for a disease phenotype to be under the control of two loci.", "sc:name": "TLINKAGE", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.jurgott.org/linkage/tlinkage.htm" } \ No newline at end of file diff --git a/data/tls_motion_determination/tls_motion_determinationbioschemas.jsonld b/data/tls_motion_determination/tls_motion_determinationbioschemas.jsonld index fa7dca889f0e2..bd798b8e2597b 100644 --- a/data/tls_motion_determination/tls_motion_determinationbioschemas.jsonld +++ b/data/tls_motion_determination/tls_motion_determinationbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "TLS Motion Determination analyzes a macromolecular crystal structure for evidence of flexibility, e.g. local or inter-domain motions. It does this by partitioning individual chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a maximum number of segments.", "sc:name": "TLS Motion Determination", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://skuld.bmsc.washington.edu/~tlsmd/index.html" diff --git a/data/tm-aligner/tm-alignerbioschemas.jsonld b/data/tm-aligner/tm-alignerbioschemas.jsonld index 3e816cb390377..1d49a7631a5f3 100644 --- a/data/tm-aligner/tm-alignerbioschemas.jsonld +++ b/data/tm-aligner/tm-alignerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy.", "sc:name": "TM-Aligner", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://lms.snu.edu.in/TM-Aligner/" } \ No newline at end of file diff --git a/data/tma_navigator/tma_navigatorbioschemas.jsonld b/data/tma_navigator/tma_navigatorbioschemas.jsonld index 531f24bcdc4e2..75d630c4c0037 100644 --- a/data/tma_navigator/tma_navigatorbioschemas.jsonld +++ b/data/tma_navigator/tma_navigatorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "TMA Navigator is a suite of tools developed specifically for tissue microarray data. It allows network inference, patient stratification and survival analysis from tissue microarray data.", "sc:name": "TMA Navigator", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.tmanavigator.org" diff --git a/data/tmaj/tmajbioschemas.jsonld b/data/tmaj/tmajbioschemas.jsonld index 5b5cfd94203a9..f8fbc30a83183 100644 --- a/data/tmaj/tmajbioschemas.jsonld +++ b/data/tmaj/tmajbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "It is for Tissue MicroArrays (TMA’s). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.", "sc:name": "TMAJ", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://tmaj.pathology.jhmi.edu/", diff --git a/data/tmap/tmapbioschemas.jsonld b/data/tmap/tmapbioschemas.jsonld index 3f2ffd429208d..f7106cf868746 100644 --- a/data/tmap/tmapbioschemas.jsonld +++ b/data/tmap/tmapbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2164-15-264", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/tmap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "GitHub Issues", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC4051166", "pubmed:24708189", { "@id": "https://doi.org/10.1186/1471-2164-15-264" - }, - "pmcid:PMC4051166" + } ], "sc:description": "A short read aligner specifically tuned for data from the Ion Torrent PGM.", "sc:featureList": { @@ -31,10 +27,14 @@ }, "sc:name": "TMAP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/iontorrent/TS/tree/master/Analysis/TMAP" + }, + { + "@id": "https://doi.org/10.1186/1471-2164-15-264", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tmax/tmaxbioschemas.jsonld b/data/tmax/tmaxbioschemas.jsonld index d8ef65ac327cb..ce79f78520650 100644 --- a/data/tmax/tmaxbioschemas.jsonld +++ b/data/tmax/tmaxbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A program for performing association analysis on a set of linked loci within a targeted region.", "sc:name": "tmax", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://wpicr.wpic.pitt.edu/WPICCompGen/tmax.html" } \ No newline at end of file diff --git a/data/tmcrys/tmcrysbioschemas.jsonld b/data/tmcrys/tmcrysbioschemas.jsonld index 0aefcebf2172c..e5ad9f8058ff1 100644 --- a/data/tmcrys/tmcrysbioschemas.jsonld +++ b/data/tmcrys/tmcrysbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "TMCrys", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/brgenzim/tmcrys" } \ No newline at end of file diff --git a/data/tmh_benchmark/tmh_benchmarkbioschemas.jsonld b/data/tmh_benchmark/tmh_benchmarkbioschemas.jsonld index d3cf93367a7d3..cb655c0b3d95b 100644 --- a/data/tmh_benchmark/tmh_benchmarkbioschemas.jsonld +++ b/data/tmh_benchmark/tmh_benchmarkbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods.", "sc:name": "TMH Benchmark", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://rostlab.org/owiki/index.php/TMHBenchmark" } \ No newline at end of file diff --git a/data/tmhcon/tmhconbioschemas.jsonld b/data/tmhcon/tmhconbioschemas.jsonld index ac3945b5de451..b337fa2a61418 100644 --- a/data/tmhcon/tmhconbioschemas.jsonld +++ b/data/tmhcon/tmhconbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It predicts helix-helix contacts specifically within the transmembrane parts of membrane proteins. It includes predictions by two different neural networks, one developed for helix-helix contacts on all transmembrane helix pairs and one specifically tailored for the prediction of helix-helix contacts lying on non-neighboring transmembrane helices.", "sc:name": "TMHcon", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://webclu.bio.wzw.tum.de/tmhcon/index.html", "sc:version": "20101215" diff --git a/data/tmhhcp/tmhhcpbioschemas.jsonld b/data/tmhhcp/tmhhcpbioschemas.jsonld index b25829f381069..8c577eaf63fb7 100644 --- a/data/tmhhcp/tmhhcpbioschemas.jsonld +++ b/data/tmhhcp/tmhhcpbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It is developed to predict residue-residue contacts in alpha-helix transmembrane proteins. The predicted contacts could be further used to predict helix-helix interactions between helices.", "sc:name": "TMhhcp", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://systbio.cau.edu.cn/tmhhcp/" } \ No newline at end of file diff --git a/data/tmhmm/tmhmmbioschemas.jsonld b/data/tmhmm/tmhmmbioschemas.jsonld index 394c562e45093..fe3c9c32d63ce 100644 --- a/data/tmhmm/tmhmmbioschemas.jsonld +++ b/data/tmhmm/tmhmmbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/tmhmm", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web service", "Command-line tool", + "Web service", "Web application" ], "sc:description": "Prediction of transmembrane helices in proteins.", "sc:license": "Other", "sc:name": "TMHMM", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": "CBS", "sc:url": "http://cbs.dtu.dk/services/TMHMM/", diff --git a/data/tmkink/tmkinkbioschemas.jsonld b/data/tmkink/tmkinkbioschemas.jsonld index 9b608df1f79f4..10297a08ec7f5 100644 --- a/data/tmkink/tmkinkbioschemas.jsonld +++ b/data/tmkink/tmkinkbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A method to predict transmembrane helix kinks.", "sc:name": "TMKink", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://tmkinkpredictor.mbi.ucla.edu/" diff --git a/data/tml-mp/tml-mpbioschemas.jsonld b/data/tml-mp/tml-mpbioschemas.jsonld index 934220daadd70..07d9c34bbeb9f 100644 --- a/data/tml-mp/tml-mpbioschemas.jsonld +++ b/data/tml-mp/tml-mpbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predictor for protein folding free energy change upon single point mutation for soluble proteins.", "sc:name": "TML-MP", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://weilab.math.msu.edu/TML/TML-MP/" } \ No newline at end of file diff --git a/data/tmpad/tmpadbioschemas.jsonld b/data/tmpad/tmpadbioschemas.jsonld index e9c4354f178d4..7cba3d47b56e9 100644 --- a/data/tmpad/tmpadbioschemas.jsonld +++ b/data/tmpad/tmpadbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Integrates experimentally observed helix-helix interactions and related structural information of membrane proteins. It offers pre-calculated geometric descriptors at the helix-packing interface. It also includes the corresponding sequence, topology, lipid accessibility, ligand-binding information and supports structural classification, schematic diagrams and visualization of the above structural features of TM helix-packing.", "sc:name": "TMPad", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bio-cluster.iis.sinica.edu.tw/TMPad" diff --git a/data/tmpd/tmpdbioschemas.jsonld b/data/tmpd/tmpdbioschemas.jsonld index 521af274461a4..aabea4dd65e93 100644 --- a/data/tmpd/tmpdbioschemas.jsonld +++ b/data/tmpd/tmpdbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC6020451", - "pubmed:29945549", { "@id": "https://doi.org/10.1186/s12864-018-4878-4" - } + }, + "pmcid:PMC6020451", + "pubmed:29945549" ], "sc:description": "The Tobacco Markers & Primers Database.", "sc:featureList": { @@ -27,9 +27,9 @@ }, "sc:name": "TMPD", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://biodb.sdau.edu.cn/tmpd/index.html" }, diff --git a/data/tmpred/tmpredbioschemas.jsonld b/data/tmpred/tmpredbioschemas.jsonld index 3ce350875b10f..f4467e5457e51 100644 --- a/data/tmpred/tmpredbioschemas.jsonld +++ b/data/tmpred/tmpredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins", "sc:name": "TMPred", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://embnet.vital-it.ch/software/TMPRED_form.html" } \ No newline at end of file diff --git a/data/tmseg/tmsegbioschemas.jsonld b/data/tmseg/tmsegbioschemas.jsonld index 87ca7ef4fdd91..551064c39949c 100644 --- a/data/tmseg/tmsegbioschemas.jsonld +++ b/data/tmseg/tmsegbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Predict transmembrane proteins (TMP) and transmembrane helices (TMH) using position-specific scoring matrices (PSSM) generated by PSI-BLAST and the physico-chemical properties of the amino acids.", "sc:name": "TMSEG", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "tum.de", "sc:url": "https://github.com/Rostlab/TMSEG", diff --git a/data/tmsoc/tmsocbioschemas.jsonld b/data/tmsoc/tmsocbioschemas.jsonld index 8e359d124d6b9..9d1ca35ae79e3 100644 --- a/data/tmsoc/tmsocbioschemas.jsonld +++ b/data/tmsoc/tmsocbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Transmembrane helix: Simple Or Complex (TMSOC) webserver identifies the simple and complex transmembrane helices in a protein sequence. Simple TM helices are then masked prior to sequence similarity searches to decrease the false discovery rate of similarity searches.", "sc:name": "TMSOC", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://tmsoc.bii.a-star.edu.sg" } \ No newline at end of file diff --git a/data/tmvar/tmvarbioschemas.jsonld b/data/tmvar/tmvarbioschemas.jsonld index 5e3219038f785..184bf5f573ac7 100644 --- a/data/tmvar/tmvarbioschemas.jsonld +++ b/data/tmvar/tmvarbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btx541", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/tmvar", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5860583", - "pubmed:28968638", { "@id": "https://doi.org/10.1093/bioinformatics/btx541" - } + }, + "pubmed:28968638", + "pmcid:PMC5860583" ], "sc:description": "Text-mining approach based on conditional random field (CRF) for extracting a wide range of sequence variants in both protein and gene levels according to a standard sequence variants nomenclature developed by the human genome variation society (HGVS).", "sc:featureList": { @@ -27,10 +31,6 @@ "sc:name": "tmVar", "sc:operatingSystem": "Linux", "sc:url": "https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/tmvar/" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btx541", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tnt/tntbioschemas.jsonld b/data/tnt/tntbioschemas.jsonld index 7aa84234fdc3e..cd02edd25f44f 100644 --- a/data/tnt/tntbioschemas.jsonld +++ b/data/tnt/tntbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "TnT", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TnT.html", "sc:version": "1.2.0" diff --git a/data/toehold/toeholdbioschemas.jsonld b/data/toehold/toeholdbioschemas.jsonld index 610937838ee29..bdfe79ce9b0cd 100644 --- a/data/toehold/toeholdbioschemas.jsonld +++ b/data/toehold/toeholdbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "toehold", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://yiplab.cse.cuhk.edu.hk/toehold/" diff --git a/data/toffee/toffeebioschemas.jsonld b/data/toffee/toffeebioschemas.jsonld index f25c7acc017cf..4ae6ab9cd5e63 100644 --- a/data/toffee/toffeebioschemas.jsonld +++ b/data/toffee/toffeebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/toffee", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "Toffee – A highly efficient, lossless file format for DIA-MS | A library for fast access to Time of Flight SWATH-MS data — toffee latest documentation | Free document hosting provided by Read the Docs", "sc:license": "MIT", diff --git a/data/toggle/togglebioschemas.jsonld b/data/toggle/togglebioschemas.jsonld index dbba62bd85b2f..cdc971792ece9 100644 --- a/data/toggle/togglebioschemas.jsonld +++ b/data/toggle/togglebioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/S12859-015-0795-6", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/toggle", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:26552596", "pmcid:PMC4640241", { "@id": "https://doi.org/10.1186/S12859-015-0795-6" - }, - "pubmed:26552596" + } ], "sc:description": "Toolbox for generic NGS analyses.", "sc:featureList": { @@ -28,10 +32,6 @@ "sc:name": "TOGGLE", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/SouthGreenPlatform/TOGGLE" - }, - { - "@id": "https://doi.org/10.1186/S12859-015-0795-6", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/togogenome/togogenomebioschemas.jsonld b/data/togogenome/togogenomebioschemas.jsonld index 2cd8cf9f49794..aabbbcc182d61 100644 --- a/data/togogenome/togogenomebioschemas.jsonld +++ b/data/togogenome/togogenomebioschemas.jsonld @@ -18,30 +18,30 @@ "Web application" ], "sc:citation": [ - "pmcid:PMC6323299", + "pubmed:30624651", { "@id": "https://doi.org/10.1093/database/bay132" }, - "pubmed:30624651" + "pmcid:PMC6323299" ], "sc:description": "Genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches.", "sc:featureList": [ - { - "@id": "edam:operation_3431" - }, { "@id": "edam:operation_0337" }, { "@id": "edam:operation_0224" + }, + { + "@id": "edam:operation_3431" } ], "sc:license": "MIT", "sc:name": "TogoGenome", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://togogenome.org/" }, diff --git a/data/togostanza/togostanzabioschemas.jsonld b/data/togostanza/togostanzabioschemas.jsonld index e81882023c66e..d079538b3593e 100644 --- a/data/togostanza/togostanzabioschemas.jsonld +++ b/data/togostanza/togostanzabioschemas.jsonld @@ -15,30 +15,30 @@ "biotools:primaryContact": "Keita Urashima", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6323299", - "pubmed:30624651", { "@id": "https://doi.org/10.1093/database/bay132" - } + }, + "pubmed:30624651", + "pmcid:PMC6323299" ], "sc:description": "Generic Web framework for rendering an information block.", "sc:featureList": [ { - "@id": "edam:operation_3431" + "@id": "edam:operation_0337" }, { "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0337" + "@id": "edam:operation_3431" } ], "sc:license": "MIT", "sc:name": "TogoStanza", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://togostanza.org/" }, diff --git a/data/togotable/togotablebioschemas.jsonld b/data/togotable/togotablebioschemas.jsonld index 929d3748e47dc..eac1ea6bd039e 100644 --- a/data/togotable/togotablebioschemas.jsonld +++ b/data/togotable/togotablebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "TogoTable", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://togotable.dbcls.jp/" } \ No newline at end of file diff --git a/data/tomato_genome_browser/tomato_genome_browserbioschemas.jsonld b/data/tomato_genome_browser/tomato_genome_browserbioschemas.jsonld index c74f80fac8212..d8002905ceec8 100644 --- a/data/tomato_genome_browser/tomato_genome_browserbioschemas.jsonld +++ b/data/tomato_genome_browser/tomato_genome_browserbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Unlicense", "sc:name": "Tomato Genome Browser", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://cab.unina.it/cgi-bin/gb2/gbrowse/SL250/", "sc:version": "1" diff --git a/data/tome/tomebioschemas.jsonld b/data/tome/tomebioschemas.jsonld index 8c47f52a1a04f..a6ee17eb03876 100644 --- a/data/tome/tomebioschemas.jsonld +++ b/data/tome/tomebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.", "sc:name": "aTOME-2", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://abcis.cbs.cnrs.fr/AT2/" } \ No newline at end of file diff --git a/data/tomoj/tomojbioschemas.jsonld b/data/tomoj/tomojbioschemas.jsonld index d3c62d728e5c2..07b157b9ef86e 100644 --- a/data/tomoj/tomojbioschemas.jsonld +++ b/data/tomoj/tomojbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-8-288", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/tomoj", "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ - "pubmed:17683598", - "pmcid:PMC1976622", { "@id": "https://doi.org/10.1186/1471-2105-8-288" - } + }, + "pmcid:PMC1976622", + "pubmed:17683598" ], "sc:description": "A plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ.", "sc:featureList": { @@ -30,12 +26,16 @@ }, "sc:name": "TOMOJ", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://sourceforge.net/projects/tomoj/", "sc:version": "2.30" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-8-288", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tomominer/tomominerbioschemas.jsonld b/data/tomominer/tomominerbioschemas.jsonld index c1a7c168b52ad..d2a9bf95be4e7 100644 --- a/data/tomominer/tomominerbioschemas.jsonld +++ b/data/tomominer/tomominerbioschemas.jsonld @@ -15,10 +15,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pmcid:PMC5567730", - "pubmed:28552576", { "@id": "https://doi.org/10.1016/j.str.2017.04.016" - } + }, + "pubmed:28552576" ], "sc:description": "Large-scale subtomogram classification, template matching, subtomogram averaging, and alignment. Also provides a pre-configured TomoMinerCloud computing service permitting users without sufficient computing resources instant access to TomoMiners high-performance features.", "sc:featureList": { diff --git a/data/tomophantom/tomophantombioschemas.jsonld b/data/tomophantom/tomophantombioschemas.jsonld index c03b0c4a6e726..88edeb2e5b98c 100644 --- a/data/tomophantom/tomophantombioschemas.jsonld +++ b/data/tomophantom/tomophantombioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "TomoPhantom", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/ElsevierSoftwareX/SOFTX_2018_19", "sc:version": "1.1" diff --git a/data/toner/tonerbioschemas.jsonld b/data/toner/tonerbioschemas.jsonld index 0049770b1d449..8f7678f6559d7 100644 --- a/data/toner/tonerbioschemas.jsonld +++ b/data/toner/tonerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for statistical modeling of enrichment from RNA-seq data comprising enriched and unenriched control libraries.", "sc:name": "ToNER", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www4a.biotec.or.th/GI/tools/toner" } \ No newline at end of file diff --git a/data/toolbox-romano-et-al/toolbox-romano-et-albioschemas.jsonld b/data/toolbox-romano-et-al/toolbox-romano-et-albioschemas.jsonld index 644f2766ef00e..7b683ad70cc1e 100644 --- a/data/toolbox-romano-et-al/toolbox-romano-et-albioschemas.jsonld +++ b/data/toolbox-romano-et-al/toolbox-romano-et-albioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sebastián A. Romano", "sc:additionalType": [ - "Desktop application", - "Workflow" + "Workflow", + "Desktop application" ], "sc:description": "A computational data processing pipeline for the analysis of neuronal population calcium dynamics from fluorescence imaging.", "sc:license": "GPL-3.0", diff --git a/data/topas-nbio/topas-nbiobioschemas.jsonld b/data/topas-nbio/topas-nbiobioschemas.jsonld index cd02130613a80..a90b4519de9a5 100644 --- a/data/topas-nbio/topas-nbiobioschemas.jsonld +++ b/data/topas-nbio/topas-nbiobioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1667/RR15226.1", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/TOPAS-nBio", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Thomas Bortfeld", - "Joost Verburg" + "Joost Verburg", + "Thomas Bortfeld" ], "sc:additionalType": "Web application", "sc:citation": [ "pubmed:30609382", - "pmcid:PMC6377808", { "@id": "https://doi.org/10.1667/RR15226.1" - } + }, + "pmcid:PMC6377808" ], "sc:description": "Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology.", "sc:name": "TOPAS-nBio", @@ -35,6 +31,10 @@ "Linux" ], "sc:url": "https://gray.mgh.harvard.edu/software/258-topas-nbio" + }, + { + "@id": "https://doi.org/10.1667/RR15226.1", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/topas/topasbioschemas.jsonld b/data/topas/topasbioschemas.jsonld index 181fdb73521be..a713971fe673a 100644 --- a/data/topas/topasbioschemas.jsonld +++ b/data/topas/topasbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Joseph Perl", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:23127075", "pmcid:PMC3493036", { "@id": "https://doi.org/10.1118/1.4758060" - }, - "pubmed:23127075" + } ], "sc:description": "Proton Monte Carlo platform for research and clinical applications.", "sc:featureList": { @@ -28,8 +28,8 @@ "sc:license": "Proprietary", "sc:name": "TOPAS", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.topasmc.org/home" }, diff --git a/data/topaseq/topaseqbioschemas.jsonld b/data/topaseq/topaseqbioschemas.jsonld index 79e35bebdd6e9..fb4d2fbad679c 100644 --- a/data/topaseq/topaseqbioschemas.jsonld +++ b/data/topaseq/topaseqbioschemas.jsonld @@ -15,33 +15,33 @@ "biotools:primaryContact": "Ivana Ihnatova", "edam:has_input": [ { - "@id": "edam:data_2600" + "@id": "edam:data_2603" }, { - "@id": "edam:data_2603" + "@id": "edam:data_2600" } ], "edam:has_output": [ { - "@id": "edam:data_2884" + "@id": "edam:data_0951" }, { - "@id": "edam:data_0951" + "@id": "edam:data_2884" } ], "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3308" + "@id": "edam:topic_0602" }, { "@id": "edam:topic_3170" }, { - "@id": "edam:topic_0602" + "@id": "edam:topic_3308" } ], "sc:citation": [ @@ -58,8 +58,8 @@ "sc:license": "GPL-3.0", "sc:name": "ToPASeq", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/ToPASeq.html", diff --git a/data/topconfects/topconfectsbioschemas.jsonld b/data/topconfects/topconfectsbioschemas.jsonld index e84b3d0eb9cf5..7cd248e10d83d 100644 --- a/data/topconfects/topconfectsbioschemas.jsonld +++ b/data/topconfects/topconfectsbioschemas.jsonld @@ -9,24 +9,28 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13059-019-1674-7", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/Topconfects", "@type": "sc:SoftwareApplication", "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC6437914", { "@id": "https://doi.org/10.1186/s13059-019-1674-7" }, - "pubmed:30922379" + "pubmed:30922379", + "pmcid:PMC6437914" ], "sc:description": "R package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list.", "sc:featureList": [ { - "@id": "edam:operation_3800" + "@id": "edam:operation_3680" }, { - "@id": "edam:operation_3680" + "@id": "edam:operation_3800" }, { "@id": "edam:operation_3223" @@ -35,16 +39,12 @@ "sc:license": "LGPL-2.1", "sc:name": "Topconfects", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/topconfects.html", "sc:version": "1.0.0" - }, - { - "@id": "https://doi.org/10.1186/s13059-019-1674-7", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/topcons/topconsbioschemas.jsonld b/data/topcons/topconsbioschemas.jsonld index c4b47742fcfce..6d74f8f3c66e3 100644 --- a/data/topcons/topconsbioschemas.jsonld +++ b/data/topcons/topconsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "TOPCONS", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "bils.se", "sc:url": "http://topcons.cbr.su.se/", diff --git a/data/topdb/topdbbioschemas.jsonld b/data/topdb/topdbbioschemas.jsonld index 2b7d5b8cf7782..3ba3b86c0d723 100644 --- a/data/topdb/topdbbioschemas.jsonld +++ b/data/topdb/topdbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Transmembrane protein datasets containing experimentally derived topology information.", "sc:name": "Topology Data Bank of Transmembrane Proteins", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://toPDB.enzim.hu" } \ No newline at end of file diff --git a/data/topfind/topfindbioschemas.jsonld b/data/topfind/topfindbioschemas.jsonld index 1e8f387636b60..844b6e752ed5a 100644 --- a/data/topfind/topfindbioschemas.jsonld +++ b/data/topfind/topfindbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "First public knowledgebase for protein termini and protease processing.", "sc:name": "TopFIND", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://clipserve.clip.ubc.ca/topfind" } \ No newline at end of file diff --git a/data/topgo/topgobioschemas.jsonld b/data/topgo/topgobioschemas.jsonld index 519ef83e492f5..ef9f9f11ed504 100644 --- a/data/topgo/topgobioschemas.jsonld +++ b/data/topgo/topgobioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "topGO", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/topGO.html", diff --git a/data/tophat/tophatbioschemas.jsonld b/data/tophat/tophatbioschemas.jsonld index 413a234b68fee..a84a45ccdd334 100644 --- a/data/tophat/tophatbioschemas.jsonld +++ b/data/tophat/tophatbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. A stable SAMtools version is now packaged with the program.", "sc:name": "TopHat", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ccb.jhu.edu/software/tophat/index.shtml", "sc:version": "2.1.1" diff --git a/data/tophat2/tophat2bioschemas.jsonld b/data/tophat2/tophat2bioschemas.jsonld index 738b0752b8ef3..43a6875f5944b 100644 --- a/data/tophat2/tophat2bioschemas.jsonld +++ b/data/tophat2/tophat2bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Gapped-read mapper for RNA-seq data.", "sc:name": "tophat2", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://ccb.jhu.edu/software/tophat/index.shtml", "sc:version": "2.0.10" diff --git a/data/topmatch/topmatchbioschemas.jsonld b/data/topmatch/topmatchbioschemas.jsonld index cfdb70fe9886b..d01f5cebce0d3 100644 --- a/data/topmatch/topmatchbioschemas.jsonld +++ b/data/topmatch/topmatchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Computational tools for the alignment and superposition of protein structures are essential instruments in structural biology. TopMatch-web provides an easy-to-use interface to a suite of techniques for protein structure alignments. Given a pair of protein structures, TopMatch calculates a list of alignments ordered by structural similarity. The corresponding superpositions can be explored in a 3D molecule viewer which highlights the structurally equivalent parts of the proteins.", "sc:name": "TopMatch", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://topmatch.services.came.sbg.ac.at/" } \ No newline at end of file diff --git a/data/topo2/topo2bioschemas.jsonld b/data/topo2/topo2bioschemas.jsonld index a84621652099c..2a350f867a37e 100644 --- a/data/topo2/topo2bioschemas.jsonld +++ b/data/topo2/topo2bioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "It is an open source program written in Python for the creation of transmembrane protein 2D topology images. It makes no attempt to predict the TMDs that it displays. The user needs to supply that information. Residues of interest can be highlighted, if desired.", "sc:name": "TOPO2", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.sacs.ucsf.edu/TOPO2/" } \ No newline at end of file diff --git a/data/topogsa/topogsabioschemas.jsonld b/data/topogsa/topogsabioschemas.jsonld index bf2139854cd7b..1f0aca836a473 100644 --- a/data/topogsa/topogsabioschemas.jsonld +++ b/data/topogsa/topogsabioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "TopoGSA", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.topogsa.net" } \ No newline at end of file diff --git a/data/topolink/topolinkbioschemas.jsonld b/data/topolink/topolinkbioschemas.jsonld index eb7b329e27724..947384969fed4 100644 --- a/data/topolink/topolinkbioschemas.jsonld +++ b/data/topolink/topolinkbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "TopoLink", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://leandro.iqm.unicamp.br/topolink/home.shtml" } \ No newline at end of file diff --git a/data/topologygsa/topologygsabioschemas.jsonld b/data/topologygsa/topologygsabioschemas.jsonld index fc1a345899791..247b22f2e2dcf 100644 --- a/data/topologygsa/topologygsabioschemas.jsonld +++ b/data/topologygsa/topologygsabioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Chiara Romualdi", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:20809931", + "pmcid:PMC2945950", { "@id": "https://doi.org/10.1186/1752-0509-4-121" - }, - "pmcid:PMC2945950", - "pubmed:20809931" + } ], "sc:description": "Novel approach to perform pathway analysis using gene expression data. Given the structure of a graph (a pathway) it introduces two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques).", "sc:featureList": { @@ -33,8 +33,8 @@ "sc:name": "TopologyGSA", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://cran.r-project.org/web/packages/topologyGSA/index.html", diff --git a/data/toppcluster/toppclusterbioschemas.jsonld b/data/toppcluster/toppclusterbioschemas.jsonld index 5d59409454158..0ac5fabdbf34f 100644 --- a/data/toppcluster/toppclusterbioschemas.jsonld +++ b/data/toppcluster/toppclusterbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ToppCluster is a human/mammalian genomes-centered web server application for comparative enrichment and network analysis of multiple gene lists. Features such as Gene Ontology terms, protein interactions,disease or disease-associated mammalian phenotypes, promoter cis-elements, miR binding sites, etc. that are differentially represented in the gene lists can be clustered or transformed into high dimensional Cytoscape or Gephi -compatible networks.", "sc:name": "ToppCluster", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://toppcluster.cchmc.org" } \ No newline at end of file diff --git a/data/toppgene_suite/toppgene_suitebioschemas.jsonld b/data/toppgene_suite/toppgene_suitebioschemas.jsonld index 6b1feac8ee920..257e0c7df39e3 100644 --- a/data/toppgene_suite/toppgene_suitebioschemas.jsonld +++ b/data/toppgene_suite/toppgene_suitebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome.", "sc:name": "ToppGene Suite", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://toppgene.cchmc.org" } \ No newline at end of file diff --git a/data/toppic/toppicbioschemas.jsonld b/data/toppic/toppicbioschemas.jsonld index 6c84c70f5df69..63887699a7591 100644 --- a/data/toppic/toppicbioschemas.jsonld +++ b/data/toppic/toppicbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Xiaowen Liu", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:22027200", "sc:description": "Proteoform identification/characterizaion at the proteome level using database search.", diff --git a/data/toppmir/toppmirbioschemas.jsonld b/data/toppmir/toppmirbioschemas.jsonld index 33dd65cc11d09..2537f97d95943 100644 --- a/data/toppmir/toppmirbioschemas.jsonld +++ b/data/toppmir/toppmirbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "ToppMiR web server ranks microRNAs and their mRNA targets based on biological functions and context.", "sc:name": "ToppMiR", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://toppmir.cchmc.org" } \ No newline at end of file diff --git a/data/topsearch/topsearchbioschemas.jsonld b/data/topsearch/topsearchbioschemas.jsonld index f2f9fa19be6cb..f5db919642fcf 100644 --- a/data/topsearch/topsearchbioschemas.jsonld +++ b/data/topsearch/topsearchbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "TopSearch is a new powerful gateway to protein structures and their structural relationships. Given a query structure the search engine instantly returns a list of known protein structures sorted by structural similarity. TopSearch operates on three structural levels: chains, biological assemblies and quaternary structures, and asymmetric units.", "sc:name": "TopSearch", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://topsearch.services.came.sbg.ac.at/" } \ No newline at end of file diff --git a/data/torque/torquebioschemas.jsonld b/data/torque/torquebioschemas.jsonld index f58957cf9bffa..29209c681f3ca 100644 --- a/data/torque/torquebioschemas.jsonld +++ b/data/torque/torquebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web server for querying of protein-protein interaction networks or pathways across species. Networks of up to 25 proteins may be input.", "sc:name": "Torque", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.cs.tau.ac.il/~bnet/torque.html" diff --git a/data/totem/totembioschemas.jsonld b/data/totem/totembioschemas.jsonld index 9bb4ec60725ca..4ae6ef28beb98 100644 --- a/data/totem/totembioschemas.jsonld +++ b/data/totem/totembioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-018-2227-x", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/totem", "@type": "sc:SoftwareApplication", @@ -27,15 +31,11 @@ }, "sc:name": "ToTem", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://totem.software/login/?backlink=iplpf&_fid=t22e" - }, - { - "@id": "https://doi.org/10.1186/s12859-018-2227-x", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/toucan_2/toucan_2bioschemas.jsonld b/data/toucan_2/toucan_2bioschemas.jsonld index 3fc7c1039ea64..571bc5e1fb048 100644 --- a/data/toucan_2/toucan_2bioschemas.jsonld +++ b/data/toucan_2/toucan_2bioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms.", "sc:name": "TOUCAN 2", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php" } \ No newline at end of file diff --git a/data/tp-db/tp-dbbioschemas.jsonld b/data/tp-db/tp-dbbioschemas.jsonld index b45c408956cbe..c3f7f6ef4b3e5 100644 --- a/data/tp-db/tp-dbbioschemas.jsonld +++ b/data/tp-db/tp-dbbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Chung-Yu Lan", - "Lee-Wei Yang", - "Hua-Wen Fu" + "Hua-Wen Fu", + "Lee-Wei Yang" ], "sc:additionalType": "Web application", "sc:description": "Therapeutic Peptide Design DataBase.", "sc:license": "Unlicense", "sc:name": "TP-DB", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://dyn.life.nthu.edu.tw/design" } \ No newline at end of file diff --git a/data/tpes/tpesbioschemas.jsonld b/data/tpes/tpesbioschemas.jsonld index f055bdfa654a8..8b59a8b5666b0 100644 --- a/data/tpes/tpesbioschemas.jsonld +++ b/data/tpes/tpesbioschemas.jsonld @@ -21,8 +21,8 @@ "sc:name": "TPES", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://bitbucket.org/l0ka/tpes.git" } \ No newline at end of file diff --git a/data/tpmcalculator/tpmcalculatorbioschemas.jsonld b/data/tpmcalculator/tpmcalculatorbioschemas.jsonld index 0c80326bffc45..dad2e3134316d 100644 --- a/data/tpmcalculator/tpmcalculatorbioschemas.jsonld +++ b/data/tpmcalculator/tpmcalculatorbioschemas.jsonld @@ -11,10 +11,10 @@ "@id": "https://bio.tools/TPMCalculator", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Leonardo Mariño-Ramírez", "Roberto Vera Alvarez", - "Lorinc Pongor", - "David Landsman" + "David Landsman", + "Leonardo Mariño-Ramírez", + "Lorinc Pongor" ], "sc:additionalType": "Command-line tool", "sc:description": "Software to quantify mRNA abundance of genomic features.", diff --git a/data/tpp/tppbioschemas.jsonld b/data/tpp/tppbioschemas.jsonld index 73fc191a7e1d7..5b043a8dae6d3 100644 --- a/data/tpp/tppbioschemas.jsonld +++ b/data/tpp/tppbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Artistic-2.0", "sc:name": "TPP", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bioconductor.org/packages/TPP/", "sc:version": "3.4.2" diff --git a/data/tpwy/tpwybioschemas.jsonld b/data/tpwy/tpwybioschemas.jsonld index ef8b5c1d6fee9..dfbf822c244b3 100644 --- a/data/tpwy/tpwybioschemas.jsonld +++ b/data/tpwy/tpwybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "tpWY", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.cbil.upenn.edu/tpWY/" } \ No newline at end of file diff --git a/data/tqdist/tqdistbioschemas.jsonld b/data/tqdist/tqdistbioschemas.jsonld index 5d2ff815a2d90..264161546b7fc 100644 --- a/data/tqdist/tqdistbioschemas.jsonld +++ b/data/tqdist/tqdistbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Computation of the triplet- and Quartet-distance between evolutionary trees.", "sc:name": "tqDist", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": "birc.au.dk", diff --git a/data/trace-rrbs/trace-rrbsbioschemas.jsonld b/data/trace-rrbs/trace-rrbsbioschemas.jsonld index 508ef154382e4..a9b0d02b716fc 100644 --- a/data/trace-rrbs/trace-rrbsbioschemas.jsonld +++ b/data/trace-rrbs/trace-rrbsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A full pipeline for mapping bisulfite se-quencing data using bowtie2 and then generating CpG level data.", "sc:name": "TRACE-RRBS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioinformaticstools.mayo.edu/research/trace-rrbs/" diff --git a/data/tracembler/tracemblerbioschemas.jsonld b/data/tracembler/tracemblerbioschemas.jsonld index 82932fdf2b221..dc71567a65965 100644 --- a/data/tracembler/tracemblerbioschemas.jsonld +++ b/data/tracembler/tracemblerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads.", "sc:name": "Tracembler", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.plantgdb.org/tool/tracembler/" } \ No newline at end of file diff --git a/data/tracer/tracerbioschemas.jsonld b/data/tracer/tracerbioschemas.jsonld index b9dbdcc4db542..2cf6860d41729 100644 --- a/data/tracer/tracerbioschemas.jsonld +++ b/data/tracer/tracerbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Graphical tool for visualization and diagnostics of MCMC (Markov chain Monte Carlo) output. It can read output files from MrBayesand BEAST.", "sc:name": "Tracer", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://tree.bio.ed.ac.uk/software/tracer/" } \ No newline at end of file diff --git a/data/tracktables/bioconda_tracktables.yaml b/data/tracktables/bioconda_tracktables.yaml index fe776c312fd58..9e405653ab726 100644 --- a/data/tracktables/bioconda_tracktables.yaml +++ b/data/tracktables/bioconda_tracktables.yaml @@ -4,7 +4,6 @@ description: Methods to create complex IGV genome browser sessions and dynamic I home: https://bioconductor.org/packages/3.10/bioc/html/tracktables.html identifiers: - biotools:tracktables -- doi:10.1038/nmeth.3252 license: GPL (>= 3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-tracktables diff --git a/data/tracktables/tracktablesbioschemas.jsonld b/data/tracktables/tracktablesbioschemas.jsonld index 3487f8b1591f5..4d530db241a72 100644 --- a/data/tracktables/tracktablesbioschemas.jsonld +++ b/data/tracktables/tracktablesbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "tracktables", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/tracktables.html", diff --git a/data/trackviewer/bioconda_trackviewer.yaml b/data/trackviewer/bioconda_trackviewer.yaml index e277307b9c586..4e36d8f3d0c7c 100644 --- a/data/trackviewer/bioconda_trackviewer.yaml +++ b/data/trackviewer/bioconda_trackviewer.yaml @@ -4,7 +4,6 @@ description: Visualize mapped reads along with annotation as track layers for NG home: https://bioconductor.org/packages/3.10/bioc/html/trackViewer.html identifiers: - biotools:trackviewer -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-trackviewer diff --git a/data/trackviewer/trackviewerbioschemas.jsonld b/data/trackviewer/trackviewerbioschemas.jsonld index 8f02ba457cadd..a9a8c9d3c8e73 100644 --- a/data/trackviewer/trackviewerbioschemas.jsonld +++ b/data/trackviewer/trackviewerbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-2.0", "sc:name": "trackViewer", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/trackViewer.html", diff --git a/data/tracmit/tracmitbioschemas.jsonld b/data/tracmit/tracmitbioschemas.jsonld index e15990d1778ff..ecd221126d4a2 100644 --- a/data/tracmit/tracmitbioschemas.jsonld +++ b/data/tracmit/tracmitbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "TRACMIT", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://github.com/lacan/TRACMIT" } \ No newline at end of file diff --git a/data/tractaviewer/tractaviewerbioschemas.jsonld b/data/tractaviewer/tractaviewerbioschemas.jsonld index 7d0ce2c58e2b5..3751c30204712 100644 --- a/data/tractaviewer/tractaviewerbioschemas.jsonld +++ b/data/tractaviewer/tractaviewerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "TractaViewer", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/NeilPearson-Lilly/TractaViewer" } \ No newline at end of file diff --git a/data/tractoflow/tractoflowbioschemas.jsonld b/data/tractoflow/tractoflowbioschemas.jsonld index dec5e51c72bd2..c7ba09c310a74 100644 --- a/data/tractoflow/tractoflowbioschemas.jsonld +++ b/data/tractoflow/tractoflowbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "TractoFlow", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://github.com/scilus/tractoflow" } \ No newline at end of file diff --git a/data/trafac/trafacbioschemas.jsonld b/data/trafac/trafacbioschemas.jsonld index d22f17c238242..48c47cb38f979 100644 --- a/data/trafac/trafacbioschemas.jsonld +++ b/data/trafac/trafacbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "TraFaC", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://trafac.cchmc.org/trafac/index.jsp" } \ No newline at end of file diff --git a/data/trainable_weka_segmentation/trainable_weka_segmentationbioschemas.jsonld b/data/trainable_weka_segmentation/trainable_weka_segmentationbioschemas.jsonld index 49f57bdb0a235..65734b05aa23e 100644 --- a/data/trainable_weka_segmentation/trainable_weka_segmentationbioschemas.jsonld +++ b/data/trainable_weka_segmentation/trainable_weka_segmentationbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Trainable Weka Segmentation", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://imagej.net/Trainable_Weka_Segmentation", "sc:version": "3.2.33" diff --git a/data/traitar/traitarbioschemas.jsonld b/data/traitar/traitarbioschemas.jsonld index 24d15d64f99e4..9e7a3dc91ea75 100644 --- a/data/traitar/traitarbioschemas.jsonld +++ b/data/traitar/traitarbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Alice McHardy", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5192078", + "pubmed:28066816", { "@id": "https://doi.org/10.1128/mSystems.00101-16" - }, - "pubmed:28066816", - "pmcid:PMC5192078" + } ], "sc:description": "Traitar is a fully automated software package for deriving phenotypes from a genome sequence.", "sc:featureList": { diff --git a/data/traitrateprop/traitratepropbioschemas.jsonld b/data/traitrateprop/traitratepropbioschemas.jsonld index ff5a8060b3a91..0a0cd2a5b1200 100644 --- a/data/traitrateprop/traitratepropbioschemas.jsonld +++ b/data/traitrateprop/traitratepropbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKX288", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-5045-0857", "@type": "schema:Person" @@ -38,6 +34,10 @@ "sc:name": "TraitRateProp", "sc:operatingSystem": "Linux", "sc:url": "http://traitrate.tau.ac.il/prop" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKX288", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tral/tralbioschemas.jsonld b/data/tral/tralbioschemas.jsonld index a92b116bceebb..2db7d4b80cf34 100644 --- a/data/tral/tralbioschemas.jsonld +++ b/data/tral/tralbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "It makes annotation of tandem repeats in amino acid and nucleic data simple. It includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs; statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.", "sc:name": "TRAL", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://github.com/acg-team/tral" diff --git a/data/trample/tramplebioschemas.jsonld b/data/trample/tramplebioschemas.jsonld index fd3c63b389dd7..57bad5b8a4ab9 100644 --- a/data/trample/tramplebioschemas.jsonld +++ b/data/trample/tramplebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.", "sc:name": "TRAMPLE", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://gpcr.biocomp.unibo.it/biodec/" } \ No newline at end of file diff --git a/data/tranalign/tranalignbioschemas.jsonld b/data/tranalign/tranalignbioschemas.jsonld index 89dbc7282ad97..f8158203354e0 100644 --- a/data/tranalign/tranalignbioschemas.jsonld +++ b/data/tranalign/tranalignbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "EMBOSS Contributors", + "UK MRC", "UK BBSRC", "Wellcome Trust" ], @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "tranalign", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": [ "EMBL EBI", diff --git a/data/tranalign_ws_husar/tranalign_ws_husarbioschemas.jsonld b/data/tranalign_ws_husar/tranalign_ws_husarbioschemas.jsonld index d12a6c174c5f1..f78937d474781 100644 --- a/data/tranalign_ws_husar/tranalign_ws_husarbioschemas.jsonld +++ b/data/tranalign_ws_husar/tranalign_ws_husarbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Align nucleic coding regions given the aligned proteins.", "sc:name": "tranalign WS (husar)", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/tranalign.html", diff --git a/data/transalign/transalignbioschemas.jsonld b/data/transalign/transalignbioschemas.jsonld index 3f4374e85c65f..944de667e3b36 100644 --- a/data/transalign/transalignbioschemas.jsonld +++ b/data/transalign/transalignbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Calculate more accurate pairwise alignments by making use of a (large) database of uncurated sequences to aid matching against a (small) database of curated target sequences.", "sc:name": "transalign", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "imr.no", "sc:url": "http://malde.org/~ketil/biohaskell/transalign/", diff --git a/data/transclust/transclustbioschemas.jsonld b/data/transclust/transclustbioschemas.jsonld index ece7c8633c0cb..d3f586eb3665c 100644 --- a/data/transclust/transclustbioschemas.jsonld +++ b/data/transclust/transclustbioschemas.jsonld @@ -21,17 +21,17 @@ }, "sc:additionalType": [ "Desktop application", - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:author": "Jan Baumbach", "sc:citation": "pubmed:20508635", "sc:description": "Comprehensive clustering tool that incorporates the hidden transitive nature occuring e.g. within biomedical data sets. It is based on Weighted Transitive Graph Projection problem.", "sc:name": "TransClust", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "bmb.sdu.dk", "sc:url": "https://transclust.compbio.sdu.dk/main_page/index.php", diff --git a/data/transcriptogramer/transcriptogramerbioschemas.jsonld b/data/transcriptogramer/transcriptogramerbioschemas.jsonld index 8e52dc80b0cdf..22b5e6cb7403b 100644 --- a/data/transcriptogramer/transcriptogramerbioschemas.jsonld +++ b/data/transcriptogramer/transcriptogramerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "transcriptogramer", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/transcriptogramer.html", "sc:version": "1.2.1" diff --git a/data/transcriptr/bioconda_transcriptr.yaml b/data/transcriptr/bioconda_transcriptr.yaml index 53271ad97026c..93c8de7d57848 100644 --- a/data/transcriptr/bioconda_transcriptr.yaml +++ b/data/transcriptr/bioconda_transcriptr.yaml @@ -19,7 +19,6 @@ description: The differences in the RNA types being sequenced have an impact on home: https://bioconductor.org/packages/3.10/bioc/html/transcriptR.html identifiers: - biotools:transcriptr -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-transcriptr diff --git a/data/transcriptr/transcriptrbioschemas.jsonld b/data/transcriptr/transcriptrbioschemas.jsonld index 0aab4cc7c4c12..4697854a49ede 100644 --- a/data/transcriptr/transcriptrbioschemas.jsonld +++ b/data/transcriptr/transcriptrbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Armen R. Karapetyan", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "An R package for identifying and quantifying de novo continuous regions of transcription across the genome. The package uses ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs) to divide closely spaced transcripts into individually transcriped units.", "sc:license": "GPL-3.0", "sc:name": "transcriptR", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/transcriptR.html", diff --git a/data/transeq/transeqbioschemas.jsonld b/data/transeq/transeqbioschemas.jsonld index c858e43ee8cd7..61f926426648b 100644 --- a/data/transeq/transeqbioschemas.jsonld +++ b/data/transeq/transeqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK BBSRC", "UK MRC", - "Wellcome Trust" + "Wellcome Trust", + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Translate nucleic acid sequences.", "sc:funder": [ - "UK MRC", "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "transeq", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/transeq.html", "sc:version": "r6" diff --git a/data/transfind/transfindbioschemas.jsonld b/data/transfind/transfindbioschemas.jsonld index 05e942a44092c..3f59007df0792 100644 --- a/data/transfind/transfindbioschemas.jsonld +++ b/data/transfind/transfindbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "TransFind web server predicts transcription factor binding sites in promoter regions of co-regulated gene sets.", "sc:name": "TransFind", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://transfind.sys-bio.net/" } \ No newline at end of file diff --git a/data/transfold/transfoldbioschemas.jsonld b/data/transfold/transfoldbioschemas.jsonld index 3ffbb7b0f1f74..63997471a1771 100644 --- a/data/transfold/transfoldbioschemas.jsonld +++ b/data/transfold/transfoldbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "transFold predicts the super-secondary structure of transmembrane beta-barrel (TMB) proteins including side-chain orientation and topology of transmembrane segments.", "sc:name": "transFold", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioinformatics.bc.edu/clotelab/transFold" } \ No newline at end of file diff --git a/data/transit/transitbioschemas.jsonld b/data/transit/transitbioschemas.jsonld index 31cd37b898a53..4efa453897628 100644 --- a/data/transit/transitbioschemas.jsonld +++ b/data/transit/transitbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:description": "A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.", "sc:name": "TRANSIT", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://saclab.tamu.edu/essentiality/transit/" }, diff --git a/data/translate/translatebioschemas.jsonld b/data/translate/translatebioschemas.jsonld index a1957f2f5ced2..a20d0e54930f6 100644 --- a/data/translate/translatebioschemas.jsonld +++ b/data/translate/translatebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Translation of a nucleotide (DNA/RNA) sequence to a protein sequence.", "sc:name": "Translate", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://web.expasy.org/translate/" diff --git a/data/translatome/translatomebioschemas.jsonld b/data/translatome/translatomebioschemas.jsonld index a90034e512f51..a6f79727d73f0 100644 --- a/data/translatome/translatomebioschemas.jsonld +++ b/data/translatome/translatomebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/translatome", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Erik Dassi", - "Toma Tebaldi" + "Toma Tebaldi", + "Erik Dassi" ], "sc:additionalType": [ "Library", @@ -22,9 +22,9 @@ "sc:license": "GPL-3.0", "sc:name": "tRanslatome", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/tRanslatome.html", "sc:version": "1.16.0" diff --git a/data/translatorx/translatorxbioschemas.jsonld b/data/translatorx/translatorxbioschemas.jsonld index 649e5882eebec..94bce3bb91051 100644 --- a/data/translatorx/translatorxbioschemas.jsonld +++ b/data/translatorx/translatorxbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "TranslatorX", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://translatorx.co.uk" } \ No newline at end of file diff --git a/data/translig/transligbioschemas.jsonld b/data/translig/transligbioschemas.jsonld index 52ca1bd2c00bf..37a4ccd76dcf1 100644 --- a/data/translig/transligbioschemas.jsonld +++ b/data/translig/transligbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "TransLiG", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://sourceforge.net/projects/transcriptomeassembly/files/" } \ No newline at end of file diff --git a/data/transposons/transposonsbioschemas.jsonld b/data/transposons/transposonsbioschemas.jsonld index f64825ba998cc..6106eee26a279 100644 --- a/data/transposons/transposonsbioschemas.jsonld +++ b/data/transposons/transposonsbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/S41598-019-43403-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/Transposons", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Maria Poptsova", "sc:additionalType": "Script", "sc:citation": [ + "pmcid:PMC6510757", "pubmed:31076573", { "@id": "https://doi.org/10.1038/S41598-019-43403-3" - }, - "pmcid:PMC6510757" + } ], "sc:description": "Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models.", "sc:featureList": { @@ -32,11 +28,15 @@ "sc:license": "Unlicense", "sc:name": "Transposons", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/AlexShein/transposons/" + }, + { + "@id": "https://doi.org/10.1038/S41598-019-43403-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/transview/bioconda_transview.yaml b/data/transview/bioconda_transview.yaml index 12adcaef1e62d..3cb2121808bb3 100644 --- a/data/transview/bioconda_transview.yaml +++ b/data/transview/bioconda_transview.yaml @@ -4,7 +4,6 @@ description: This package provides efficient tools to generate, access and displ home: https://bioconductor.org/packages/3.10/bioc/html/TransView.html identifiers: - biotools:transview -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-transview diff --git a/data/transview/transviewbioschemas.jsonld b/data/transview/transviewbioschemas.jsonld index 2ca2ddcf772e4..bc27bfe44b40c 100644 --- a/data/transview/transviewbioschemas.jsonld +++ b/data/transview/transviewbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "TransView", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TransView.html", "sc:version": "1.22.0" diff --git a/data/trapid/trapidbioschemas.jsonld b/data/trapid/trapidbioschemas.jsonld index cbd9c03846f06..af9194e8437ac 100644 --- a/data/trapid/trapidbioschemas.jsonld +++ b/data/trapid/trapidbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Online tool for the fast, reliable and user-friendly analysis of de novo transcriptomes.", "sc:name": "TRAPID", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:provider": "PSB", "sc:url": "http://bioinformatics.psb.ugent.be/webtools/trapid/trapid/", diff --git a/data/trapline/traplinebioschemas.jsonld b/data/trapline/traplinebioschemas.jsonld index f87c56ce22932..05c68f80537da 100644 --- a/data/trapline/traplinebioschemas.jsonld +++ b/data/trapline/traplinebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "RNAseq data processing, evaluation, and prediction tool optimized for Illumina FASTQ reads, and other sequencing platforms like SOLiD or Solexa. Predictions are based on modules which are able to identify protein-protein interactions, miRNA targets and alternatively splicing variants or promoter enriched sites.", "sc:name": "TRAPLINE", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://www.sbi.uni-rostock.de/TRAPLINE", diff --git a/data/trapp/trappbioschemas.jsonld b/data/trapp/trappbioschemas.jsonld index 4b32a3f3a5730..094b4c0293034 100644 --- a/data/trapp/trappbioschemas.jsonld +++ b/data/trapp/trappbioschemas.jsonld @@ -9,22 +9,26 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKX277", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/trapp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Daria Kokh", { "@id": "http://orcid.org/0000-0001-5951-8670" - }, - "Daria Kokh" + } ], "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28431137", "pmcid:PMC5570179", { "@id": "https://doi.org/10.1093/NAR/GKX277" - } + }, + "pubmed:28431137" ], "sc:description": "TRAnsient Pockets in Proteins. Discovery of ligands that bind in transient subpockets in proteins. Explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion.", "sc:featureList": { @@ -33,15 +37,11 @@ "sc:name": "TRAPP", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://trapp.h-its.org/" }, - { - "@id": "https://doi.org/10.1093/NAR/GKX277", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0001-5951-8670", "@type": "schema:Person" diff --git a/data/trapr/traprbioschemas.jsonld b/data/trapr/traprbioschemas.jsonld index becf9858ece34..33c529893cbe4 100644 --- a/data/trapr/traprbioschemas.jsonld +++ b/data/trapr/traprbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.5808/GI.2017.15.1.51", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/trapr", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jae Hyun Lim", "sc:additionalType": "Library", "sc:citation": [ + "pubmed:28416950", "pmcid:PMC5389949", { "@id": "https://doi.org/10.5808/GI.2017.15.1.51" - }, - "pubmed:28416950" + } ], "sc:description": "Statistical analysis and visualization of RNA-Seq data.", "sc:featureList": { @@ -32,12 +28,16 @@ "sc:license": "GPL-2.0", "sc:name": "TRAPR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.snubi.org/software/trapr/", "sc:version": "1.0" + }, + { + "@id": "https://doi.org/10.5808/GI.2017.15.1.51", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/traser/traserbioschemas.jsonld b/data/traser/traserbioschemas.jsonld index 3661e84e218ce..3c720476f9b39 100644 --- a/data/traser/traserbioschemas.jsonld +++ b/data/traser/traserbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "li chen", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.", "sc:license": "GPL-3.0", "sc:name": "traseR", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/traseR.html", "sc:version": "1.4.0" diff --git a/data/trawlerweb/trawlerwebbioschemas.jsonld b/data/trawlerweb/trawlerwebbioschemas.jsonld index 293509cfff857..4f2b1d1b8d688 100644 --- a/data/trawlerweb/trawlerwebbioschemas.jsonld +++ b/data/trawlerweb/trawlerwebbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12864-018-4630-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/trawlerweb", "@type": "sc:SoftwareApplication", @@ -21,11 +25,11 @@ "Command-line tool" ], "sc:citation": [ - "pmcid:PMC5887194", + "pubmed:29621972", { "@id": "https://doi.org/10.1186/s12864-018-4630-0" }, - "pubmed:29621972" + "pmcid:PMC5887194" ], "sc:description": "De novo motif discovery tool for next-generation sequencing datasets.", "sc:featureList": { @@ -39,10 +43,6 @@ "Mac" ], "sc:url": "https://trawler.erc.monash.edu.au/" - }, - { - "@id": "https://doi.org/10.1186/s12864-018-4630-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/trc/trcbioschemas.jsonld b/data/trc/trcbioschemas.jsonld index 337d98fcdaccc..3e7bebfa00ac0 100644 --- a/data/trc/trcbioschemas.jsonld +++ b/data/trc/trcbioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "TRC", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sites.google.com/site/dhyeonyu/software" } \ No newline at end of file diff --git a/data/trdistiller/trdistillerbioschemas.jsonld b/data/trdistiller/trdistillerbioschemas.jsonld index b09cf300f675d..922a0d762dbaa 100644 --- a/data/trdistiller/trdistillerbioschemas.jsonld +++ b/data/trdistiller/trdistillerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A rapid filter that is based on the comparison of composition and order of short strings in the adjacent sequence motifs.", "sc:name": "TRDistiller", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinfo.montp.cnrs.fr/?r=TRDistiller" } \ No newline at end of file diff --git a/data/treat/treatbioschemas.jsonld b/data/treat/treatbioschemas.jsonld index 137725f5fbc0e..b884d0bba95e1 100644 --- a/data/treat/treatbioschemas.jsonld +++ b/data/treat/treatbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "An R package for detecting complex joint effects in case-control studies. The test statistic is derived from a tree-structure model by recursive partitioning the data. Ultra-fast algorithm is designed to evaluate the significance of association between candidate gene and disease outcome.", "sc:name": "TREAT", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://www.hanzhang.name/softwares/treat" diff --git a/data/treatable-id/treatable-idbioschemas.jsonld b/data/treatable-id/treatable-idbioschemas.jsonld index e36c60b011d98..4e5504be86bf9 100644 --- a/data/treatable-id/treatable-idbioschemas.jsonld +++ b/data/treatable-id/treatable-idbioschemas.jsonld @@ -19,18 +19,18 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:22824307", + "pmcid:PMC3458980", { "@id": "https://doi.org/10.1186/1750-1172-7-47" - }, - "pmcid:PMC3458980" + } ], "sc:description": "Interactive tool for the clinician and scientist presenting identified 81 inborn errors of metabolism which are causally related to Intellectual Disability and amenable to therapy.", "sc:license": "Other", "sc:name": "treatable-id", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://treatable-id.org" } diff --git a/data/tree-hmm/tree-hmmbioschemas.jsonld b/data/tree-hmm/tree-hmmbioschemas.jsonld index b4a9761fcd04d..081b3bd31d356 100644 --- a/data/tree-hmm/tree-hmmbioschemas.jsonld +++ b/data/tree-hmm/tree-hmmbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "An extension of the popular ChromHMM for doing clustering of epigenetic markers. Given a complete set of epigenetic markers for several cell types, and the phylogeny describing their relationship, Tree-HMM will perform approximate inference on the graphical model induced by connecting genomic positions of a certain cell type in a chain while also connecting different species according to the tree.", "sc:name": "Tree-HMM", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://cbcl.ics.uci.edu//doku.php/software#tree-hmm", "sc:version": "0.1.0" diff --git a/data/tree-puzzle/tree-puzzlebioschemas.jsonld b/data/tree-puzzle/tree-puzzlebioschemas.jsonld index 62f7b83b81c04..140058b156cd6 100644 --- a/data/tree-puzzle/tree-puzzlebioschemas.jsonld +++ b/data/tree-puzzle/tree-puzzlebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/tree-puzzle", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Heiko A. Schmidt", - "Arndt von Haeseler" + "Arndt von Haeseler", + "Heiko A. Schmidt" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:11934758", diff --git a/data/treecon/treeconbioschemas.jsonld b/data/treecon/treeconbioschemas.jsonld index 4547b33fa7fb9..d51c8581e6bbf 100644 --- a/data/treecon/treeconbioschemas.jsonld +++ b/data/treecon/treeconbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences.", "sc:name": "TREECON", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/TREECON", diff --git a/data/treedyn/treedynbioschemas.jsonld b/data/treedyn/treedynbioschemas.jsonld index d109befe39c01..cc890f245cb59 100644 --- a/data/treedyn/treedynbioschemas.jsonld +++ b/data/treedyn/treedynbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "François Chevenet", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:description": "Dynamic graphics and annotations for tree investigations.", "sc:license": "GPL-2.0", diff --git a/data/treeexp/treeexpbioschemas.jsonld b/data/treeexp/treeexpbioschemas.jsonld index b35ccffdc9f18..656fe9ca84da0 100644 --- a/data/treeexp/treeexpbioschemas.jsonld +++ b/data/treeexp/treeexpbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/TreeExp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Xun Gu", - "Hang Ruan" + "Hang Ruan", + "Xun Gu" ], "sc:additionalType": "Library", "sc:citation": "pubmed:31114853", @@ -21,8 +21,8 @@ "sc:name": "TreeExp", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/hr1912/TreeExp" } \ No newline at end of file diff --git a/data/treegibbssampler/treegibbssamplerbioschemas.jsonld b/data/treegibbssampler/treegibbssamplerbioschemas.jsonld index eee1b3f67c7ba..966ecd30d02df 100644 --- a/data/treegibbssampler/treegibbssamplerbioschemas.jsonld +++ b/data/treegibbssampler/treegibbssamplerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software for identifying motifs by simultaneously using the motif overrepresentation property and the motif evolutionary conservation property. It identifies motifs without depending on pre-aligned orthologous sequences, which makes it useful for the extraction of regulatory elements in multiple genomes of both closely related and distant species.", "sc:name": "TreeGibbsSampler", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://hulab.ucf.edu/software" } \ No newline at end of file diff --git a/data/treegraph_2/treegraph_2bioschemas.jsonld b/data/treegraph_2/treegraph_2bioschemas.jsonld index db8ff4b479559..9675d9c064b7b 100644 --- a/data/treegraph_2/treegraph_2bioschemas.jsonld +++ b/data/treegraph_2/treegraph_2bioschemas.jsonld @@ -23,8 +23,8 @@ "sc:license": "GPL-3.0", "sc:name": "TreeGraph 2", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://treegraph.bioinfweb.info/", diff --git a/data/treeio/treeiobioschemas.jsonld b/data/treeio/treeiobioschemas.jsonld index f7ffb59c8cbdf..a0ea9977be5c5 100644 --- a/data/treeio/treeiobioschemas.jsonld +++ b/data/treeio/treeiobioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "treeio", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/treeio.html", "sc:version": "1.4.2" diff --git a/data/treejuxtaposer/treejuxtaposerbioschemas.jsonld b/data/treejuxtaposer/treejuxtaposerbioschemas.jsonld index 6e8fbb32d87ce..bb6e8dd24b192 100644 --- a/data/treejuxtaposer/treejuxtaposerbioschemas.jsonld +++ b/data/treejuxtaposer/treejuxtaposerbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/treejuxtaposer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Mailing list", - "Bug report" + "Bug report", + "Mailing list" ], "sc:additionalType": "Web application", "sc:description": "TreeJuxtaposer is a free software tool that allows a visual comparison of two trees in Newick format (phylogenies, taxonomies, gene trees, etc.). It can work with trees having up to 500,000 nodes, and automatically calculates and marks the differences.", "sc:name": "TreeJuxtaposer", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://olduvai.sourceforge.net/" } \ No newline at end of file diff --git a/data/treeko/treekobioschemas.jsonld b/data/treeko/treekobioschemas.jsonld index e4e6d09fb215e..86431ad843182 100644 --- a/data/treeko/treekobioschemas.jsonld +++ b/data/treeko/treekobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "A python package that allows the comparison of any two phylogenetic tree topologies, even those with missing leaves and duplications", "sc:name": "TreeKO", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://treeko.cgenomics.org/" diff --git a/data/treeld/treeldbioschemas.jsonld b/data/treeld/treeldbioschemas.jsonld index f3eda3b625c38..f6958d1d0266e 100644 --- a/data/treeld/treeldbioschemas.jsonld +++ b/data/treeld/treeldbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "TreeLD", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sph.umich.edu/csg/software_pages/treeld.html" } \ No newline at end of file diff --git a/data/treeman/treemanbioschemas.jsonld b/data/treeman/treemanbioschemas.jsonld index 0a61f9c5e280c..23507b9bf3f82 100644 --- a/data/treeman/treemanbioschemas.jsonld +++ b/data/treeman/treemanbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s13104-016-2340-8", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/treeman", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Dominic J. Bennett", "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC5219798", { "@id": "https://doi.org/10.1186/s13104-016-2340-8" }, - "pubmed:28061884", - "pmcid:PMC5219798" + "pubmed:28061884" ], "sc:description": "An R package for manipulating phylogentic trees.", "sc:featureList": { @@ -32,10 +28,14 @@ "sc:license": "GPL-2.0", "sc:name": "treeman", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/DomBennett/TreeMan" + }, + { + "@id": "https://doi.org/10.1186/s13104-016-2340-8", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/treesaap/treesaapbioschemas.jsonld b/data/treesaap/treesaapbioschemas.jsonld index 194a53cfcc72e..1d88fe22fe326 100644 --- a/data/treesaap/treesaapbioschemas.jsonld +++ b/data/treesaap/treesaapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during clade-genesis, and performs goodness-of-fit and categorical statistical tests.", "sc:name": "TreeSAAP", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://dna.cs.byu.edu/treesaap/" diff --git a/data/treesample/treesamplebioschemas.jsonld b/data/treesample/treesamplebioschemas.jsonld index 22684688c13ab..50d8c460ba12b 100644 --- a/data/treesample/treesamplebioschemas.jsonld +++ b/data/treesample/treesamplebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A program for simulating phylogenetic trees with a fixed number of species.", "sc:name": "TreeSample", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "https://code.google.com/p/treesample/" } \ No newline at end of file diff --git a/data/treesim/treesimbioschemas.jsonld b/data/treesim/treesimbioschemas.jsonld index 5347ec7350fbe..95bb53f93e807 100644 --- a/data/treesim/treesimbioschemas.jsonld +++ b/data/treesim/treesimbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An R package for simulating phylogenetic trees.", "sc:name": "TreeSim", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://cran.r-project.org/web/packages/TreeSim/index.html" } \ No newline at end of file diff --git a/data/treevis/treevisbioschemas.jsonld b/data/treevis/treevisbioschemas.jsonld index 9af515615b632..0351b72d4241c 100644 --- a/data/treevis/treevisbioschemas.jsonld +++ b/data/treevis/treevisbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "New visualization algorithm to generate clear two-dimensional layouts of complex tree structures.", "sc:name": "TreeVis", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://pengqiu.gatech.edu/software/TreeVis/index.htm" } \ No newline at end of file diff --git a/data/treewas/treewasbioschemas.jsonld b/data/treewas/treewasbioschemas.jsonld index 06fdfa97fab1c..2519287ab11e5 100644 --- a/data/treewas/treewasbioschemas.jsonld +++ b/data/treewas/treewasbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes", "sc:name": "treeWAS", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://github.com/caitiecollins/treeWAS" } \ No newline at end of file diff --git a/data/tremap/tremapbioschemas.jsonld b/data/tremap/tremapbioschemas.jsonld index 820ff8e69c107..5fe8f5bdcdc70 100644 --- a/data/tremap/tremapbioschemas.jsonld +++ b/data/tremap/tremapbioschemas.jsonld @@ -9,42 +9,42 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1145/3233547.3233551", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/tREMAP", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Lei Xie", "sc:additionalType": "Script", "sc:citation": [ + "pubmed:31061989", + "pmcid:PMC6500446", { "@id": "https://doi.org/10.1145/3233547.3233551" - }, - "pmcid:PMC6500446", - "pubmed:31061989" + } ], "sc:description": "Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm.", "sc:featureList": [ { - "@id": "edam:operation_2492" + "@id": "edam:operation_0441" }, { - "@id": "edam:operation_3439" + "@id": "edam:operation_2492" }, { - "@id": "edam:operation_0441" + "@id": "edam:operation_3439" } ], "sc:license": "Unlicense", "sc:name": "tREMAP", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/hansaimlim/REMAP/tree/master/TriFacREMAP" - }, - { - "@id": "https://doi.org/10.1145/3233547.3233551", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/trend/trendbioschemas.jsonld b/data/trend/trendbioschemas.jsonld index d245a10f9c3c7..b013651210859 100644 --- a/data/trend/trendbioschemas.jsonld +++ b/data/trend/trendbioschemas.jsonld @@ -13,20 +13,16 @@ "@id": "http://orcid.org/0000-0002-0189-5833", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.1016/j.bpj.2016.12.018", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/trend", "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:citation": [ + "pmcid:PMC5266145", { "@id": "https://doi.org/10.1016/j.bpj.2016.12.018" }, - "pubmed:28122211", - "pmcid:PMC5266145" + "pubmed:28122211" ], "sc:contributor": { "@id": "http://orcid.org/0000-0002-0189-5833" @@ -43,6 +39,10 @@ "Mac" ], "sc:url": "https://biochem.missouri.edu/trend/" + }, + { + "@id": "https://doi.org/10.1016/j.bpj.2016.12.018", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/trendsceek/trendsceekbioschemas.jsonld b/data/trendsceek/trendsceekbioschemas.jsonld index 4c51948646572..bd02f39f2a0a4 100644 --- a/data/trendsceek/trendsceekbioschemas.jsonld +++ b/data/trendsceek/trendsceekbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Freeware", "sc:name": "trendsceek", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/edsgard/trendsceek" } \ No newline at end of file diff --git a/data/trendy/trendybioschemas.jsonld b/data/trendy/trendybioschemas.jsonld index f26c056232b93..1a256c9081528 100644 --- a/data/trendy/trendybioschemas.jsonld +++ b/data/trendy/trendybioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Trendy", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Trendy.html", "sc:version": "1.2.2" diff --git a/data/trespex/trespexbioschemas.jsonld b/data/trespex/trespexbioschemas.jsonld index 60b48c8289c27..5196f47c65c78 100644 --- a/data/trespex/trespexbioschemas.jsonld +++ b/data/trespex/trespexbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals.", "sc:name": "TreSpEx", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://annelida.de/research/bioinformatics/software/index.html" diff --git a/data/trf/trfbioschemas.jsonld b/data/trf/trfbioschemas.jsonld index 374239ba44eda..77153a7259db7 100644 --- a/data/trf/trfbioschemas.jsonld +++ b/data/trf/trfbioschemas.jsonld @@ -15,8 +15,8 @@ "Command-line tool" ], "sc:citation": [ - "pubmed:9862982", - "pmcid:PMC148217" + "pmcid:PMC148217", + "pubmed:9862982" ], "sc:description": "Tandem Repeats Finder. Find tandem repeats in DNA sequences without the need to specify either the pattern or pattern size. It uses the method of k-tuple matching to avoid the need for full scale alignment matrix computations. It requires no a priori knowledge of the pattern, pattern size or number of copies. There are no restrictions on the size of the repeats that can be detected. It determines a consensus pattern for the smallest repetitive unit in the tandem repeat.", "sc:license": "Other", diff --git a/data/tri_tool/tri_toolbioschemas.jsonld b/data/tri_tool/tri_toolbioschemas.jsonld index 31417406e8a1c..ee7a8078340e1 100644 --- a/data/tri_tool/tri_toolbioschemas.jsonld +++ b/data/tri_tool/tri_toolbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "TRI_tool", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.vin.bg.ac.rs/180/tools/tfpred.php" } \ No newline at end of file diff --git a/data/triagetools/triagetoolsbioschemas.jsonld b/data/triagetools/triagetoolsbioschemas.jsonld index 99e363094cb00..2e854f7bff8e9 100644 --- a/data/triagetools/triagetoolsbioschemas.jsonld +++ b/data/triagetools/triagetoolsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects.", "sc:name": "TriageTools", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://sourceforge.net/projects/triagetools/" } \ No newline at end of file diff --git a/data/trichdb/trichdbbioschemas.jsonld b/data/trichdb/trichdbbioschemas.jsonld index 10be7e82ed42d..246e0f83d776f 100644 --- a/data/trichdb/trichdbbioschemas.jsonld +++ b/data/trichdb/trichdbbioschemas.jsonld @@ -27,11 +27,11 @@ "@id": "edam:topic_0621" }, "sc:citation": [ - "pmcid:PMC2686445", - "pubmed:18824479", { "@id": "https://doi.org/10.1093/nar/gkn631" - } + }, + "pubmed:18824479", + "pmcid:PMC2686445" ], "sc:description": "Genomic-scale datasets associated with the eukaryotic Trichomonas.", "sc:featureList": { @@ -39,9 +39,9 @@ }, "sc:name": "Trichomonas genome resources (TrichDB)", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://trichdb.org/trichdb/" } diff --git a/data/tridamp/tridampbioschemas.jsonld b/data/tridamp/tridampbioschemas.jsonld index 5cabcd3d8f89b..159d4f56c4760 100644 --- a/data/tridamp/tridampbioschemas.jsonld +++ b/data/tridamp/tridampbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A MathDAMP extension for the visualization of three-way comparisons between metabolite profiles. An intuitive color-coding is used to represent the three-way differences on density plots.", "sc:name": "TriDAMP", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://mathdamp.iab.keio.ac.jp/tridamp/" } \ No newline at end of file diff --git a/data/trifle/triflebioschemas.jsonld b/data/trifle/triflebioschemas.jsonld index 32359e057081f..c7be14ca2159d 100644 --- a/data/trifle/triflebioschemas.jsonld +++ b/data/trifle/triflebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "TRiFLe is a program for simulating TRFs and identifying species by TRF profiling", "sc:name": "TriFLe", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://cegg.unige.ch/trifle_docs" } \ No newline at end of file diff --git a/data/triform/triformbioschemas.jsonld b/data/triform/triformbioschemas.jsonld index 82badc191cec5..fcccecd7f3b1f 100644 --- a/data/triform/triformbioschemas.jsonld +++ b/data/triform/triformbioschemas.jsonld @@ -14,12 +14,12 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Thomas Carroll", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:22827163", "pmcid:PMC3480842", + "pubmed:22827163", { "@id": "https://doi.org/10.1186/1471-2105-13-176" } @@ -29,21 +29,21 @@ { "@id": "edam:operation_3501" }, - { - "@id": "edam:operation_2238" - }, { "@id": "edam:operation_3222" }, { "@id": "edam:operation_0445" + }, + { + "@id": "edam:operation_2238" } ], "sc:license": "GPL-2.0", "sc:name": "triform", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/triform.html", diff --git a/data/trifusion/trifusionbioschemas.jsonld b/data/trifusion/trifusionbioschemas.jsonld index f1bbc1b593067..2d93bf21d9689 100644 --- a/data/trifusion/trifusionbioschemas.jsonld +++ b/data/trifusion/trifusionbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:license": "GPL-3.0", "sc:name": "TriFusion", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://odiogosilva.github.io/TriFusion/", "sc:version": "0.5.0" diff --git a/data/trigger/bioconda_trigger.yaml b/data/trigger/bioconda_trigger.yaml index d824f280d73ac..401d103bb4eb3 100644 --- a/data/trigger/bioconda_trigger.yaml +++ b/data/trigger/bioconda_trigger.yaml @@ -11,7 +11,6 @@ description: 'This R package provides tools for the statistical analysis of inte home: https://bioconductor.org/packages/3.10/bioc/html/trigger.html identifiers: - biotools:trigger -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-trigger diff --git a/data/trigger/triggerbioschemas.jsonld b/data/trigger/triggerbioschemas.jsonld index 6d52eca78f814..4c67b7a24e8a0 100644 --- a/data/trigger/triggerbioschemas.jsonld +++ b/data/trigger/triggerbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "trigger", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/trigger.html", "sc:version": "1.24.0" diff --git a/data/trimadaptor/trimadaptorbioschemas.jsonld b/data/trimadaptor/trimadaptorbioschemas.jsonld index dc18423467a2d..ce0b70205e1f8 100644 --- a/data/trimadaptor/trimadaptorbioschemas.jsonld +++ b/data/trimadaptor/trimadaptorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Remove the 3' adaptor of a list of reads.", "sc:name": "trimadaptor", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/trimal/trimalbioschemas.jsonld b/data/trimal/trimalbioschemas.jsonld index c2663e0bb2e17..0b08756fc0b9f 100644 --- a/data/trimal/trimalbioschemas.jsonld +++ b/data/trimal/trimalbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.", "sc:name": "trimAl", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://trimal.cgenomics.org", "sc:version": "1.4" diff --git a/data/trimest/trimestbioschemas.jsonld b/data/trimest/trimestbioschemas.jsonld index c02f2e3868b92..0e10528d5e938 100644 --- a/data/trimest/trimestbioschemas.jsonld +++ b/data/trimest/trimestbioschemas.jsonld @@ -13,15 +13,15 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", + "EMBOSS Contributors", "Wellcome Trust", - "UK MRC", - "EMBOSS Contributors" + "UK MRC" ], "sc:description": "Remove poly-A tails from nucleotide sequences.", "sc:funder": [ - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "trimest", diff --git a/data/trimitomics/trimitomicsbioschemas.jsonld b/data/trimitomics/trimitomicsbioschemas.jsonld index 5a40caec96c09..974c3a25042cf 100644 --- a/data/trimitomics/trimitomicsbioschemas.jsonld +++ b/data/trimitomics/trimitomicsbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/Trimitomics", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Ana Riesgo", - "Bruna Plese" + "Bruna Plese", + "Ana Riesgo" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:31070854", @@ -21,8 +21,8 @@ "sc:name": "Trimitomics", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/bplese/Trimitomics" } \ No newline at end of file diff --git a/data/trimseq/trimseqbioschemas.jsonld b/data/trimseq/trimseqbioschemas.jsonld index 6b9ee33cd7332..ac70ba860abc7 100644 --- a/data/trimseq/trimseqbioschemas.jsonld +++ b/data/trimseq/trimseqbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK BBSRC", "UK MRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK BBSRC", + "Wellcome Trust" ], "sc:description": "Remove unwanted characters from start and end of sequence(s).", "sc:funder": [ - "UK MRC", "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "trimseq", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/trimseq.html", "sc:version": "r6" diff --git a/data/trimsequences/trimsequencesbioschemas.jsonld b/data/trimsequences/trimsequencesbioschemas.jsonld index 2e731ec7a1e02..5bf395c479c22 100644 --- a/data/trimsequences/trimsequencesbioschemas.jsonld +++ b/data/trimsequences/trimsequencesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Remove the 5' and/or 3' adaptors of a list of reads.", "sc:name": "trimsequences", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://urgi.versailles.inra.fr/Tools/REPET", "sc:version": "1.0.0" diff --git a/data/trimspace/trimspacebioschemas.jsonld b/data/trimspace/trimspacebioschemas.jsonld index 22c62d88cb0cd..312ae70ac69da 100644 --- a/data/trimspace/trimspacebioschemas.jsonld +++ b/data/trimspace/trimspacebioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ + "UK BBSRC", "Wellcome Trust", - "EMBOSS Contributors", "UK MRC", - "UK BBSRC" + "EMBOSS Contributors" ], "sc:description": "Remove extra whitespace from an ASCII text file.", "sc:funder": [ + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "trimspace", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/trimspace.html", "sc:version": "r6" diff --git a/data/trinculo/trinculobioschemas.jsonld b/data/trinculo/trinculobioschemas.jsonld index 869ed90eeeed4..161d89f43ad8b 100644 --- a/data/trinculo/trinculobioschemas.jsonld +++ b/data/trinculo/trinculobioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Program that implements a wide range of multinomial analyses in a single fast package that is designed to be easy to use by users of standard genome-wide association study software.", "sc:name": "Trinculo", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/trinculo/" } \ No newline at end of file diff --git a/data/trinity/trinitybioschemas.jsonld b/data/trinity/trinitybioschemas.jsonld index 849e277f597c9..d721ac3258df9 100644 --- a/data/trinity/trinitybioschemas.jsonld +++ b/data/trinity/trinitybioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/trinity", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Aviv Regev", - "Nir Friedman" + "Nir Friedman", + "Aviv Regev" ], "sc:additionalType": "Suite", "sc:citation": "pubmed:21572440", diff --git a/data/trinotate/trinotatebioschemas.jsonld b/data/trinotate/trinotatebioschemas.jsonld index d5c05fefdac4d..95f908bd5d97c 100644 --- a/data/trinotate/trinotatebioschemas.jsonld +++ b/data/trinotate/trinotatebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1016/j.celrep.2016.12.063", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/trinotate", "@type": "sc:SoftwareApplication", @@ -21,11 +17,11 @@ "Suite" ], "sc:citation": [ + "pubmed:28099853", + "pmcid:PMC5419050", { "@id": "https://doi.org/10.1016/j.celrep.2016.12.063" - }, - "pubmed:28099853", - "pmcid:PMC5419050" + } ], "sc:description": "Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.", "sc:featureList": { @@ -33,6 +29,10 @@ }, "sc:name": "Trinotate", "sc:url": "https://github.com/Trinotate/Trinotate.github.io" + }, + { + "@id": "https://doi.org/10.1016/j.celrep.2016.12.063", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/trio/bioconda_trio.yaml b/data/trio/bioconda_trio.yaml index 871ed661e2d75..bafb9f6933c31 100644 --- a/data/trio/bioconda_trio.yaml +++ b/data/trio/bioconda_trio.yaml @@ -8,7 +8,6 @@ description: Testing SNPs and SNP interactions with a genotypic TDT. This packag home: https://bioconductor.org/packages/3.10/bioc/html/trio.html identifiers: - biotools:trio -- doi:10.1038/nmeth.3252 license: LGPL-2 license_file: /lib/R/share/licenses/LGPL-2 name: bioconductor-trio diff --git a/data/trio/triobioschemas.jsonld b/data/trio/triobioschemas.jsonld index d65f39b2cf5c4..9e60aa7e5e1fb 100644 --- a/data/trio/triobioschemas.jsonld +++ b/data/trio/triobioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Holger Schwender", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.", "sc:license": "GPL-2.0", "sc:name": "trio", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/trio.html", "sc:version": "3.16.0" diff --git a/data/triocaller/triocallerbioschemas.jsonld b/data/triocaller/triocallerbioschemas.jsonld index 711f59bc9284d..a68122c4d2a06 100644 --- a/data/triocaller/triocallerbioschemas.jsonld +++ b/data/triocaller/triocallerbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/triocaller", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Goncalo Abecasis", - "Wei Chen" + "Wei Chen", + "Goncalo Abecasis" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:26772743", diff --git a/data/tripal/tripalbioschemas.jsonld b/data/tripal/tripalbioschemas.jsonld index f4f87e8d941fd..4db09f5f31bb4 100644 --- a/data/tripal/tripalbioschemas.jsonld +++ b/data/tripal/tripalbioschemas.jsonld @@ -9,27 +9,27 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/DATABASE/BAT075", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/tripal", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support Forum", "sc:additionalType": "Suite", "sc:citation": [ + "pubmed:21959868", "pmcid:PMC3808541", - "pubmed:24163125", { "@id": "https://doi.org/10.1093/DATABASE/BAT075" }, - "pubmed:21959868" + "pubmed:24163125" ], "sc:description": "Tripal is a collection of open-source, freely-available Drupal modules that serves as a web interface for a GMOD Chado database. It is designed to allow anyone with genomic data to quickly create an online genomic database using community supported tools. Tripal is part of the open-source tool collection available through the Generic Model Organism Database (GMOD) project.", "sc:name": "Tripal", "sc:operatingSystem": "Linux", "sc:url": "http://tripal.sourceforge.net/" - }, - { - "@id": "https://doi.org/10.1093/DATABASE/BAT075", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tripal_elasticsearch/tripal_elasticsearchbioschemas.jsonld b/data/tripal_elasticsearch/tripal_elasticsearchbioschemas.jsonld index c2c4a497c8e55..508ce5cf5e91f 100644 --- a/data/tripal_elasticsearch/tripal_elasticsearchbioschemas.jsonld +++ b/data/tripal_elasticsearch/tripal_elasticsearchbioschemas.jsonld @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "Tripal Elasticsearch", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/tripal/tripal_elasticsearch" } diff --git a/data/triplex/triplexbioschemas.jsonld b/data/triplex/triplexbioschemas.jsonld index 1dd3598cf7911..b03f3fe7ae205 100644 --- a/data/triplex/triplexbioschemas.jsonld +++ b/data/triplex/triplexbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-3321-9629", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/triplex", "@type": "sc:SoftwareApplication", @@ -24,16 +28,12 @@ "sc:license": "BSD-4-Clause", "sc:name": "triplex", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/triplex.html", "sc:version": "1.14.0" - }, - { - "@id": "http://orcid.org/0000-0002-3321-9629", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/triplexrna/triplexrnabioschemas.jsonld b/data/triplexrna/triplexrnabioschemas.jsonld index d06cc1ee27730..43de345f7c82d 100644 --- a/data/triplexrna/triplexrnabioschemas.jsonld +++ b/data/triplexrna/triplexrnabioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Database of cooperating miRNAs and their mutual targets which enables researchers explore novel patterns in gene regulation.", "sc:name": "TriplexRNA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://triplexrna.org" } \ No newline at end of file diff --git a/data/tripoint/tripointbioschemas.jsonld b/data/tripoint/tripointbioschemas.jsonld index a3ff918884def..73aaf3cf378bd 100644 --- a/data/tripoint/tripointbioschemas.jsonld +++ b/data/tripoint/tripointbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "TriPOINT", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.uconn.edu/ajt06004/TriPOINT" } \ No newline at end of file diff --git a/data/tritex/tritexbioschemas.jsonld b/data/tritex/tritexbioschemas.jsonld index 5fab30e2652c0..b9edb40d00c70 100644 --- a/data/tritex/tritexbioschemas.jsonld +++ b/data/tritex/tritexbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "TRITEX", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://tritexassembly.bitbucket.io" } \ No newline at end of file diff --git a/data/trnadb-ce/trnadb-cebioschemas.jsonld b/data/trnadb-ce/trnadb-cebioschemas.jsonld index 636d54ee74cc5..e711d0a32b486 100644 --- a/data/trnadb-ce/trnadb-cebioschemas.jsonld +++ b/data/trnadb-ce/trnadb-cebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "The tRNA Gene DataBase Curated by Experts \"\"tRNADB-CE\"\" contains tRNA sequences.", "sc:name": "tRNADB-CE", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://trna.nagahama-i-bio.ac.jp" diff --git a/data/trnamodpred/trnamodpredbioschemas.jsonld b/data/trnamodpred/trnamodpredbioschemas.jsonld index 7fb9e37e65025..ccc8621af6992 100644 --- a/data/trnamodpred/trnamodpredbioschemas.jsonld +++ b/data/trnamodpred/trnamodpredbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/trnamodpred", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Magdalena Machnicka", - "Janusz Bujnicki" + "Janusz Bujnicki", + "Magdalena Machnicka" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:27016142", "sc:description": "A method for predicting modifications in tRNA using the MODOMICS database of RNA modification pathways as a reference.", "sc:name": "tRNAmodpred", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://genesilico.pl/trnamodpred/" } \ No newline at end of file diff --git a/data/trnascan-se/trnascan-sebioschemas.jsonld b/data/trnascan-se/trnascan-sebioschemas.jsonld index e7bfe2efc8114..0eaeb914d7a17 100644 --- a/data/trnascan-se/trnascan-sebioschemas.jsonld +++ b/data/trnascan-se/trnascan-sebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A program for improved detection of transfer RNA genes in genomic sequence.", "sc:name": "Trnascan-SE", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://trna.ucsc.edu/tRNAscan-SE/" } \ No newline at end of file diff --git a/data/trnascanimport/trnascanimportbioschemas.jsonld b/data/trnascanimport/trnascanimportbioschemas.jsonld index bebb28e282f1c..705fd971b6faf 100644 --- a/data/trnascanimport/trnascanimportbioschemas.jsonld +++ b/data/trnascanimport/trnascanimportbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "tRNAscanImport", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/tRNAscanImport.html", "sc:version": "1.0.1" diff --git a/data/trnaviz/trnavizbioschemas.jsonld b/data/trnaviz/trnavizbioschemas.jsonld index 90e441c0807f2..b061bb5110d70 100644 --- a/data/trnaviz/trnavizbioschemas.jsonld +++ b/data/trnaviz/trnavizbioschemas.jsonld @@ -17,8 +17,8 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31127306", "pmcid:PMC6602477", + "pubmed:31127306", { "@id": "https://doi.org/10.1093/NAR/GKZ438" } @@ -35,9 +35,9 @@ "sc:license": "GPL-3.0", "sc:name": "tRNAviz", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://trna.ucsc.edu/tRNAviz/summary/" }, diff --git a/data/trod/trodbioschemas.jsonld b/data/trod/trodbioschemas.jsonld index 0b45c845e6e99..182df9ef3fbb9 100644 --- a/data/trod/trodbioschemas.jsonld +++ b/data/trod/trodbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.", "sc:name": "TROD", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.cellbio.unige.ch/RNAi.html" } \ No newline at end of file diff --git a/data/trom/trombioschemas.jsonld b/data/trom/trombioschemas.jsonld index 44df1702bced7..47120205f8a33 100644 --- a/data/trom/trombioschemas.jsonld +++ b/data/trom/trombioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1007/s12561-016-9163-y", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/trom", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jingyi Jessica Li", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5542419", + "pubmed:28781712", { "@id": "https://doi.org/10.1007/s12561-016-9163-y" }, - "pubmed:28781712" + "pmcid:PMC5542419" ], "sc:description": "TROM (Transcriptome Overlap Measure) is an R package for comparing transcriptomes within or between different species, and provide a different perspective, in contrast to traditional correlation analyses, about capturing transcriptomic similarity.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "GPL-2.0", "sc:name": "TROM", "sc:operatingSystem": [ - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.stat.ucla.edu/~jingyi.li/software-and-data/trom.html", "sc:version": "1.3" - }, - { - "@id": "https://doi.org/10.1007/s12561-016-9163-y", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tromer/tromerbioschemas.jsonld b/data/tromer/tromerbioschemas.jsonld index ef32ca1fb6efc..518cbea652d8d 100644 --- a/data/tromer/tromerbioschemas.jsonld +++ b/data/tromer/tromerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The transcriptome analyser project aims to provide tools to determine and document all the transcribed parts of a genome. The transcribed parts are defined by analysing experimental evidence, like expressed sequence tags (EST) and other mRNA sequences.", "sc:name": "tromer", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://ccg.vital-it.ch/tromer/" } \ No newline at end of file diff --git a/data/tronco/troncobioschemas.jsonld b/data/tronco/troncobioschemas.jsonld index 9f343271c57cd..4c4c19ae45ec2 100644 --- a/data/tronco/troncobioschemas.jsonld +++ b/data/tronco/troncobioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/bioinformatics/btw035", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/tronco", "@type": "sc:SoftwareApplication", @@ -32,10 +36,6 @@ "sc:provider": "ELIXIR-ITA-BICOCCA", "sc:url": "https://sites.google.com/site/troncopackage/", "sc:version": "2" - }, - { - "@id": "https://doi.org/10.1093/bioinformatics/btw035", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/trove/trovebioschemas.jsonld b/data/trove/trovebioschemas.jsonld index 25f7c93168336..de2aee0017ebb 100644 --- a/data/trove/trovebioschemas.jsonld +++ b/data/trove/trovebioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/TROVE", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Huey Eng Chua", - "Sourav S. Bhowmick" + "Sourav S. Bhowmick", + "Huey Eng Chua" ], "sc:additionalType": "Desktop application", "sc:description": "Tool for visualizing and analyzing cancer hallmarks in signaling networks.", "sc:license": "EPL-1.0", "sc:name": "TROVE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://github.com/trove2017/Trove" } \ No newline at end of file diff --git a/data/trumpet/trumpetbioschemas.jsonld b/data/trumpet/trumpetbioschemas.jsonld index 194e652df2afc..54b9c0d64c95a 100644 --- a/data/trumpet/trumpetbioschemas.jsonld +++ b/data/trumpet/trumpetbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "trumpet", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://github.com/skyhorsetomoon/Trumpet", "sc:version": "0.3.6" diff --git a/data/tscan/tscanbioschemas.jsonld b/data/tscan/tscanbioschemas.jsonld index 17e8fdde0048f..681a95de266ff 100644 --- a/data/tscan/tscanbioschemas.jsonld +++ b/data/tscan/tscanbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "TSCAN", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TSCAN.html", "sc:version": "1.16.0" diff --git a/data/tsdd/tsddbioschemas.jsonld b/data/tsdd/tsddbioschemas.jsonld index 51709cf23b81a..94c2851d7e72e 100644 --- a/data/tsdd/tsddbioschemas.jsonld +++ b/data/tsdd/tsddbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "TSDD", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html" diff --git a/data/tsema/tsemabioschemas.jsonld b/data/tsema/tsemabioschemas.jsonld index 85f9407ec3541..05dc2be33f774 100644 --- a/data/tsema/tsemabioschemas.jsonld +++ b/data/tsema/tsemabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Server for Efficient Mapping Assessment (TSEMA) predicts possible protein-protein interactions based on the comparision of phylogenetic trees derived from sequences of associated protein families.", "sc:name": "TSEMA", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://tsema.bioinfo.cnio.es/" } \ No newline at end of file diff --git a/data/tsir/tsirbioschemas.jsonld b/data/tsir/tsirbioschemas.jsonld index 444a846199c8d..0de65e2ef74a9 100644 --- a/data/tsir/tsirbioschemas.jsonld +++ b/data/tsir/tsirbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "tsiR", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/adbecker/tsiR" } \ No newline at end of file diff --git a/data/tsis/tsisbioschemas.jsonld b/data/tsis/tsisbioschemas.jsonld index d46b99df00c03..6f1486dd98852 100644 --- a/data/tsis/tsisbioschemas.jsonld +++ b/data/tsis/tsisbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Infer alternative splicing isoform switches for time-series data.", "sc:name": "TSIS", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://github.com/wyguo/TSIS" diff --git a/data/tsni/tsnibioschemas.jsonld b/data/tsni/tsnibioschemas.jsonld index fb80f72f8011d..584ecdf33772c 100644 --- a/data/tsni/tsnibioschemas.jsonld +++ b/data/tsni/tsnibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The algorithm can infer the local network of gene-gene interactions surrounding a gene of interest from time-series gene expression profiles.", "sc:name": "TSNI", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://dibernardo.tigem.it/softwares/time-series-network-identification-tsni" } \ No newline at end of file diff --git a/data/tspair/tspairbioschemas.jsonld b/data/tspair/tspairbioschemas.jsonld index 4c76241b61117..a45fe0ac2390d 100644 --- a/data/tspair/tspairbioschemas.jsonld +++ b/data/tspair/tspairbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jeffrey T. Leek", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "These functions calculate the pair of genes that show the maximum difference in ranking between two user specified groups. This \"top scoring pair\" maximizes the average of sensitivity and specificity over all rank based classifiers using a pair of genes in the data set. The advantage of this method is that the classifiers are much simpler and often easily interpretable and if arrays can be classified using only a pair of genes, PCR based tests could be used for classification of samples.", "sc:license": "GPL-2.0", "sc:name": "tspair", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/tspair.html", "sc:version": "1.36.0" diff --git a/data/tspmap/tspmapbioschemas.jsonld b/data/tspmap/tspmapbioschemas.jsonld index 1c8151f307ffe..7d42d5e85d8c3 100644 --- a/data/tspmap/tspmapbioschemas.jsonld +++ b/data/tspmap/tspmapbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s13040-017-0158-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/tspmap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "J. Grey Monroe", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:29270228", { "@id": "https://doi.org/10.1186/s13040-017-0158-0" }, - "pmcid:PMC5735504", - "pubmed:29270228" + "pmcid:PMC5735504" ], "sc:description": "Method which implements both approximate and exact Traveling Salesperson Problem solvers to generate linkage maps.", "sc:featureList": { @@ -27,14 +31,10 @@ }, "sc:name": "TSPmap", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/mckaylab/TSPmap" - }, - { - "@id": "https://doi.org/10.1186/s13040-017-0158-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tsrchitect/tsrchitectbioschemas.jsonld b/data/tsrchitect/tsrchitectbioschemas.jsonld index 196ff69b1a896..d67784928464c 100644 --- a/data/tsrchitect/tsrchitectbioschemas.jsonld +++ b/data/tsrchitect/tsrchitectbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-3.0", "sc:name": "TSRchitect", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TSRchitect.html", diff --git a/data/tssar/tssarbioschemas.jsonld b/data/tssar/tssarbioschemas.jsonld index 74f6b73934862..89092238b6d0f 100644 --- a/data/tssar/tssarbioschemas.jsonld +++ b/data/tssar/tssarbioschemas.jsonld @@ -9,24 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-15-89", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/tssar", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": [ - "Desktop application", - "Web application" + "Web application", + "Desktop application" ], "sc:citation": [ "pmcid:PMC4098767", + "pubmed:24674136", { "@id": "https://doi.org/10.1186/1471-2105-15-89" - }, - "pubmed:24674136" + } ], "sc:description": "A tool for automated de novo TSS annotation from dRNA-seq data that respects the statistics of dRNA-seq libraries.", "sc:featureList": { @@ -34,11 +30,15 @@ }, "sc:name": "TSSAR", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://rna.tbi.univie.ac.at/TSSAR" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-15-89", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tssv/tssvbioschemas.jsonld b/data/tssv/tssvbioschemas.jsonld index 35a5e3cb11b3f..ea5203b843d9b 100644 --- a/data/tssv/tssvbioschemas.jsonld +++ b/data/tssv/tssvbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Program that does targeted characterisation of short structural variation. It can be used for STR analysis, or any other type of targeted analysis. It characterises any variation between a set of user-defined markers.", "sc:name": "TSSV", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://git.lumc.nl/j.f.j.laros/tssv/blob/master/README.md" } \ No newline at end of file diff --git a/data/ttd/ttdbioschemas.jsonld b/data/ttd/ttdbioschemas.jsonld index 72e4c1a45e051..20e5d118f20bd 100644 --- a/data/ttd/ttdbioschemas.jsonld +++ b/data/ttd/ttdbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Therapeutic Target Database (TTD) has been developed to provide information about therapeutic targets and corresponding drugs. TTD includes information about successful, clinical trial and research targets, approved, clinical trial and experimental drugs linked to their primary targets, new ways to access data by drug mode of action, recursive search of related targets or drugs, similarity target and drug searching, customized and whole data download, and standardized target ID.", "sc:name": "TTD", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://bidd.nus.edu.sg/group/cjttd/" } \ No newline at end of file diff --git a/data/tts_mapping/tts_mappingbioschemas.jsonld b/data/tts_mapping/tts_mappingbioschemas.jsonld index 15e5d549fb7f9..a3e1945db755a 100644 --- a/data/tts_mapping/tts_mappingbioschemas.jsonld +++ b/data/tts_mapping/tts_mappingbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "TTS mapping", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://ggeda.bii.a-star.edu.sg/~piroonj/TTS_mapping/TTS_mapping.php" } \ No newline at end of file diff --git a/data/tuberq/tuberqbioschemas.jsonld b/data/tuberq/tuberqbioschemas.jsonld index a7deb45670a87..0759cffa9e7ad 100644 --- a/data/tuberq/tuberqbioschemas.jsonld +++ b/data/tuberq/tuberqbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/database/bau035", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/tuberq", "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ - "pmcid:PMC4014675", + "pubmed:24816183", { "@id": "https://doi.org/10.1093/database/bau035" }, - "pubmed:24816183" + "pmcid:PMC4014675" ], "sc:description": "Mycobacterium tuberculosis protein druggability database", "sc:featureList": { @@ -27,10 +31,6 @@ "sc:name": "TuberQ", "sc:url": "http://tuberq.proteinq.com.ar/", "sc:version": "1.4.3" - }, - { - "@id": "https://doi.org/10.1093/database/bau035", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tuiuiu/tuiuiubioschemas.jsonld b/data/tuiuiu/tuiuiubioschemas.jsonld index 55928ad529d15..e2b6bef51e3a8 100644 --- a/data/tuiuiu/tuiuiubioschemas.jsonld +++ b/data/tuiuiu/tuiuiubioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Filter designed for multiple repeats and for dealing with error rates greater than 10% of the repeats length.", "sc:name": "Tuiuiu", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://training.genouest.org/claroline/claroline/learnPath/learningPathList.php?cidReset=true&cidReq=TUIUIU", "sc:version": "1" diff --git a/data/tulip/tulipbioschemas.jsonld b/data/tulip/tulipbioschemas.jsonld index 4dacc89c6a584..604b329325251 100644 --- a/data/tulip/tulipbioschemas.jsonld +++ b/data/tulip/tulipbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Tulip", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "https://github.com/gymreklab/Tulip" } \ No newline at end of file diff --git a/data/tumorcnv/tumorcnvbioschemas.jsonld b/data/tumorcnv/tumorcnvbioschemas.jsonld index d0f8150990f11..819bbb92d6242 100644 --- a/data/tumorcnv/tumorcnvbioschemas.jsonld +++ b/data/tumorcnv/tumorcnvbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "MIT", "sc:name": "TumorCNV", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/yongzhuang/TumorCNV" } \ No newline at end of file diff --git a/data/tumorhpd/tumorhpdbioschemas.jsonld b/data/tumorhpd/tumorhpdbioschemas.jsonld index 7f53146c19fef..d54199f9930ed 100644 --- a/data/tumorhpd/tumorhpdbioschemas.jsonld +++ b/data/tumorhpd/tumorhpdbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web server for predicting and designing tumor homing peptides. This server is extremely useful for the researchers working in the field of therapeutic peptides.", "sc:name": "TumorHPD", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://crdd.osdd.net/raghava/tumorhpd/" } \ No newline at end of file diff --git a/data/turbonorm/turbonormbioschemas.jsonld b/data/turbonorm/turbonormbioschemas.jsonld index 1f25d7aaaff0f..34f09d18d3b05 100644 --- a/data/turbonorm/turbonormbioschemas.jsonld +++ b/data/turbonorm/turbonormbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-3.0", "sc:name": "TurboNorm", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TurboNorm.html", "sc:version": "1.26.0" diff --git a/data/turf-e/turf-ebioschemas.jsonld b/data/turf-e/turf-ebioschemas.jsonld index 6dfc3dbccadbd..442be1faf6eab 100644 --- a/data/turf-e/turf-ebioschemas.jsonld +++ b/data/turf-e/turf-ebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Program for SNP interaction filtering. Could be directly applied to GWA datasets with millions of SNPs.", "sc:name": "TuRF-E", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://code.google.com/p/ensemble-of-filters/" } \ No newline at end of file diff --git a/data/tvt_viewer/tvt_viewerbioschemas.jsonld b/data/tvt_viewer/tvt_viewerbioschemas.jsonld index 5c5b66f8d37f2..f540d54d4c206 100644 --- a/data/tvt_viewer/tvt_viewerbioschemas.jsonld +++ b/data/tvt_viewer/tvt_viewerbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "Unlicense", "sc:name": "TVT viewer", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://elk.med.harvard.edu/gfy/www/modules/single_standard" } \ No newline at end of file diff --git a/data/tvtb/bioconda_tvtb.yaml b/data/tvtb/bioconda_tvtb.yaml index 5967c82876dc5..9eb60d4823054 100644 --- a/data/tvtb/bioconda_tvtb.yaml +++ b/data/tvtb/bioconda_tvtb.yaml @@ -7,7 +7,6 @@ description: The package provides S4 classes and methods to filter, summarise an home: https://bioconductor.org/packages/3.10/bioc/html/TVTB.html identifiers: - biotools:tvtb -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-tvtb summary: 'TVTB: The VCF Tool Box' diff --git a/data/tvtb/tvtbbioschemas.jsonld b/data/tvtb/tvtbbioschemas.jsonld index 6d2d995d4f6a8..ca7a52f07e456 100644 --- a/data/tvtb/tvtbbioschemas.jsonld +++ b/data/tvtb/tvtbbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Kevin Rue-Albrecht", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The VCF Tool Box (TVTB) is a suite of S4 classes and methods for filtering, summarizing and visualizing genetic variation data stored in VCF files. Functionalities are integrated and demonstrated in a programming free Shiny web-application, the Shiny Variant Explorer (tSVE).", "sc:license": "Artistic-2.0", "sc:name": "TVTB", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TVTB.html", "sc:version": "1.4.0" diff --git a/data/tweedeseq/tweedeseqbioschemas.jsonld b/data/tweedeseq/tweedeseqbioschemas.jsonld index d1c765d94eb00..bc8b830f413d7 100644 --- a/data/tweedeseq/tweedeseqbioschemas.jsonld +++ b/data/tweedeseq/tweedeseqbioschemas.jsonld @@ -18,26 +18,26 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Juan R Gonzalez", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ - "pubmed:23965047", { "@id": "https://doi.org/10.1186/1471-2105-14-254" }, - "pmcid:PMC3849762" + "pmcid:PMC3849762", + "pubmed:23965047" ], "sc:description": "An R package for analyzing differential expression from RNA-seq data using the Poisson-Tweedie family of distributions.", "sc:featureList": [ { - "@id": "edam:operation_2238" + "@id": "edam:operation_3223" }, { - "@id": "edam:operation_3763" + "@id": "edam:operation_2238" }, { - "@id": "edam:operation_3223" + "@id": "edam:operation_3763" }, { "@id": "edam:operation_3680" @@ -46,9 +46,9 @@ "sc:license": "GPL-2.0", "sc:name": "tweeDEseq", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/tweeDEseq.html", "sc:version": "1.24.0" diff --git a/data/twigs/twigsbioschemas.jsonld b/data/twigs/twigsbioschemas.jsonld index 21064707fb770..99321922d5190 100644 --- a/data/twigs/twigsbioschemas.jsonld +++ b/data/twigs/twigsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for advanced analysis of three-way data (e.g., patient-gene-time in gene expression or subject-voxel-time in fMRI). It identifies both core modules that appear in multiple patients and patient-specific augmentations of these core modules that contain additional genes.", "sc:name": "TWIGS", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://acgt.cs.tau.ac.il/twigs/" } \ No newline at end of file diff --git a/data/twilight-ligand/twilight-ligandbioschemas.jsonld b/data/twilight-ligand/twilight-ligandbioschemas.jsonld index 454d19f9260c5..29ad9c488cf7d 100644 --- a/data/twilight-ligand/twilight-ligandbioschemas.jsonld +++ b/data/twilight-ligand/twilight-ligandbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A standalone script for analysis, visualization, and annotation of a pre-filtered set of protein/ligand complexes deposited with the PDB with ligand RSCC values that are below a threshold of 0.6.", "sc:name": "Twilight", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.ruppweb.org/twilight/default.htm" } \ No newline at end of file diff --git a/data/twilight/twilightbioschemas.jsonld b/data/twilight/twilightbioschemas.jsonld index b8e5610443e91..ba788bd336a4a 100644 --- a/data/twilight/twilightbioschemas.jsonld +++ b/data/twilight/twilightbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "twilight", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/twilight.html", "sc:version": "1.50.0" diff --git a/data/twinscan/twinscanbioschemas.jsonld b/data/twinscan/twinscanbioschemas.jsonld index 8dcae8fa0937b..009ddc4bb22ea 100644 --- a/data/twinscan/twinscanbioschemas.jsonld +++ b/data/twinscan/twinscanbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Twinscan is a system for predicting gene-structure in eukaryotic genomic sequences. In order to make its predictions, Twinscan combines the information from predicted coding regions and splice sites with conserservation measurements between the target sequence and sequences from a closely related genome. Currently sequences from mammalian genomes, and those of Arabidopsis thaliana, C. elegans, C. briggsae and strains JEC21 and H99 of Cryptococcus neoformans can be processed using Twinscan.", "sc:name": "Twinscan", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://genes.cs.wustl.edu/" } \ No newline at end of file diff --git a/data/twoddpcr/twoddpcrbioschemas.jsonld b/data/twoddpcr/twoddpcrbioschemas.jsonld index 4ec22fbdc7874..c89cd9f49fee9 100644 --- a/data/twoddpcr/twoddpcrbioschemas.jsonld +++ b/data/twoddpcr/twoddpcrbioschemas.jsonld @@ -21,10 +21,10 @@ }, "sc:additionalType": "Library", "sc:citation": [ - "pmcid:PMC5860069", { "@id": "https://doi.org/10.1093/bioinformatics/btx308" }, + "pmcid:PMC5860069", "pubmed:28475662" ], "sc:description": "The package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad's QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data.", @@ -34,9 +34,9 @@ "sc:license": "GPL-3.0", "sc:name": "twoddpcr", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/twoddpcr.html", "sc:version": "1.4.1" diff --git a/data/twofeat/twofeatbioschemas.jsonld b/data/twofeat/twofeatbioschemas.jsonld index 1216ede1360c9..017ff084f5bf8 100644 --- a/data/twofeat/twofeatbioschemas.jsonld +++ b/data/twofeat/twofeatbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "Wellcome Trust", "EMBOSS Contributors", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:description": "Find neighbouring pairs of features in sequence(s).", "sc:funder": [ - "UK BBSRC", "Wellcome Trust", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "twofeat", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/twofeat.html", "sc:version": "r6" diff --git a/data/tximport/tximportbioschemas.jsonld b/data/tximport/tximportbioschemas.jsonld index 0603019296257..0f502e7cd904e 100644 --- a/data/tximport/tximportbioschemas.jsonld +++ b/data/tximport/tximportbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0001-8401-0545", - "@type": "schema:Person" + "@id": "https://doi.org/10.12688/f1000research.7563.2", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/tximport", @@ -20,14 +20,14 @@ "@id": "http://orcid.org/0000-0001-8401-0545" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:citation": [ + "pmcid:PMC4712774", { "@id": "https://doi.org/10.12688/f1000research.7563.2" }, - "pmcid:PMC4712774", "pubmed:26925227" ], "sc:description": "An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.", @@ -36,25 +36,25 @@ "@id": "edam:operation_0335" }, { - "@id": "edam:operation_3680" + "@id": "edam:operation_2497" }, { - "@id": "edam:operation_2497" + "@id": "edam:operation_3680" } ], "sc:license": "GPL-2.0", "sc:name": "tximport", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/tximport.html", "sc:version": "1.6.0" }, { - "@id": "https://doi.org/10.12688/f1000research.7563.2", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0001-8401-0545", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/txreginfra/txreginfrabioschemas.jsonld b/data/txreginfra/txreginfrabioschemas.jsonld index 0842783f93146..f74c2b4f4c93a 100644 --- a/data/txreginfra/txreginfrabioschemas.jsonld +++ b/data/txreginfra/txreginfrabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "TxRegInfra", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/TxRegInfra.html", diff --git a/data/tygs/tygsbioschemas.jsonld b/data/tygs/tygsbioschemas.jsonld index 666ce1ff5bba6..71981886bc042 100644 --- a/data/tygs/tygsbioschemas.jsonld +++ b/data/tygs/tygsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1038/S41467-019-10210-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0001-9105-9814", "@type": "schema:Person" @@ -20,15 +24,15 @@ "@id": "https://orcid.org/0000-0001-9105-9814" }, "sc:additionalType": [ - "Web application", - "Web service" + "Web service", + "Web application" ], "sc:citation": [ + "pubmed:31097708", + "pmcid:PMC6522516", { "@id": "https://doi.org/10.1038/S41467-019-10210-3" - }, - "pubmed:31097708", - "pmcid:PMC6522516" + } ], "sc:description": "Automated high-throughput platform for state-of-the-art genome-based taxonomy.", "sc:featureList": [ @@ -36,24 +40,20 @@ "@id": "edam:operation_3460" }, { - "@id": "edam:operation_3431" + "@id": "edam:operation_0544" }, { - "@id": "edam:operation_0544" + "@id": "edam:operation_3431" } ], "sc:license": "Unlicense", "sc:name": "TYGS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://tygs.dsmz.de" - }, - { - "@id": "https://doi.org/10.1038/S41467-019-10210-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/tyna/tynabioschemas.jsonld b/data/tyna/tynabioschemas.jsonld index c72927d7c562a..2813ab8c1fd1b 100644 --- a/data/tyna/tynabioschemas.jsonld +++ b/data/tyna/tynabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Web system for managing, comparing and mining multiple networks, both directed and undirected.", "sc:name": "tyna", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://tyna.gersteinlab.org/tyna/", diff --git a/data/typeinfo/typeinfobioschemas.jsonld b/data/typeinfo/typeinfobioschemas.jsonld index b884b5c5ab6e0..cb287fbd26147 100644 --- a/data/typeinfo/typeinfobioschemas.jsonld +++ b/data/typeinfo/typeinfobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Duncan Temple Lang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "A prototype for a mechanism for specifying the types of parameters and the return value for an R function.", "sc:license": "BSD-4-Clause", diff --git a/data/ualcan/ualcanbioschemas.jsonld b/data/ualcan/ualcanbioschemas.jsonld index bbb9d42777230..55e5ea217ce37 100644 --- a/data/ualcan/ualcanbioschemas.jsonld +++ b/data/ualcan/ualcanbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/UALCAN", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:description": "Comprehensive, user-friendly, and interactive web resource for analyzing cancer OMICS data.", "sc:license": "Unlicense", "sc:name": "UALCAN", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://ualcan.path.uab.edu/analysis.html" } \ No newline at end of file diff --git a/data/ub-isap/ub-isapbioschemas.jsonld b/data/ub-isap/ub-isapbioschemas.jsonld index 434da750d04da..a7bbb4c6a3e3f 100644 --- a/data/ub-isap/ub-isapbioschemas.jsonld +++ b/data/ub-isap/ub-isapbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1719-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ub-isap", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Atul Kamboj", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:28623888", { "@id": "https://doi.org/10.1186/s12859-017-1719-4" }, - "pmcid:PMC5474025" + "pmcid:PMC5474025", + "pubmed:28623888" ], "sc:description": "UNIX-based vector integration site analysis pipeline that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads.", "sc:featureList": { @@ -32,6 +28,10 @@ "sc:name": "Ub-ISAP", "sc:operatingSystem": "Linux", "sc:url": "https://sourceforge.net/projects/ub-isap/" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1719-4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ubine/ubinebioschemas.jsonld b/data/ubine/ubinebioschemas.jsonld index 8abac6108bd38..5e81ac0d47056 100644 --- a/data/ubine/ubinebioschemas.jsonld +++ b/data/ubine/ubinebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/DATABASE/BAW054", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ubine", "@type": "sc:SoftwareApplication", @@ -36,6 +32,10 @@ "Linux" ], "sc:url": "http://140.138.144.145/~ubinet/index.php" + }, + { + "@id": "https://doi.org/10.1093/DATABASE/BAW054", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ubisite/ubisitebioschemas.jsonld b/data/ubisite/ubisitebioschemas.jsonld index b95afd8ed0ed1..977ee197a61b8 100644 --- a/data/ubisite/ubisitebioschemas.jsonld +++ b/data/ubisite/ubisitebioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S12918-015-0246-Z", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ubisite", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4895383", { "@id": "https://doi.org/10.1186/S12918-015-0246-Z" }, + "pmcid:PMC4895383", "pubmed:26818456" ], "sc:description": "Incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.", @@ -31,11 +27,15 @@ }, "sc:name": "UbiSite", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://csb.cse.yzu.edu.tw/UbiSite/" + }, + { + "@id": "https://doi.org/10.1186/S12918-015-0246-Z", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ucl_web_services/ucl_web_servicesbioschemas.jsonld b/data/ucl_web_services/ucl_web_servicesbioschemas.jsonld index 4aaf8f23e45a3..62e0d548673f1 100644 --- a/data/ucl_web_services/ucl_web_servicesbioschemas.jsonld +++ b/data/ucl_web_services/ucl_web_servicesbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "This tool has multiple functions, including: Protein Structure Prediction, Protein Sequence Analysis, Genome Analysis, Protein Structure Classification, Transmembrane Protein Modelling.", "sc:name": "UCL Web Services", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://bioinf.cs.ucl.ac.uk/web_servers/web_services/", "sc:version": "1" diff --git a/data/ucsc_cancer_genomics_browser/ucsc_cancer_genomics_browserbioschemas.jsonld b/data/ucsc_cancer_genomics_browser/ucsc_cancer_genomics_browserbioschemas.jsonld index 16d8cd2776a8b..f79243c0d2370 100644 --- a/data/ucsc_cancer_genomics_browser/ucsc_cancer_genomics_browserbioschemas.jsonld +++ b/data/ucsc_cancer_genomics_browser/ucsc_cancer_genomics_browserbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/ucsc_cancer_genomics_browser", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Cancer Genomics Browser Support", - "Genomics Browser Forum" + "Genomics Browser Forum", + "Cancer Genomics Browser Support" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:21059681", diff --git a/data/ucsc_genome_browser/ucsc_genome_browserbioschemas.jsonld b/data/ucsc_genome_browser/ucsc_genome_browserbioschemas.jsonld index 2edca484c07ec..300acb0376135 100644 --- a/data/ucsc_genome_browser/ucsc_genome_browserbioschemas.jsonld +++ b/data/ucsc_genome_browser/ucsc_genome_browserbioschemas.jsonld @@ -13,10 +13,6 @@ "@id": "https://doi.org/10.1093/nar/gkr1055", "@type": "sc:CreativeWork" }, - { - "@id": "https://doi.org/10.1093/nar/gkr1012", - "@type": "sc:CreativeWork" - }, { "@id": "https://doi.org/10.1093/nar/gkp939", "@type": "sc:CreativeWork" @@ -26,52 +22,56 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Brooke Rhead", "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ - { - "@id": "https://doi.org/10.1093/nar/gkr1012" - }, - "pmcid:PMC3245018", "pmcid:PMC2808870", + "pubmed:22086951", { "@id": "https://doi.org/10.1093/nar/gkr1055" }, "pmcid:PMC3245183", - "pubmed:19906737", "pubmed:22075998", - "pubmed:22086951", + "pubmed:19906737", + "pmcid:PMC3245018", { "@id": "https://doi.org/10.1093/nar/gkp939" + }, + { + "@id": "https://doi.org/10.1093/nar/gkr1012" } ], "sc:description": "Large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users own annotation data.", "sc:featureList": [ { - "@id": "edam:operation_0292" + "@id": "edam:operation_0308" }, { "@id": "edam:operation_3197" }, { - "@id": "edam:operation_2421" + "@id": "edam:operation_3208" }, { - "@id": "edam:operation_3208" + "@id": "edam:operation_2421" }, { - "@id": "edam:operation_0308" + "@id": "edam:operation_0292" } ], "sc:license": "Apache-2.0", "sc:name": "UCSC Genome Browser", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "https://genome.ucsc.edu/" + }, + { + "@id": "https://doi.org/10.1093/nar/gkr1012", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ucsc_genome_browser_utilities/ucsc_genome_browser_utilitiesbioschemas.jsonld b/data/ucsc_genome_browser_utilities/ucsc_genome_browser_utilitiesbioschemas.jsonld index 198c1122c9c2f..d4c8f872a75f4 100644 --- a/data/ucsc_genome_browser_utilities/ucsc_genome_browser_utilitiesbioschemas.jsonld +++ b/data/ucsc_genome_browser_utilities/ucsc_genome_browser_utilitiesbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Other", "sc:name": "UCSC Genome Browser Utilities", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://hgdownload.cse.ucsc.edu/downloads.html" } \ No newline at end of file diff --git a/data/ucsc_interaction_browser/ucsc_interaction_browserbioschemas.jsonld b/data/ucsc_interaction_browser/ucsc_interaction_browserbioschemas.jsonld index 8f522848fc2ef..a6981650eb5e5 100644 --- a/data/ucsc_interaction_browser/ucsc_interaction_browserbioschemas.jsonld +++ b/data/ucsc_interaction_browser/ucsc_interaction_browserbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Online tool fo biologists to view high-throughput data sets simultaenously for the analysis of functional relationships between biological entities. Users can access several public interaction networks and functional genomics datasets through the portal as well as upload their own data for analysis. Using CircleMap, multiple genomic datasets can be viewed simultaneously.", "sc:name": "UCSC Interaction Browser", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://sysbio.soe.ucsc.edu/nets" } \ No newline at end of file diff --git a/data/ufboot2/ufboot2bioschemas.jsonld b/data/ufboot2/ufboot2bioschemas.jsonld index 3539483b70233..cb5d80212537b 100644 --- a/data/ufboot2/ufboot2bioschemas.jsonld +++ b/data/ufboot2/ufboot2bioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Le Sy Vinh", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5850222", { "@id": "https://doi.org/10.1093/molbev/msx281" }, - "pmcid:PMC5850222", "pubmed:29077904" ], "sc:description": "Improving the Ultrafast Bootstrap Approximation.", diff --git a/data/ugahash/ugahashbioschemas.jsonld b/data/ugahash/ugahashbioschemas.jsonld index 30a0dec3a935b..be9100f76f632 100644 --- a/data/ugahash/ugahashbioschemas.jsonld +++ b/data/ugahash/ugahashbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "UGAHash", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://ugahash.uni-frankfurt.de/" } \ No newline at end of file diff --git a/data/ugene/ugenebioschemas.jsonld b/data/ugene/ugenebioschemas.jsonld index 8c6c3075164e9..05d08bc0cce16 100644 --- a/data/ugene/ugenebioschemas.jsonld +++ b/data/ugene/ugenebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "UGENE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://ugene.unipro.ru" } \ No newline at end of file diff --git a/data/uicluster/uiclusterbioschemas.jsonld b/data/uicluster/uiclusterbioschemas.jsonld index 0574ce921ee60..4d4d2a61661c8 100644 --- a/data/uicluster/uiclusterbioschemas.jsonld +++ b/data/uicluster/uiclusterbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Updated version of tlcluster that is much faster and adds new features such as reverse complement checking. In addition to optimization and reverse checking, it performs an extended search of all primaries for each sequence being clustered.", "sc:name": "UIcluster", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://genome.uiowa.edu/home.old/pubsoft/clustering/index.html", "sc:version": "3.0.5" diff --git a/data/ukbtools/ukbtoolsbioschemas.jsonld b/data/ukbtools/ukbtoolsbioschemas.jsonld index b239bdc031b3a..14dbea6ca1b1a 100644 --- a/data/ukbtools/ukbtoolsbioschemas.jsonld +++ b/data/ukbtools/ukbtoolsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/journal.pone.0214311", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ukbtools", "@type": "sc:SoftwareApplication", @@ -20,31 +16,35 @@ "sc:additionalType": "Library", "sc:citation": [ "pmcid:PMC6544205", + "pubmed:31150407", { "@id": "https://doi.org/10.1371/journal.pone.0214311" - }, - "pubmed:31150407" + } ], "sc:description": "R package to manage and query UK Biobank data.", "sc:featureList": [ - { - "@id": "edam:operation_2422" - }, { "@id": "edam:operation_2428" }, { "@id": "edam:operation_3196" + }, + { + "@id": "edam:operation_2422" } ], "sc:license": "GPL-2.0", "sc:name": "ukbtools", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://cran.r-project.org/package=ukbtools" + }, + { + "@id": "https://doi.org/10.1371/journal.pone.0214311", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ukpmc/ukpmcbioschemas.jsonld b/data/ukpmc/ukpmcbioschemas.jsonld index 42e7826d80764..289e0bf375575 100644 --- a/data/ukpmc/ukpmcbioschemas.jsonld +++ b/data/ukpmc/ukpmcbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "UK PubMed Central is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. Now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. Furthermore, UKPMC contains 'Cited By' information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources.", "sc:name": "UKPMC", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://ukpmc.ac.uk" diff --git a/data/ultra/ultrabioschemas.jsonld b/data/ultra/ultrabioschemas.jsonld index 261387f65dad1..85370833a3354 100644 --- a/data/ultra/ultrabioschemas.jsonld +++ b/data/ultra/ultrabioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Daniel Olson", "sc:citation": [ - "pmcid:PMC6508075", - "pubmed:31080962", { "@id": "https://doi.org/10.1145/3233547.3233604" - } + }, + "pmcid:PMC6508075", + "pubmed:31080962" ], "sc:description": "> MEDIUM CONFIDENCE! | A Model Based Tool to Detect Tandem Repeats | ULTRA Locates Tandemly Repetitive Areas | To contribute to ULTRA development, you want to be on the develop branch, which is where we are currently integrating feature branches. For more information, see the ULTRA wiki", "sc:featureList": [ @@ -36,9 +36,9 @@ "sc:license": "BSD-3-Clause", "sc:name": "ULTRA", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/TravisWheelerLab/ULTRA" } diff --git a/data/ultrapse/ultrapsebioschemas.jsonld b/data/ultrapse/ultrapsebioschemas.jsonld index a8b0c6a7b82fc..2e321de73bcea 100644 --- a/data/ultrapse/ultrapsebioschemas.jsonld +++ b/data/ultrapse/ultrapsebioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3390/ijms18112400", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ultrapse", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Pu-Feng Du", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:29135934", - "pmcid:PMC5713368", { "@id": "https://doi.org/10.3390/ijms18112400" - } + }, + "pmcid:PMC5713368", + "pubmed:29135934" ], "sc:description": "A universal and extensible software platform for biological sequence representations.", "sc:featureList": { @@ -29,10 +33,6 @@ "sc:name": "UltraPse", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/pufengdu/UltraPse" - }, - { - "@id": "https://doi.org/10.3390/ijms18112400", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/ulysses/ulyssesbioschemas.jsonld b/data/ulysses/ulyssesbioschemas.jsonld index 5b572763be778..1cd614a5f140e 100644 --- a/data/ulysses/ulyssesbioschemas.jsonld +++ b/data/ulysses/ulyssesbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Chimeric python/R tool that is designed to provide an accurate detection of low-frequency structural variations in large insert-size sequencing libraries.", "sc:name": "Ulysses", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.lcqb.upmc.fr/ulysses/" } \ No newline at end of file diff --git a/data/umd-predictor/umd-predictorbioschemas.jsonld b/data/umd-predictor/umd-predictorbioschemas.jsonld index dd5afa694843d..dda8f16f96a77 100644 --- a/data/umd-predictor/umd-predictorbioschemas.jsonld +++ b/data/umd-predictor/umd-predictorbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/umd-predictor", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Christophe Beroud", - "David Salgado" + "David Salgado", + "Christophe Beroud" ], "sc:additionalType": "Web application", "sc:description": "A tool that provides a combinatorial approach to identify potential pathogenic variations, that associates the following data: localization within the protein, conservation, biochemical properties of the mutant and wild-type residues, and the potential impact of the variation on mRNA.", diff --git a/data/umd/umdbioschemas.jsonld b/data/umd/umdbioschemas.jsonld index bab987ba0ab8c..bb26161df1e60 100644 --- a/data/umd/umdbioschemas.jsonld +++ b/data/umd/umdbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Unlicense", "sc:name": "UMD", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.umd.be/" } \ No newline at end of file diff --git a/data/umi-tools/umi-toolsbioschemas.jsonld b/data/umi-tools/umi-toolsbioschemas.jsonld index 35fa77af2cbde..9df5202d58149 100644 --- a/data/umi-tools/umi-toolsbioschemas.jsonld +++ b/data/umi-tools/umi-toolsbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1101/gr.209601.116", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/umi-tools", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ian Sudbery", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:28100584", + "pmcid:PMC5340976", { "@id": "https://doi.org/10.1101/gr.209601.116" - }, - "pubmed:28100584", - "pmcid:PMC5340976" + } ], "sc:description": "Tools for handling Unique Molecular Identifiers in NGS data sets.", "sc:featureList": { @@ -29,10 +33,6 @@ "sc:name": "UMI-tools", "sc:operatingSystem": "Linux", "sc:url": "https://github.com/CGATOxford/UMI-tools" - }, - { - "@id": "https://doi.org/10.1101/gr.209601.116", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/umx/umxbioschemas.jsonld b/data/umx/umxbioschemas.jsonld index f09cbbaf13dcc..02ef4a2676b9a 100644 --- a/data/umx/umxbioschemas.jsonld +++ b/data/umx/umxbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "umx", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://cran.r-project.org/package=umx", "sc:version": "2.10.0" diff --git a/data/unafold/unafoldbioschemas.jsonld b/data/unafold/unafoldbioschemas.jsonld index 8fb205f29d988..36db1997f6f5b 100644 --- a/data/unafold/unafoldbioschemas.jsonld +++ b/data/unafold/unafoldbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Unified Nucleic Acid Folding. Simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folding prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, entire melting profiles are computed , not just melting temperatures.", "sc:name": "UNAFold", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://mfold.rna.albany.edu/", "sc:version": "3.9-1" diff --git a/data/unccombo/unccombobioschemas.jsonld b/data/unccombo/unccombobioschemas.jsonld index 694f2724d7224..28278975c5f80 100644 --- a/data/unccombo/unccombobioschemas.jsonld +++ b/data/unccombo/unccombobioschemas.jsonld @@ -18,8 +18,8 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Plug-in", "sc:citation": [ - "pmcid:PMC4668777", "pubmed:25979475", + "pmcid:PMC4668777", { "@id": "https://doi.org/10.1093/bioinformatics/btv307" } @@ -36,9 +36,9 @@ "sc:license": "Not licensed", "sc:name": "UNCcombo", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://yunliweb.its.unc.edu/UNCcombo/" } diff --git a/data/unceqr/unceqrbioschemas.jsonld b/data/unceqr/unceqrbioschemas.jsonld index d148186bbd08b..8993b8ae52c48 100644 --- a/data/unceqr/unceqrbioschemas.jsonld +++ b/data/unceqr/unceqrbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Matt Wilkerson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Method and associated software for discovering somatic mutations using the integration of DNA and RNA sequencing.", "sc:license": "MIT", diff --git a/data/uncover/uncoverbioschemas.jsonld b/data/uncover/uncoverbioschemas.jsonld index 6bcd4129bed7d..e8729e809ec06 100644 --- a/data/uncover/uncoverbioschemas.jsonld +++ b/data/uncover/uncoverbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006802", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0003-2244-2320", "@type": "schema:Person" @@ -24,8 +28,8 @@ { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006802" }, - "pmcid:PMC6550413", - "pubmed:31120875" + "pubmed:31120875", + "pmcid:PMC6550413" ], "sc:description": "Efficient algorithms to discover alterations with complementary functional association in cancer.", "sc:featureList": [ @@ -44,10 +48,6 @@ "Mac" ], "sc:url": "https://github.com/VandinLab/UNCOVER" - }, - { - "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1006802", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/undo/undobioschemas.jsonld b/data/undo/undobioschemas.jsonld index 6589810e64f3d..2185170e7f179 100644 --- a/data/undo/undobioschemas.jsonld +++ b/data/undo/undobioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-2.0", "sc:name": "UNDO", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/UNDO.html", "sc:version": "1.16.0" diff --git a/data/unfold/unfoldbioschemas.jsonld b/data/unfold/unfoldbioschemas.jsonld index 29dc7960d6869..7346379c3b309 100644 --- a/data/unfold/unfoldbioschemas.jsonld +++ b/data/unfold/unfoldbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Predict the sequence of protein (un)folding events by recursive min-cut on a weighted secondary structure element graph.", "sc:name": "UNFOLD", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.cs.rpi.edu/~zaki/www-new/pmwiki.php/Software/Software#toc34" } \ No newline at end of file diff --git a/data/unialign/unialignbioschemas.jsonld b/data/unialign/unialignbioschemas.jsonld index ecc8a59d60300..495d0828a84d3 100644 --- a/data/unialign/unialignbioschemas.jsonld +++ b/data/unialign/unialignbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Protein pairwise structure alignment algorithm that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles, and residue conservation.", "sc:name": "UniAlign", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://sacan.biomed.drexel.edu/unialign" } \ No newline at end of file diff --git a/data/unicarb-db/unicarb-dbbioschemas.jsonld b/data/unicarb-db/unicarb-dbbioschemas.jsonld index a52b23f0cc38a..3a8c3b34c0ce3 100644 --- a/data/unicarb-db/unicarb-dbbioschemas.jsonld +++ b/data/unicarb-db/unicarb-dbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A database of LC-MS structural data for oligosaccharides.", "sc:name": "UniCarb-DB", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:provider": "bils.se", "sc:url": "http://unicarb-db.biomedicine.gu.se/" diff --git a/data/unicarbkb/unicarbkbbioschemas.jsonld b/data/unicarbkb/unicarbkbbioschemas.jsonld index 28075bbab6e2c..c1644ed6218df 100644 --- a/data/unicarbkb/unicarbkbbioschemas.jsonld +++ b/data/unicarbkb/unicarbkbbioschemas.jsonld @@ -29,28 +29,28 @@ ], "sc:contributor": [ "SIB Swiss Institute of Bioinformatics", - "Max Planck Institute of Colloids and Interfaces, Germany", "Macquarie University, Australia", - "University of Gothenburg, Sweden", "National Institute for Bioprocessing Research and Training (NIBRT), Ireland", "UNSW, Australia", + "Soka University, Japan", "CCRC, USA", - "Soka University, Japan" + "Max Planck Institute of Colloids and Interfaces, Germany", + "University of Gothenburg, Sweden" ], "sc:description": "Curated and annotated glycan database which curates information from the scientific literature on glycoprotein derived glycan structures.", "sc:featureList": [ { - "@id": "edam:operation_0417" + "@id": "edam:operation_0416" }, { - "@id": "edam:operation_0416" + "@id": "edam:operation_0417" } ], "sc:name": "UniCarbKB", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://unicarb-db.expasy.org/" }, diff --git a/data/unicycler/unicyclerbioschemas.jsonld b/data/unicycler/unicyclerbioschemas.jsonld index e6c0f885653a6..94628bb6e4fce 100644 --- a/data/unicycler/unicyclerbioschemas.jsonld +++ b/data/unicycler/unicyclerbioschemas.jsonld @@ -26,13 +26,13 @@ "sc:additionalType": "Command-line tool", "sc:applicationSubCategory": [ { - "@id": "edam:topic_3301" + "@id": "edam:topic_0196" }, { - "@id": "edam:topic_3168" + "@id": "edam:topic_3301" }, { - "@id": "edam:topic_0196" + "@id": "edam:topic_3168" }, { "@id": "edam:topic_0622" @@ -42,16 +42,16 @@ { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1005595" }, - "pubmed:28594827", - "pmcid:PMC5481147" + "pmcid:PMC5481147", + "pubmed:28594827" ], "sc:description": "A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.", "sc:featureList": [ { - "@id": "edam:operation_0525" + "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3436" + "@id": "edam:operation_0525" } ], "sc:isAccessibleForFree": true, diff --git a/data/unifiedwmwqpcr/unifiedwmwqpcrbioschemas.jsonld b/data/unifiedwmwqpcr/unifiedwmwqpcrbioschemas.jsonld index b8b671c859aa9..1141f27552174 100644 --- a/data/unifiedwmwqpcr/unifiedwmwqpcrbioschemas.jsonld +++ b/data/unifiedwmwqpcr/unifiedwmwqpcrbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "GPL-2.0", "sc:name": "unifiedWMWqPCR", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/unifiedWMWqPCR.html", "sc:version": "1.10.0" diff --git a/data/unigene/unigenebioschemas.jsonld b/data/unigene/unigenebioschemas.jsonld index fd689faa709cf..d5b61e2f76931 100644 --- a/data/unigene/unigenebioschemas.jsonld +++ b/data/unigene/unigenebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Each entry is a set of transcript (expressed sequence tag) sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.", "sc:name": "UniGene gene-oriented nucleotide sequence clusters", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=UniGene" diff --git a/data/unimod/unimodbioschemas.jsonld b/data/unimod/unimodbioschemas.jsonld index c859e5521620b..d3b8a6a1fe12b 100644 --- a/data/unimod/unimodbioschemas.jsonld +++ b/data/unimod/unimodbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "UniMod", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.unimod.org" } \ No newline at end of file diff --git a/data/unimog/unimogbioschemas.jsonld b/data/unimog/unimogbioschemas.jsonld index 068a49132a369..0fbbf1ef245e1 100644 --- a/data/unimog/unimogbioschemas.jsonld +++ b/data/unimog/unimogbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Software tool unifying five genome rearrangement distance models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion only and translocation only. It allows computing all of these five distances between pairs of genomes represented as sequences of oriented common blocks.", "sc:name": "UniMoG", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bibiserv.techfak.uni-bielefeld.de/dcj/" diff --git a/data/uninovo/uninovobioschemas.jsonld b/data/uninovo/uninovobioschemas.jsonld index c7d109ce6c802..2bbebd11ccf09 100644 --- a/data/uninovo/uninovobioschemas.jsonld +++ b/data/uninovo/uninovobioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "K. Jeong", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC3722526", - "pubmed:23766417", { "@id": "https://doi.org/10.1093/bioinformatics/btt338" - } + }, + "pmcid:PMC3722526", + "pubmed:23766417" ], "sc:description": "A universal tool for de novo peptide sequencing.", "sc:featureList": { diff --git a/data/union/unionbioschemas.jsonld b/data/union/unionbioschemas.jsonld index bc2dc7f5b9f94..bff2d33fc2d9a 100644 --- a/data/union/unionbioschemas.jsonld +++ b/data/union/unionbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "UK BBSRC", + "EMBOSS Contributors", "UK MRC", - "EMBOSS Contributors" + "Wellcome Trust" ], "sc:description": "Concatenate multiple sequences into a single sequence.", "sc:funder": [ - "UK MRC", + "Wellcome Trust", "UK BBSRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "union", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/union.html", "sc:version": "r6" diff --git a/data/uniparc/uniparcbioschemas.jsonld b/data/uniparc/uniparcbioschemas.jsonld index 040af31f4809a..3277b0e7b021d 100644 --- a/data/uniparc/uniparcbioschemas.jsonld +++ b/data/uniparc/uniparcbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "UniParc is a comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world. Proteins may exist in different source databases and in multiple copies in the same database. UniParc avoids such redundancy by storing each unique sequence only once and giving it a stable and unique identifier (UPI).", "sc:name": "UniParc", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "UniProt Consortium", "sc:url": "http://www.uniprot.org/uniparc/" diff --git a/data/unipept/unipeptbioschemas.jsonld b/data/unipept/unipeptbioschemas.jsonld index 73a6d9f011772..41d32730c4775 100644 --- a/data/unipept/unipeptbioschemas.jsonld +++ b/data/unipept/unipeptbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "Unipept", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://unipept.ugent.be/", diff --git a/data/unipept_cli/unipept_clibioschemas.jsonld b/data/unipept_cli/unipept_clibioschemas.jsonld index a11f0e754c7cf..120053aa0a56e 100644 --- a/data/unipept_cli/unipept_clibioschemas.jsonld +++ b/data/unipept_cli/unipept_clibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Unipept CLI", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://unipept.ugent.be/clidocs", "sc:version": "1.3.0" diff --git a/data/unipept_visualizations/unipept_visualizationsbioschemas.jsonld b/data/unipept_visualizations/unipept_visualizationsbioschemas.jsonld index e12df0669c13a..b209b34edaa30 100644 --- a/data/unipept_visualizations/unipept_visualizationsbioschemas.jsonld +++ b/data/unipept_visualizations/unipept_visualizationsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Unipept visualizations", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/unipept/unipept-visualizations", "sc:version": "1.5.0" diff --git a/data/uniprobe/uniprobebioschemas.jsonld b/data/uniprobe/uniprobebioschemas.jsonld index 65343122bdb8f..868cfb4f3b497 100644 --- a/data/uniprobe/uniprobebioschemas.jsonld +++ b/data/uniprobe/uniprobebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Universal PBM Resource for Oligonucleotide-Binding Evaluation database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants of length k, as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data.", "sc:name": "UniPROBE", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://uniprobe.org" } \ No newline at end of file diff --git a/data/uniprot.ws/bioconda_uniprot.ws.yaml b/data/uniprot.ws/bioconda_uniprot.ws.yaml index b93ab4c90b09a..ac64e3697bf68 100644 --- a/data/uniprot.ws/bioconda_uniprot.ws.yaml +++ b/data/uniprot.ws/bioconda_uniprot.ws.yaml @@ -4,7 +4,6 @@ description: A collection of functions for retrieving, processing and repackagin home: https://bioconductor.org/packages/3.10/bioc/html/UniProt.ws.html identifiers: - biotools:uniprot.ws -- doi:10.1038/nmeth.3252 license: Artistic License 2.0 name: bioconductor-uniprot.ws summary: R Interface to UniProt Web Services diff --git a/data/uniprot_align/uniprot_alignbioschemas.jsonld b/data/uniprot_align/uniprot_alignbioschemas.jsonld index 8fbd9ec202569..427d8fbb285fb 100644 --- a/data/uniprot_align/uniprot_alignbioschemas.jsonld +++ b/data/uniprot_align/uniprot_alignbioschemas.jsonld @@ -16,13 +16,13 @@ "sc:license": "CC-BY-ND-3.0", "sc:name": "UniProt Align", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "EMBL-EBI", - "UniProt Consortium" + "UniProt Consortium", + "EMBL-EBI" ], "sc:url": "http://www.uniprot.org/align", "sc:version": "1" diff --git a/data/uniprot_blast/uniprot_blastbioschemas.jsonld b/data/uniprot_blast/uniprot_blastbioschemas.jsonld index 3fa18a3635851..7f78ed24fe8db 100644 --- a/data/uniprot_blast/uniprot_blastbioschemas.jsonld +++ b/data/uniprot_blast/uniprot_blastbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "UniProt BLAST", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "UniProt Consortium", diff --git a/data/uniprot_id_mapping/uniprot_id_mappingbioschemas.jsonld b/data/uniprot_id_mapping/uniprot_id_mappingbioschemas.jsonld index 1c4ccbf820384..3aa5bc0735d4c 100644 --- a/data/uniprot_id_mapping/uniprot_id_mappingbioschemas.jsonld +++ b/data/uniprot_id_mapping/uniprot_id_mappingbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Maps identifiers to or from UniProtKB.", "sc:name": "UniProt ID Mapping", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:provider": "UniProt Consortium", "sc:url": "http://www.uniprot.org/mapping/", diff --git a/data/uniprotkb_swiss-prot/uniprotkb_swiss-protbioschemas.jsonld b/data/uniprotkb_swiss-prot/uniprotkb_swiss-protbioschemas.jsonld index d9633ca4e96eb..f9440c7c486e7 100644 --- a/data/uniprotkb_swiss-prot/uniprotkb_swiss-protbioschemas.jsonld +++ b/data/uniprotkb_swiss-prot/uniprotkb_swiss-protbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "UniProtKB Swiss-Prot", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://web.expasy.org/docs/swiss-prot_guideline.html" } \ No newline at end of file diff --git a/data/uniquorn/uniquornbioschemas.jsonld b/data/uniquorn/uniquornbioschemas.jsonld index 4d5387c42f074..73842cf8ab695 100644 --- a/data/uniquorn/uniquornbioschemas.jsonld +++ b/data/uniquorn/uniquornbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "'Raik Otto'", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This packages enables users to identify cancer cell lines based on the locations of somatic and germline mutations. The implemented method is optimized for the next-generation whole exome and whole genome DNA-sequencing technology.", "sc:license": "Artistic-2.0", "sc:name": "Uniquorn", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Uniquorn.html", diff --git a/data/unitas/unitasbioschemas.jsonld b/data/unitas/unitasbioschemas.jsonld index 009df40332aae..8b5969d8af80f 100644 --- a/data/unitas/unitasbioschemas.jsonld +++ b/data/unitas/unitasbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Daniel Gebert", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5567656", { "@id": "https://doi.org/10.1186/s12864-017-4031-9" }, - "pubmed:28830358", - "pmcid:PMC5567656" + "pubmed:28830358" ], "sc:description": "Complete annotation of small RNA datasets from NGS.", "sc:featureList": { @@ -32,9 +32,9 @@ "sc:license": "GPL-3.0", "sc:name": "unitas", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://sourceforge.net/projects/unitas/files/" } diff --git a/data/unite_rdna/unite_rdnabioschemas.jsonld b/data/unite_rdna/unite_rdnabioschemas.jsonld index 193a4f0792180..3649e07122e25 100644 --- a/data/unite_rdna/unite_rdnabioschemas.jsonld +++ b/data/unite_rdna/unite_rdnabioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "rDNA sequence database focused on ectomycorrhizal asco- and basidiomycetes.", "sc:name": "UNITE rDNA", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://unite.ut.ee/" diff --git a/data/unitrap/unitrapbioschemas.jsonld b/data/unitrap/unitrapbioschemas.jsonld index ce2580865a64d..91f2e8abc7904 100644 --- a/data/unitrap/unitrapbioschemas.jsonld +++ b/data/unitrap/unitrapbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Tools for the biologist enabling optimized use of gene trap clones.", "sc:name": "UniTrap gene trap clones", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://unitrap.crg.es/about.php" } \ No newline at end of file diff --git a/data/universal_ttss/universal_ttssbioschemas.jsonld b/data/universal_ttss/universal_ttssbioschemas.jsonld index ff12d4f639d30..709958536c74d 100644 --- a/data/universal_ttss/universal_ttssbioschemas.jsonld +++ b/data/universal_ttss/universal_ttssbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Yulia A. Medvedeva", "sc:additionalType": "Script", "sc:citation": [ + "pmcid:PMC6518440", { "@id": "https://doi.org/10.12688/F1000RESEARCH.13522.2" }, - "pubmed:31131080", - "pmcid:PMC6518440" + "pubmed:31131080" ], "sc:description": "The code to identify the universal Triplex Target Sites (TTSs) DNA regions", "sc:featureList": [ @@ -27,18 +27,18 @@ "@id": "edam:operation_2495" }, { - "@id": "edam:operation_3222" + "@id": "edam:operation_3501" }, { - "@id": "edam:operation_3501" + "@id": "edam:operation_3222" } ], "sc:license": "GPL-3.0", "sc:name": "universal TTSs", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/vanya-antonov/universal_tts" }, diff --git a/data/unoseq/unoseqbioschemas.jsonld b/data/unoseq/unoseqbioschemas.jsonld index 88782781318f1..ccda25f06f601 100644 --- a/data/unoseq/unoseqbioschemas.jsonld +++ b/data/unoseq/unoseqbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "UnoSeq", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://sourceforge.net/projects/unoseq/" } \ No newline at end of file diff --git a/data/unravel/unravelbioschemas.jsonld b/data/unravel/unravelbioschemas.jsonld index c7baf74f5c9d8..08b1809d23e4d 100644 --- a/data/unravel/unravelbioschemas.jsonld +++ b/data/unravel/unravelbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "UNRAVEL", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://www.unravelrdp.nl" } \ No newline at end of file diff --git a/data/upb/upbbioschemas.jsonld b/data/upb/upbbioschemas.jsonld index 83d25e55aa25d..ac4291b4de3a2 100644 --- a/data/upb/upbbioschemas.jsonld +++ b/data/upb/upbbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "UPB is an Urinary Protein Biomarker database to collect existing studies of urinary protein biomarkers from published literature.", "sc:name": "UPB", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://59.108.16.249/biomarker/web/indexdb", "sc:version": "20130710" diff --git a/data/upf/upfbioschemas.jsonld b/data/upf/upfbioschemas.jsonld index 07eb439b02059..673ce40a69e4a 100644 --- a/data/upf/upfbioschemas.jsonld +++ b/data/upf/upfbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "The standalone tool UPF offers the possibility for a highly efficient and simple detection of unique peptides. In a first step a SQL-based database of theoretically digested peptides from a given FASTA formatted protein database is generated by choosing a protease. In a second step, in silico generated peptides from a pre-defined protein sequence are compared to this peptide database in order to identify unique peptides.", "sc:name": "Unique Peptide Finder (UPF)", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "PD Dr. Martin Eisenacher", "sc:url": "http://www.ruhr-uni-bochum.de/mpc/software/UPF/index.html.en", diff --git a/data/upic/upicbioschemas.jsonld b/data/upic/upicbioschemas.jsonld index fb39a0f03c7f7..9304930b1b44e 100644 --- a/data/upic/upicbioschemas.jsonld +++ b/data/upic/upicbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "UPIC", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ars.usda.gov/Main/docs.htm?docid=18376" } \ No newline at end of file diff --git a/data/uproc/uprocbioschemas.jsonld b/data/uproc/uprocbioschemas.jsonld index 33be750d39aaf..adbac304de856 100644 --- a/data/uproc/uprocbioschemas.jsonld +++ b/data/uproc/uprocbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The toolbox implements a novel algorithm (“Mosaic Matching”) for large-scale sequence analysis and is now available in terms of an open source C library. It is up to three orders of magnitude faster than profile-based methods and achieved up to 80% higher sensitivity on unassembled short reads (100 bp) from simulated metagenomes.", "sc:name": "UProC", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://uproc.gobics.de/" } \ No newline at end of file diff --git a/data/uqlust/uqlustbioschemas.jsonld b/data/uqlust/uqlustbioschemas.jsonld index 09b5265688305..0956c8965fc19 100644 --- a/data/uqlust/uqlustbioschemas.jsonld +++ b/data/uqlust/uqlustbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC5198500", + "pubmed:28031034", { "@id": "https://doi.org/10.1186/S12859-016-1381-2" }, - "pubmed:28031034" + "pmcid:PMC5198500" ], "sc:description": "Combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data.", "sc:featureList": { diff --git a/data/urlget/urlgetbioschemas.jsonld b/data/urlget/urlgetbioschemas.jsonld index 885c2e14e875e..ceee0e6f81957 100644 --- a/data/urlget/urlgetbioschemas.jsonld +++ b/data/urlget/urlgetbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK MRC", - "EMBOSS Contributors", + "UK BBSRC", "Wellcome Trust", - "UK BBSRC" + "EMBOSS Contributors" ], "sc:description": "Get URLs of data resources.", "sc:funder": [ - "UK BBSRC", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "urlget", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/ursgal/ursgalbioschemas.jsonld b/data/ursgal/ursgalbioschemas.jsonld index b09c0a3c8b113..bdfcd58ae0cb7 100644 --- a/data/ursgal/ursgalbioschemas.jsonld +++ b/data/ursgal/ursgalbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "MIT", "sc:name": "Ursgal", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/ursgal/ursgal", "sc:version": "0.6.5" diff --git a/data/usearch/usearchbioschemas.jsonld b/data/usearch/usearchbioschemas.jsonld index 65d9def2f026c..9bb0c880c050b 100644 --- a/data/usearch/usearchbioschemas.jsonld +++ b/data/usearch/usearchbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Algorithm designed to enable high-throughput, sensitive search of very large sequence databases.", "sc:name": "USEARCH", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://www.drive5.com/usearch/" } \ No newline at end of file diff --git a/data/usort/usortbioschemas.jsonld b/data/usort/usortbioschemas.jsonld index 5c7147e8a267c..ca0a3d00fd1df 100644 --- a/data/usort/usortbioschemas.jsonld +++ b/data/usort/usortbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Hao Chen", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization.", "sc:license": "Artistic-2.0", "sc:name": "uSORT", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/uSORT.html", "sc:version": "1.4.0" diff --git a/data/usr-vs/usr-vsbioschemas.jsonld b/data/usr-vs/usr-vsbioschemas.jsonld index 016e986fba6ce..f2d477c037085 100644 --- a/data/usr-vs/usr-vsbioschemas.jsonld +++ b/data/usr-vs/usr-vsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Webserver for large-scale prospective virtual screening using USR and USRCAT, two ultrafast ligand-based 3D molecular similarity methods that have been retrospectively validated.", "sc:name": "USR-VS", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://usr.marseille.inserm.fr/" } \ No newline at end of file diff --git a/data/utap/utapbioschemas.jsonld b/data/utap/utapbioschemas.jsonld index 5b1d5b4ea3f06..10104067c4625 100644 --- a/data/utap/utapbioschemas.jsonld +++ b/data/utap/utapbioschemas.jsonld @@ -19,22 +19,22 @@ "biotools:primaryContact": "Refael Kohen", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6434621", "pubmed:30909881", { "@id": "https://doi.org/10.1186/s12859-019-2728-2" - } + }, + "pmcid:PMC6434621" ], "sc:description": "User-friendly Transcriptome Analysis Pipeline.(UTAP) is open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently and accurately analyse transcriptome sequence data.", "sc:featureList": [ - { - "@id": "edam:operation_3680" - }, { "@id": "edam:operation_3223" }, { "@id": "edam:operation_3800" + }, + { + "@id": "edam:operation_3680" } ], "sc:name": "UTAP", diff --git a/data/utgb_toolkit/utgb_toolkitbioschemas.jsonld b/data/utgb_toolkit/utgb_toolkitbioschemas.jsonld index 340eafb41f840..7703b8f983662 100644 --- a/data/utgb_toolkit/utgb_toolkitbioschemas.jsonld +++ b/data/utgb_toolkit/utgb_toolkitbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Apache-2.0", "sc:name": "UTGB Toolkit", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://utgenome.org/index.html", "sc:version": "1.5.8" diff --git a/data/utrdb/utrdbbioschemas.jsonld b/data/utrdb/utrdbbioschemas.jsonld index d6efe28fbd6c8..3858935667c76 100644 --- a/data/utrdb/utrdbbioschemas.jsonld +++ b/data/utrdb/utrdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "UTRdb", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "ELIXIR-ITA-CNR", "sc:url": "http://utrdb.ba.itb.cnr.it/" diff --git a/data/utrsite/utrsitebioschemas.jsonld b/data/utrsite/utrsitebioschemas.jsonld index 2346de29cadd7..cb681921d97c6 100644 --- a/data/utrsite/utrsitebioschemas.jsonld +++ b/data/utrsite/utrsitebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A collection of functional sequence patterns located in UTR sequences.", "sc:name": "UTRSite", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": "ELIXIR-ITA-CNR", "sc:url": "http://utrsite.ba.itb.cnr.it/" diff --git a/data/uvp/uvpbioschemas.jsonld b/data/uvp/uvpbioschemas.jsonld index 85f63be70c3d3..42413fbe91226 100644 --- a/data/uvp/uvpbioschemas.jsonld +++ b/data/uvp/uvpbioschemas.jsonld @@ -17,8 +17,8 @@ "@id": "https://bio.tools/UVP", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Workflow" + "Workflow", + "Command-line tool" ], "sc:author": { "@id": "https://orcid.org/0000-0003-1064-6895" @@ -27,8 +27,8 @@ "sc:license": "MIT", "sc:name": "UVP", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/CPTR-ReSeqTB/UVP", "sc:version": [ diff --git a/data/v-pipe/v-pipebioschemas.jsonld b/data/v-pipe/v-pipebioschemas.jsonld index c45656d28cbc6..1f26b01b2e2a7 100644 --- a/data/v-pipe/v-pipebioschemas.jsonld +++ b/data/v-pipe/v-pipebioschemas.jsonld @@ -9,20 +9,12 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0003-4739-5110", - "@type": "schema:Person" - }, - { - "@id": "https://orcid.org/0000-0002-0573-6119", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/v-pipe", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Workflow", - "Command-line tool" + "Command-line tool", + "Workflow" ], "sc:author": [ { @@ -44,9 +36,17 @@ ], "sc:url": "https://cbg-ethz.github.io/V-pipe/" }, + { + "@id": "https://orcid.org/0000-0003-4739-5110", + "@type": "schema:Person" + }, { "@id": "https://orcid.org/0000-0002-7459-8186", "@type": "schema:Person" + }, + { + "@id": "https://orcid.org/0000-0002-0573-6119", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/vaccimm/vaccimmbioschemas.jsonld b/data/vaccimm/vaccimmbioschemas.jsonld index 07b46d54f61d5..fefdd865326a3 100644 --- a/data/vaccimm/vaccimmbioschemas.jsonld +++ b/data/vaccimm/vaccimmbioschemas.jsonld @@ -13,15 +13,15 @@ "@id": "https://bio.tools/vaccimm", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Robert Preissner", - "Joachim von Eichborn" + "Joachim von Eichborn", + "Robert Preissner" ], "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC3651379", { "@id": "https://doi.org/10.1186/1471-2105-14-127" }, + "pmcid:PMC3651379", "pubmed:23586423" ], "sc:description": "Simulating peptide vaccination in cancer therapy.", diff --git a/data/vacsol/vacsolbioschemas.jsonld b/data/vacsol/vacsolbioschemas.jsonld index f8dcd040cd77c..8158c95544f3b 100644 --- a/data/vacsol/vacsolbioschemas.jsonld +++ b/data/vacsol/vacsolbioschemas.jsonld @@ -9,20 +9,24 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-017-1540-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/vacsol", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Muhammad Rizwan", "sc:additionalType": [ - "Workflow", - "Desktop application" + "Desktop application", + "Workflow" ], "sc:citation": [ - "pubmed:28193166", "pmcid:PMC5307925", { "@id": "https://doi.org/10.1186/s12859-017-1540-0" - } + }, + "pubmed:28193166" ], "sc:description": "Automate the high throughput in silico vaccine candidate prediction process for the identification of putative vaccine candidates against the proteome of bacterial pathogens.", "sc:featureList": { @@ -31,14 +35,10 @@ "sc:name": "VacSol", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://sourceforge.net/projects/vacsol/" - }, - { - "@id": "https://doi.org/10.1186/s12859-017-1540-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/vadar/vadarbioschemas.jsonld b/data/vadar/vadarbioschemas.jsonld index c3a4f17f29fdf..d7a73a34a2373 100644 --- a/data/vadar/vadarbioschemas.jsonld +++ b/data/vadar/vadarbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.", "sc:name": "VADAR", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://redpoll.pharmacy.ualberta.ca/vadar/" } \ No newline at end of file diff --git a/data/valfold/valfoldbioschemas.jsonld b/data/valfold/valfoldbioschemas.jsonld index 6dbf50d371d2e..e33f3d06acd8d 100644 --- a/data/valfold/valfoldbioschemas.jsonld +++ b/data/valfold/valfoldbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The program is capable of predicting secondary structures with improved accuracy based on unique aptamer characteristics. It predicts not only the canonical Watson-Crick pairs but also G-G pairs derived from G-quadruplex (known structure for many aptamers) using the stem candidate selection algorithm.", "sc:name": "ValFold", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://code.google.com/p/valfold/" } \ No newline at end of file diff --git a/data/validatordb/validatordbbioschemas.jsonld b/data/validatordb/validatordbbioschemas.jsonld index 7b3346187f8f2..5d044f2cd5369 100644 --- a/data/validatordb/validatordbbioschemas.jsonld +++ b/data/validatordb/validatordbbioschemas.jsonld @@ -13,17 +13,17 @@ "sc:additionalType": "Database portal", "sc:author": "David Sehnal", "sc:contributor": [ - "Deepti Jaiswal", - "Lukáš Pravda", "Crina-Maria Ionescu", - "Radka Svobodová Vařeková" + "Lukáš Pravda", + "Radka Svobodová Vařeková", + "Deepti Jaiswal" ], "sc:description": "Database of validation results for ligands and non-standard residues in the Protein Data Bank.", "sc:name": "ValidatorDB", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "Masaryk University, Brno, Czech Republic", "sc:url": "http://webchem.ncbr.muni.cz/Platform/ValidatorDB" diff --git a/data/valtrendsdb/valtrendsdbbioschemas.jsonld b/data/valtrendsdb/valtrendsdbbioschemas.jsonld index cd1c062bfac6f..1c37aa4246d58 100644 --- a/data/valtrendsdb/valtrendsdbbioschemas.jsonld +++ b/data/valtrendsdb/valtrendsdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A web database of biomacromolecular structure validation trends.", "sc:name": "ValTrendsDB", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://webchem.ncbr.muni.cz/ValTrendsDB/index.php" } \ No newline at end of file diff --git a/data/valworkbench/valworkbenchbioschemas.jsonld b/data/valworkbench/valworkbenchbioschemas.jsonld index 8a39a2ce55740..0ba29f215b8b5 100644 --- a/data/valworkbench/valworkbenchbioschemas.jsonld +++ b/data/valworkbench/valworkbenchbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "ValWorkBench", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.math.unipa.it/~raffaele/valworkbench/" } \ No newline at end of file diff --git a/data/vampire/vampirebioschemas.jsonld b/data/vampire/vampirebioschemas.jsonld index c85f6f5acc9a1..965ebea9540bf 100644 --- a/data/vampire/vampirebioschemas.jsonld +++ b/data/vampire/vampirebioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "VAMPIRE", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://genome.ucsd.edu/microarray/" } \ No newline at end of file diff --git a/data/vamps/vampsbioschemas.jsonld b/data/vamps/vampsbioschemas.jsonld index 433d6c7a8ac66..2dda664da03b2 100644 --- a/data/vamps/vampsbioschemas.jsonld +++ b/data/vamps/vampsbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2105-15-41", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/vamps", "@type": "sc:SoftwareApplication", @@ -20,10 +16,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:24499292", - "pmcid:PMC3922339", { "@id": "https://doi.org/10.1186/1471-2105-15-41" - } + }, + "pmcid:PMC3922339" ], "sc:description": "A website for visualization and analysis of microbial population structures.", "sc:featureList": { @@ -31,11 +27,15 @@ }, "sc:name": "VAMPS", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://vamps.mbl.edu/" + }, + { + "@id": "https://doi.org/10.1186/1471-2105-15-41", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/vancomycin_tdm/vancomycin_tdmbioschemas.jsonld b/data/vancomycin_tdm/vancomycin_tdmbioschemas.jsonld index daa56f80d49d3..816c6b2b9d3fd 100644 --- a/data/vancomycin_tdm/vancomycin_tdmbioschemas.jsonld +++ b/data/vancomycin_tdm/vancomycin_tdmbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.3390/PHARMACEUTICS11050224", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/vancomycin_TDM", "@type": "sc:SoftwareApplication", @@ -31,12 +27,16 @@ "sc:license": "Unlicense", "sc:name": "vancomycin TDM", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://pipet.shinyapps.io/vancomycin" }, + { + "@id": "https://doi.org/10.3390/PHARMACEUTICS11050224", + "@type": "sc:CreativeWork" + }, { "@id": "https://orcid.org/0000-0002-9976-5120", "@type": "schema:Person" diff --git a/data/vanesa/vanesabioschemas.jsonld b/data/vanesa/vanesabioschemas.jsonld index 8bd9e752d3751..b64ad934e3eef 100644 --- a/data/vanesa/vanesabioschemas.jsonld +++ b/data/vanesa/vanesabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software application for the visualization and analysis of biomedical networks in system biology applications to create systems that can answer fundamental questions and moreover, imitate cell behavior.", "sc:name": "VANESA", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://agbi.techfak.uni-bielefeld.de/vanesa/" } \ No newline at end of file diff --git a/data/vanillaice/vanillaicebioschemas.jsonld b/data/vanillaice/vanillaicebioschemas.jsonld index b33ca7319ece1..3df90e94320be 100644 --- a/data/vanillaice/vanillaicebioschemas.jsonld +++ b/data/vanillaice/vanillaicebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1214/07-AOAS155", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/vanillaice", "@type": "sc:SoftwareApplication", @@ -18,37 +22,33 @@ "Command-line tool" ], "sc:citation": [ + "pmcid:PMC2710854", "pubmed:19609370", { "@id": "https://doi.org/10.1214/07-AOAS155" - }, - "pmcid:PMC2710854" + } ], "sc:description": "An R package that uses Hidden Markov Model for characterizing chromosomal alterations in high throughput SNP arrays.", "sc:featureList": [ { - "@id": "edam:operation_2238" + "@id": "edam:operation_3228" }, { "@id": "edam:operation_3196" }, { - "@id": "edam:operation_3228" + "@id": "edam:operation_2238" } ], "sc:license": "GPL-2.0", "sc:name": "VanillaICE", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/VanillaICE.html", "sc:version": "1.36.0" - }, - { - "@id": "https://doi.org/10.1214/07-AOAS155", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/vanno/vannobioschemas.jsonld b/data/vanno/vannobioschemas.jsonld index 20bbdc9ebc80e..f7c2469ff9434 100644 --- a/data/vanno/vannobioschemas.jsonld +++ b/data/vanno/vannobioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Visualization-aided variant annotation tool.", "sc:name": "Vanno", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://cgts.cgu.edu.tw/vanno/" } \ No newline at end of file diff --git a/data/vanted/vantedbioschemas.jsonld b/data/vanted/vantedbioschemas.jsonld index f3cadb6385f59..1fa301e607e79 100644 --- a/data/vanted/vantedbioschemas.jsonld +++ b/data/vanted/vantedbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation.", "sc:name": "VANTED", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://immersive-analytics.infotech.monash.edu/vanted/", "sc:version": "2.5.3" diff --git a/data/vap/vapbioschemas.jsonld b/data/vap/vapbioschemas.jsonld index b7db6a3893481..9c687ffbdcd0c 100644 --- a/data/vap/vapbioschemas.jsonld +++ b/data/vap/vapbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "VAP is a versatile aggregate profiler for efficient genome-wide data representation and discovery. VAP was designed to be used by biologists and bioinformaticians to analyze genomic datasets to generate aggregate or individual profiles of groups of genes / annotations / regions of interest from their genome of interest.", "sc:name": "VAP", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://lab-jacques.recherche.usherbrooke.ca/vap/" } \ No newline at end of file diff --git a/data/vapros/vaprosbioschemas.jsonld b/data/vapros/vaprosbioschemas.jsonld index 82b147ed116fd..d7416f0c482d0 100644 --- a/data/vapros/vaprosbioschemas.jsonld +++ b/data/vapros/vaprosbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1007/S10969-016-9211-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/vapros", "@type": "sc:SoftwareApplication", @@ -31,6 +27,10 @@ }, "sc:name": "VaProS", "sc:url": "http://pford.info/vapros/" + }, + { + "@id": "https://doi.org/10.1007/S10969-016-9211-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/vardetect/vardetectbioschemas.jsonld b/data/vardetect/vardetectbioschemas.jsonld index cdb10c83b6668..39fd12ec58779 100644 --- a/data/vardetect/vardetectbioschemas.jsonld +++ b/data/vardetect/vardetectbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces.", "sc:name": "VarDetect", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www4a.biotec.or.th/GI/tools/vardetect" } \ No newline at end of file diff --git a/data/vargenius/vargeniusbioschemas.jsonld b/data/vargenius/vargeniusbioschemas.jsonld index ed38a78ccbfaf..2ab11dd56f913 100644 --- a/data/vargenius/vargeniusbioschemas.jsonld +++ b/data/vargenius/vargeniusbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0001-9440-1080", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-018-2532-4", "@type": "sc:CreativeWork" }, + { + "@id": "https://orcid.org/0000-0001-9440-1080", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/VarGenius", "@type": "sc:SoftwareApplication", @@ -25,11 +25,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ + "pubmed:30541431", + "pmcid:PMC6291943", { "@id": "https://doi.org/10.1186/s12859-018-2532-4" - }, - "pubmed:30541431", - "pmcid:PMC6291943" + } ], "sc:description": "VarGenius is a platform for analysis of variants from DNA sequencing data. Currently it can be used for WES and Panels. Starting from fastq files it can execute the GATK Best Practices pipeline doing both single calling and joint calling. Then it executes Annovar for variant annotation and generates a readable output in tabular and XLS format. All the data extracted from the samples (variants, genotypes, etc..) are uploaded into a Postgres database which can be used for further downstream analyses.", "sc:name": "VarGenius", diff --git a/data/variancepartition/variancepartitionbioschemas.jsonld b/data/variancepartition/variancepartitionbioschemas.jsonld index 2ea4e1c752b4e..4cb9fb54075b0 100644 --- a/data/variancepartition/variancepartitionbioschemas.jsonld +++ b/data/variancepartition/variancepartitionbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-0957-0224", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/variancepartition", "@type": "sc:SoftwareApplication", @@ -22,8 +26,8 @@ "@id": "edam:data_2884" }, "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:applicationSubCategory": [ { @@ -52,17 +56,13 @@ "sc:license": "GPL-2.0", "sc:name": "variancePartition", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/variancePartition.html", "sc:version": "1.4.1" }, - { - "@id": "http://orcid.org/0000-0002-0957-0224", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/s12859-016-1323-z", "@type": "sc:CreativeWork" diff --git a/data/variant/variantbioschemas.jsonld b/data/variant/variantbioschemas.jsonld index ee6c7f7667f11..56c333310cc14 100644 --- a/data/variant/variantbioschemas.jsonld +++ b/data/variant/variantbioschemas.jsonld @@ -12,20 +12,20 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "babelomics@cipf.es (Francisco García)", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Command line, web service, and web interface for fast and accurate functional characterization of variants found by Next Generation Sequencing.", "sc:name": "VARIANT", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": [ "http://bioinfo.cipf.es", - "Computational Genomics Department. Prince Felipe Research Center (CIPF)", - "cipf.es" + "cipf.es", + "Computational Genomics Department. Prince Felipe Research Center (CIPF)" ], "sc:url": "http://variant.bioinfo.cipf.es/", "sc:version": "1" diff --git a/data/variant_combinaton_pathogenicity_predictor/variant_combinaton_pathogenicity_predictorbioschemas.jsonld b/data/variant_combinaton_pathogenicity_predictor/variant_combinaton_pathogenicity_predictorbioschemas.jsonld index 7c32c45494d4a..fc57c251b4948 100644 --- a/data/variant_combinaton_pathogenicity_predictor/variant_combinaton_pathogenicity_predictorbioschemas.jsonld +++ b/data/variant_combinaton_pathogenicity_predictor/variant_combinaton_pathogenicity_predictorbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0003-3645-1455", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/Variant_Combinaton_Pathogenicity_Predictor", "@type": "sc:SoftwareApplication", @@ -21,17 +25,13 @@ "sc:license": "CC-BY-NC-ND-4.0", "sc:name": "Variant Combination Pathogenicity Predictor (VarCoPP)", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "Interuniversity Institute of Bioinformatics in Brussels", "sc:url": "http://varcopp.ibsquare.be", "sc:version": "1.0" - }, - { - "@id": "https://orcid.org/0000-0003-3645-1455", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/variant_ranker/variant_rankerbioschemas.jsonld b/data/variant_ranker/variant_rankerbioschemas.jsonld index fd59c11b5c075..1ad995169e00c 100644 --- a/data/variant_ranker/variant_rankerbioschemas.jsonld +++ b/data/variant_ranker/variant_rankerbioschemas.jsonld @@ -9,21 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-017-1752-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/variant_ranker", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "John Alexander", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC5514526", + "pubmed:28716001", { "@id": "https://doi.org/10.1186/s12859-017-1752-3" - }, - "pmcid:PMC5514526", - "pubmed:28716001" + } ], "sc:description": "Performs ranking and annotation of variants in genomic datasets, integrating information from multiple sources to prioritize each variant by its deleteriousness, novelty and existing information.", "sc:featureList": { @@ -36,6 +32,10 @@ "Linux" ], "sc:url": "http://paschou-lab.mbg.duth.gr/html5up/index.html" + }, + { + "@id": "https://doi.org/10.1186/s12859-017-1752-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/variant_score_ranker/variant_score_rankerbioschemas.jsonld b/data/variant_score_ranker/variant_score_rankerbioschemas.jsonld index fe0373f6b3b84..2ee46dd2707ca 100644 --- a/data/variant_score_ranker/variant_score_rankerbioschemas.jsonld +++ b/data/variant_score_ranker/variant_score_rankerbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "Unlicense", "sc:name": "Variant Score Ranker", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://vsranker.broadinstitute.org" } \ No newline at end of file diff --git a/data/variantannotation/variantannotationbioschemas.jsonld b/data/variantannotation/variantannotationbioschemas.jsonld index 553e882e60679..e1be674d10df1 100644 --- a/data/variantannotation/variantannotationbioschemas.jsonld +++ b/data/variantannotation/variantannotationbioschemas.jsonld @@ -26,22 +26,22 @@ "Library" ], "sc:citation": [ + "pubmed:24681907", { "@id": "https://doi.org/10.1093/bioinformatics/btu168" }, - "pubmed:24681907", "pmcid:PMC4080743" ], "sc:description": "Annotate variants, compute amino acid coding changes, predict coding outcomes.", "sc:featureList": [ - { - "@id": "edam:operation_3661" - }, { "@id": "edam:operation_3202" }, { "@id": "edam:operation_3225" + }, + { + "@id": "edam:operation_3661" } ], "sc:license": "Artistic-2.0", diff --git a/data/variantclassifier/variantclassifierbioschemas.jsonld b/data/variantclassifier/variantclassifierbioschemas.jsonld index 5d83a683c9d4e..7ebcfd9021d09 100644 --- a/data/variantclassifier/variantclassifierbioschemas.jsonld +++ b/data/variantclassifier/variantclassifierbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Software tool for hierarchically classifying variants based on the genome annotation that is provided. Instead of looking at a region of the genome and seeing all the features relative to each other on the genomic axis, the tool inverts the process so that novel variants can be tested for interest, based on the known features on the genomic axis. Furthermore, our hierarchical classification provides a prioritisation of the variants that should be considered for more intensive study.", "sc:name": "VariantClassifier", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.jcvi.org/cms/research/projects/variantclassifier" } \ No newline at end of file diff --git a/data/variantfiltering/bioconda_variantfiltering.yaml b/data/variantfiltering/bioconda_variantfiltering.yaml index 23ded52c7bb4c..78942f229dc4d 100644 --- a/data/variantfiltering/bioconda_variantfiltering.yaml +++ b/data/variantfiltering/bioconda_variantfiltering.yaml @@ -5,7 +5,6 @@ description: Filter genetic variants using different criteria such as inheritanc home: https://bioconductor.org/packages/3.10/bioc/html/VariantFiltering.html identifiers: - biotools:variantfiltering -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-variantfiltering summary: Filtering of coding and non-coding genetic variants diff --git a/data/variantfiltering/variantfilteringbioschemas.jsonld b/data/variantfiltering/variantfilteringbioschemas.jsonld index 96b686a6f2799..2981b6e616b3d 100644 --- a/data/variantfiltering/variantfilteringbioschemas.jsonld +++ b/data/variantfiltering/variantfilteringbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Robert Castelo", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.", "sc:license": "Artistic-2.0", "sc:name": "VariantFiltering", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/VariantFiltering.html", diff --git a/data/variantmetacaller/variantmetacallerbioschemas.jsonld b/data/variantmetacaller/variantmetacallerbioschemas.jsonld index a8dc6a2536534..8139467a29c29 100644 --- a/data/variantmetacaller/variantmetacallerbioschemas.jsonld +++ b/data/variantmetacaller/variantmetacallerbioschemas.jsonld @@ -15,11 +15,11 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC4625715", + "pubmed:26510841", { "@id": "https://doi.org/10.1186/S12864-015-2050-Y" }, - "pubmed:26510841" + "pmcid:PMC4625715" ], "sc:description": "Automated fusion of variant calling pipelines for quantitative, precision-based filtering.", "sc:featureList": { diff --git a/data/varianttools/varianttoolsbioschemas.jsonld b/data/varianttools/varianttoolsbioschemas.jsonld index a24b80dd44339..34fbeb12a2a80 100644 --- a/data/varianttools/varianttoolsbioschemas.jsonld +++ b/data/varianttools/varianttoolsbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "VariantTools", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/VariantTools.html", "sc:version": "1.16.0" diff --git a/data/variational_bayes_approach_gemini/variational_bayes_approach_geminibioschemas.jsonld b/data/variational_bayes_approach_gemini/variational_bayes_approach_geminibioschemas.jsonld index d221908be2102..d3e0c9f5fc7b0 100644 --- a/data/variational_bayes_approach_gemini/variational_bayes_approach_geminibioschemas.jsonld +++ b/data/variational_bayes_approach_gemini/variational_bayes_approach_geminibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "BSD-3-Clause", "sc:name": "Variational Bayes approach (GEMINI)", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "https://github.com/sellerslab/gemini" diff --git a/data/variationget/variationgetbioschemas.jsonld b/data/variationget/variationgetbioschemas.jsonld index 38a953442ff27..b965f2b143659 100644 --- a/data/variationget/variationgetbioschemas.jsonld +++ b/data/variationget/variationgetbioschemas.jsonld @@ -13,26 +13,26 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "UK MRC", "EMBOSS Contributors", + "UK MRC", "UK BBSRC" ], "sc:description": "An Emboss tool that reads sequence variation data and writes the data in one of the EMBOSS variation output formats", "sc:funder": [ + "UK MRC", "UK BBSRC", - "Wellcome Trust", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "variationget", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://www.bioinformatics.nl/cgi-bin/emboss/variationget", "sc:version": "r6" diff --git a/data/varibench/varibenchbioschemas.jsonld b/data/varibench/varibenchbioschemas.jsonld index 21de503a4ce62..2d9e266ef143b 100644 --- a/data/varibench/varibenchbioschemas.jsonld +++ b/data/varibench/varibenchbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Unlicense", "sc:name": "VariBench", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://structure.bmc.lu.se/VariBench/" diff --git a/data/varid/varidbioschemas.jsonld b/data/varid/varidbioschemas.jsonld index 031217204eb25..58bcedb718e64 100644 --- a/data/varid/varidbioschemas.jsonld +++ b/data/varid/varidbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "VARID", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://compbio.cs.utoronto.ca/varid/" } \ No newline at end of file diff --git a/data/variobox/varioboxbioschemas.jsonld b/data/variobox/varioboxbioschemas.jsonld index 1ec23689362e2..5f0b593598c11 100644 --- a/data/variobox/varioboxbioschemas.jsonld +++ b/data/variobox/varioboxbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "VarioBox", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinformatics.ua.pt/software/variobox/" } \ No newline at end of file diff --git a/data/variowatch/variowatchbioschemas.jsonld b/data/variowatch/variowatchbioschemas.jsonld index e333012a6ff4b..65366a1fca7e4 100644 --- a/data/variowatch/variowatchbioschemas.jsonld +++ b/data/variowatch/variowatchbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Unlicense", "sc:name": "VarioWatch", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://grch38.genepipe.ncgm.sinica.edu.tw/variowatch/main.do" } \ No newline at end of file diff --git a/data/varmap/varmapbioschemas.jsonld b/data/varmap/varmapbioschemas.jsonld index 4a1f37fa5d91c..aad0852e4c312 100644 --- a/data/varmap/varmapbioschemas.jsonld +++ b/data/varmap/varmapbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "VarMap", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/DisaStr/GetPage.pl?varmap=TRUE" diff --git a/data/varmod/varmodbioschemas.jsonld b/data/varmod/varmodbioschemas.jsonld index 82fb3d23905fe..811a48d6fee28 100644 --- a/data/varmod/varmodbioschemas.jsonld +++ b/data/varmod/varmodbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "VarMod", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.wasslab.org/varmod" } \ No newline at end of file diff --git a/data/varprism/varprismbioschemas.jsonld b/data/varprism/varprismbioschemas.jsonld index 8772bbba4a97f..0556636d3e55b 100644 --- a/data/varprism/varprismbioschemas.jsonld +++ b/data/varprism/varprismbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Contact form", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:27562213", - "pmcid:PMC4997702", { "@id": "https://doi.org/10.1186/S13073-016-0341-9" - } + }, + "pubmed:27562213", + "pmcid:PMC4997702" ], "sc:description": "Incorporating variant prioritization in tests of de novo mutation association.", "sc:featureList": { diff --git a/data/varscan/varscanbioschemas.jsonld b/data/varscan/varscanbioschemas.jsonld index 19fd0cb639fe5..7d6cc13256903 100644 --- a/data/varscan/varscanbioschemas.jsonld +++ b/data/varscan/varscanbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "VarScan", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://dkoboldt.github.io/varscan/" } \ No newline at end of file diff --git a/data/varsifter/varsifterbioschemas.jsonld b/data/varsifter/varsifterbioschemas.jsonld index 7e794ff32286b..b71b88e7ae061 100644 --- a/data/varsifter/varsifterbioschemas.jsonld +++ b/data/varsifter/varsifterbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Graphical java program designed to display, sort, filter, and generally sift variation data from massively parallel sequencing experiments.It is designed to read exome-scale variation data in either a tab-delimited text file with header, or an uncompressed VCF file (see User Guide for details.) These files should be pre-generated with desired annotation information one would like to view.", "sc:name": "VarSifter", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://research.nhgri.nih.gov/software/VarSifter/" } \ No newline at end of file diff --git a/data/varsome/varsomebioschemas.jsonld b/data/varsome/varsomebioschemas.jsonld index 5b8c8ec12075d..85b1c47d84b23 100644 --- a/data/varsome/varsomebioschemas.jsonld +++ b/data/varsome/varsomebioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "A search engine for human genomic variants.", "sc:name": "VarSome", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://varsome.com/" } \ No newline at end of file diff --git a/data/vas/vasbioschemas.jsonld b/data/vas/vasbioschemas.jsonld index 916dca922984b..787e20e8e3e99 100644 --- a/data/vas/vasbioschemas.jsonld +++ b/data/vas/vasbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Kevin Y Yip", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC4210471", { "@id": "https://doi.org/10.1186/1471-2164-15-886" }, + "pmcid:PMC4210471", "pubmed:25306238" ], "sc:description": "A convenient web portal for efficient integration of genomic features with millions of genetic variants.", diff --git a/data/vasp/vaspbioschemas.jsonld b/data/vasp/vaspbioschemas.jsonld index d51996cd16187..8a349a706df1b 100644 --- a/data/vasp/vaspbioschemas.jsonld +++ b/data/vasp/vaspbioschemas.jsonld @@ -18,11 +18,11 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:20814581", - "pmcid:PMC2930297", { "@id": "https://doi.org/10.1371/JOURNAL.PCBI.1000881" - } + }, + "pubmed:20814581", + "pmcid:PMC2930297" ], "sc:description": "Vienna Ab initio Simulation Package. Tool for comparison of binding sites in aligned protein structures. Uses solid volumes to represent protein shape and the shape of surface cavities, clefts and tunnels that are defined with other methods.", "sc:featureList": [ diff --git a/data/vast/vastbioschemas.jsonld b/data/vast/vastbioschemas.jsonld index 0f704038947d1..7aa3b59522fc6 100644 --- a/data/vast/vastbioschemas.jsonld +++ b/data/vast/vastbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "VAST", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml" } \ No newline at end of file diff --git a/data/vastdb/vastdbbioschemas.jsonld b/data/vastdb/vastdbbioschemas.jsonld index fa0ac4a647586..4d5942dcdcb23 100644 --- a/data/vastdb/vastdbbioschemas.jsonld +++ b/data/vastdb/vastdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "Freeware", "sc:name": "VastDB", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://vastdb.crg.eu/" } \ No newline at end of file diff --git a/data/vat/vatbioschemas.jsonld b/data/vat/vatbioschemas.jsonld index c06c513ba17a2..17d3a417bca58 100644 --- a/data/vat/vatbioschemas.jsonld +++ b/data/vat/vatbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1111/cge.12257", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/vat", "@type": "sc:SoftwareApplication", @@ -38,11 +34,15 @@ ], "sc:name": "VAT", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://opengenetics.ca/2015/02/25/variant-assessment-tool-vat/" + }, + { + "@id": "https://doi.org/10.1111/cge.12257", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/vbmp/vbmpbioschemas.jsonld b/data/vbmp/vbmpbioschemas.jsonld index 94e2889e5e6b4..19a707672f9de 100644 --- a/data/vbmp/vbmpbioschemas.jsonld +++ b/data/vbmp/vbmpbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Nicola Lama", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package implements multinomial probit regression with Gaussian Process priors and\nestimates class membership posterior probability employing variational and sparse approximation\nto the full posterior.", "sc:license": "GPL-2.0", "sc:name": "vbmp", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/vbmp.html", "sc:version": "1.46.0" diff --git a/data/vcf-server/vcf-serverbioschemas.jsonld b/data/vcf-server/vcf-serverbioschemas.jsonld index 007dc500dac9f..9f9b0fb203d8a 100644 --- a/data/vcf-server/vcf-serverbioschemas.jsonld +++ b/data/vcf-server/vcf-serverbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0001-8347-0830", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/VCF-Server", "@type": "sc:SoftwareApplication", @@ -18,36 +22,32 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:31127704", + "pmcid:PMC6625089", { "@id": "https://doi.org/10.1002/MGG3.641" - }, - "pmcid:PMC6625089" + } ], "sc:description": "A web-based visualization tool for high-throughput variant data mining and management.", "sc:featureList": [ - { - "@id": "edam:operation_3227" - }, { "@id": "edam:operation_1812" }, { "@id": "edam:operation_3675" + }, + { + "@id": "edam:operation_3227" } ], "sc:license": "GPL-3.0", "sc:name": "VCF-Server", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://diseasegps.sjtu.edu.cn/VCF-Server?lan=eng" }, - { - "@id": "https://orcid.org/0000-0001-8347-0830", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1002/MGG3.641", "@type": "sc:CreativeWork" diff --git a/data/vcf_consensus/vcf_consensusbioschemas.jsonld b/data/vcf_consensus/vcf_consensusbioschemas.jsonld index 98de9c1e2a8b1..ac3ee9a5e9b69 100644 --- a/data/vcf_consensus/vcf_consensusbioschemas.jsonld +++ b/data/vcf_consensus/vcf_consensusbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Apply VCF variants to a fasta file to create a new consensus sequence.", "sc:name": "vcf_consensus", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://bio.tools/vcftools", "sc:version": "0.1" diff --git a/data/vcf_remove_filtered/vcf_remove_filteredbioschemas.jsonld b/data/vcf_remove_filtered/vcf_remove_filteredbioschemas.jsonld index 5dc7c8dc27387..5ad0c2f7e86ae 100644 --- a/data/vcf_remove_filtered/vcf_remove_filteredbioschemas.jsonld +++ b/data/vcf_remove_filtered/vcf_remove_filteredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Remove filtered lines from vcf files.", "sc:name": "vcf_remove_filtered", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://bio.tools/vcftools", "sc:version": "1.0.0" diff --git a/data/vcf_substract/vcf_substractbioschemas.jsonld b/data/vcf_substract/vcf_substractbioschemas.jsonld index 2a74297ee0d7f..bf3fa7c59c645 100644 --- a/data/vcf_substract/vcf_substractbioschemas.jsonld +++ b/data/vcf_substract/vcf_substractbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "vcf_substract", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://bio.tools/vcftools", "sc:version": "1.0.0" diff --git a/data/vcffilterjs/vcffilterjsbioschemas.jsonld b/data/vcffilterjs/vcffilterjsbioschemas.jsonld index 367c1c39c413c..7cb289de7311e 100644 --- a/data/vcffilterjs/vcffilterjsbioschemas.jsonld +++ b/data/vcffilterjs/vcffilterjsbioschemas.jsonld @@ -17,12 +17,12 @@ "sc:license": "MIT", "sc:name": "VCFFilterJS", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ - "Institut du Thorax, Nantes, France", - "univ-nantes.fr" + "univ-nantes.fr", + "Institut du Thorax, Nantes, France" ], "sc:url": "https://github.com/lindenb/jvarkit/wiki/VCFFilterJS", "sc:version": "1.0" diff --git a/data/vcfhead/vcfheadbioschemas.jsonld b/data/vcfhead/vcfheadbioschemas.jsonld index 824140b084dc0..7d6321b6b355c 100644 --- a/data/vcfhead/vcfheadbioschemas.jsonld +++ b/data/vcfhead/vcfheadbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "MIT", "sc:name": "VcfHead", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ "Institut du Thorax, Nantes, France", diff --git a/data/vcflib/vcflibbioschemas.jsonld b/data/vcflib/vcflibbioschemas.jsonld index 5d36accef9746..0077cb7a5212c 100644 --- a/data/vcflib/vcflibbioschemas.jsonld +++ b/data/vcflib/vcflibbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "MIT", "sc:name": "Vcflib", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/vcflib/vcflib" } \ No newline at end of file diff --git a/data/vcfr/vcfrbioschemas.jsonld b/data/vcfr/vcfrbioschemas.jsonld index 67c8830cc8361..787ae63581631 100644 --- a/data/vcfr/vcfrbioschemas.jsonld +++ b/data/vcfr/vcfrbioschemas.jsonld @@ -29,8 +29,8 @@ "sc:name": "vcfR", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/vcfR/index.html", "sc:version": "1.8.0" diff --git a/data/vcftools/vcftoolsbioschemas.jsonld b/data/vcftools/vcftoolsbioschemas.jsonld index 1c1c5be175a03..092d1978b9b3a 100644 --- a/data/vcftools/vcftoolsbioschemas.jsonld +++ b/data/vcftools/vcftoolsbioschemas.jsonld @@ -15,29 +15,29 @@ "biotools:primaryContact": "Mailing list", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC3137218", - "pubmed:21653522", { "@id": "https://doi.org/10.1093/bioinformatics/btr330" - } + }, + "pmcid:PMC3137218", + "pubmed:21653522" ], "sc:description": "Provide easily accessible methods for working with complex genetic variation data in the form of VCF files.", "sc:featureList": [ - { - "@id": "edam:operation_2409" - }, { "@id": "edam:operation_3197" }, { "@id": "edam:operation_3675" + }, + { + "@id": "edam:operation_2409" } ], "sc:license": "GPL-3.0", "sc:name": "VCFtools", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://vcftools.github.io/index.html" }, diff --git a/data/vcftotree/vcftotreebioschemas.jsonld b/data/vcftotree/vcftotreebioschemas.jsonld index b95bcb46a219c..9a80d955f9938 100644 --- a/data/vcftotree/vcftotreebioschemas.jsonld +++ b/data/vcftotree/vcftotreebioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Duo Xu", "sc:additionalType": "Desktop application", "sc:citation": [ - "pmcid:PMC5615795", { "@id": "https://doi.org/10.1186/s12859-017-1844-0" }, + "pmcid:PMC5615795", "pubmed:28950836" ], "sc:description": "User-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.", diff --git a/data/vcfutils/vcfutilsbioschemas.jsonld b/data/vcfutils/vcfutilsbioschemas.jsonld index 1aa1bea53146c..5239b332ba18d 100644 --- a/data/vcfutils/vcfutilsbioschemas.jsonld +++ b/data/vcfutils/vcfutilsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "vcfutils", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.htslib.org/", "sc:version": "0.1.18" diff --git a/data/vcnet/vcnetbioschemas.jsonld b/data/vcnet/vcnetbioschemas.jsonld index 0613b4ba3f29a..891a61272f749 100644 --- a/data/vcnet/vcnetbioschemas.jsonld +++ b/data/vcnet/vcnetbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "GPL-3.0", "sc:name": "VCNet", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/wangzengmiao/VCNet" } \ No newline at end of file diff --git a/data/vcpa/vcpabioschemas.jsonld b/data/vcpa/vcpabioschemas.jsonld index f22d072274956..07a177e7790f7 100644 --- a/data/vcpa/vcpabioschemas.jsonld +++ b/data/vcpa/vcpabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "MIT", "sc:name": "VCPA", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://www.niagads.org/resources/tools-and-software/vcpa" } \ No newline at end of file diff --git a/data/vdjpuzzle/vdjpuzzlebioschemas.jsonld b/data/vdjpuzzle/vdjpuzzlebioschemas.jsonld index 23ec0e7b20408..0f3e321c84547 100644 --- a/data/vdjpuzzle/vdjpuzzlebioschemas.jsonld +++ b/data/vdjpuzzle/vdjpuzzlebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "B-cell receptor reconstruction from single-cell RNA-seq.", "sc:name": "VDJPuzzle", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://bitbucket.org/kirbyvisp/vdjpuzzle2" } \ No newline at end of file diff --git a/data/vdjsolver/vdjsolverbioschemas.jsonld b/data/vdjsolver/vdjsolverbioschemas.jsonld index cdd2a13a095f6..c62e3f68e3e14 100644 --- a/data/vdjsolver/vdjsolverbioschemas.jsonld +++ b/data/vdjsolver/vdjsolverbioschemas.jsonld @@ -16,8 +16,8 @@ "@id": "http://orcid.org/0000-0001-7885-4311" }, "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:17005006", "sc:description": "Tool for analysing human immunoglobulin VDJ recombination.", diff --git a/data/vdjviz/vdjvizbioschemas.jsonld b/data/vdjviz/vdjvizbioschemas.jsonld index 2954b5cd3f0df..3c9ce6ad7d800 100644 --- a/data/vdjviz/vdjvizbioschemas.jsonld +++ b/data/vdjviz/vdjvizbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "Mikhail Shugay", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:27297497", { "@id": "https://doi.org/10.1186/S12864-016-2799-7" }, - "pmcid:PMC4907000" + "pmcid:PMC4907000", + "pubmed:27297497" ], "sc:description": "Versatile browser for immunogenomics data.", "sc:featureList": { @@ -32,8 +32,8 @@ "sc:name": "VDJviz", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/antigenomics/vdjviz" } diff --git a/data/vect/vectbioschemas.jsonld b/data/vect/vectbioschemas.jsonld index 6f090a2077112..19ddf3c454a71 100644 --- a/data/vect/vectbioschemas.jsonld +++ b/data/vect/vectbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Visual extraction conversion program that provides biomedical researches with minimal computer programming background a way to generate data extraction and conversion programs. It provides a convenient graphical user interface that allows using common point and click methods to extract and arrange data in the way that is useful to their purposes and then provides the computer program to generate such results on other documents with the same formatting.", "sc:name": "Vect", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.complex.iastate.edu/download/Vect/" } \ No newline at end of file diff --git a/data/vectorbase/vectorbasebioschemas.jsonld b/data/vectorbase/vectorbasebioschemas.jsonld index 5629bc62a1f20..5ad641587f32a 100644 --- a/data/vectorbase/vectorbasebioschemas.jsonld +++ b/data/vectorbase/vectorbasebioschemas.jsonld @@ -29,20 +29,20 @@ "sc:additionalType": "Database portal", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0078" + "@id": "edam:topic_0622" }, { - "@id": "edam:topic_0622" + "@id": "edam:topic_0078" }, { "@id": "edam:topic_0114" } ], "sc:citation": [ + "pubmed:19028744", { "@id": "https://doi.org/10.1093/nar/gkn857" }, - "pubmed:19028744", "pmcid:PMC2686483" ], "sc:description": "Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. It annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, it contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis.", @@ -51,8 +51,8 @@ }, "sc:name": "VectorBase", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "Identifiers.org", diff --git a/data/vectornti/vectorntibioschemas.jsonld b/data/vectornti/vectorntibioschemas.jsonld index 291111d6a49af..f894e04df5669 100644 --- a/data/vectornti/vectorntibioschemas.jsonld +++ b/data/vectornti/vectorntibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Application for integrated for molecular sequence analysis including primer design, virtual cloning, alignments, and sequence assembly. The free license needs to be renewed every year.", "sc:name": "VectorNTI", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://www.thermofisher.com/dk/en/home/life-science/cloning/vector-nti-software.html" } \ No newline at end of file diff --git a/data/vectorstrip/vectorstripbioschemas.jsonld b/data/vectorstrip/vectorstripbioschemas.jsonld index c20696f8993a7..caffa7ed0244d 100644 --- a/data/vectorstrip/vectorstripbioschemas.jsonld +++ b/data/vectorstrip/vectorstripbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "UK MRC", + "EMBOSS Contributors", "UK BBSRC", "Wellcome Trust" ], "sc:description": "Remove vectors from the ends of nucleotide sequence(s).", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", - "UK MRC" + "UK MRC", + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "vectorstrip", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/vectorstrip.html", "sc:version": "r6" diff --git a/data/vega/vegabioschemas.jsonld b/data/vega/vegabioschemas.jsonld index d065eaac563fb..d2889241e520a 100644 --- a/data/vega/vegabioschemas.jsonld +++ b/data/vega/vegabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sandro Morganella", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The Variational Estimator for Genomic Aberrations is an algorithm that adapts a very popular variational model (Mumford and Shah) used in image segmentation so that chromosomal aberrant regions can be efficiently detected.", "sc:license": "GPL-2.0", "sc:name": "Vega", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/Vega.html", "sc:version": "1.22.0" diff --git a/data/vega_annotation_browser/vega_annotation_browserbioschemas.jsonld b/data/vega_annotation_browser/vega_annotation_browserbioschemas.jsonld index 5b446f3e1e393..a43fc9de12040 100644 --- a/data/vega_annotation_browser/vega_annotation_browserbioschemas.jsonld +++ b/data/vega_annotation_browser/vega_annotation_browserbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality curation of finished sequence.", "sc:name": "Vega Annotation Browser", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://vega.sanger.ac.uk" } \ No newline at end of file diff --git a/data/vegamc/vegamcbioschemas.jsonld b/data/vegamc/vegamcbioschemas.jsonld index b061fd339acfe..34123f728cd6b 100644 --- a/data/vegamc/vegamcbioschemas.jsonld +++ b/data/vegamc/vegamcbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "VegaMC", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/VegaMC.html", "sc:version": "3.12.0" diff --git a/data/vegas2/vegas2bioschemas.jsonld b/data/vegas2/vegas2bioschemas.jsonld index 9b44cefc09f10..248d4b4609cd2 100644 --- a/data/vegas2/vegas2bioschemas.jsonld +++ b/data/vegas2/vegas2bioschemas.jsonld @@ -15,16 +15,16 @@ "A. Mishra" ], "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:25518859", "sc:description": "An extension that uses 1,000 Genomes data to model SNP correlations across the autosomes and chromosome X. It allows greater flexibility when defining gene boundaries.", "sc:name": "VEGAS2", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://vegas2.qimrberghofer.edu.au/" } \ No newline at end of file diff --git a/data/velvet/velvetbioschemas.jsonld b/data/velvet/velvetbioschemas.jsonld index eba55ed4997ad..dca3ded40f915 100644 --- a/data/velvet/velvetbioschemas.jsonld +++ b/data/velvet/velvetbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "GPL-3.0", "sc:name": "Velvet", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/dzerbino/velvet" } \ No newline at end of file diff --git a/data/velvetoptimiser/velvetoptimiserbioschemas.jsonld b/data/velvetoptimiser/velvetoptimiserbioschemas.jsonld index 18ad3a20d917d..f3e91f0c2b2c6 100644 --- a/data/velvetoptimiser/velvetoptimiserbioschemas.jsonld +++ b/data/velvetoptimiser/velvetoptimiserbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/velvetoptimiser", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Torsten Seemann", "Australia", - "Simon Gladman" + "Simon Gladman", + "Torsten Seemann" ], "sc:additionalType": "Command-line tool", "sc:author": [ diff --git a/data/venn_diagrams/venn_diagramsbioschemas.jsonld b/data/venn_diagrams/venn_diagramsbioschemas.jsonld index 695874a66fb73..683b7fba722ae 100644 --- a/data/venn_diagrams/venn_diagramsbioschemas.jsonld +++ b/data/venn_diagrams/venn_diagramsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "With this tool you can calculate the intersection(s) of list of elements. It will generate a textual output indicating which elements are in each intersection or are unique to a certain list. If the number of lists is lower than 6 it will also produce a graphical output in the form of a venn diagram. You have the choice between symmetric (default) or non symmetric venn diagrams. Currently you are able to calculate the intersections of at maximum 30 lists.", "sc:name": "Venn Diagrams", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": "PSB", "sc:url": "http://bioinformatics.psb.ugent.be/webtools/Venn/", diff --git a/data/vennpainter/vennpainterbioschemas.jsonld b/data/vennpainter/vennpainterbioschemas.jsonld index 8b5115b19e6c1..4db6a33a57ea7 100644 --- a/data/vennpainter/vennpainterbioschemas.jsonld +++ b/data/vennpainter/vennpainterbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0154315", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/vennpainter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Wei Zhou", "sc:additionalType": "Desktop application", "sc:citation": [ + "pubmed:27120465", { "@id": "https://doi.org/10.1371/journal.pone.0154315" }, - "pmcid:PMC4847855", - "pubmed:27120465" + "pmcid:PMC4847855" ], "sc:description": "VennPainter is a program for depicting unique and shared sets of genes lists and generating Venn diagrams.", "sc:featureList": { @@ -28,15 +32,11 @@ "sc:license": "Other", "sc:name": "VennPainter", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://github.com/linguoliang/VennPainter/" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0154315", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/vep/vepbioschemas.jsonld b/data/vep/vepbioschemas.jsonld index 9fc0a7d4550fe..fec0b85336a07 100644 --- a/data/vep/vepbioschemas.jsonld +++ b/data/vep/vepbioschemas.jsonld @@ -12,19 +12,19 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Contact Form", "sc:additionalType": [ - "Web application", - "Command-line tool", "Script", - "Web service" + "Command-line tool", + "Web service", + "Web application" ], "sc:author": "Ensembl", "sc:description": "Tool for predicting effects of variants for any genome in Ensembl or with genome annotation (via GFF). This includes vertebrates and also plants, fungi, protists, metazoa and bacteria. There is a web and a REST API version but the most powerful is the Perl script version. See McLaren et al., 2016, Genome Biology", "sc:license": "Apache-2.0", "sc:name": "Variant Effect Predictor (VEP)", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://www.ensembl.org/vep" } \ No newline at end of file diff --git a/data/verifybamid/verifybamidbioschemas.jsonld b/data/verifybamid/verifybamidbioschemas.jsonld index fdb2fb46af174..b84b6aeb3f7ca 100644 --- a/data/verifybamid/verifybamidbioschemas.jsonld +++ b/data/verifybamid/verifybamidbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "verifyBamID", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": [ "sanger.ac.uk", diff --git a/data/verina3d/verina3dbioschemas.jsonld b/data/verina3d/verina3dbioschemas.jsonld index 5b4e796f0f2cb..a24e8579acdb9 100644 --- a/data/verina3d/verina3dbioschemas.jsonld +++ b/data/verina3d/verina3dbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/VeriNA3d", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Pablo D. Dans", - "Modesto Orozco" + "Modesto Orozco", + "Pablo D. Dans" ], "sc:additionalType": "Library", "sc:description": "R package for the analysis of nucleic acids structural data, with an emphasis in complex RNA structures.", "sc:license": "GPL-3.0", "sc:name": "VeriNA3d", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://mmb.irbbarcelona.org/gitlab/dgallego/veriNA3d" diff --git a/data/vermont/vermontbioschemas.jsonld b/data/vermont/vermontbioschemas.jsonld index a1a881758e697..2c41a621bd597 100644 --- a/data/vermont/vermontbioschemas.jsonld +++ b/data/vermont/vermontbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Multi-perspective visual interactive platform for mutational analysis.", "sc:name": "Vermont", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinfo.dcc.ufmg.br/vermont/" } \ No newline at end of file diff --git a/data/veselect/veselectbioschemas.jsonld b/data/veselect/veselectbioschemas.jsonld index 2b65f9534aee9..41d5b49351ff3 100644 --- a/data/veselect/veselectbioschemas.jsonld +++ b/data/veselect/veselectbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/veselect", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Christian Stigloher", - "Thomas Dandekar" + "Thomas Dandekar", + "Christian Stigloher" ], "sc:additionalType": "Desktop application", "sc:description": "3D automated reconstruction tool for vesicle structures of electron tomograms.", diff --git a/data/vesiclepedia/vesiclepediabioschemas.jsonld b/data/vesiclepedia/vesiclepediabioschemas.jsonld index 4446d15ef1cb2..2be5ebd1a3a6a 100644 --- a/data/vesiclepedia/vesiclepediabioschemas.jsonld +++ b/data/vesiclepedia/vesiclepediabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Manually curated compendium of molecular data (lipid, RNA and protein) identified in different classes of extracellular vesicles.", "sc:name": "Vesiclepedia", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://microvesicles.org/index.html" } \ No newline at end of file diff --git a/data/vespa/vespabioschemas.jsonld b/data/vespa/vespabioschemas.jsonld index f4925b6a6e0e7..a15423b410d2e 100644 --- a/data/vespa/vespabioschemas.jsonld +++ b/data/vespa/vespabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates.", "sc:name": "VESPA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cbb.pnnl.gov/portal/software/vespa.html" } \ No newline at end of file diff --git a/data/vexor/vexorbioschemas.jsonld b/data/vexor/vexorbioschemas.jsonld index 7c4ae88f88905..b1e5f8be78920 100644 --- a/data/vexor/vexorbioschemas.jsonld +++ b/data/vexor/vexorbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Integrative environment for prioritization of functional variants in fine-mapping analysis.", "sc:name": "VEXOR", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://romix.genome.ulaval.ca/vexor/" } \ No newline at end of file diff --git a/data/vfdb/vfdbbioschemas.jsonld b/data/vfdb/vfdbbioschemas.jsonld index 9514b917b29ca..899d0b8b43674 100644 --- a/data/vfdb/vfdbbioschemas.jsonld +++ b/data/vfdb/vfdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Comprehensive repository of bacterial virulence factors.", "sc:name": "VFDB", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.mgc.ac.cn/VFs/" } \ No newline at end of file diff --git a/data/vga/vgabioschemas.jsonld b/data/vga/vgabioschemas.jsonld index 326e17a22dac0..9894a8baeb361 100644 --- a/data/vga/vgabioschemas.jsonld +++ b/data/vga/vgabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Method for accurate assembly of a heterogeneous viral population consisting of individuals viral genomes (also known as quasi-species).", "sc:name": "VGA", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://genetics.cs.ucla.edu/vga/" } \ No newline at end of file diff --git a/data/vhldb/vhldbbioschemas.jsonld b/data/vhldb/vhldbbioschemas.jsonld index 968745071d4ea..4774f64f76187 100644 --- a/data/vhldb/vhldbbioschemas.jsonld +++ b/data/vhldb/vhldbbioschemas.jsonld @@ -20,8 +20,8 @@ "@id": "edam:data_0896" }, "sc:additionalType": [ - "Database portal", "Web API", + "Database portal", "Web application" ], "sc:applicationSubCategory": [ @@ -33,19 +33,19 @@ } ], "sc:citation": [ + "pubmed:27511743", { "@id": "https://doi.org/10.1038/srep31128" }, - "pubmed:27511743", "pmcid:PMC4980628" ], "sc:description": "A database of interactors and mutations of the human von Hippel-Lindau tumor suppressor protein (pVHL).", "sc:featureList": [ { - "@id": "edam:operation_2414" + "@id": "edam:operation_0224" }, { - "@id": "edam:operation_0224" + "@id": "edam:operation_2414" } ], "sc:isAccessibleForFree": true, diff --git a/data/vica/vicabioschemas.jsonld b/data/vica/vicabioschemas.jsonld index 6a2bbeb77dd3e..eb9638191fc40 100644 --- a/data/vica/vicabioschemas.jsonld +++ b/data/vica/vicabioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Other", "sc:name": "Vica", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/USDA-ARS-GBRU/vica", "sc:version": "v0.1.6" diff --git a/data/vicmpred/vicmpredbioschemas.jsonld b/data/vicmpred/vicmpredbioschemas.jsonld index 6ef244208838f..8d89f2a5410cf 100644 --- a/data/vicmpred/vicmpredbioschemas.jsonld +++ b/data/vicmpred/vicmpredbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Classification of bacterial proteins into virulence factors, information molecule, cellular process and metabolism molecule.", "sc:name": "VICMpred", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.imtech.res.in/raghava/vicmpred/" } \ No newline at end of file diff --git a/data/victor/victorbioschemas.jsonld b/data/victor/victorbioschemas.jsonld index ed328afa60d96..5663b0e8824f3 100644 --- a/data/victor/victorbioschemas.jsonld +++ b/data/victor/victorbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Open-source project dedicated to providing tools for analyzing and manipulating protein structures.", "sc:name": "Victor", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-PADOVA", "sc:url": "http://protein.bio.unipd.it/victor/index.php/Main_Page", diff --git a/data/vida/vidabioschemas.jsonld b/data/vida/vidabioschemas.jsonld index 4239e783a40f1..bda2f84edfe1d 100644 --- a/data/vida/vidabioschemas.jsonld +++ b/data/vida/vidabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Complete collection of homologous protein families derived from open reading frames from complete and partial virus genomes.", "sc:name": "Virus Database (VIDA)", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:provider": "rki.de", "sc:url": "http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA3/VIDA.html" diff --git a/data/vidger/vidgerbioschemas.jsonld b/data/vidger/vidgerbioschemas.jsonld index 05e7a3a9f1ce2..66d2f954172c3 100644 --- a/data/vidger/vidgerbioschemas.jsonld +++ b/data/vidger/vidgerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "GPL-2.0", "sc:name": "vidger", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/vidger.html", diff --git a/data/vidjil/vidjilbioschemas.jsonld b/data/vidjil/vidjilbioschemas.jsonld index ddcef8eca2e31..0f0a3e96ad3eb 100644 --- a/data/vidjil/vidjilbioschemas.jsonld +++ b/data/vidjil/vidjilbioschemas.jsonld @@ -13,15 +13,15 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5106020", - "pubmed:27835690" + "pubmed:27835690", + "pmcid:PMC5106020" ], "sc:description": "Open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time.", "sc:name": "Vidjil", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.vidjil.org/" } \ No newline at end of file diff --git a/data/vienna-ptm/vienna-ptmbioschemas.jsonld b/data/vienna-ptm/vienna-ptmbioschemas.jsonld index 5a6faba81f90d..06ed74f585c28 100644 --- a/data/vienna-ptm/vienna-ptmbioschemas.jsonld +++ b/data/vienna-ptm/vienna-ptmbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Vienna-PTM web server is a platform for automated introduction of post-translational modifications (PTMs) of choice to protein 3D structures.", "sc:name": "Vienna-PTM", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://vienna-ptm.univie.ac.at" } \ No newline at end of file diff --git a/data/vienna_rna_package/vienna_rna_packagebioschemas.jsonld b/data/vienna_rna_package/vienna_rna_packagebioschemas.jsonld index cf80cfdf7a120..4a289717b8389 100644 --- a/data/vienna_rna_package/vienna_rna_packagebioschemas.jsonld +++ b/data/vienna_rna_package/vienna_rna_packagebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.", "sc:name": "Vienna RNA Package", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.tbi.univie.ac.at/~ivo/RNA/" } \ No newline at end of file diff --git a/data/vienna_rna_websuite/vienna_rna_websuitebioschemas.jsonld b/data/vienna_rna_websuite/vienna_rna_websuitebioschemas.jsonld index 37f2b8d57677e..48a024d0a8a85 100644 --- a/data/vienna_rna_websuite/vienna_rna_websuitebioschemas.jsonld +++ b/data/vienna_rna_websuite/vienna_rna_websuitebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. Tools include folding of single and aligned sequences, prediction of RNA-RNA interactions, design of sequences with a given structure, analysis of folding landscapes and structural RNA alignments using LocARNA.", "sc:name": "Vienna RNA Websuite", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://rna.tbi.univie.ac.at/" diff --git a/data/viennngs/viennngsbioschemas.jsonld b/data/viennngs/viennngsbioschemas.jsonld index ee70dbea4c87d..03d9d59bdbf5d 100644 --- a/data/viennngs/viennngsbioschemas.jsonld +++ b/data/viennngs/viennngsbioschemas.jsonld @@ -10,32 +10,24 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0003-0925-5205", + "@id": "http://orcid.org/0000-0001-9564-7525", "@type": "schema:Person" }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.6157.2", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-4573-9939", "@type": "schema:Person" }, - { - "@id": "http://orcid.org/0000-0001-9564-7525", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/viennngs", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ { - "@id": "http://orcid.org/0000-0001-9564-7525" + "@id": "http://orcid.org/0000-0003-0925-5205" }, - "Fabian Amman", { - "@id": "http://orcid.org/0000-0003-0925-5205" + "@id": "http://orcid.org/0000-0001-9564-7525" }, + "Fabian Amman", { "@id": "http://orcid.org/0000-0002-4573-9939" } @@ -51,21 +43,29 @@ "sc:description": "Build efficient pipelines for NGS data processing. Extracts and converts features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, It allows identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.", "sc:featureList": [ { - "@id": "edam:operation_3800" + "@id": "edam:operation_3198" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3800" }, { "@id": "edam:operation_3435" }, { - "@id": "edam:operation_3198" + "@id": "edam:operation_2495" } ], "sc:name": "ViennNGS", "sc:url": "https://metacpan.org/release/Bio-ViennaNGS", "sc:version": "0.19" + }, + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.6157.2", + "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0003-0925-5205", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/ving/vingbioschemas.jsonld b/data/ving/vingbioschemas.jsonld index b7e165036e4d9..c9d4a6afc0904 100644 --- a/data/ving/vingbioschemas.jsonld +++ b/data/ving/vingbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/S13104-015-1404-5", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/ving", "@type": "sc:SoftwareApplication", @@ -37,6 +33,10 @@ "Mac" ], "sc:url": "http://vm-gb.curie.fr/ving/" + }, + { + "@id": "https://doi.org/10.1186/S13104-015-1404-5", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/viper/viperbioschemas.jsonld b/data/viper/viperbioschemas.jsonld index 94e5122ada2cb..23f2713905c3e 100644 --- a/data/viper/viperbioschemas.jsonld +++ b/data/viper/viperbioschemas.jsonld @@ -26,20 +26,20 @@ ], "sc:description": "The package uses gene expression data to Infer protein activity. The package uses VIPER and msVIPER algorithms.", "sc:featureList": [ - { - "@id": "edam:operation_0314" - }, { "@id": "edam:operation_3562" }, { "@id": "edam:operation_3630" + }, + { + "@id": "edam:operation_0314" } ], "sc:name": "viper", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/viper.html", diff --git a/data/viperdb/viperdbbioschemas.jsonld b/data/viperdb/viperdbbioschemas.jsonld index d0a029e91313a..10bf54b2fd3dd 100644 --- a/data/viperdb/viperdbbioschemas.jsonld +++ b/data/viperdb/viperdbbioschemas.jsonld @@ -22,12 +22,12 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:18981051", - "pmcid:PMC2686430", - "pubmed:16205712", { "@id": "https://doi.org/10.1093/nar/gkn840" - } + }, + "pubmed:16205712", + "pmcid:PMC2686430", + "pubmed:18981051" ], "sc:contributor": { "@id": "http://orcid.org/0000-0003-0060-6486" @@ -36,8 +36,8 @@ "sc:name": "VIPERdb", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "rki.de", "sc:url": "http://viperdb.scripps.edu/" diff --git a/data/vipr/viprbioschemas.jsonld b/data/vipr/viprbioschemas.jsonld index 11feaae6969db..cbf161ac748e6 100644 --- a/data/vipr/viprbioschemas.jsonld +++ b/data/vipr/viprbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkr859", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/vipr", "@type": "sc:SoftwareApplication", @@ -16,32 +20,28 @@ "@id": "http://orcid.org/0000-0001-7930-8160" }, "sc:additionalType": [ + "Database portal", "Web application", - "Workbench", - "Database portal" + "Workbench" ], "sc:citation": [ - "pubmed:22006842", "pmcid:PMC3245011", { "@id": "https://doi.org/10.1093/nar/gkr859" }, + "pubmed:22006842", "pubmed:23202522" ], "sc:description": "This database supports the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank, etc.), direct submissions, and internal curation and analysis pipelines, and provides a suite of bioinformatics analysis and visualization tools to expedite virology research.", "sc:name": "Virus Pathogen Resource (ViPR)", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:provider": "rki.de", "sc:url": "http://www.viprbrc.org/brc/home.spg?decorator=vipr" }, - { - "@id": "https://doi.org/10.1093/nar/gkr859", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0001-7930-8160", "@type": "schema:Person" diff --git a/data/viralmbd/viralmbdbioschemas.jsonld b/data/viralmbd/viralmbdbioschemas.jsonld index 0a0bc0147c8bd..0bcf710b15174 100644 --- a/data/viralmbd/viralmbdbioschemas.jsonld +++ b/data/viralmbd/viralmbdbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Viral fragment detection in MBD-seq data.", "sc:name": "ViralMBD", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://www.biobix.be/viralmbd/", diff --git a/data/viralmir/viralmirbioschemas.jsonld b/data/viralmir/viralmirbioschemas.jsonld index eb3d7d81fb7ad..51039747c9dd7 100644 --- a/data/viralmir/viralmirbioschemas.jsonld +++ b/data/viralmir/viralmirbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "First public resource dedicated to identify the microRNA precursor in virus.", "sc:name": "ViralMir", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://csb.cse.yzu.edu.tw/viralmir/" diff --git a/data/viralorfeome/viralorfeomebioschemas.jsonld b/data/viralorfeome/viralorfeomebioschemas.jsonld index 3ef0bca9f255f..b46b69b718821 100644 --- a/data/viralorfeome/viralorfeomebioschemas.jsonld +++ b/data/viralorfeome/viralorfeomebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/viralorfeome", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "C. Rabourdin-Combe", - "P. O. Vidalain" + "P. O. Vidalain", + "C. Rabourdin-Combe" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:20007148", "sc:description": "Database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. It provides an interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. It has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain.", "sc:name": "ViralORFeome", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://doi.org/10.1093/nar/gkp1000" diff --git a/data/viralphos/viralphosbioschemas.jsonld b/data/viralphos/viralphosbioschemas.jsonld index 7e73eb7614e6a..fb4f99c3a410a 100644 --- a/data/viralphos/viralphosbioschemas.jsonld +++ b/data/viralphos/viralphosbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "ViralPhos is a web server for identifying potential virus phosphorylation sites with substrate motifs.", "sc:name": "ViralPhos", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://csb.cse.yzu.edu.tw/ViralPhos/" } \ No newline at end of file diff --git a/data/viralpro/viralprobioschemas.jsonld b/data/viralpro/viralprobioschemas.jsonld index d8d4947b65aae..30ee2f59b540a 100644 --- a/data/viralpro/viralprobioschemas.jsonld +++ b/data/viralpro/viralprobioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Predictor capable of identifying capsid and tail protein sequences using support vector machines (SVM) with an accuracy estimated to be between 90% and 97%.", "sc:name": "VIRALpro", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://scratch.proteomics.ics.uci.edu" } \ No newline at end of file diff --git a/data/viralzone/viralzonebioschemas.jsonld b/data/viralzone/viralzonebioschemas.jsonld index e02c5317bb1a0..685c8ce8e6364 100644 --- a/data/viralzone/viralzonebioschemas.jsonld +++ b/data/viralzone/viralzonebioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkq901", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/viralzone", "@type": "sc:SoftwareApplication", "sc:additionalType": "Database portal", "sc:citation": [ + "pubmed:20947564", + "pmcid:PMC3013774", { "@id": "https://doi.org/10.1093/nar/gkq901" - }, - "pubmed:20947564", - "pmcid:PMC3013774" + } ], "sc:description": "A web resource for all viral genus and families, providing general molecular and epidemiological informations, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries.", "sc:featureList": [ @@ -36,11 +32,15 @@ "sc:name": "ViralZone", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": "SIB Swiss Institute of Bioinformatics", "sc:url": "http://viralzone.expasy.org" + }, + { + "@id": "https://doi.org/10.1093/nar/gkq901", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/viramp/virampbioschemas.jsonld b/data/viramp/virampbioschemas.jsonld index ce35c2a3f6042..ac8cff85b5054 100644 --- a/data/viramp/virampbioschemas.jsonld +++ b/data/viramp/virampbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. It is a collection of existing tools, combined into a single Galaxy interface. Users without further computational knowledge can easily operate the pipeline.", "sc:name": "VirAmp", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://docs.viramp.com/en/latest/introduction.html" } \ No newline at end of file diff --git a/data/virapipe/virapipebioschemas.jsonld b/data/virapipe/virapipebioschemas.jsonld index 43fc8f40b90f0..bf15830e514b1 100644 --- a/data/virapipe/virapipebioschemas.jsonld +++ b/data/virapipe/virapipebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "MIT", "sc:name": "ViraPipe", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/NGSeq/ViraPipe" } \ No newline at end of file diff --git a/data/virhostnet/virhostnetbioschemas.jsonld b/data/virhostnet/virhostnetbioschemas.jsonld index 8838dc7ba6b45..b3d4d607ee79c 100644 --- a/data/virhostnet/virhostnetbioschemas.jsonld +++ b/data/virhostnet/virhostnetbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Virus-Host Network is a knowledge-base system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains). VirHostNet contains high quality and up-to-date information gathered and curated from public databases.", "sc:name": "VirHostnet", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://virhostnet.prabi.fr/" diff --git a/data/viromescan/viromescanbioschemas.jsonld b/data/viromescan/viromescanbioschemas.jsonld index 3423e50046185..110bb9436d382 100644 --- a/data/viromescan/viromescanbioschemas.jsonld +++ b/data/viromescan/viromescanbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "https://doi.org/10.1186/s12864-016-2446-3", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0002-5655-6695", + "@type": "schema:Person" }, { "@id": "https://bio.tools/viromescan", @@ -34,14 +34,14 @@ "sc:license": "BSD-2-Clause-FreeBSD", "sc:name": "ViromeScan", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://sourceforge.net/projects/viromescan/" }, { - "@id": "http://orcid.org/0000-0002-5655-6695", - "@type": "schema:Person" + "@id": "https://doi.org/10.1186/s12864-016-2446-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/virsirnadb/virsirnadbbioschemas.jsonld b/data/virsirnadb/virsirnadbbioschemas.jsonld index 9cc47553f4091..3f0a431f1810a 100644 --- a/data/virsirnadb/virsirnadbbioschemas.jsonld +++ b/data/virsirnadb/virsirnadbbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "VIRsiRNAdb", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://crdd.osdd.net/servers/virsirnadb/" } \ No newline at end of file diff --git a/data/virtual_folder_for_structural_biology_projects/virtual_folder_for_structural_biology_projectsbioschemas.jsonld b/data/virtual_folder_for_structural_biology_projects/virtual_folder_for_structural_biology_projectsbioschemas.jsonld index 30bdbc2af5fe3..3a74b522d83fd 100644 --- a/data/virtual_folder_for_structural_biology_projects/virtual_folder_for_structural_biology_projectsbioschemas.jsonld +++ b/data/virtual_folder_for_structural_biology_projects/virtual_folder_for_structural_biology_projectsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "It provides internal file repository with limited scratch disc space available within virtual machine and accessible via WEBDAV protocol. The internal file repository can be used by installed application to execute processing tasks etc. It provides integration of external file repositories specific to user/group. Currently user specific EUDAT (B2DROP) can be mounted and data processed.", "sc:name": "Virtual Folder for Structural Biology Projects", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:provider": "STFC", diff --git a/data/virtual_pharmacist/virtual_pharmacistbioschemas.jsonld b/data/virtual_pharmacist/virtual_pharmacistbioschemas.jsonld index 14e64f09e0b89..a197c3873bd66 100644 --- a/data/virtual_pharmacist/virtual_pharmacistbioschemas.jsonld +++ b/data/virtual_pharmacist/virtual_pharmacistbioschemas.jsonld @@ -11,9 +11,9 @@ "@id": "https://bio.tools/virtual_pharmacist", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Zhoufang Li", + "Jiankui He", "Ross Ka-Kit Leung", - "Jiankui He" + "Zhoufang Li" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:26496198", @@ -21,8 +21,8 @@ "sc:name": "Virtual Pharmacist", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.sustc-genome.org.cn/vp/" } \ No newline at end of file diff --git a/data/virtual_ribosome/virtual_ribosomebioschemas.jsonld b/data/virtual_ribosome/virtual_ribosomebioschemas.jsonld index 33892f11bdd40..be6f3e1cf547b 100644 --- a/data/virtual_ribosome/virtual_ribosomebioschemas.jsonld +++ b/data/virtual_ribosome/virtual_ribosomebioschemas.jsonld @@ -18,8 +18,8 @@ "sc:name": "Virtual Ribosome", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.cbs.dtu.dk/services/VirtualRibosome/" } \ No newline at end of file diff --git a/data/virtualscreening/virtualscreeningbioschemas.jsonld b/data/virtualscreening/virtualscreeningbioschemas.jsonld index 0c1e4a8cd986e..f0de0fc1e242c 100644 --- a/data/virtualscreening/virtualscreeningbioschemas.jsonld +++ b/data/virtualscreening/virtualscreeningbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "BioExcel Virtual Screening pipeline", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://github.com/bioexcel/virtualscreening", "sc:version": "Alpha" diff --git a/data/virus_genotyping_tools/virus_genotyping_toolsbioschemas.jsonld b/data/virus_genotyping_tools/virus_genotyping_toolsbioschemas.jsonld index da98e7d3097e1..df6e4e7d16828 100644 --- a/data/virus_genotyping_tools/virus_genotyping_toolsbioschemas.jsonld +++ b/data/virus_genotyping_tools/virus_genotyping_toolsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis.", "sc:name": "Virus Genotyping Tools", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioafrica.mrc.ac.za/rega-genotype/html/" diff --git a/data/virusbanker/virusbankerbioschemas.jsonld b/data/virusbanker/virusbankerbioschemas.jsonld index ac9907a547ac2..ff93bca26d532 100644 --- a/data/virusbanker/virusbankerbioschemas.jsonld +++ b/data/virusbanker/virusbankerbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "MySQL database of virus sequences and alignments that is accessed via a Java program.", "sc:name": "Virusbanker", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioinformatics.org/virusbanker/" diff --git a/data/virusmentha/virusmenthabioschemas.jsonld b/data/virusmentha/virusmenthabioschemas.jsonld index 83dfb368ae470..4954564ae097e 100644 --- a/data/virusmentha/virusmenthabioschemas.jsonld +++ b/data/virusmentha/virusmenthabioschemas.jsonld @@ -17,17 +17,17 @@ "@id": "https://bio.tools/virusmentha", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Alberto Calderone", - "Luana Licata" + "Luana Licata", + "Alberto Calderone" ], "sc:additionalType": "Web application", "sc:author": "Alberto Calderone", "sc:citation": [ - "pmcid:PMC4384001", { "@id": "https://doi.org/10.1093/nar/gku830" }, - "pubmed:25217587" + "pubmed:25217587", + "pmcid:PMC4384001" ], "sc:contributor": "Gianni Cesareni", "sc:description": "This tool archives evidence about viral interactions collected from different manually curated protein-protein interaction databases that have adhered to the IMEx consortium.", @@ -46,8 +46,8 @@ "Windows" ], "sc:provider": [ - "ELIXIR-ITA-TORVERGATA", - "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" + "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy", + "ELIXIR-ITA-TORVERGATA" ], "sc:url": "http://virusmentha.uniroma2.it/", "sc:version": "1" diff --git a/data/virusmint/virusmintbioschemas.jsonld b/data/virusmint/virusmintbioschemas.jsonld index aa04fe07bcfc6..f01152afbee4d 100644 --- a/data/virusmint/virusmintbioschemas.jsonld +++ b/data/virusmint/virusmintbioschemas.jsonld @@ -10,8 +10,8 @@ }, "@graph": [ { - "@id": "http://orcid.org/0000-0001-9533-4246", - "@type": "schema:Person" + "@id": "https://doi.org/10.1093/nar/gkn739", + "@type": "sc:CreativeWork" }, { "@id": "https://bio.tools/virusmint", @@ -22,12 +22,12 @@ "@id": "http://orcid.org/0000-0001-9533-4246" }, "sc:citation": [ - "pmcid:PMC2686573", - "pubmed:23900247", + "pubmed:18974184", { "@id": "https://doi.org/10.1093/nar/gkn739" }, - "pubmed:18974184" + "pubmed:23900247", + "pmcid:PMC2686573" ], "sc:contributor": [ "Daniele Peluso", @@ -36,14 +36,14 @@ "sc:description": "This database aims at collecting and annotating in a structured format all the interactions between human and viral proteins and to integrate this information in the human protein interaction network.", "sc:name": "VirusMINT", "sc:provider": [ - "ELIXIR-ITA-TORVERGATA", - "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" + "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy", + "ELIXIR-ITA-TORVERGATA" ], "sc:url": "http://mint.bio.uniroma2.it/virusmint/" }, { - "@id": "https://doi.org/10.1093/nar/gkn739", - "@type": "sc:CreativeWork" + "@id": "http://orcid.org/0000-0001-9533-4246", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/virusseq/virusseqbioschemas.jsonld b/data/virusseq/virusseqbioschemas.jsonld index 33cda25384c09..367a609e3723e 100644 --- a/data/virusseq/virusseqbioschemas.jsonld +++ b/data/virusseq/virusseqbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on RNA-Seq data of 256 TCGA human cancer samples. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole genome sequencing data of human tissue.", "sc:name": "VirusSeq", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html" } \ No newline at end of file diff --git a/data/visant/visantbioschemas.jsonld b/data/visant/visantbioschemas.jsonld index 408c5b8626356..03666554ff273 100644 --- a/data/visant/visantbioschemas.jsonld +++ b/data/visant/visantbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions allow determination of over-representation and expression enrichment, integrated search and navigation of disease and drug hierarchies, drug/disease annotation, etc.", "sc:name": "VisANT", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://visant.bu.edu/" } \ No newline at end of file diff --git a/data/viscose/viscosebioschemas.jsonld b/data/viscose/viscosebioschemas.jsonld index 4a6d8b19df235..85cad562b0d25 100644 --- a/data/viscose/viscosebioschemas.jsonld +++ b/data/viscose/viscosebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "VisCoSe", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bio.math-inf.uni-greifswald.de/viscose/" } \ No newline at end of file diff --git a/data/visen/visenbioschemas.jsonld b/data/visen/visenbioschemas.jsonld index bcfa14195d926..8b2f635c4d7eb 100644 --- a/data/visen/visenbioschemas.jsonld +++ b/data/visen/visenbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "It provides a graphical visualization for statistical epistasis.  Pairwise and three-way epistatic interactions are measured using information gain and are represented using networks.", "sc:name": "ViSEN", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "https://sourceforge.net/projects/visen/" diff --git a/data/vishic/vishicbioschemas.jsonld b/data/vishic/vishicbioschemas.jsonld index 933461b04da21..fb80756e7372d 100644 --- a/data/vishic/vishicbioschemas.jsonld +++ b/data/vishic/vishicbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters.", "sc:name": "VisHiC", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://biit.cs.ut.ee/vishic" diff --git a/data/visinets/visinetsbioschemas.jsonld b/data/visinets/visinetsbioschemas.jsonld index 45aaaf9db4b8a..51c91bb40488c 100644 --- a/data/visinets/visinetsbioschemas.jsonld +++ b/data/visinets/visinetsbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1371/journal.pone.0123773", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/visinets", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC4447416", + "pubmed:26020230", { "@id": "https://doi.org/10.1371/journal.pone.0123773" - }, - "pubmed:26020230", - "pmcid:PMC4447416" + } ], "sc:description": "Visinets is a graphically oriented method for pathway modeling and a software package that allows for both modeling and visualization of biological networks in a user-friendly format.", "sc:featureList": { @@ -27,15 +31,11 @@ "sc:license": "MIT", "sc:name": "Visinets", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://www.visinets.com/index.htm" - }, - { - "@id": "https://doi.org/10.1371/journal.pone.0123773", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/visionet/visionetbioschemas.jsonld b/data/visionet/visionetbioschemas.jsonld index bfdb7be3e3d86..46618188d894c 100644 --- a/data/visionet/visionetbioschemas.jsonld +++ b/data/visionet/visionetbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Streamlined visualization to transform large and dense overlapping transcription factor networks into sparse human-readable graphs via numerically filtering.", "sc:name": "VISIONET", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://visionet.erc.monash.edu.au/index.html" diff --git a/data/vispig/vispigbioschemas.jsonld b/data/vispig/vispigbioschemas.jsonld index 01e379e9836e7..71dc5f3465686 100644 --- a/data/vispig/vispigbioschemas.jsonld +++ b/data/vispig/vispigbioschemas.jsonld @@ -14,15 +14,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": [ - "Library", - "Web application" + "Web application", + "Library" ], "sc:citation": [ - "pubmed:25208325", { "@id": "https://doi.org/10.1371/journal.pone.0107497" }, - "pmcid:PMC4160258" + "pmcid:PMC4160258", + "pubmed:25208325" ], "sc:description": "A web application to produce multi-track, multi-scale, multi-region plots of genetic data.", "sc:featureList": { @@ -31,9 +31,9 @@ "sc:license": "GPL-3.0", "sc:name": "visPIG", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://vispig.icr.ac.uk/" }, diff --git a/data/visr/visrbioschemas.jsonld b/data/visr/visrbioschemas.jsonld index 94d2d77908735..327688ceb94c1 100644 --- a/data/visr/visrbioschemas.jsonld +++ b/data/visr/visrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "VisR", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://visrsoftware.github.io", "sc:version": "0.9.4" diff --git a/data/vissr/vissrbioschemas.jsonld b/data/vissr/vissrbioschemas.jsonld index 30fb34148cb41..fe80e76a93c56 100644 --- a/data/vissr/vissrbioschemas.jsonld +++ b/data/vissr/vissrbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "VisSR (Visualisation of sRNAs): generate a visual representation of sRNAs and user-imported genomic features.", "sc:name": "VisSR", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://srna-workbench.cmp.uea.ac.uk" diff --git a/data/vista/vistabioschemas.jsonld b/data/vista/vistabioschemas.jsonld index 3937522f4f8b4..9e52f1a8c78b0 100644 --- a/data/vista/vistabioschemas.jsonld +++ b/data/vista/vistabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Vista Support", "sc:additionalType": [ - "Database portal", - "Web application" + "Web application", + "Database portal" ], "sc:citation": "pubmed:15033870", "sc:description": "Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.", "sc:name": "VISTA", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://genome.lbl.gov/vista/index.shtml" } \ No newline at end of file diff --git a/data/vista_enhancer_browser/vista_enhancer_browserbioschemas.jsonld b/data/vista_enhancer_browser/vista_enhancer_browserbioschemas.jsonld index 08b60a4708fda..f39d1f6f4c246 100644 --- a/data/vista_enhancer_browser/vista_enhancer_browserbioschemas.jsonld +++ b/data/vista_enhancer_browser/vista_enhancer_browserbioschemas.jsonld @@ -21,29 +21,29 @@ "Web application" ], "sc:citation": [ - "pubmed:17130149", + "pmcid:PMC1716724", { "@id": "https://doi.org/10.1093/nar/gkl822" }, - "pmcid:PMC1716724" + "pubmed:17130149" ], "sc:description": "A resource for experimentally validated human and mouse enhancers. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to a particular tissue, or download entire collections of enhancers with a defined tissue specificity or conservation depth.", "sc:featureList": [ - { - "@id": "edam:operation_1781" - }, { "@id": "edam:operation_0361" }, { "@id": "edam:operation_2421" + }, + { + "@id": "edam:operation_1781" } ], "sc:name": "VISTA Enhancer Browser", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "https://enhancer.lbl.gov/frnt_page_n.shtml" } diff --git a/data/vistrajectory/vistrajectorybioschemas.jsonld b/data/vistrajectory/vistrajectorybioschemas.jsonld index 17222f1e1ffe5..0e067082d6402 100644 --- a/data/vistrajectory/vistrajectorybioschemas.jsonld +++ b/data/vistrajectory/vistrajectorybioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Bayesian unidimensional scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations.", "sc:name": "visTrajectory", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "https://nlhuong.shinyapps.io/visTrajectory/" diff --git a/data/visualcna/visualcnabioschemas.jsonld b/data/visualcna/visualcnabioschemas.jsonld index 9e4d50dd11284..0578b1a966248 100644 --- a/data/visualcna/visualcnabioschemas.jsonld +++ b/data/visualcna/visualcnabioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "PyMOL plug-in for interactive Constraint Network Analysis and protein engineering for improving thermostability", "sc:name": "VisualCNA", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cpclab.uni-duesseldorf.de/software" } \ No newline at end of file diff --git a/data/vitapad/vitapadbioschemas.jsonld b/data/vitapad/vitapadbioschemas.jsonld index 1b5be1a3833ee..c9f68706d0d6c 100644 --- a/data/vitapad/vitapadbioschemas.jsonld +++ b/data/vitapad/vitapadbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Application used to visualize biological pathways and map experimental data to them.", "sc:name": "VitaPad", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://sourceforge.net/projects/vitapad/" } \ No newline at end of file diff --git a/data/vitram/vitrambioschemas.jsonld b/data/vitram/vitrambioschemas.jsonld index b3fe576faf1c9..9049c048d84f0 100644 --- a/data/vitram/vitrambioschemas.jsonld +++ b/data/vitram/vitrambioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Visualization of transcriptional modules.", "sc:name": "ViTraM", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.intec.ugent.be/kmarchal/ViTraM/Index.html", diff --git a/data/vivaldi/vivaldibioschemas.jsonld b/data/vivaldi/vivaldibioschemas.jsonld index 6aa596ebe2127..fb4ba44df34b9 100644 --- a/data/vivaldi/vivaldibioschemas.jsonld +++ b/data/vivaldi/vivaldibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). It provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information.", "sc:name": "Vivaldi", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://www.ebi.ac.uk/pdbe/vivaldi/" } \ No newline at end of file diff --git a/data/vivan/vivanbioschemas.jsonld b/data/vivan/vivanbioschemas.jsonld index 3926a1b4c5559..7f9f78b6b6436 100644 --- a/data/vivan/vivanbioschemas.jsonld +++ b/data/vivan/vivanbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations.", "sc:name": "ViVan", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://vivan.tau.ac.il/index.php" } \ No newline at end of file diff --git a/data/vivaxgen/vivaxgenbioschemas.jsonld b/data/vivaxgen/vivaxgenbioschemas.jsonld index 90fa1c56269ef..e0dc23b85ef34 100644 --- a/data/vivaxgen/vivaxgenbioschemas.jsonld +++ b/data/vivaxgen/vivaxgenbioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1371/JOURNAL.PNTD.0005465", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/vivaxgen", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Sarah Auburn", "sc:additionalType": "Web application", "sc:citation": [ + "pmcid:PMC5389845", { "@id": "https://doi.org/10.1371/JOURNAL.PNTD.0005465" }, - "pmcid:PMC5389845", "pubmed:28362818" ], "sc:description": "Open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations.", @@ -36,11 +32,15 @@ ], "sc:name": "VivaxGEN", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "http://vivaxgen.menzies.edu.au/" + }, + { + "@id": "https://doi.org/10.1371/JOURNAL.PNTD.0005465", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/vizardous/vizardousbioschemas.jsonld b/data/vizardous/vizardousbioschemas.jsonld index 42313312dfe13..0fa597a75a878 100644 --- a/data/vizardous/vizardousbioschemas.jsonld +++ b/data/vizardous/vizardousbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software for the evaluation of single-cell experiments. While its core functionality is the visualization of time-resolved, single-cell but also population data, it can be used for the automated/scripted analysis of data as well.", "sc:name": "Vizardous", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://github.com/modsim/vizardous" } \ No newline at end of file diff --git a/data/vizgvar/vizgvarbioschemas.jsonld b/data/vizgvar/vizgvarbioschemas.jsonld index 5066159f39c1a..1aa6679d90c32 100644 --- a/data/vizgvar/vizgvarbioschemas.jsonld +++ b/data/vizgvar/vizgvarbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/VizGVar", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Antonio Solano-Román", - "Allan Orozco-Solano" + "Allan Orozco-Solano", + "Antonio Solano-Román" ], "sc:description": "Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains.", "sc:name": "VizGVar", diff --git a/data/vizstruct/vizstructbioschemas.jsonld b/data/vizstruct/vizstructbioschemas.jsonld index e730cd15e50c4..d0b990554a7af 100644 --- a/data/vizstruct/vizstructbioschemas.jsonld +++ b/data/vizstruct/vizstructbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "Not licensed", "sc:name": "VizStruct", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "https://www.cse.buffalo.edu/DBGROUP/bioinformatics/supplementary/vizstruct/index.html" } \ No newline at end of file diff --git a/data/vkcdb/vkcdbbioschemas.jsonld b/data/vkcdb/vkcdbbioschemas.jsonld index c4fb68f34a987..072479db74cf0 100644 --- a/data/vkcdb/vkcdbbioschemas.jsonld +++ b/data/vkcdb/vkcdbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The Voltage-gated K(+) Channel DataBase contains full-length or nearly full-length unique channel sequences from Bacteria, Archaea and Eukaryotes. Corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses.", "sc:name": "VKCDB", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://vkcdb.biology.ualberta.ca" } \ No newline at end of file diff --git a/data/vldp/vldpbioschemas.jsonld b/data/vldp/vldpbioschemas.jsonld index 709bacedb5d11..e1872a45b33ce 100644 --- a/data/vldp/vldpbioschemas.jsonld +++ b/data/vldp/vldpbioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/vldp", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sylvain Leonard", + "Alexandre G. de Brevern", "Jeremy Esque", - "Alexandre G. de Brevern" + "Sylvain Leonard" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:23761450", "sc:description": "Web server designed to determine protein contacts, accessibility and residue volume using Laguerre diagram.", "sc:name": "VLDP", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.dsimb.inserm.fr/dsimb_tools/vldp" diff --git a/data/vmcmc/vmcmcbioschemas.jsonld b/data/vmcmc/vmcmcbioschemas.jsonld index 013286d479c1a..642e1c407f5c1 100644 --- a/data/vmcmc/vmcmcbioschemas.jsonld +++ b/data/vmcmc/vmcmcbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-017-1505-3", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/vmcmc", "@type": "sc:SoftwareApplication", @@ -27,15 +31,11 @@ }, "sc:name": "VMCMC", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://bitbucket.org/rhali/visualmcmc/" - }, - { - "@id": "https://doi.org/10.1186/s12859-017-1505-3", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/vmh/vmhbioschemas.jsonld b/data/vmh/vmhbioschemas.jsonld index 5d6b557beaf22..80d8f4a374e68 100644 --- a/data/vmh/vmhbioschemas.jsonld +++ b/data/vmh/vmhbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://orcid.org/0000-0002-8071-7110", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/VMH", "@type": "sc:SoftwareApplication", @@ -27,11 +23,15 @@ "sc:license": "Unlicense", "sc:name": "VMH", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://vmh.life" + }, + { + "@id": "https://orcid.org/0000-0002-8071-7110", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/vntrfinder/vntrfinderbioschemas.jsonld b/data/vntrfinder/vntrfinderbioschemas.jsonld index 8f0a128f3e622..bf3aef2f58a86 100644 --- a/data/vntrfinder/vntrfinderbioschemas.jsonld +++ b/data/vntrfinder/vntrfinderbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The program enables the detection of sequence length variation between arrays of inter-specific or intra-specific tandem repeats. In the absence of comparable sequences to explore observed variation, predictions are provided describing which tandem repeats are more likely to be variable, to help guide and focus further experimental evaluation.", "sc:name": "VNTRfinder", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://sites.google.com/a/codushlaine.com/colm-o-dushlaine/Data" } \ No newline at end of file diff --git a/data/vocs/vocsbioschemas.jsonld b/data/vocs/vocsbioschemas.jsonld index 07d96bd42ed88..aad9a37cb5e69 100644 --- a/data/vocs/vocsbioschemas.jsonld +++ b/data/vocs/vocsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "An easy-to-use Java GUI used to access the VBRC genome databases.", "sc:name": "VOCS", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://virology.uvic.ca/virology-ca-tools/vocs/" } \ No newline at end of file diff --git a/data/voe/voebioschemas.jsonld b/data/voe/voebioschemas.jsonld index 87fc1b9becc0f..c7343cadc3704 100644 --- a/data/voe/voebioschemas.jsonld +++ b/data/voe/voebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "A cross-platform portal for interactive data visualization.", "sc:name": "Visual Omics Explorer (VOE)", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bcil.github.io/VOE/" } \ No newline at end of file diff --git a/data/vogdb/vogdbbioschemas.jsonld b/data/vogdb/vogdbbioschemas.jsonld index b38610104662e..b8598f1917f2f 100644 --- a/data/vogdb/vogdbbioschemas.jsonld +++ b/data/vogdb/vogdbbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Virus Orthologous Groups.", "sc:name": "VOGDB", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://vogdb.org/" } \ No newline at end of file diff --git a/data/void_editor/void_editorbioschemas.jsonld b/data/void_editor/void_editorbioschemas.jsonld index 6fc1f844ada35..9ad2409941591 100644 --- a/data/void_editor/void_editorbioschemas.jsonld +++ b/data/void_editor/void_editorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "VoID Editor", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:provider": "manchester.ac.uk", "sc:url": "http://voideditor.cs.man.ac.uk/", diff --git a/data/volarea/volareabioschemas.jsonld b/data/volarea/volareabioschemas.jsonld index 51998f3da1057..957f7c7148aeb 100644 --- a/data/volarea/volareabioschemas.jsonld +++ b/data/volarea/volareabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Plug-in of the widely spread molecular graphics software Visual Molecular Dynamics (VMD), which allows the calculation of the volume as well as the surface area of any chemical structure. The surface area can be used also to map or calculate the exposed area of the structure to the solvent or to another chemical structure.", "sc:name": "Volarea", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://www.fc.up.pt/PortoBioComp/Software/Volarea/Home.html" diff --git a/data/volocity/volocitybioschemas.jsonld b/data/volocity/volocitybioschemas.jsonld index f9b3429fbd734..4b4bfe7b60118 100644 --- a/data/volocity/volocitybioschemas.jsonld +++ b/data/volocity/volocitybioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "It is the universal solution for 3D analysis of fluorescence microscopy images.  A collection of high performance 3D imaging software products, Volocity lets you turn images into understanding, relate cellular structure to function and deliver quantitative measurements for publication.", "sc:name": "Volocity Demo", "sc:operatingSystem": [ - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://www.perkinelmer.co.uk/lab-solutions/resources/docs/BRO_VolocityBrochure_PerkinElmer.pdf", "sc:version": "6.3" diff --git a/data/volpes/volpesbioschemas.jsonld b/data/volpes/volpesbioschemas.jsonld index d8a58f302b2bb..54367099aed9a 100644 --- a/data/volpes/volpesbioschemas.jsonld +++ b/data/volpes/volpesbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKZ407", - "@type": "sc:CreativeWork" - }, - { - "@id": "https://orcid.org/0000-0003-3814-3675", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/VOLPES", "@type": "sc:SoftwareApplication", @@ -25,11 +17,11 @@ }, "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:31114895", { "@id": "https://doi.org/10.1093/NAR/GKZ407" }, - "pmcid:PMC6602475" + "pmcid:PMC6602475", + "pubmed:31114895" ], "sc:description": "VOLPES (Visualization Of PhysicochEmical Sequence properties) - interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences.", "sc:featureList": [ @@ -37,10 +29,10 @@ "@id": "edam:operation_3095" }, { - "@id": "edam:operation_2518" + "@id": "edam:operation_0279" }, { - "@id": "edam:operation_0279" + "@id": "edam:operation_2518" } ], "sc:license": "Unlicense", @@ -51,6 +43,14 @@ "Mac" ], "sc:url": "http://volpes.univie.ac.at" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKZ407", + "@type": "sc:CreativeWork" + }, + { + "@id": "https://orcid.org/0000-0003-3814-3675", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/vpac/vpacbioschemas.jsonld b/data/vpac/vpacbioschemas.jsonld index 5a7c2ebf64cc8..e9557d8e65cc2 100644 --- a/data/vpac/vpacbioschemas.jsonld +++ b/data/vpac/vpacbioschemas.jsonld @@ -15,22 +15,22 @@ "biotools:primaryContact": "Rui Jiang", "sc:additionalType": "Script", "sc:citation": [ + "pmcid:PMC6509870", + "pubmed:31074382", { "@id": "https://doi.org/10.1186/S12859-019-2742-4" - }, - "pmcid:PMC6509870", - "pubmed:31074382" + } ], "sc:description": "Variational projection for accurate clustering of single-cell transcriptomic data.", "sc:featureList": [ { - "@id": "edam:operation_3557" + "@id": "edam:operation_3891" }, { - "@id": "edam:operation_3432" + "@id": "edam:operation_3557" }, { - "@id": "edam:operation_3891" + "@id": "edam:operation_3432" } ], "sc:license": "MIT", diff --git a/data/vphylomm/vphylommbioschemas.jsonld b/data/vphylomm/vphylommbioschemas.jsonld index f6633307f5f49..ebe42f4b046b0 100644 --- a/data/vphylomm/vphylommbioschemas.jsonld +++ b/data/vphylomm/vphylommbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "The purpose of the tool is to generate a transition model showing the mutational pathways of drug resistance for viruses under drug pressure.", "sc:name": "vPhyloMM", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://vphylomm.sourceforge.net/" } \ No newline at end of file diff --git a/data/vplg/vplgbioschemas.jsonld b/data/vplg/vplgbioschemas.jsonld index b07cf57457cba..abdda0c981bab 100644 --- a/data/vplg/vplgbioschemas.jsonld +++ b/data/vplg/vplgbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "This uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, e.g. usually alpha helices and beta sheets) or ligand molecules while the edges model contacts and spatial relations between them.", "sc:name": "VPLG", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.bioinformatik.uni-frankfurt.de/tools/vplg/index.html" } \ No newline at end of file diff --git a/data/vsdmip/vsdmipbioschemas.jsonld b/data/vsdmip/vsdmipbioschemas.jsonld index d2bdb4ce16707..3fac490b06d03 100644 --- a/data/vsdmip/vsdmipbioschemas.jsonld +++ b/data/vsdmip/vsdmipbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Virtual Screening Data Management on an Integrated Platform  is divided in two parts: programs which actually do things (local packages) and program which translate those things to the database (cluster packages and cartridge).", "sc:name": "VSDMIP", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://ub.cbm.uam.es/software/vsdmip/" } \ No newline at end of file diff --git a/data/vseams/vseamsbioschemas.jsonld b/data/vseams/vseamsbioschemas.jsonld index aa2c019747fe9..b3d9e57f9b256 100644 --- a/data/vseams/vseamsbioschemas.jsonld +++ b/data/vseams/vseamsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Pipeline for investigating whether a set of gene/genomic intervals is enriched for genome wide association study (GWAS) p-values for a particular trait.", "sc:name": "VSEAMS", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://github.com/ollyburren/vseams/wiki" } \ No newline at end of file diff --git a/data/vsearch/vsearchbioschemas.jsonld b/data/vsearch/vsearchbioschemas.jsonld index 01eef5fb69d88..db17a02f57f4a 100644 --- a/data/vsearch/vsearchbioschemas.jsonld +++ b/data/vsearch/vsearchbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "GPL-3.0", "sc:name": "VSEARCH", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": "UiO", "sc:url": "https://github.com/torognes/vsearch", diff --git a/data/vsn/vsnbioschemas.jsonld b/data/vsn/vsnbioschemas.jsonld index a744cddec3c60..cf2ca46076264 100644 --- a/data/vsn/vsnbioschemas.jsonld +++ b/data/vsn/vsnbioschemas.jsonld @@ -24,9 +24,9 @@ "sc:license": "Artistic-2.0", "sc:name": "vsn", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/vsn.html", "sc:version": "3.46.0" diff --git a/data/vtbuilder/vtbuilderbioschemas.jsonld b/data/vtbuilder/vtbuilderbioschemas.jsonld index 1a08386b6239f..27cc4164c03d1 100644 --- a/data/vtbuilder/vtbuilderbioschemas.jsonld +++ b/data/vtbuilder/vtbuilderbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "It is for the inference of non-chimeric contigs from read data that has been sequenced from complex multi-isoformic transcriptomes, such as snake venom glands, or rapidly evolving viral populations, such as HIV-1.", "sc:name": "VTBuilder", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.lstmed.ac.uk/vtbuilder" } \ No newline at end of file diff --git a/data/vtpnet/vtpnetbioschemas.jsonld b/data/vtpnet/vtpnetbioschemas.jsonld index faf432b46e4f4..2a241d90389e5 100644 --- a/data/vtpnet/vtpnetbioschemas.jsonld +++ b/data/vtpnet/vtpnetbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "Artistic-2.0", "sc:name": "vtpnet", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/vtpnet.html", diff --git a/data/vulcan/vulcanbioschemas.jsonld b/data/vulcan/vulcanbioschemas.jsonld index 429898933b750..5e79ef6b6d421 100644 --- a/data/vulcan/vulcanbioschemas.jsonld +++ b/data/vulcan/vulcanbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1038/ng.3593", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-7325-9908", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1038/ng.3593", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/vulcan", "@type": "sc:SoftwareApplication", @@ -25,11 +25,11 @@ }, "sc:additionalType": "Library", "sc:citation": [ - "pubmed:27322546", - "pmcid:PMC5040167", { "@id": "https://doi.org/10.1038/ng.3593" - } + }, + "pmcid:PMC5040167", + "pubmed:27322546" ], "sc:description": "VirtUaL ChIP-Seq Analysis through Networks is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data.", "sc:featureList": { @@ -38,9 +38,9 @@ "sc:license": "LGPL-3.0", "sc:name": "vulcan", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/vulcan.html", "sc:version": "1.2.0" diff --git a/data/vulcanspot/vulcanspotbioschemas.jsonld b/data/vulcanspot/vulcanspotbioschemas.jsonld index fa397681618c3..7abbf1ff5f8cd 100644 --- a/data/vulcanspot/vulcanspotbioschemas.jsonld +++ b/data/vulcanspot/vulcanspotbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "vulcanSpot", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.vulcanspot.org/" } \ No newline at end of file diff --git a/data/w-chipmotifs/w-chipmotifsbioschemas.jsonld b/data/w-chipmotifs/w-chipmotifsbioschemas.jsonld index 039223e2f6f85..b9c6378fc6e69 100644 --- a/data/w-chipmotifs/w-chipmotifsbioschemas.jsonld +++ b/data/w-chipmotifs/w-chipmotifsbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Web application tool for de novo motif discovery from ChIP-based high throughput data.", "sc:name": "W-ChIPMotifs", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://compbio.uthscsa.edu/ChIPMotifs/" } \ No newline at end of file diff --git a/data/w-iq-tree/w-iq-treebioschemas.jsonld b/data/w-iq-tree/w-iq-treebioschemas.jsonld index aa013f9b8c44b..f9b710709633b 100644 --- a/data/w-iq-tree/w-iq-treebioschemas.jsonld +++ b/data/w-iq-tree/w-iq-treebioschemas.jsonld @@ -9,20 +9,16 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/NAR/GKW256", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/w-iq-tree", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Minh BQ", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:27084950", { "@id": "https://doi.org/10.1093/NAR/GKW256" }, + "pubmed:27084950", "pmcid:PMC4987875" ], "sc:description": "A fast online phylogenetic tool for maximum likelihood analysis.", @@ -31,11 +27,15 @@ }, "sc:name": "W-IQ-TREE", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://iqtree.cibiv.univie.ac.at/" + }, + { + "@id": "https://doi.org/10.1093/NAR/GKW256", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/w3dna/w3dnabioschemas.jsonld b/data/w3dna/w3dnabioschemas.jsonld index 76fea9b0c5f39..477640608fece 100644 --- a/data/w3dna/w3dnabioschemas.jsonld +++ b/data/w3dna/w3dnabioschemas.jsonld @@ -13,37 +13,37 @@ "@id": "https://bio.tools/w3DNA", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Wilma K Olson", - "Xiang-Jun Lu" + "Xiang-Jun Lu", + "Wilma K Olson" ], "sc:additionalType": [ "Web application", "Web service" ], "sc:citation": [ - "pubmed:31114927", { "@id": "https://doi.org/10.1093/NAR/GKZ394" }, + "pubmed:31114927", "pmcid:PMC6602438" ], "sc:description": "Analysis, visualization, and modeling of 3D nucleic acid structures.", "sc:featureList": [ { - "@id": "edam:operation_0279" + "@id": "edam:operation_2518" }, { "@id": "edam:operation_3095" }, { - "@id": "edam:operation_2518" + "@id": "edam:operation_0279" } ], "sc:license": "Unlicense", "sc:name": "w3DNA", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://web.x3dna.org/" diff --git a/data/w4cseq/w4cseqbioschemas.jsonld b/data/w4cseq/w4cseqbioschemas.jsonld index 16e12ab9af1c0..62141c64584d2 100644 --- a/data/w4cseq/w4cseqbioschemas.jsonld +++ b/data/w4cseq/w4cseqbioschemas.jsonld @@ -14,15 +14,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Mingyang Cai", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": [ + "pubmed:27378289", + "pmcid:PMC5079477", { "@id": "https://doi.org/10.1093/bioinformatics/btw408" - }, - "pmcid:PMC5079477", - "pubmed:27378289" + } ], "sc:description": "w4CSeq is a software package that applies a computational and statistical approach to analyze 4C-Seq data generated from both enzyme digestion and sonication fragmentation-based methods.", "sc:featureList": { diff --git a/data/waffect/waffectbioschemas.jsonld b/data/waffect/waffectbioschemas.jsonld index 5139d43fe407e..206f387e8458c 100644 --- a/data/waffect/waffectbioschemas.jsonld +++ b/data/waffect/waffectbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Package to simulate phenotypic (case or control) datasets under a disease model H1 such that the total number of cases is constant across all the simulations (the constrain in the title).", "sc:name": "WAFFECT", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://nuel.perso.math.cnrs.fr/#software" diff --git a/data/waggawagga/waggawaggabioschemas.jsonld b/data/waggawagga/waggawaggabioschemas.jsonld index 4f2615610e89b..e2173f067c317 100644 --- a/data/waggawagga/waggawaggabioschemas.jsonld +++ b/data/waggawagga/waggawaggabioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "Web-based and command-line tool for the comparative visualization of coiled-coil predictions and the detection of stable single a-helices (SAH domains).", "sc:name": "Waggawagga", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://waggawagga.motorprotein.de/" } \ No newline at end of file diff --git a/data/war/warbioschemas.jsonld b/data/war/warbioschemas.jsonld index 897024b87259a..5b1f13c32d311 100644 --- a/data/war/warbioschemas.jsonld +++ b/data/war/warbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Easy-to-use webserver that makes it possible to simultaneously use the best methods for aligning and predicting the consensus secondary structure for a set of non-coding RNA sequences.", "sc:name": "WAR", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:provider": "binf.ku.dk", "sc:url": "http://genome.ku.dk/resources/war/", diff --git a/data/warpgroup/warpgroupbioschemas.jsonld b/data/warpgroup/warpgroupbioschemas.jsonld index b6625d10fb37b..b376a1c97ec9a 100644 --- a/data/warpgroup/warpgroupbioschemas.jsonld +++ b/data/warpgroup/warpgroupbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Warpgroup", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/nathaniel-mahieu/warpgroup" } \ No newline at end of file diff --git a/data/wasabi/wasabibioschemas.jsonld b/data/wasabi/wasabibioschemas.jsonld index 153cb67a49c29..548f92562849d 100644 --- a/data/wasabi/wasabibioschemas.jsonld +++ b/data/wasabi/wasabibioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for visualisation and manipulation of rich MSAs and a graphical interface to command-line programs.", "sc:name": "Wasabi", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://wasabiapp.org/" } \ No newline at end of file diff --git a/data/wasp/waspbioschemas.jsonld b/data/wasp/waspbioschemas.jsonld index 4c614f0945b4e..dc9b4cfaed384 100644 --- a/data/wasp/waspbioschemas.jsonld +++ b/data/wasp/waspbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "http://orcid.org/0000-0002-1491-1839", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/wasp", "@type": "sc:SoftwareApplication", @@ -17,11 +21,11 @@ }, "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC1976135", - "pubmed:17697334", { "@id": "https://doi.org/10.1186/1471-2164-8-275" - } + }, + "pmcid:PMC1976135", + "pubmed:17697334" ], "sc:description": "Application that designs allele-specific (AS) primers for detecting SNPs and mutations. WASP input can be either key searches (Section A) or SNPs with flanking sequences (Section B).", "sc:featureList": { @@ -29,19 +33,15 @@ }, "sc:name": "WASP", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www4a.biotec.or.th/GI/tools/wasp" }, { "@id": "https://doi.org/10.1186/1471-2164-8-275", "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-1491-1839", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/watclust/watclustbioschemas.jsonld b/data/watclust/watclustbioschemas.jsonld index 6c9f30b19bb12..fd958b4f252d8 100644 --- a/data/watclust/watclustbioschemas.jsonld +++ b/data/watclust/watclustbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "WATCLUST", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "https://watclust.wordpress.com/" } \ No newline at end of file diff --git a/data/water-ebi/water-ebibioschemas.jsonld b/data/water-ebi/water-ebibioschemas.jsonld index 6c1380ec852b3..ff91cb781036a 100644 --- a/data/water-ebi/water-ebibioschemas.jsonld +++ b/data/water-ebi/water-ebibioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "water (EBI)", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/Tools/psa/emboss_water/", diff --git a/data/water/waterbioschemas.jsonld b/data/water/waterbioschemas.jsonld index 2825c171dcb3b..4cfc238e4a932 100644 --- a/data/water/waterbioschemas.jsonld +++ b/data/water/waterbioschemas.jsonld @@ -13,8 +13,8 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "Wellcome Trust", - "EMBOSS Contributors", "UK MRC", + "EMBOSS Contributors", "UK BBSRC" ], "sc:description": "Smith-Waterman local alignment of sequences.", @@ -26,9 +26,9 @@ "sc:license": "GPL-3.0", "sc:name": "water", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:provider": [ "EMBL EBI", diff --git a/data/water_api-ebi/water_api-ebibioschemas.jsonld b/data/water_api-ebi/water_api-ebibioschemas.jsonld index 6516fe3d81d64..060e38d66fada 100644 --- a/data/water_api-ebi/water_api-ebibioschemas.jsonld +++ b/data/water_api-ebi/water_api-ebibioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "water_api (EBI)", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/Tools/webservices/services/psa/emboss_water_rest", "sc:version": "1" diff --git a/data/watermelon/watermelonbioschemas.jsonld b/data/watermelon/watermelonbioschemas.jsonld index ece8399fdfea2..952da1a2c6b3d 100644 --- a/data/watermelon/watermelonbioschemas.jsonld +++ b/data/watermelon/watermelonbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2164-14-293", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0001-7030-5756", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/1471-2164-14-293", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/watermelon", "@type": "sc:SoftwareApplication", @@ -24,33 +24,33 @@ "@id": "http://orcid.org/0000-0001-7030-5756" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": [ - "pubmed:23631413", - "pmcid:PMC3769145", { "@id": "https://doi.org/10.1186/1471-2164-14-293" - } + }, + "pmcid:PMC3769145", + "pubmed:23631413" ], "sc:description": "The package makes it convenient to use data quality metrics and normalization methods for Illumina 450 methylation array. The functions also use minfi, methylumi and IMA packages.", "sc:featureList": [ { - "@id": "edam:operation_3435" + "@id": "edam:operation_3763" }, { - "@id": "edam:operation_3204" + "@id": "edam:operation_3435" }, { - "@id": "edam:operation_3763" + "@id": "edam:operation_3204" } ], "sc:license": "GPL-3.0", "sc:name": "wateRmelon", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/wateRmelon.html", diff --git a/data/wattos/wattosbioschemas.jsonld b/data/wattos/wattosbioschemas.jsonld index aca5ab0a61c64..b7ab320bf4de9 100644 --- a/data/wattos/wattosbioschemas.jsonld +++ b/data/wattos/wattosbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Collection of Java programs for structural biology and NMR spectroscopy. It’s programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.", "sc:name": "Wattos", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "https://code.google.com/p/wattos/" diff --git a/data/wavcluster/wavclusterbioschemas.jsonld b/data/wavcluster/wavclusterbioschemas.jsonld index a400c11945ed1..d14afd9122129 100644 --- a/data/wavcluster/wavclusterbioschemas.jsonld +++ b/data/wavcluster/wavclusterbioschemas.jsonld @@ -9,14 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-015-0470-y", - "@type": "sc:CreativeWork" - }, { "@id": "http://orcid.org/0000-0002-8970-6610", "@type": "schema:Person" }, + { + "@id": "https://doi.org/10.1186/s12859-015-0470-y", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/wavcluster", "@type": "sc:SoftwareApplication", @@ -30,42 +30,42 @@ "@id": "edam:data_3495" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:applicationSubCategory": [ { - "@id": "edam:topic_3170" + "@id": "edam:topic_0659" }, { - "@id": "edam:topic_0659" + "@id": "edam:topic_3170" } ], "sc:citation": [ + "pmcid:PMC4339748", + "pubmed:25638391", { "@id": "https://doi.org/10.1186/s12859-015-0470-y" - }, - "pubmed:25638391", - "pmcid:PMC4339748" + } ], "sc:description": "The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework.", "sc:featureList": [ { - "@id": "edam:operation_0361" + "@id": "edam:operation_0278" }, { - "@id": "edam:operation_2441" + "@id": "edam:operation_0361" }, { - "@id": "edam:operation_0278" + "@id": "edam:operation_2441" } ], "sc:license": "GPL-2.0", "sc:name": "wavClusteR", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/wavClusteR.html", "sc:version": "2.8.0" diff --git a/data/wave-crest/wave-crestbioschemas.jsonld b/data/wave-crest/wave-crestbioschemas.jsonld index 69894a4485753..198f05a5bef2c 100644 --- a/data/wave-crest/wave-crestbioschemas.jsonld +++ b/data/wave-crest/wave-crestbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Li-Fang Chu", "sc:additionalType": [ - "Desktop application", - "Library" + "Library", + "Desktop application" ], "sc:description": "Statistical approach to reconstruct gene expression trajectory in single cell RNA-seq experiments with ordered conditions.", "sc:license": "Apache-2.0", "sc:name": "Wave-Crest", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "https://github.com/lengning/WaveCrest" } \ No newline at end of file diff --git a/data/waveread/wavereadbioschemas.jsonld b/data/waveread/wavereadbioschemas.jsonld index aff329abbc85a..8446aad3874dc 100644 --- a/data/waveread/wavereadbioschemas.jsonld +++ b/data/waveread/wavereadbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "WaveRead", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioinformatics.fccc.edu/software/OpenSource/waveread/index.shtml" } \ No newline at end of file diff --git a/data/waveseqr/waveseqrbioschemas.jsonld b/data/waveseqr/waveseqrbioschemas.jsonld index 46ff02455b8b5..dbaa180b9bbc8 100644 --- a/data/waveseqr/waveseqrbioschemas.jsonld +++ b/data/waveseqr/waveseqrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "WaveSeqR", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://rdrr.io/rforge/WaveSeqR/" } \ No newline at end of file diff --git a/data/wavis/wavisbioschemas.jsonld b/data/wavis/wavisbioschemas.jsonld index 42b8802c74d05..a94ba98d99317 100644 --- a/data/wavis/wavisbioschemas.jsonld +++ b/data/wavis/wavisbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "WAViS", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://wavis.img.cas.cz/" } \ No newline at end of file diff --git a/data/wclique/wcliquebioschemas.jsonld b/data/wclique/wcliquebioschemas.jsonld index ecad917847210..d270858178ae4 100644 --- a/data/wclique/wcliquebioschemas.jsonld +++ b/data/wclique/wcliquebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "wclique is a C++ program that helps select genetic or RH markers for framework mapping.", "sc:name": "wclique", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.hpcf.upr.edu/~humberto/software/BPE/wclique/index.html", diff --git a/data/wdac/wdacbioschemas.jsonld b/data/wdac/wdacbioschemas.jsonld index edf06e1034252..5cdee20ff1c29 100644 --- a/data/wdac/wdacbioschemas.jsonld +++ b/data/wdac/wdacbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The WDAC (Weighted Domain Architecture Comparison Tool) is a web-based server to perform protein homology search by comparing protein domain architectures, defined as a sequential order of domains in a protein.", "sc:name": "WDAC", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://pat.kobic.re.kr/wdac/index.htm" } \ No newline at end of file diff --git a/data/wdl-rf/wdl-rfbioschemas.jsonld b/data/wdl-rf/wdl-rfbioschemas.jsonld index d6e9222c91665..8cd3c3b016bc7 100644 --- a/data/wdl-rf/wdl-rfbioschemas.jsonld +++ b/data/wdl-rf/wdl-rfbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Novel pipeline for bioactivity prediction of GPCR-associated ligand molecules.", "sc:name": "WDL-RF", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:url": "https://zhanglab.ccmb.med.umich.edu/WDL-RF/" } \ No newline at end of file diff --git a/data/weaver/bioconda_weaver.yaml b/data/weaver/bioconda_weaver.yaml index 2a939d85d28b9..cfc86119a3f5d 100644 --- a/data/weaver/bioconda_weaver.yaml +++ b/data/weaver/bioconda_weaver.yaml @@ -4,7 +4,6 @@ description: This package provides enhancements on the Sweave() function in the home: https://bioconductor.org/packages/3.10/bioc/html/weaver.html identifiers: - biotools:weaver -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-weaver diff --git a/data/weaver/weaverbioschemas.jsonld b/data/weaver/weaverbioschemas.jsonld index 2d6501d52baed..eb3d78cc6f3fd 100644 --- a/data/weaver/weaverbioschemas.jsonld +++ b/data/weaver/weaverbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Seth Falcon", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package provides enhancements on the Sweave() function in the base package. The focus\nof the extensions is on caching computationally expensive (time consuming) code chunks in Sweave\ndocuments.", "sc:license": "GPL-2.0", "sc:name": "weaver", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/weaver.html", "sc:version": "1.44.0" diff --git a/data/web-beagle/web-beaglebioschemas.jsonld b/data/web-beagle/web-beaglebioschemas.jsonld index 702f9d6bd3c9f..1bafa3853d68d 100644 --- a/data/web-beagle/web-beaglebioschemas.jsonld +++ b/data/web-beagle/web-beaglebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkv489", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/web-beagle", "@type": "sc:SoftwareApplication", @@ -17,34 +21,34 @@ "@id": "edam:data_2526" }, "edam:has_output": [ - { - "@id": "edam:data_2968" - }, { "@id": "edam:data_2526" }, { "@id": "edam:data_1394" + }, + { + "@id": "edam:data_2968" } ], "sc:additionalType": "Web application", "sc:applicationSubCategory": [ { - "@id": "edam:topic_0097" + "@id": "edam:topic_0659" }, { "@id": "edam:topic_0082" }, { - "@id": "edam:topic_0659" + "@id": "edam:topic_0097" } ], "sc:citation": [ "pubmed:25977293", + "pmcid:PMC4489221", { "@id": "https://doi.org/10.1093/nar/gkv489" - }, - "pmcid:PMC4489221" + } ], "sc:description": "BEar Alignment Global and Local. Perform pairwise alignments of RNA secondary structure. The method exploits a new encoding for RNA secondary structure (BEAR) and a substitution matrix for RNA structural elements (MBR) .", "sc:featureList": [ @@ -55,18 +59,14 @@ "@id": "edam:operation_2439" }, { - "@id": "edam:operation_0510" + "@id": "edam:operation_0503" }, { - "@id": "edam:operation_0503" + "@id": "edam:operation_0510" } ], "sc:name": "Web-Beagle", "sc:url": "http://beagle.bio.uniroma2.it/index.php" - }, - { - "@id": "https://doi.org/10.1093/nar/gkv489", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/web-rmkl/web-rmklbioschemas.jsonld b/data/web-rmkl/web-rmklbioschemas.jsonld index 1adc6843f3629..11db850268db5 100644 --- a/data/web-rmkl/web-rmklbioschemas.jsonld +++ b/data/web-rmkl/web-rmklbioschemas.jsonld @@ -9,13 +9,17 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/NAR/GKZ422", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/web-rMKL", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Nico Pfeifer", "Marius Herr", - "Nicolas Kersten" + "Nicolas Kersten", + "Nico Pfeifer" ], "sc:additionalType": [ "Web application", @@ -23,19 +27,19 @@ "Web service" ], "sc:citation": [ - "pubmed:31114892", { "@id": "https://doi.org/10.1093/NAR/GKZ422" }, + "pubmed:31114892", "pmcid:PMC6602472" ], "sc:description": "Web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning.", "sc:featureList": [ { - "@id": "edam:operation_3501" + "@id": "edam:operation_3891" }, { - "@id": "edam:operation_3891" + "@id": "edam:operation_3501" } ], "sc:license": "Unlicense", @@ -46,10 +50,6 @@ "Windows" ], "sc:url": "http://web-rMKL.org" - }, - { - "@id": "https://doi.org/10.1093/NAR/GKZ422", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/web3dmol/web3dmolbioschemas.jsonld b/data/web3dmol/web3dmolbioschemas.jsonld index 66a65c3b25c24..8c227b385b2c9 100644 --- a/data/web3dmol/web3dmolbioschemas.jsonld +++ b/data/web3dmol/web3dmolbioschemas.jsonld @@ -9,32 +9,32 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gkx383", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/web3dmol", "@type": "sc:SoftwareApplication", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28482028", { "@id": "https://doi.org/10.1093/nar/gkx383" }, + "pubmed:28482028", "pmcid:PMC5570197" ], "sc:description": "Protein structure visualization in modern web browsers. Users submit a PDB identification code or select a PDB archive from their local disk, and it will display and allow interactive manipulation of the 3D structure. Featured functions, such as sequence plot, fragment segmentation, measure tool and meta-information display, are offered for users to gain a better understanding of protein structure.", "sc:featureList": [ { - "@id": "edam:operation_0337" + "@id": "edam:operation_0245" }, { - "@id": "edam:operation_0245" + "@id": "edam:operation_0337" } ], "sc:name": "Web3DMol", "sc:url": "http://web3dmol.duapp.com/" - }, - { - "@id": "https://doi.org/10.1093/nar/gkx383", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/web_3dna/web_3dnabioschemas.jsonld b/data/web_3dna/web_3dnabioschemas.jsonld index bef3fa067477a..f784b751326ae 100644 --- a/data/web_3dna/web_3dnabioschemas.jsonld +++ b/data/web_3dna/web_3dnabioschemas.jsonld @@ -11,17 +11,17 @@ "@id": "https://bio.tools/web_3dna", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Dr. Lu", - "Prof. Olson" + "Prof. Olson", + "Dr. Lu" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:19474339", "sc:description": "The web 3DNA server is the web interface for the 3DNA suite of programs developed for the analysis, reconstruction and visualization of 3D nucleic acid containing structures.", "sc:name": "Web 3DNA", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://w3dna.rutgers.edu" } \ No newline at end of file diff --git a/data/web_weeder/web_weederbioschemas.jsonld b/data/web_weeder/web_weederbioschemas.jsonld index e3d2065055a1d..9b3f944f34f95 100644 --- a/data/web_weeder/web_weederbioschemas.jsonld +++ b/data/web_weeder/web_weederbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.", "sc:name": "Web Weeder", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://159.149.160.51/modtools/" diff --git a/data/webapollo/webapollobioschemas.jsonld b/data/webapollo/webapollobioschemas.jsonld index 6b656adc745d3..0757d6b053ef9 100644 --- a/data/webapollo/webapollobioschemas.jsonld +++ b/data/webapollo/webapollobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "WebApollo", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://gmod.org/wiki/WebApollo" } \ No newline at end of file diff --git a/data/webaugustus/webaugustusbioschemas.jsonld b/data/webaugustus/webaugustusbioschemas.jsonld index 25dcc9130e3de..3c08682817971 100644 --- a/data/webaugustus/webaugustusbioschemas.jsonld +++ b/data/webaugustus/webaugustusbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "WebAUGUSTUS is a web server for the prediction of genes in eukaryotic genomic sequences. This web server provides an interface for training AUGUSTUS for predicting genes in genomes of novel species. It also enables users to predict genes in a genome sequence with already trained parameters.", "sc:name": "WebAUGUSTUS", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://bioinf.uni-greifswald.de/webaugustus" diff --git a/data/webbioc/webbiocbioschemas.jsonld b/data/webbioc/webbiocbioschemas.jsonld index ba7e4f14b8292..4ed99cc2d64cb 100644 --- a/data/webbioc/webbiocbioschemas.jsonld +++ b/data/webbioc/webbiocbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Colin A. Smith", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "An integrated web interface for doing microarray analysis using several of the BioConductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users, although currently only Affymetrix oligonucleotide analysis is supported.", "sc:license": "GPL-2.0", "sc:name": "webbioc", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/webbioc.html", "sc:version": "1.50.0" diff --git a/data/webcmd/webcmdbioschemas.jsonld b/data/webcmd/webcmdbioschemas.jsonld index 95643a4d6f5e6..b1c1710928c22 100644 --- a/data/webcmd/webcmdbioschemas.jsonld +++ b/data/webcmd/webcmdbioschemas.jsonld @@ -22,8 +22,8 @@ { "@id": "https://doi.org/10.12688/wellcomeopenres.12201.1" }, - "pubmed:28951892", - "pmcid:PMC5571890" + "pmcid:PMC5571890", + "pubmed:28951892" ], "sc:description": "A cross-platform interface for the BCMD modelling framework.", "sc:featureList": { diff --git a/data/webfr3d/webfr3dbioschemas.jsonld b/data/webfr3d/webfr3dbioschemas.jsonld index 19c3d52468c32..4dcf560f50f31 100644 --- a/data/webfr3d/webfr3dbioschemas.jsonld +++ b/data/webfr3d/webfr3dbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "WebFR3D is the online version of Find RNA 3D, a program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate RNA 3D structural motifs such as hairpin, internal or junction loops and sarcin-ricin and kink tun internal loops.", "sc:name": "WebFR3D", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://rna.bgsu.edu/webfr3d" } \ No newline at end of file diff --git a/data/webgestalt/webgestaltbioschemas.jsonld b/data/webgestalt/webgestaltbioschemas.jsonld index b2d0b00d7c6cf..965fbb19f9b6f 100644 --- a/data/webgestalt/webgestaltbioschemas.jsonld +++ b/data/webgestalt/webgestaltbioschemas.jsonld @@ -12,17 +12,17 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Zhiao Shi", - "Bing Zhang", - "Suhas Vasaikar" + "Suhas Vasaikar", + "Bing Zhang" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:15980575", "sc:description": "System facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected. Pathway maps.", "sc:name": "WebGestalt", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://www.webgestalt.org/option.php" } \ No newline at end of file diff --git a/data/webgester_db/webgester_dbbioschemas.jsonld b/data/webgester_db/webgester_dbbioschemas.jsonld index 3da087d750a25..6762b41459adc 100644 --- a/data/webgester_db/webgester_dbbioschemas.jsonld +++ b/data/webgester_db/webgester_dbbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database of intrinsic transcription terminators identified in bacterial genome sequences and plasmids. Users can obtain both graphic and tabular results on putative terminators based on default or user-defined parameters. The results are arranged in different tiers to facilitate retrieval, as per the specific requirements. An interactive map has been incorporated to visualize the distribution of terminators across the whole genome.", "sc:name": "WebGeSTer DB", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://pallab.serc.iisc.ernet.in/gester" } \ No newline at end of file diff --git a/data/webgivi/webgivibioschemas.jsonld b/data/webgivi/webgivibioschemas.jsonld index 63ac5823c18ca..64d395d888ad9 100644 --- a/data/webgivi/webgivibioschemas.jsonld +++ b/data/webgivi/webgivibioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12859-017-1664-2", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/webgivi", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Liang Sun", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:28472919", "pmcid:PMC5418709", { "@id": "https://doi.org/10.1186/s12859-017-1664-2" - } + }, + "pubmed:28472919" ], "sc:description": "The tool can accept a gene list that will be used to retrieve a gene symbol and iTerm list. This list can be resubmitted to visualize the gene-iTerm pairs using Cytoscape or Concept Map.", "sc:featureList": [ @@ -33,15 +37,11 @@ "sc:license": "BSD-Protection", "sc:name": "WebGIVI", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://raven.anr.udel.edu/webgivi/" - }, - { - "@id": "https://doi.org/10.1186/s12859-017-1664-2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/webikey/webikeybioschemas.jsonld b/data/webikey/webikeybioschemas.jsonld index 6daaa6b4abce9..a9141546f300b 100644 --- a/data/webikey/webikeybioschemas.jsonld +++ b/data/webikey/webikeybioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.3732/apps.1500128", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/webikey", "@type": "sc:SoftwareApplication", @@ -29,10 +33,6 @@ "sc:name": "WEBiKEY", "sc:operatingSystem": "Windows", "sc:url": "https://github.com/WEBiKEY/InteractiveKey" - }, - { - "@id": "https://doi.org/10.3732/apps.1500128", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/webknossos/webknossosbioschemas.jsonld b/data/webknossos/webknossosbioschemas.jsonld index 96de9fc56fe73..9af4c8e190a34 100644 --- a/data/webknossos/webknossosbioschemas.jsonld +++ b/data/webknossos/webknossosbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "AGPL-3.0", "sc:name": "webKnossos", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "https://webknossos.org/" } \ No newline at end of file diff --git a/data/weblab/weblabbioschemas.jsonld b/data/weblab/weblabbioschemas.jsonld index 6d85c70105a62..1ca3c6b3220f0 100644 --- a/data/weblab/weblabbioschemas.jsonld +++ b/data/weblab/weblabbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "An integrative knowledge sharing system that supports collaboration of biological researchers from various fields. WebLab allows users to fetch, analyze with more than 260 integrated bioinformatic tools, manipulate and share data under an intuitive web interface. These tools can be further organized as customized workflows.", "sc:name": "WebLab", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://weblab.cbi.pku.edu.cn" } \ No newline at end of file diff --git a/data/weblogo/weblogobioschemas.jsonld b/data/weblogo/weblogobioschemas.jsonld index b48c121abc03a..b47a7554dab51 100644 --- a/data/weblogo/weblogobioschemas.jsonld +++ b/data/weblogo/weblogobioschemas.jsonld @@ -17,9 +17,9 @@ "sc:description": "Web-based application designed to make generate sequence logos.", "sc:name": "WebLogo", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://weblogo.berkeley.edu/" } \ No newline at end of file diff --git a/data/weblogo_3/weblogo_3bioschemas.jsonld b/data/weblogo_3/weblogo_3bioschemas.jsonld index baf4977c6440b..4c9d35f7dcd8b 100644 --- a/data/weblogo_3/weblogo_3bioschemas.jsonld +++ b/data/weblogo_3/weblogo_3bioschemas.jsonld @@ -13,23 +13,23 @@ "@id": "https://bio.tools/weblogo_3", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": [ - "pmcid:PMC419797", { "@id": "https://doi.org/10.1101/gr.849004" }, - "pubmed:15173120" + "pubmed:15173120", + "pmcid:PMC419797" ], "sc:description": "Web-based application designed to make generate sequence logos.", "sc:featureList": [ { - "@id": "edam:operation_0239" + "@id": "edam:operation_0564" }, { - "@id": "edam:operation_0564" + "@id": "edam:operation_0239" }, { "@id": "edam:operation_0566" diff --git a/data/webmetabase/webmetabasebioschemas.jsonld b/data/webmetabase/webmetabasebioschemas.jsonld index 0c9ddca40337e..c03cdd574cbbd 100644 --- a/data/webmetabase/webmetabasebioschemas.jsonld +++ b/data/webmetabase/webmetabasebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/WebMetabase", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Web service", - "Web application" + "Web application", + "Web service" ], "sc:description": "Cleavage sites analysis tool for natural and unnatural substrates from diverse data source.", "sc:license": "Other", "sc:name": "WebMetabase", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://webmetabase.com:8182/WebMetabaseBioinformatics/" } \ No newline at end of file diff --git a/data/webmotifs/webmotifsbioschemas.jsonld b/data/webmotifs/webmotifsbioschemas.jsonld index 836952532122d..edf56521fcdc2 100644 --- a/data/webmotifs/webmotifsbioschemas.jsonld +++ b/data/webmotifs/webmotifsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.", "sc:name": "WebMOTIFS", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://fraenkel.mit.edu/webmotifs/" } \ No newline at end of file diff --git a/data/webnma/webnmabioschemas.jsonld b/data/webnma/webnmabioschemas.jsonld index 9b880ca173a6f..10daa8f67ad29 100644 --- a/data/webnma/webnmabioschemas.jsonld +++ b/data/webnma/webnmabioschemas.jsonld @@ -15,27 +15,27 @@ "Web service" ], "sc:author": [ + "Kidane M Tekle", + "Gisle Salensminde", + "Lars Skjærven", "Nathalie Reuter", "Svenn H Grindhaug", - "Edvin Fuglebakk", - "Lars Skjærven", - "Gisle Salensminde", + "Siv M Hollup", "Tristan Cragnolini", "Sandhya P Tiwari", - "Siv M Hollup", - "Kidane M Tekle" + "Edvin Fuglebakk" ], "sc:description": "Quick, automated computation and analysis of low-frequency normal modes for protein structures.", "sc:name": "WEBnma", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "Computational Biology Unit, Department of Informatics, University of Bergen, Norway", + "Department of Molecular Biology, University of Bergen, Norway", "UiB", - "Department of Molecular Biology, University of Bergen, Norway" + "Computational Biology Unit, Department of Informatics, University of Bergen, Norway" ], "sc:url": "http://apps.cbu.uib.no/webnma", "sc:version": "2.0" diff --git a/data/webprank/webprankbioschemas.jsonld b/data/webprank/webprankbioschemas.jsonld index e3c757ad3ff8a..2c434e50e40b9 100644 --- a/data/webprank/webprankbioschemas.jsonld +++ b/data/webprank/webprankbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:description": "Multiple sequence alignment tool.", "sc:name": "webPRANK", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": "EMBL-EBI", "sc:url": "http://www.ebi.ac.uk/goldman-srv/webprank/", diff --git a/data/webprc/webprcbioschemas.jsonld b/data/webprc/webprcbioschemas.jsonld index 967e960e5fe71..b462c47562db3 100644 --- a/data/webprc/webprcbioschemas.jsonld +++ b/data/webprc/webprcbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web server for searching for distant homologs or similar alignment in domain databases. Results may be provided as either multiple sequence alignments or aligned hidden Markov models. An alignment editor allows for user editing of output alignments.", "sc:name": "webPRC", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.ibi.vu.nl/programs/prcwww/" } \ No newline at end of file diff --git a/data/webprinses/webprinsesbioschemas.jsonld b/data/webprinses/webprinsesbioschemas.jsonld index 1353ebd9e809d..52808bdfdfdfb 100644 --- a/data/webprinses/webprinsesbioschemas.jsonld +++ b/data/webprinses/webprinsesbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "WebPrInSeS", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://updeplasrv1.epfl.ch/prinses/" } \ No newline at end of file diff --git a/data/webproanalyst/webproanalystbioschemas.jsonld b/data/webproanalyst/webproanalystbioschemas.jsonld index f77aeebeaebb0..69bde48bf490b 100644 --- a/data/webproanalyst/webproanalystbioschemas.jsonld +++ b/data/webproanalyst/webproanalystbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Tool for searching for residues whose substitutions are correlated with variations in protein activity. Key physicochemical characteristics of these sites can be calculated.", "sc:name": "WebProAnalyst", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/" } \ No newline at end of file diff --git a/data/webrtc/webrtcbioschemas.jsonld b/data/webrtc/webrtcbioschemas.jsonld index 5a6dc5a2e49af..8fc98b6a8329c 100644 --- a/data/webrtc/webrtcbioschemas.jsonld +++ b/data/webrtc/webrtcbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "webRTC", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://webrtc.org/" } \ No newline at end of file diff --git a/data/websat/websatbioschemas.jsonld b/data/websat/websatbioschemas.jsonld index e092c23af132b..c67b143e8394d 100644 --- a/data/websat/websatbioschemas.jsonld +++ b/data/websat/websatbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software for microsatellite molecular marker prediction and development. It allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification.", "sc:name": "WebSat", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://wsmartins.net/websat/" } \ No newline at end of file diff --git a/data/webscipio/webscipiobioschemas.jsonld b/data/webscipio/webscipiobioschemas.jsonld index fbfd0cbca6f8d..353363b192f44 100644 --- a/data/webscipio/webscipiobioschemas.jsonld +++ b/data/webscipio/webscipiobioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Scipio is a tool to determine the precise exon-intron gene structure given a protein sequence and a genome. It identifies splice sites and is able to cope with sequencing errors and genes spanning several contigs. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in related species. WebScipio, allows to search for mutually exclusive spliced exons and tandemly arrayed gene duplicates.", "sc:name": "WebScipio", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.webscipio.org" diff --git a/data/weeder/weederbioschemas.jsonld b/data/weeder/weederbioschemas.jsonld index 7cdb467a1da06..f74e8d364ea2b 100644 --- a/data/weeder/weederbioschemas.jsonld +++ b/data/weeder/weederbioschemas.jsonld @@ -19,8 +19,8 @@ "sc:license": "GPL-3.0", "sc:name": "Weeder", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:provider": "ELIXIR-ITA-MILANO", "sc:url": "http://www.beaconlab.it/modtools", diff --git a/data/weget/wegetbioschemas.jsonld b/data/weget/wegetbioschemas.jsonld index 945d7c7abc626..c95881231b956 100644 --- a/data/weget/wegetbioschemas.jsonld +++ b/data/weget/wegetbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "WeGET is a computational tool to find mammalian genes that strongly co-express with a human query gene set of interest.", "sc:name": "WeGet", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://weget.cmbi.umcn.nl/" } \ No newline at end of file diff --git a/data/weighbor/weighborbioschemas.jsonld b/data/weighbor/weighborbioschemas.jsonld index 8dfcbdc16af77..40b23e1f6d4a9 100644 --- a/data/weighbor/weighborbioschemas.jsonld +++ b/data/weighbor/weighborbioschemas.jsonld @@ -11,13 +11,13 @@ "@id": "https://bio.tools/weighbor", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "N. D. Socci", "W. Bruno", + "N. D. Socci", "A. Halpern" ], "sc:additionalType": [ - "Web application", - "Command-line tool" + "Command-line tool", + "Web application" ], "sc:citation": "pubmed:10666718", "sc:description": "Tool for building phylogenetic trees from distance matrices. It employs a weighted version of the neighbour-joining method in which longer distances in the matrix are given less weight.", diff --git a/data/weighted_fdr/weighted_fdrbioschemas.jsonld b/data/weighted_fdr/weighted_fdrbioschemas.jsonld index 25abda6224b20..860783a9c5606 100644 --- a/data/weighted_fdr/weighted_fdrbioschemas.jsonld +++ b/data/weighted_fdr/weighted_fdrbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Software to Apply Weighted False Discovery Rate for Multiple Testing. When testing a large number of hypotheses, such as an association genome scan, the power to detect modest effects can be low, due to the penalty for multiple testing.  This is especially true when traditional approaches such as the Bonferroni correction are employed.", "sc:name": "weighted_FDR", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://wpicr.wpic.pitt.edu/WPICCompGen/fdr/" } \ No newline at end of file diff --git a/data/wellinverter/wellinverterbioschemas.jsonld b/data/wellinverter/wellinverterbioschemas.jsonld index 8fc11c46acd48..cd6fd7b3b4918 100644 --- a/data/wellinverter/wellinverterbioschemas.jsonld +++ b/data/wellinverter/wellinverterbioschemas.jsonld @@ -9,27 +9,23 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2920-4", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/WellInverter", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Johannes Geiselmann", - "Hidde de Jong" + "Hidde de Jong", + "Johannes Geiselmann" ], "sc:additionalType": [ "Web application", "Desktop application" ], "sc:citation": [ - "pubmed:31185910", - "pmcid:PMC6558888", { "@id": "https://doi.org/10.1186/s12859-019-2920-4" - } + }, + "pmcid:PMC6558888", + "pubmed:31185910" ], "sc:description": "Web application for the analysis of fluorescent reporter gene data.", "sc:featureList": [ @@ -44,10 +40,14 @@ "sc:name": "WellInverter", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://team.inria.fr/ibis/wellinverter/" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2920-4", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/wenmr_gromacs/wenmr_gromacsbioschemas.jsonld b/data/wenmr_gromacs/wenmr_gromacsbioschemas.jsonld index 3686ecfd0ff32..8680cc06f07f2 100644 --- a/data/wenmr_gromacs/wenmr_gromacsbioschemas.jsonld +++ b/data/wenmr_gromacs/wenmr_gromacsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The WeNMR web portal combines the versatility of this molecular dynamics package with the calculation power of the eNMR grid. This will enable you to perform many simulations from the comfort of your internet browser anywhere in the world. The server is furthermore aimed to provide a user friendly and efficient MD experience by performing many preparation and optimization steps automatically.", "sc:name": "WeNMR GROMACS", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://haddock.science.uu.nl/enmr/services/GROMACS/main.php" diff --git a/data/wft4galaxy/wft4galaxybioschemas.jsonld b/data/wft4galaxy/wft4galaxybioschemas.jsonld index ed207af754150..d3fd2e554ec93 100644 --- a/data/wft4galaxy/wft4galaxybioschemas.jsonld +++ b/data/wft4galaxy/wft4galaxybioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "wft4galaxy", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/phnmnl/wft4galaxy" } \ No newline at end of file diff --git a/data/wgaviewer/wgaviewerbioschemas.jsonld b/data/wgaviewer/wgaviewerbioschemas.jsonld index afc9e92b1b6e3..379b0e4d3ff29 100644 --- a/data/wgaviewer/wgaviewerbioschemas.jsonld +++ b/data/wgaviewer/wgaviewerbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study.", "sc:name": "WGAViewer", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://igm.cumc.columbia.edu/WGAViewer/" } \ No newline at end of file diff --git a/data/wgcna/wgcnabioschemas.jsonld b/data/wgcna/wgcnabioschemas.jsonld index af62357427243..9f71b69aed047 100644 --- a/data/wgcna/wgcnabioschemas.jsonld +++ b/data/wgcna/wgcnabioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.", "sc:name": "WGCNA", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "https://cran.r-project.org/web/packages/WGCNA/" } \ No newline at end of file diff --git a/data/wgddetector/wgddetectorbioschemas.jsonld b/data/wgddetector/wgddetectorbioschemas.jsonld index 6ba3aa27d9e03..dc88a455f3f88 100644 --- a/data/wgddetector/wgddetectorbioschemas.jsonld +++ b/data/wgddetector/wgddetectorbioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/s12859-019-2670-3", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/WGDdetector", "@type": "sc:SoftwareApplication", @@ -31,11 +27,15 @@ }, "sc:name": "WGDdetector", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/yongzhiyang2012/WGDdetector" + }, + { + "@id": "https://doi.org/10.1186/s12859-019-2670-3", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/wge/wgebioschemas.jsonld b/data/wge/wgebioschemas.jsonld index 6ce4188fd27f1..a06542b61efb5 100644 --- a/data/wge/wgebioschemas.jsonld +++ b/data/wge/wgebioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:25979474", + "pmcid:PMC4565030", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTV308" - }, - "pmcid:PMC4565030" + } ], "sc:description": "A CRISPR database for genome engineering.", "sc:featureList": { diff --git a/data/whamm/whammbioschemas.jsonld b/data/whamm/whammbioschemas.jsonld index 8afd73f2464d3..ee01b93d5a560 100644 --- a/data/whamm/whammbioschemas.jsonld +++ b/data/whamm/whammbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:license": "Not licensed", "sc:name": "Whamm", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://coruscant.itmat.upenn.edu/whamm/index.html" } \ No newline at end of file diff --git a/data/what_if/what_ifbioschemas.jsonld b/data/what_if/what_ifbioschemas.jsonld index 9642269a4f0b2..db487cbc0e070 100644 --- a/data/what_if/what_ifbioschemas.jsonld +++ b/data/what_if/what_ifbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "WHAT IF", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://swift.cmbi.ru.nl/servers/html/index.html" } \ No newline at end of file diff --git a/data/whatizit/whatizitbioschemas.jsonld b/data/whatizit/whatizitbioschemas.jsonld index f96f2bc0ab16b..58b48562c6ea8 100644 --- a/data/whatizit/whatizitbioschemas.jsonld +++ b/data/whatizit/whatizitbioschemas.jsonld @@ -13,16 +13,16 @@ "biotools:primaryContact": "Jee-Hyub Kim", "sc:additionalType": "Web application", "sc:author": [ + "Johanna McEntyre", "Dietrich Rebholz-Schuhmann", - "Literature Services", "Jee-Hyub Kim", - "Johanna McEntyre" + "Literature Services" ], "sc:description": "A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases.", "sc:name": "Whatizit", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:provider": "EMBL-EBI", diff --git a/data/wheat_genome/wheat_genomebioschemas.jsonld b/data/wheat_genome/wheat_genomebioschemas.jsonld index 8935c3ab323af..269a0b6ef1c89 100644 --- a/data/wheat_genome/wheat_genomebioschemas.jsonld +++ b/data/wheat_genome/wheat_genomebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Wheat Genome", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": "unimelb.edu.au", "sc:url": "http://www.wheatgenome.info/wheat_genome_databases.php" diff --git a/data/wheat_zapper/wheat_zapperbioschemas.jsonld b/data/wheat_zapper/wheat_zapperbioschemas.jsonld index 00ed34806e370..2fdba89a31d7e 100644 --- a/data/wheat_zapper/wheat_zapperbioschemas.jsonld +++ b/data/wheat_zapper/wheat_zapperbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Fast and flexible on-line application to predict orthologus relationships with the model species Oryza sativa, Brachypodium dystachyon, and Sorghum bicolor.", "sc:name": "Wheat Zapper", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://wge.ndsu.nodak.edu/wheatzapper/" } \ No newline at end of file diff --git a/data/whichcyp/whichcypbioschemas.jsonld b/data/whichcyp/whichcypbioschemas.jsonld index b1af50a36931a..9b97c93e0574d 100644 --- a/data/whichcyp/whichcypbioschemas.jsonld +++ b/data/whichcyp/whichcypbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "WhichCyp", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.farma.ku.dk/whichcyp/index.php" } \ No newline at end of file diff --git a/data/whichdb/whichdbbioschemas.jsonld b/data/whichdb/whichdbbioschemas.jsonld index 138b9378e2d45..55cbd00d12726 100644 --- a/data/whichdb/whichdbbioschemas.jsonld +++ b/data/whichdb/whichdbbioschemas.jsonld @@ -13,22 +13,22 @@ "sc:additionalType": "Command-line tool", "sc:contributor": [ "UK BBSRC", - "Wellcome Trust", + "EMBOSS Contributors", "UK MRC", - "EMBOSS Contributors" + "Wellcome Trust" ], "sc:description": "Search all sequence databases for an entry and retrieve it.", "sc:funder": [ - "UK MRC", "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "whichdb", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/whichgenes/whichgenesbioschemas.jsonld b/data/whichgenes/whichgenesbioschemas.jsonld index 7e1a01ff701cc..659280d7f590a 100644 --- a/data/whichgenes/whichgenesbioschemas.jsonld +++ b/data/whichgenes/whichgenesbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:description": "WhichGenes is a web based tool for gathering, building, storing and exporting gene sets with application to gene set enrichment analysis. The user may export a gene set in any desired output format with multiple gene identifiers.", "sc:name": "WhichGenes", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.whichgenes.org/" } \ No newline at end of file diff --git a/data/whiteboard/whiteboardbioschemas.jsonld b/data/whiteboard/whiteboardbioschemas.jsonld index b44542f3947f6..af28d7b7bb730 100644 --- a/data/whiteboard/whiteboardbioschemas.jsonld +++ b/data/whiteboard/whiteboardbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Class library implemented in C++, allowing for easy graphing any kind of data into any format. It provides all basic tool sets for drawing simple objects, as well as color manipulation methods, a rich set of compound graphs, and documentation.", "sc:name": "Whiteboard", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://whiteboard-class.sourceforge.net/" diff --git a/data/whopgenome/whopgenomebioschemas.jsonld b/data/whopgenome/whopgenomebioschemas.jsonld index e53d908ab75c6..acae5aacb73b4 100644 --- a/data/whopgenome/whopgenomebioschemas.jsonld +++ b/data/whopgenome/whopgenomebioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-2.0", "sc:name": "WhopGenome", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://cran.r-project.org/web/packages/WhopGenome/", "sc:version": "0.97" diff --git a/data/widgettools/widgettoolsbioschemas.jsonld b/data/widgettools/widgettoolsbioschemas.jsonld index 9d71b4d287663..a48f7e32ea24b 100644 --- a/data/widgettools/widgettoolsbioschemas.jsonld +++ b/data/widgettools/widgettoolsbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Jianhua Zhang", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This packages enables users to build interactive widgets. Although the underlying implementation of any widget built is through the R tcltk package, users of widgetTools do not need to know all of the lowlevel\nTcl/Tk commands, because the widget functionality is encapsulated in S4 classes which interact directly with standard R objects.", "sc:license": "GPL-3.0", "sc:name": "widgetTools", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/widgetTools.html", diff --git a/data/wiggleplotr/wiggleplotrbioschemas.jsonld b/data/wiggleplotr/wiggleplotrbioschemas.jsonld index fa10a85d56fc7..a3134b321c968 100644 --- a/data/wiggleplotr/wiggleplotrbioschemas.jsonld +++ b/data/wiggleplotr/wiggleplotrbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Apache-2.0", "sc:name": "wiggleplotr", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/wiggleplotr.html" diff --git a/data/wikipathways/wikipathwaysbioschemas.jsonld b/data/wikipathways/wikipathwaysbioschemas.jsonld index 6ffa8a157ba0d..192b0ee3e469a 100644 --- a/data/wikipathways/wikipathwaysbioschemas.jsonld +++ b/data/wikipathways/wikipathwaysbioschemas.jsonld @@ -11,22 +11,22 @@ "@id": "https://bio.tools/wikipathways", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Martina Kutmon", - "Alexander R. Pico" + "Alexander R. Pico", + "Martina Kutmon" ], "sc:additionalType": [ "Web service", "Database portal", - "Web application", - "Web API" + "Web API", + "Web application" ], "sc:description": "WikiPathways is a database of biological pathways maintained by and for the scientific community.", "sc:license": "Apache-2.0", "sc:name": "WikiPathways", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.wikipathways.org" } \ No newline at end of file diff --git a/data/wikipathways_app/wikipathways_appbioschemas.jsonld b/data/wikipathways_app/wikipathways_appbioschemas.jsonld index 9d5ce8881139c..b75d647ed7179 100644 --- a/data/wikipathways_app/wikipathways_appbioschemas.jsonld +++ b/data/wikipathways_app/wikipathways_appbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.12688/F1000RESEARCH.4254.2", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/wikipathways_app", "@type": "sc:SoftwareApplication", @@ -17,18 +21,18 @@ }, "sc:additionalType": "Plug-in", "sc:citation": [ + "pmcid:PMC4168754", { "@id": "https://doi.org/10.12688/F1000RESEARCH.4254.2" }, - "pubmed:25254103", - "pmcid:PMC4168754" + "pubmed:25254103" ], "sc:description": "Easy access to pathway content at WikiPathways.org from Cytoscape.", "sc:license": "Apache-2.0", "sc:name": "WikiPathways App", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://apps.cytoscape.org/apps/wikipathways", @@ -37,10 +41,6 @@ { "@id": "http://orcid.org/0000-0002-7699-8191", "@type": "schema:Person" - }, - { - "@id": "https://doi.org/10.12688/F1000RESEARCH.4254.2", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/wisard/wisardbioschemas.jsonld b/data/wisard/wisardbioschemas.jsonld index 97f9a56b44752..6af2963fac3e1 100644 --- a/data/wisard/wisardbioschemas.jsonld +++ b/data/wisard/wisardbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Workbench for Integrated Superfast Association study with Related Data is a comprehensive Statistical Analysis toolkit for omics data. Large-scale SNP, CNV and NGS data with related and unrelated samples can be analyzed in computationally optimized and efficient way by using muti-core system.", "sc:name": "WISARD", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://statgen.snu.ac.kr/wisard/" diff --git a/data/wiws/wiwsbioschemas.jsonld b/data/wiws/wiwsbioschemas.jsonld index 5e041d1dcb6cd..66a6dcc40712e 100644 --- a/data/wiws/wiwsbioschemas.jsonld +++ b/data/wiws/wiwsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web service based on the WHAT IF software package for macromolecular analysis, visualization, modeling and structure validation. This protein structure bioinformatics web service collection has over 1600 different functions.", "sc:name": "WIWS", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://swift.cmbi.ru.nl/" diff --git a/data/wkinmut/wkinmutbioschemas.jsonld b/data/wkinmut/wkinmutbioschemas.jsonld index 88d2c1ffcc1ca..04073cc14004e 100644 --- a/data/wkinmut/wkinmutbioschemas.jsonld +++ b/data/wkinmut/wkinmutbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "wKinMut", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://kinmut2.bioinfo.cnio.es/KinMut2" } \ No newline at end of file diff --git a/data/wlake/wlakebioschemas.jsonld b/data/wlake/wlakebioschemas.jsonld index 7be1369605a79..5a03e8cfdfb28 100644 --- a/data/wlake/wlakebioschemas.jsonld +++ b/data/wlake/wlakebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A tool which allows to identify clusters of a structural water molecules in given superimposed 3D structures.", "sc:name": "wLake", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/wLake/wLake.php" } \ No newline at end of file diff --git a/data/wmap/wmapbioschemas.jsonld b/data/wmap/wmapbioschemas.jsonld index 4ce21caca519b..5f2262eb03971 100644 --- a/data/wmap/wmapbioschemas.jsonld +++ b/data/wmap/wmapbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Map high-throughput sequencing reads as well as methylated-C reads, enabling usage of such sequencing data to various fields of biological research.", "sc:name": "WMap", "sc:operatingSystem": [ - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://systemsbio.ucsd.edu/wmap/manual.html", "sc:version": "20091230" diff --git a/data/wmaxc/wmaxcbioschemas.jsonld b/data/wmaxc/wmaxcbioschemas.jsonld index 80e0f9e00a9d1..25a022cbff322 100644 --- a/data/wmaxc/wmaxcbioschemas.jsonld +++ b/data/wmaxc/wmaxcbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Weighted MAXimum Clique. Method for identifying condition specific sub-network. Reveals a subset of genes which are closely related to a particular disease. It integrates gene expression data and protein-protein interaction information to construct molecular network, and then extracts the most density connected sub-network using an integration of a global search method and efficient projection procedure.", "sc:name": "WMAXC", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://combio.gist.ac.kr/WMAXC/WMAXC.html", "sc:version": "20131115" diff --git a/data/wnv_typer/wnv_typerbioschemas.jsonld b/data/wnv_typer/wnv_typerbioschemas.jsonld index bb14f259de281..79cd005911957 100644 --- a/data/wnv_typer/wnv_typerbioschemas.jsonld +++ b/data/wnv_typer/wnv_typerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "WNV Typer", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioinfo.net.in/wnv/homepage.html" } \ No newline at end of file diff --git a/data/wobble/wobblebioschemas.jsonld b/data/wobble/wobblebioschemas.jsonld index 5dd704cb7cc4b..769f0735f32e6 100644 --- a/data/wobble/wobblebioschemas.jsonld +++ b/data/wobble/wobblebioschemas.jsonld @@ -12,9 +12,9 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "Wellcome Trust", "UK MRC", + "Wellcome Trust", + "UK BBSRC", "EMBOSS Contributors" ], "sc:description": "Plot third base position variability in a nucleotide sequence.", @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "wobble", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/wobble.html", "sc:version": "r6" diff --git a/data/wolf_psort/wolf_psortbioschemas.jsonld b/data/wolf_psort/wolf_psortbioschemas.jsonld index 224b53d92cfc7..a02c050ed9719 100644 --- a/data/wolf_psort/wolf_psortbioschemas.jsonld +++ b/data/wolf_psort/wolf_psortbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "WoLF PSORT", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://wolfpsort.hgc.jp/" } \ No newline at end of file diff --git a/data/wombat/wombatbioschemas.jsonld b/data/wombat/wombatbioschemas.jsonld index be8c0e73a6dd8..3faadc239b766 100644 --- a/data/wombat/wombatbioschemas.jsonld +++ b/data/wombat/wombatbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1631/jzus.2007.B0815", + "@type": "sc:CreativeWork" + }, { "@id": "http://orcid.org/0000-0003-2663-9059", "@type": "schema:Person" @@ -22,10 +26,10 @@ "sc:additionalType": "Command-line tool", "sc:citation": [ "pubmed:17973343", + "pmcid:PMC2064953", { "@id": "https://doi.org/10.1631/jzus.2007.B0815" - }, - "pmcid:PMC2064953" + } ], "sc:description": "Program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML).", "sc:featureList": { @@ -39,10 +43,6 @@ "Linux" ], "sc:url": "http://didgeridoo.une.edu.au/km/wombat.php" - }, - { - "@id": "https://doi.org/10.1631/jzus.2007.B0815", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/wonka/wonkabioschemas.jsonld b/data/wonka/wonkabioschemas.jsonld index 047cb3abcf0ae..20f415243e71a 100644 --- a/data/wonka/wonkabioschemas.jsonld +++ b/data/wonka/wonkabioschemas.jsonld @@ -20,10 +20,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:26387008", - "pmcid:PMC4621702", { "@id": "https://doi.org/10.1007/S10822-015-9866-Z" - } + }, + "pmcid:PMC4621702" ], "sc:description": "Objective novel complex analysis for ensembles of protein–ligand structures.", "sc:featureList": { diff --git a/data/wordcount/wordcountbioschemas.jsonld b/data/wordcount/wordcountbioschemas.jsonld index 13b3748c2cc40..511536b00f145 100644 --- a/data/wordcount/wordcountbioschemas.jsonld +++ b/data/wordcount/wordcountbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "Wellcome Trust", "UK MRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "UK BBSRC" ], "sc:description": "Count and extract unique words in molecular sequence(s).", "sc:funder": [ + "UK BBSRC", "UK MRC", - "Wellcome Trust", - "UK BBSRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "wordcount", @@ -31,8 +31,8 @@ "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/wordcount.html", "sc:version": "r6" diff --git a/data/wordfinder/wordfinderbioschemas.jsonld b/data/wordfinder/wordfinderbioschemas.jsonld index e3973320d7b1f..2b6d0b26d4da5 100644 --- a/data/wordfinder/wordfinderbioschemas.jsonld +++ b/data/wordfinder/wordfinderbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", - "UK MRC", "Wellcome Trust", - "UK BBSRC" + "UK BBSRC", + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Match large sequences against one or more other sequences.", "sc:funder": [ @@ -26,8 +26,8 @@ "sc:license": "GPL-3.0", "sc:name": "wordfinder", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:provider": [ diff --git a/data/wordmatch/wordmatchbioschemas.jsonld b/data/wordmatch/wordmatchbioschemas.jsonld index a259c29a71c9f..e57ac058b94df 100644 --- a/data/wordmatch/wordmatchbioschemas.jsonld +++ b/data/wordmatch/wordmatchbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "UK BBSRC", + "Wellcome Trust", "EMBOSS Contributors", - "Wellcome Trust" + "UK MRC" ], "sc:description": "Find regions of identity (exact matches) of two sequences.", "sc:funder": [ - "Wellcome Trust", "UK BBSRC", + "Wellcome Trust", "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "wordmatch", "sc:operatingSystem": [ + "Windows", "Mac", - "Linux", - "Windows" + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/wordmatch.html", "sc:version": "r6" diff --git a/data/worfdb/worfdbbioschemas.jsonld b/data/worfdb/worfdbbioschemas.jsonld index a34ec0150cd81..e2947317f049c 100644 --- a/data/worfdb/worfdbbioschemas.jsonld +++ b/data/worfdb/worfdbbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1101/gr.2496804", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/worfdb", "@type": "sc:SoftwareApplication", @@ -23,11 +27,11 @@ "@id": "edam:topic_0621" }, "sc:citation": [ - "pubmed:15489327", { "@id": "https://doi.org/10.1101/gr.2496804" }, - "pmcid:PMC528921" + "pmcid:PMC528921", + "pubmed:15489327" ], "sc:description": "The Caenorhabditis elegans ORFeome cloning project.", "sc:featureList": { @@ -35,15 +39,11 @@ }, "sc:name": "WORFDB", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://worfdb.dfci.harvard.edu/" - }, - { - "@id": "https://doi.org/10.1101/gr.2496804", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/workflow4metabolomics/workflow4metabolomicsbioschemas.jsonld b/data/workflow4metabolomics/workflow4metabolomicsbioschemas.jsonld index d8c32920199a0..ec18face6ad85 100644 --- a/data/workflow4metabolomics/workflow4metabolomicsbioschemas.jsonld +++ b/data/workflow4metabolomics/workflow4metabolomicsbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "Workflow4Metabolomics", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "https://workflow4metabolomics.org/" } \ No newline at end of file diff --git a/data/world-2dpage/world-2dpagebioschemas.jsonld b/data/world-2dpage/world-2dpagebioschemas.jsonld index 11837b9e8af8e..df9930bdf6ca0 100644 --- a/data/world-2dpage/world-2dpagebioschemas.jsonld +++ b/data/world-2dpage/world-2dpagebioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A public repository, standards compliant, for proteomics image data published in the literature.", "sc:name": "The world-2DPAGE database", "sc:operatingSystem": [ + "Windows", "Linux", - "Mac", - "Windows" + "Mac" ], "sc:url": "http://world-2dpage.expasy.org/repository/" } \ No newline at end of file diff --git a/data/world_cancer_map/world_cancer_mapbioschemas.jsonld b/data/world_cancer_map/world_cancer_mapbioschemas.jsonld index c1d08c67a5ca5..bbdb50d42ffec 100644 --- a/data/world_cancer_map/world_cancer_mapbioschemas.jsonld +++ b/data/world_cancer_map/world_cancer_mapbioschemas.jsonld @@ -9,14 +9,18 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1097/MD.0000000000015521", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/World_Cancer_Map", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Yung-Po Liaw", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC6531084", "pubmed:31096452", + "pmcid:PMC6531084", { "@id": "https://doi.org/10.1097/MD.0000000000015521" } @@ -24,10 +28,10 @@ "sc:description": "Interactive web-based platform presenting global cancer statistics , which can be used for cancer research.", "sc:featureList": [ { - "@id": "edam:operation_2429" + "@id": "edam:operation_2942" }, { - "@id": "edam:operation_2942" + "@id": "edam:operation_2429" } ], "sc:license": "Unlicense", @@ -38,10 +42,6 @@ "Windows" ], "sc:url": "http://worldmap.csmu-liawyp.tw" - }, - { - "@id": "https://doi.org/10.1097/MD.0000000000015521", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/wormgender/wormgenderbioschemas.jsonld b/data/wormgender/wormgenderbioschemas.jsonld index c4856c5de8593..f6a162654c369 100644 --- a/data/wormgender/wormgenderbioschemas.jsonld +++ b/data/wormgender/wormgenderbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Open-source software which designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions include, i) automatic recognition and counting of adult hermaphrodites and males, ii) a manual inspection feature that enables manual correction of errors, and iii) flexibility to use new training images to optimize the software for different imaging conditions.", "sc:name": "WormGender", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.quantworm.org/" diff --git a/data/wormhole/wormholebioschemas.jsonld b/data/wormhole/wormholebioschemas.jsonld index 326f58a0dccdd..689bc4edcca3c 100644 --- a/data/wormhole/wormholebioschemas.jsonld +++ b/data/wormhole/wormholebioschemas.jsonld @@ -27,9 +27,9 @@ }, "sc:name": "WORMHOLE", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://wormhole.jax.org/" }, diff --git a/data/wormnet_v3/wormnet_v3bioschemas.jsonld b/data/wormnet_v3/wormnet_v3bioschemas.jsonld index 0b1f84bb754e8..b28b11dc7bbb8 100644 --- a/data/wormnet_v3/wormnet_v3bioschemas.jsonld +++ b/data/wormnet_v3/wormnet_v3bioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Network-assisted hypothesis-generating web server for Caenorhabditis elegans.", "sc:name": "WormNet v3", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.inetbio.org/wormnet" } \ No newline at end of file diff --git a/data/worms/wormsbioschemas.jsonld b/data/worms/wormsbioschemas.jsonld index b6758097dbf47..1887d44443922 100644 --- a/data/worms/wormsbioschemas.jsonld +++ b/data/worms/wormsbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Search the WoRMS taxonomy.", "sc:name": "World Register of Marine Species (WORMS)", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.marinespecies.org/aphia.php?p=webservice", "sc:version": "1" diff --git a/data/wossdata/wossdatabioschemas.jsonld b/data/wossdata/wossdatabioschemas.jsonld index b2842a05e5a49..f9bef181c08e0 100644 --- a/data/wossdata/wossdatabioschemas.jsonld +++ b/data/wossdata/wossdatabioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "EMBOSS Contributors", "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "EMBOSS Contributors", + "UK MRC" ], "sc:description": "Find programs by EDAM data.", "sc:funder": [ - "UK BBSRC", + "UK MRC", "Wellcome Trust", - "UK MRC" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "wossdata", diff --git a/data/wossinput/wossinputbioschemas.jsonld b/data/wossinput/wossinputbioschemas.jsonld index 4e4b63406d92e..de9c086f006be 100644 --- a/data/wossinput/wossinputbioschemas.jsonld +++ b/data/wossinput/wossinputbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "EMBOSS Contributors", + "Wellcome Trust", "UK MRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:description": "Find programs by EDAM input data.", "sc:funder": [ "Wellcome Trust", - "UK BBSRC", - "UK MRC" + "UK MRC", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "wossinput", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/wossinput.html", "sc:version": "r6" diff --git a/data/wossname/wossnamebioschemas.jsonld b/data/wossname/wossnamebioschemas.jsonld index 47e31937a66a8..88fb97db381c1 100644 --- a/data/wossname/wossnamebioschemas.jsonld +++ b/data/wossname/wossnamebioschemas.jsonld @@ -27,8 +27,8 @@ "sc:name": "wossname", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:provider": [ "EMBL EBI", diff --git a/data/wossoperation/wossoperationbioschemas.jsonld b/data/wossoperation/wossoperationbioschemas.jsonld index 53adedc0bf62c..5ce44b02573e3 100644 --- a/data/wossoperation/wossoperationbioschemas.jsonld +++ b/data/wossoperation/wossoperationbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", - "Wellcome Trust", + "UK MRC", "EMBOSS Contributors", - "UK MRC" + "Wellcome Trust", + "UK BBSRC" ], "sc:description": "Find programs by EDAM operation.", "sc:funder": [ + "Wellcome Trust", "UK BBSRC", - "UK MRC", - "Wellcome Trust" + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "wossoperation", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:provider": [ - "EMBL EBI", - "EMBOSS" + "EMBOSS", + "EMBL EBI" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/wossoperation.html", "sc:version": "r6" diff --git a/data/wossoutput/wossoutputbioschemas.jsonld b/data/wossoutput/wossoutputbioschemas.jsonld index f18db11f241f5..eec492f4b0626 100644 --- a/data/wossoutput/wossoutputbioschemas.jsonld +++ b/data/wossoutput/wossoutputbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", - "UK BBSRC", "EMBOSS Contributors", - "Wellcome Trust" + "UK BBSRC", + "Wellcome Trust", + "UK MRC" ], "sc:description": "Find programs by EDAM output data.", "sc:funder": [ "Wellcome Trust", - "UK MRC", - "UK BBSRC" + "UK BBSRC", + "UK MRC" ], "sc:license": "GPL-3.0", "sc:name": "wossoutput", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": [ "EMBOSS", diff --git a/data/wossparam/wossparambioschemas.jsonld b/data/wossparam/wossparambioschemas.jsonld index 8e8a83303f581..db19aa60df8ba 100644 --- a/data/wossparam/wossparambioschemas.jsonld +++ b/data/wossparam/wossparambioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK MRC", "UK BBSRC", - "EMBOSS Contributors" + "EMBOSS Contributors", + "Wellcome Trust", + "UK MRC" ], "sc:description": "Find programs by EDAM parameter.", "sc:funder": [ + "Wellcome Trust", "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "wossparam", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/wossparam.html", "sc:version": "r6" diff --git a/data/wosstopic/wosstopicbioschemas.jsonld b/data/wosstopic/wosstopicbioschemas.jsonld index e1a136a4e53fd..78a5cfa3903f2 100644 --- a/data/wosstopic/wosstopicbioschemas.jsonld +++ b/data/wosstopic/wosstopicbioschemas.jsonld @@ -12,27 +12,27 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK BBSRC", "UK MRC", - "EMBOSS Contributors", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC", + "EMBOSS Contributors" ], "sc:description": "Find programs by EDAM topic.", "sc:funder": [ - "Wellcome Trust", + "UK MRC", "UK BBSRC", - "UK MRC" + "Wellcome Trust" ], "sc:license": "GPL-3.0", "sc:name": "wosstopic", "sc:operatingSystem": [ "Windows", - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://emboss.open-bio.org/rel/rel6/apps/wosstopic.html", "sc:version": "r6" diff --git a/data/wrap_n_shake/wrap_n_shakebioschemas.jsonld b/data/wrap_n_shake/wrap_n_shakebioschemas.jsonld index a4fd0f268d1fe..5344fcade914a 100644 --- a/data/wrap_n_shake/wrap_n_shakebioschemas.jsonld +++ b/data/wrap_n_shake/wrap_n_shakebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "Wrap n Shake", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://www.wnsdock.xyz/" diff --git a/data/writerestohtml/writerestohtmlbioschemas.jsonld b/data/writerestohtml/writerestohtmlbioschemas.jsonld index d4c1d6ba1c60a..3aec3b86b12a0 100644 --- a/data/writerestohtml/writerestohtmlbioschemas.jsonld +++ b/data/writerestohtml/writerestohtmlbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Write all ncRNAs analysis results into an HTML file (Only for ncRNAs analysis pipeline).", "sc:name": "writerestohtml", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/urgi_tools/writeResToHTML/1.0.0", "sc:version": "1.0.0" diff --git a/data/ws_snps_and_go/ws_snps_and_gobioschemas.jsonld b/data/ws_snps_and_go/ws_snps_and_gobioschemas.jsonld index af78788499e0f..4b29ad8bc162f 100644 --- a/data/ws_snps_and_go/ws_snps_and_gobioschemas.jsonld +++ b/data/ws_snps_and_go/ws_snps_and_gobioschemas.jsonld @@ -9,18 +9,14 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "http://orcid.org/0000-0002-2323-0963", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/ws_snps_and_go", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rita Casadio", { "@id": "http://orcid.org/0000-0002-2323-0963" - } + }, + "Rita Casadio" ], "sc:additionalType": [ "Web service", @@ -33,23 +29,27 @@ } ], "sc:citation": [ - "pubmed:19514061", - "pubmed:23819482", "pmcid:PMC3194195", { "@id": "https://doi.org/10.1186/1471-2105-12-S4-S3" }, - "pubmed:21992054" + "pubmed:21992054", + "pubmed:19514061", + "pubmed:23819482" ], "sc:description": "A web server for predicting disease associated variations from protein sequence and structure.", "sc:name": "WS-SNPs and GO", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://snps.biofold.org/snps-and-go" }, + { + "@id": "http://orcid.org/0000-0002-2323-0963", + "@type": "schema:Person" + }, { "@id": "https://doi.org/10.1186/1471-2105-12-S4-S3", "@type": "sc:CreativeWork" diff --git a/data/wsgobiospace/wsgobiospacebioschemas.jsonld b/data/wsgobiospace/wsgobiospacebioschemas.jsonld index e7831d8568623..1da00cc092b06 100644 --- a/data/wsgobiospace/wsgobiospacebioschemas.jsonld +++ b/data/wsgobiospace/wsgobiospacebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Repository of sum formula with source tagged annotations for properties such as InChI strings, CAS numbers, IUPAC names, synonyms, cross references or KEGG Pathway names, among others.", "sc:name": "wsGoBioSpace", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://gmd.mpimp-golm.mpg.de/GoBioSpace.aspx", diff --git a/data/wslibrarysearch/wslibrarysearchbioschemas.jsonld b/data/wslibrarysearch/wslibrarysearchbioschemas.jsonld index 7592b820dd08c..81714a147f0e2 100644 --- a/data/wslibrarysearch/wslibrarysearchbioschemas.jsonld +++ b/data/wslibrarysearch/wslibrarysearchbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "These web services provide access to methods for matching user submitted spectra against the GMD.", "sc:name": "wsLibrarySearch", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://gmd.mpimp-golm.mpg.de/webservices/wsLibrarySearch.asmx", diff --git a/data/wsprediction/wspredictionbioschemas.jsonld b/data/wsprediction/wspredictionbioschemas.jsonld index 8129d54503343..9989a1ce7d3ba 100644 --- a/data/wsprediction/wspredictionbioschemas.jsonld +++ b/data/wsprediction/wspredictionbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Provide access to methods for prediction of chemical sub-groups by means of user submitted mass spectra.", "sc:name": "wsPrediction", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://gmd.mpimp-golm.mpg.de/webservices/wsPrediction.asmx", "sc:version": "1" diff --git a/data/wssas/wssasbioschemas.jsonld b/data/wssas/wssasbioschemas.jsonld index c3ad6d663cd32..2fc0ff634e006 100644 --- a/data/wssas/wssasbioschemas.jsonld +++ b/data/wssas/wssasbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank and provides functional residue annotation based on data from the Catalytic Site Atlas and PDBsum.", "sc:name": "SAS WS", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.ebi.ac.uk/thornton-srv/databases/WSsas/", "sc:version": "1" diff --git a/data/wtfgenes/wtfgenesbioschemas.jsonld b/data/wtfgenes/wtfgenesbioschemas.jsonld index 4df4e6b537a7a..25992e4574a76 100644 --- a/data/wtfgenes/wtfgenesbioschemas.jsonld +++ b/data/wtfgenes/wtfgenesbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/wtfgenes", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:description": "Enrichment of genes associated with particular ontology terms. Implementation of both hypergeometric and model-based approaches, that can be published as a static site with computation run in JavaScript on the user's web browser client.", "sc:license": "BSD-3-Clause", diff --git a/data/wu-crispr/wu-crisprbioschemas.jsonld b/data/wu-crispr/wu-crisprbioschemas.jsonld index 7da5cbcffbbec..62faad013bee3 100644 --- a/data/wu-crispr/wu-crisprbioschemas.jsonld +++ b/data/wu-crispr/wu-crisprbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "The Washington University gRNA designer for CRISPR/Cas9 knockouts.", "sc:name": "WU-CRISPR", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://crispr.wustl.edu/" } \ No newline at end of file diff --git a/data/wurst/wurstbioschemas.jsonld b/data/wurst/wurstbioschemas.jsonld index 4e70b700a4734..f83547facb886 100644 --- a/data/wurst/wurstbioschemas.jsonld +++ b/data/wurst/wurstbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures.", "sc:name": "Wurst", "sc:operatingSystem": [ - "Mac", "Windows", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.zbh.uni-hamburg.de/wurst/" } \ No newline at end of file diff --git a/data/wwligcsrre/wwligcsrrebioschemas.jsonld b/data/wwligcsrre/wwligcsrrebioschemas.jsonld index 95b787ea34511..40e86f8178467 100644 --- a/data/wwligcsrre/wwligcsrrebioschemas.jsonld +++ b/data/wwligcsrre/wwligcsrrebioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/wwligcsrre", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Pierre Tuffery", - "Michel Petitjean" + "Michel Petitjean", + "Pierre Tuffery" ], "sc:additionalType": "Web application", "sc:citation": "pubmed:19429687", diff --git a/data/x2h/x2hbioschemas.jsonld b/data/x2h/x2hbioschemas.jsonld index 3302e9c6ea310..4d4f53986997b 100644 --- a/data/x2h/x2hbioschemas.jsonld +++ b/data/x2h/x2hbioschemas.jsonld @@ -11,11 +11,11 @@ "@id": "https://bio.tools/X2H", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ + "Qiuru Liu", "Shuhui Su", "Jian Liu", - "Yongzhuang Liu", - "Qiuru Liu", - "Lei Zhang" + "Lei Zhang", + "Yongzhuang Liu" ], "sc:additionalType": "Command-line tool", "sc:citation": "pubmed:31094692", @@ -24,8 +24,8 @@ "sc:name": "X2H", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://github.com/lyotvincent/X2H" } \ No newline at end of file diff --git a/data/x2k/x2kbioschemas.jsonld b/data/x2k/x2kbioschemas.jsonld index a40d2278f467b..a09acb5eaca22 100644 --- a/data/x2k/x2kbioschemas.jsonld +++ b/data/x2k/x2kbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Method to identify upstream regulators likely responsible for observed patterns in genome-wide gene expression. By integrating ChIP-seq/chip and position-weight-matrices (PWMs) data, protein-protein interactions, and kinase-substrate phosphorylation reactions, it can better identify regulatory mechanisms upstream of genome-wide differences in gene expression.", "sc:name": "X2K", "sc:operatingSystem": [ - "Windows", "Linux", + "Windows", "Mac" ], "sc:url": "http://www.maayanlab.net/X2K" diff --git a/data/xanthusbase/xanthusbasebioschemas.jsonld b/data/xanthusbase/xanthusbasebioschemas.jsonld index 5b5f66dc1aaeb..5937e920090af 100644 --- a/data/xanthusbase/xanthusbasebioschemas.jsonld +++ b/data/xanthusbase/xanthusbasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Model organism database for the bacterium Myxococcus xanthus.", "sc:name": "Xanthusbase", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://ecoliwiki.net/colipedia/index.php/XanthusBase" } \ No newline at end of file diff --git a/data/xbseq/xbseqbioschemas.jsonld b/data/xbseq/xbseqbioschemas.jsonld index 6ae994c8d5d6f..7855f86e14b21 100644 --- a/data/xbseq/xbseqbioschemas.jsonld +++ b/data/xbseq/xbseqbioschemas.jsonld @@ -20,8 +20,8 @@ "sc:name": "XBSeq", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/XBSeq.html", "sc:version": "1.4.0" diff --git a/data/xcavator/xcavatorbioschemas.jsonld b/data/xcavator/xcavatorbioschemas.jsonld index 039d221fa24e5..ec38c29bb8b85 100644 --- a/data/xcavator/xcavatorbioschemas.jsonld +++ b/data/xcavator/xcavatorbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/s12864-017-4137-0", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/xcavator", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Alberto Magi", "sc:additionalType": "Command-line tool", "sc:citation": [ + "pmcid:PMC5609061", + "pubmed:28934930", { "@id": "https://doi.org/10.1186/s12864-017-4137-0" - }, - "pmcid:PMC5609061", - "pubmed:28934930" + } ], "sc:description": "Accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments.", "sc:featureList": [ @@ -34,10 +38,6 @@ "sc:name": "XCAVATOR", "sc:operatingSystem": "Linux", "sc:url": "https://sourceforge.net/projects/xcavator/" - }, - { - "@id": "https://doi.org/10.1186/s12864-017-4137-0", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/xcellerator/xcelleratorbioschemas.jsonld b/data/xcellerator/xcelleratorbioschemas.jsonld index 90d539338fb25..b3d51f4bac175 100644 --- a/data/xcellerator/xcelleratorbioschemas.jsonld +++ b/data/xcellerator/xcelleratorbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "xCellerator", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://xcellerator.info/" } \ No newline at end of file diff --git a/data/xchemexplorer/xchemexplorerbioschemas.jsonld b/data/xchemexplorer/xchemexplorerbioschemas.jsonld index 16904bef2ad0f..eb99b4c13da40 100644 --- a/data/xchemexplorer/xchemexplorerbioschemas.jsonld +++ b/data/xchemexplorer/xchemexplorerbioschemas.jsonld @@ -17,8 +17,8 @@ "@id": "https://bio.tools/xchemexplorer", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Rachael Skyner", "Frank von Delft", + "Rachael Skyner", "Tobias Krojer" ], "sc:additionalType": "Command-line tool", @@ -35,8 +35,8 @@ }, "sc:name": "XChemExplorer", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://tkrojer.github.io/XChemExplorer/" } diff --git a/data/xcms/xcmsbioschemas.jsonld b/data/xcms/xcmsbioschemas.jsonld index 104a7deda3227..8ce30edecedc3 100644 --- a/data/xcms/xcmsbioschemas.jsonld +++ b/data/xcms/xcmsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://orcid.org/0000-0002-7899-7192", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/xcms", "@type": "sc:SoftwareApplication", @@ -16,24 +20,20 @@ "@id": "https://orcid.org/0000-0002-7899-7192" }, "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:citation": "pubmed:20671148", "sc:description": "Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.", "sc:license": "GPL-2.0", "sc:name": "xcms", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/xcms.html", "sc:version": "3.0.2" - }, - { - "@id": "https://orcid.org/0000-0002-7899-7192", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/xcms_online/xcms_onlinebioschemas.jsonld b/data/xcms_online/xcms_onlinebioschemas.jsonld index c2f935d833474..8def26c930a8d 100644 --- a/data/xcms_online/xcms_onlinebioschemas.jsonld +++ b/data/xcms_online/xcms_onlinebioschemas.jsonld @@ -15,8 +15,8 @@ "sc:name": "XCMS Online", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage" } \ No newline at end of file diff --git a/data/xde/xdebioschemas.jsonld b/data/xde/xdebioschemas.jsonld index fc40b3150b675..f8729698adeb2 100644 --- a/data/xde/xdebioschemas.jsonld +++ b/data/xde/xdebioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1198/jasa.2009.ap07611", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/xde", "@type": "sc:SoftwareApplication", @@ -18,40 +22,36 @@ "Library" ], "sc:citation": [ + "pmcid:PMC2994029", "pubmed:21127725", { "@id": "https://doi.org/10.1198/jasa.2009.ap07611" - }, - "pmcid:PMC2994029" + } ], "sc:description": "A package for estimating differential gene expression from different studies with technological differences to improve the statistical power of gene expression studies.", "sc:featureList": [ { - "@id": "edam:operation_3664" + "@id": "edam:operation_2428" }, { "@id": "edam:operation_3436" }, { - "@id": "edam:operation_2495" + "@id": "edam:operation_3664" }, { - "@id": "edam:operation_2428" + "@id": "edam:operation_2495" } ], "sc:license": "GPL-2.0", "sc:name": "XDE", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/XDE.html", "sc:version": "2.24.0" - }, - { - "@id": "https://doi.org/10.1198/jasa.2009.ap07611", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/xeml-lab/xeml-labbioschemas.jsonld b/data/xeml-lab/xeml-labbioschemas.jsonld index 82b141d13926c..1069459927219 100644 --- a/data/xeml-lab/xeml-labbioschemas.jsonld +++ b/data/xeml-lab/xeml-labbioschemas.jsonld @@ -12,13 +12,13 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Desktop application", "sc:author": [ - "Benjamin Dartigues", - "Emmanuel Bouilhol" + "Emmanuel Bouilhol", + "Benjamin Dartigues" ], "sc:contributor": [ - "Yves Gibon", + "CHen Zhui", "Cecile Cabasson", - "CHen Zhui" + "Yves Gibon" ], "sc:description": "Interactive timeline visualisation that enables the intuitive design of experiments in terms of growth conditions and sampling strategy using related Ontologies (Xeo, EnvO, EO) while the corresponding metadata are automatically stored in the background in Xeml standardized format, ready for data mining.", "sc:license": "MIT", @@ -29,8 +29,8 @@ "Mac" ], "sc:provider": [ - "Centre de Bioinformatique de Bordeaux (CBiB)", - "UMR 1332 - Biologie du Fruit et Pathologie" + "UMR 1332 - Biologie du Fruit et Pathologie", + "Centre de Bioinformatique de Bordeaux (CBiB)" ], "sc:url": "https://github.com/cbib/XEML-Lab", "sc:version": "1" diff --git a/data/xenbase/xenbasebioschemas.jsonld b/data/xenbase/xenbasebioschemas.jsonld index 23e01962c3c7c..9768a90425983 100644 --- a/data/xenbase/xenbasebioschemas.jsonld +++ b/data/xenbase/xenbasebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The model organism database for Xenopus laevis and X. (Silurana) tropicalis.", "sc:name": "XenBase", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://www.xenbase.org" } \ No newline at end of file diff --git a/data/xenogi/xenogibioschemas.jsonld b/data/xenogi/xenogibioschemas.jsonld index 5fb02a687ebbe..6f281f5f9d2b7 100644 --- a/data/xenogi/xenogibioschemas.jsonld +++ b/data/xenogi/xenogibioschemas.jsonld @@ -19,25 +19,25 @@ "biotools:primaryContact": "Eliot C. Bush", "sc:additionalType": "Web application", "sc:citation": [ - "pmcid:PMC5799925", - "pubmed:29402213", { "@id": "https://doi.org/10.1186/s12859-018-2038-0" - } + }, + "pubmed:29402213", + "pmcid:PMC5799925" ], "sc:description": "Reconstructing the history of genomic island insertions in clades of closely related bacteria.", "sc:featureList": [ { - "@id": "edam:operation_0253" + "@id": "edam:operation_0324" }, { - "@id": "edam:operation_0324" + "@id": "edam:operation_0253" } ], "sc:name": "xenoGI", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://siva.cs.hmc.edu/xgicgi/wxgi.py/form" diff --git a/data/xeva/xevabioschemas.jsonld b/data/xeva/xevabioschemas.jsonld index 4681b5422ddd7..a0616bab0ed6c 100644 --- a/data/xeva/xevabioschemas.jsonld +++ b/data/xeva/xevabioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "Xeva", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/bhklab/Xeva" } \ No newline at end of file diff --git a/data/xgr/xgrbioschemas.jsonld b/data/xgr/xgrbioschemas.jsonld index b937581a74d9e..39bf913bb9553 100644 --- a/data/xgr/xgrbioschemas.jsonld +++ b/data/xgr/xgrbioschemas.jsonld @@ -14,14 +14,14 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Julian C. Knight", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": [ - "pmcid:PMC5154134", { "@id": "https://doi.org/10.1186/s13073-016-0384-y" }, + "pmcid:PMC5154134", "pubmed:27964755" ], "sc:contributor": { diff --git a/data/xheinz/xheinzbioschemas.jsonld b/data/xheinz/xheinzbioschemas.jsonld index 3e35959a68bb3..fad39995a21c4 100644 --- a/data/xheinz/xheinzbioschemas.jsonld +++ b/data/xheinz/xheinzbioschemas.jsonld @@ -12,19 +12,19 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:author": [ - "Daniela Beisser", + "Hayssam Soueidan", + "Thomas Hume", "Mohammed El-Kebir", + "Daniela Beisser", "Tobias Müller", - "Hayssam Soueidan", - "Marcus Dittrich", - "Thomas Hume" + "Marcus Dittrich" ], "sc:contributor": [ + "Jaap Heringa", + "Guillaume Blin", "Lodewyk F. A. Wessels", "Gunnar W. Klau", - "Macha Nikolski", - "Jaap Heringa", - "Guillaume Blin" + "Macha Nikolski" ], "sc:description": "Software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions. Active subnetwork modules are sets of genes, one for each species, which: - induce a connected subnetwork in a species-specific interaction network, - show overall differential behavior, and - contain a large number of orthologous genes.", "sc:license": "MIT", @@ -35,12 +35,12 @@ ], "sc:provider": [ "The Netherlands", + "The Netherlands Cancer Institute, Amsterdam", + "u-bordeaux.fr", "University Duisburg-Essen", + "Würzburg University, Germany", "Univ. Bordeaux, CNRS/LaBRI, 33405 Talence, France,", - "u-bordeaux.fr", - "The Netherlands Cancer Institute, Amsterdam", - "Bordeaux University, CBiB, France", - "Würzburg University, Germany" + "Bordeaux University, CBiB, France" ], "sc:url": "https://github.com/ls-cwi/xheinz", "sc:version": "1.0" diff --git a/data/xhm/xhmbioschemas.jsonld b/data/xhm/xhmbioschemas.jsonld index 8c0e8af8e3ade..a95333aad6ff6 100644 --- a/data/xhm/xhmbioschemas.jsonld +++ b/data/xhm/xhmbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Tool for assessment of the reliability of hybridization signals by detecting potential cross-hybridizations on DNA microarrays.", "sc:name": "XHM", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.bioinfo.no/tools/xhm/" } \ No newline at end of file diff --git a/data/xia2/xia2bioschemas.jsonld b/data/xia2/xia2bioschemas.jsonld index 8f16551c53aee..0afbcb53f925b 100644 --- a/data/xia2/xia2bioschemas.jsonld +++ b/data/xia2/xia2bioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Automated data reduction system designed to work from raw diffraction data and a little metadata, and produce usefully reduced data in a form suitable for immediately starting phasing and structure solution.", "sc:name": "XIA2", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:provider": "Instruct", diff --git a/data/xibd/xibdbioschemas.jsonld b/data/xibd/xibdbioschemas.jsonld index a5997d6c85a05..c68e3853e9543 100644 --- a/data/xibd/xibdbioschemas.jsonld +++ b/data/xibd/xibdbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "XIBD", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://bioinf.wehi.edu.au/software/XIBD/" } \ No newline at end of file diff --git a/data/xina/xinabioschemas.jsonld b/data/xina/xinabioschemas.jsonld index aa9b1626ca17e..985175c6245f7 100644 --- a/data/xina/xinabioschemas.jsonld +++ b/data/xina/xinabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/xina", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Sasha A. Singh", - "Lang Ho Lee" + "Lang Ho Lee", + "Sasha A. Singh" ], "sc:additionalType": "Library", "sc:citation": "pubmed:30370770", diff --git a/data/xip/xipbioschemas.jsonld b/data/xip/xipbioschemas.jsonld index 709ea3f2aa1e6..372ca794f14e4 100644 --- a/data/xip/xipbioschemas.jsonld +++ b/data/xip/xipbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "A flexible, editable and modular environment with a user-friendly interface that does not require previous programming skills to run,construct and edit workflows. It allows the construction of workflows by linking components written in both R and Java, the analysis of high-throughput data in grid engine systems and also the development of customized pipelines that can be encapsulated in a package and distributed.", "sc:name": "XiP", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://xip.hgc.jp/" } \ No newline at end of file diff --git a/data/xispec/xispecbioschemas.jsonld b/data/xispec/xispecbioschemas.jsonld index cd186c0b36c87..90009cbe806d7 100644 --- a/data/xispec/xispecbioschemas.jsonld +++ b/data/xispec/xispecbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/xispec", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Lars Kolbowski", "Prof Juri Rappsilber", + "Lars Kolbowski", "Colin Combe" ], "sc:additionalType": [ diff --git a/data/xlink/xlinkbioschemas.jsonld b/data/xlink/xlinkbioschemas.jsonld index 624b77badff2f..73af6ea909f7d 100644 --- a/data/xlink/xlinkbioschemas.jsonld +++ b/data/xlink/xlinkbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Set of tools for analysis of data from crosslinked and digested protein complexes.", "sc:name": "XLink", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://tools.proteomecenter.org/XLink.php" } \ No newline at end of file diff --git a/data/xlinkdb/xlinkdbbioschemas.jsonld b/data/xlinkdb/xlinkdbbioschemas.jsonld index 2679536733481..8fe07ec600cbb 100644 --- a/data/xlinkdb/xlinkdbbioschemas.jsonld +++ b/data/xlinkdb/xlinkdbbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Unlicense", "sc:name": "XLinkDB", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://xlinkdb.gs.washington.edu/xlinkdb/", diff --git a/data/xman/xmanbioschemas.jsonld b/data/xman/xmanbioschemas.jsonld index cc1efed420e81..745e02512fde3 100644 --- a/data/xman/xmanbioschemas.jsonld +++ b/data/xman/xmanbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "Simple and efficient method for the mapping of millions of query oligonucleotide fragments to the subject genome of any given length.", "sc:name": "xMAN", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://liulab.dfci.harvard.edu/WEBSITE/software.htm", "sc:version": "20060925" diff --git a/data/xmapbridge/xmapbridgebioschemas.jsonld b/data/xmapbridge/xmapbridgebioschemas.jsonld index 10f9ded64c0ff..4500da164f658 100644 --- a/data/xmapbridge/xmapbridgebioschemas.jsonld +++ b/data/xmapbridge/xmapbridgebioschemas.jsonld @@ -9,10 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1093/nar/gkm779", - "@type": "sc:CreativeWork" - }, { "@id": "https://bio.tools/xmapbridge", "@type": "sc:SoftwareApplication", @@ -31,11 +27,11 @@ "@id": "edam:topic_0102" }, "sc:citation": [ - "pmcid:PMC2238884", "pubmed:17932061", { "@id": "https://doi.org/10.1093/nar/gkm779" - } + }, + "pmcid:PMC2238884" ], "sc:description": "This package can plot graphs in the X:Map genome browser. It exports plotting files in a suitable format.", "sc:featureList": { @@ -50,6 +46,10 @@ ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/xmapbridge.html", "sc:version": "1.32.0" + }, + { + "@id": "https://doi.org/10.1093/nar/gkm779", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/xmipp/xmippbioschemas.jsonld b/data/xmipp/xmippbioschemas.jsonld index a81544531b686..9b732b893c6d6 100644 --- a/data/xmipp/xmippbioschemas.jsonld +++ b/data/xmipp/xmippbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A suite of image processing programs.", "sc:name": "XMIPP", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": "Instruct", "sc:url": "http://xmipp.cnb.csic.es/", diff --git a/data/xml2raf/xml2rafbioschemas.jsonld b/data/xml2raf/xml2rafbioschemas.jsonld index 266562093afd8..daaf2205506ea 100644 --- a/data/xml2raf/xml2rafbioschemas.jsonld +++ b/data/xml2raf/xml2rafbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "XML2RAF is a Perl software to create RAF maps from PDB XML files.The Protein Data Bank provides XML files that include a mapping between the PDB-format records SEQRES (representing the sequence of the molecule used in an experiment) and ATOM (representing the atoms experimentally observed). These XML files (along with the PDB’s chemical dictionary) also provide information on the original identity of most residues prior to any post-translational modifications, including cyclizations.", "sc:name": "XML2RAF 1.02 -Create RAF Maps from PDB XML files", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://scop.berkeley.edu/downloads/ver=1.75B" diff --git a/data/xmlget/xmlgetbioschemas.jsonld b/data/xmlget/xmlgetbioschemas.jsonld index 203a8c23f20fb..4736aaa1f6129 100644 --- a/data/xmlget/xmlgetbioschemas.jsonld +++ b/data/xmlget/xmlgetbioschemas.jsonld @@ -12,23 +12,23 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", - "UK MRC", + "UK BBSRC", "EMBOSS Contributors", - "UK BBSRC" + "UK MRC", + "Wellcome Trust" ], "sc:description": "An Emboss tool that fetches XML entry from a file or a local or remote data resource, parses it and rewrites it in various formats", "sc:funder": [ "UK MRC", - "UK BBSRC", - "Wellcome Trust" + "Wellcome Trust", + "UK BBSRC" ], "sc:license": "GPL-3.0", "sc:name": "xmlget", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:provider": [ "EMBOSS", diff --git a/data/xmltext/xmltextbioschemas.jsonld b/data/xmltext/xmltextbioschemas.jsonld index 90b915dd7caed..f7bab93644b68 100644 --- a/data/xmltext/xmltextbioschemas.jsonld +++ b/data/xmltext/xmltextbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "UK MRC", "UK BBSRC", - "Wellcome Trust", - "EMBOSS Contributors" + "UK MRC", + "EMBOSS Contributors", + "Wellcome Trust" ], "sc:description": "An Emboss tool that reads XML data and rewrites it as the original entry text", "sc:funder": [ @@ -26,13 +26,13 @@ "sc:license": "GPL-3.0", "sc:name": "xmltext", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:provider": [ - "EMBOSS", - "EMBL EBI" + "EMBL EBI", + "EMBOSS" ], "sc:url": "http://www.bioinformatics.nl/cgi-bin/emboss/xmltext", "sc:version": "r6" diff --git a/data/xmrf/xmrfbioschemas.jsonld b/data/xmrf/xmrfbioschemas.jsonld index 1b817313646b8..e1d89705fe995 100644 --- a/data/xmrf/xmrfbioschemas.jsonld +++ b/data/xmrf/xmrfbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-2.0", "sc:name": "XMRF", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "https://github.com/zhandong/XMRF" } \ No newline at end of file diff --git a/data/xmwas/xmwasbioschemas.jsonld b/data/xmwas/xmwasbioschemas.jsonld index d1542b305433d..9bbd565f7df68 100644 --- a/data/xmwas/xmwasbioschemas.jsonld +++ b/data/xmwas/xmwasbioschemas.jsonld @@ -18,9 +18,9 @@ "sc:description": "Data-driven integration and differential network analysis tool.", "sc:name": "xMWAS", "sc:operatingSystem": [ - "Windows", "Linux", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://kuppal.shinyapps.io/xmwas/" } \ No newline at end of file diff --git a/data/xp-ehh/xp-ehhbioschemas.jsonld b/data/xp-ehh/xp-ehhbioschemas.jsonld index aab89facfda80..9db51c4b38996 100644 --- a/data/xp-ehh/xp-ehhbioschemas.jsonld +++ b/data/xp-ehh/xp-ehhbioschemas.jsonld @@ -18,10 +18,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pmcid:PMC2687721", { "@id": "https://doi.org/10.1038/nature06250" }, + "pmcid:PMC2687721", "pubmed:17943131" ], "sc:description": "Program to estimate the cross population extended haplotype homozygosity as an indicator of positive selection.", diff --git a/data/xplormed/xplormedbioschemas.jsonld b/data/xplormed/xplormedbioschemas.jsonld index c655e372fd728..37ff82354f39a 100644 --- a/data/xplormed/xplormedbioschemas.jsonld +++ b/data/xplormed/xplormedbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Web tool that aids MEDLINE searching by summarizing the subjects contained in the results, thus allowing users to focus on subjects of interest.", "sc:name": "XplorMed", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://xplormed.ogic.ca/" } \ No newline at end of file diff --git a/data/xpn/xpnbioschemas.jsonld b/data/xpn/xpnbioschemas.jsonld index c4c7eeab9467c..c39619a94fdf3 100644 --- a/data/xpn/xpnbioschemas.jsonld +++ b/data/xpn/xpnbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Cross-platform normalization method for combining gene expression data from different studies. Merging two gene-expression studies via cross-platform normalization.", "sc:name": "XPN", "sc:operatingSystem": [ - "Mac", "Linux", + "Mac", "Windows" ], "sc:url": "https://genome.unc.edu/xpn/" diff --git a/data/xpress/xpressbioschemas.jsonld b/data/xpress/xpressbioschemas.jsonld index f0d0c098ba301..78c5652d47a6e 100644 --- a/data/xpress/xpressbioschemas.jsonld +++ b/data/xpress/xpressbioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/xpress", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Desktop application" + "Desktop application", + "Command-line tool" ], "sc:citation": "pubmed:11581660", "sc:description": "Calculates relative abundances from ICAT, cICAT, SILAC and other N-14/N-15 experiments.", diff --git a/data/xps/xpsbioschemas.jsonld b/data/xps/xpsbioschemas.jsonld index 0ce3399acd4e6..31298973811d5 100644 --- a/data/xps/xpsbioschemas.jsonld +++ b/data/xps/xpsbioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Christian Stratowa", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays, gene arrays and plate arrays on computers with 1 GB RAM only.", "sc:license": "GPL-2.0", "sc:name": "xps", "sc:operatingSystem": [ "Windows", - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/xps.html", "sc:version": "1.38.0" diff --git a/data/xpyder/xpyderbioschemas.jsonld b/data/xpyder/xpyderbioschemas.jsonld index e49280ce4e1fe..4e8734b2598e0 100644 --- a/data/xpyder/xpyderbioschemas.jsonld +++ b/data/xpyder/xpyderbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images.", "sc:name": "xPyder", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://xpyder.sourceforge.net/" } \ No newline at end of file diff --git a/data/xquest/xquestbioschemas.jsonld b/data/xquest/xquestbioschemas.jsonld index d1291ed08ab42..3be914209c9e4 100644 --- a/data/xquest/xquestbioschemas.jsonld +++ b/data/xquest/xquestbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Novel search engine for cross-linked peptides from complex samples.", "sc:name": "xQuest", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://proteomics.ethz.ch/orinner/public/htdocs/xquest/xquest_review.html" } \ No newline at end of file diff --git a/data/xrei/xreibioschemas.jsonld b/data/xrei/xreibioschemas.jsonld index 9b9eaf45dbecf..cb4a398dfeee9 100644 --- a/data/xrei/xreibioschemas.jsonld +++ b/data/xrei/xreibioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "xREI is a web interface that allows users to explore a range of predefined phylo-grammars or create their own phylo-grammar. Grammars are visualized via state transition graphs and substitution matrices. xREI is based on xrate, the flexible software tool for modeling structural and phylogenetic variation in multiple sequence alignments.", "sc:name": "xREI", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://biowiki.org/XreiProgram" } \ No newline at end of file diff --git a/data/xs/xsbioschemas.jsonld b/data/xs/xsbioschemas.jsonld index 2e530f62095fa..9d4d2200119e7 100644 --- a/data/xs/xsbioschemas.jsonld +++ b/data/xs/xsbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1186/1756-0500-7-40", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/xs", "@type": "sc:SoftwareApplication", @@ -31,10 +35,6 @@ "Linux" ], "sc:url": "http://bioinformatics.ua.pt/software/xs/" - }, - { - "@id": "https://doi.org/10.1186/1756-0500-7-40", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/xscape/xscapebioschemas.jsonld b/data/xscape/xscapebioschemas.jsonld index 162792e43c550..b3a9df4243861 100644 --- a/data/xscape/xscapebioschemas.jsonld +++ b/data/xscape/xscapebioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/xscape", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Library", - "Web application" + "Web application", + "Library" ], "sc:citation": "pubmed:24932009", "sc:description": "Set of Python tools for maximum parsimony phylogenetic event-based tree reconciliation in undated trees using the DTL (duplication-loss-transfer) model with applications to gene trees and species trees; parasite trees and host trees; and species trees and area cladograms.", "sc:name": "Xscape", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:url": "http://www.cs.hmc.edu/~hadas/xscape/" } \ No newline at end of file diff --git a/data/xsult/xsultbioschemas.jsonld b/data/xsult/xsultbioschemas.jsonld index b2ecb6b25b0ed..36e9adb925db5 100644 --- a/data/xsult/xsultbioschemas.jsonld +++ b/data/xsult/xsultbioschemas.jsonld @@ -21,8 +21,8 @@ { "@id": "https://doi.org/10.1093/NAR/GKX421" }, - "pmcid:PMC5793734", - "pubmed:28510698" + "pubmed:28510698", + "pmcid:PMC5793734" ], "sc:description": "Enhanced version of the protein alignment annotation program JoY,formats a submitted multiple-sequence alignment using three-dimensional (3D) structural information in order to assist in the comparative analysis of protein evolution and in the optimization of alignments for comparative modelling and construct design. It annotates each amino acid residue with residue depth, chain and ligand interactions, inter-residue contacts, sequence entropy, root mean square deviation and secondary structure and disorder prediction.", "sc:featureList": [ @@ -30,17 +30,17 @@ "@id": "edam:operation_0302" }, { - "@id": "edam:operation_2488" + "@id": "edam:operation_0267" }, { - "@id": "edam:operation_0267" + "@id": "edam:operation_2488" } ], "sc:name": "XSuLT", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://structure.bioc.cam.ac.uk/xsult/" } diff --git a/data/xsyn/xsynbioschemas.jsonld b/data/xsyn/xsynbioschemas.jsonld index fb337f9a89a41..0fa88ca284d50 100644 --- a/data/xsyn/xsynbioschemas.jsonld +++ b/data/xsyn/xsynbioschemas.jsonld @@ -9,16 +9,20 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1177/1176935117728516", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/xsyn", "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:citation": [ - "pubmed:28874883", - "pmcid:PMC5576537", { "@id": "https://doi.org/10.1177/1176935117728516" - } + }, + "pmcid:PMC5576537", + "pubmed:28874883" ], "sc:description": "xSyn is a software tool for identifying such 3-way interactions that 2 genes’ expression levels are clustered in different space locations under the control of a third gene’s expression levels. It uses cancer gene expression data based on an optimization procedure involving the usage of UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and synergy.", "sc:featureList": { @@ -27,15 +31,11 @@ "sc:license": "GPL-3.0", "sc:name": "xSyn", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://www.bdxconsult.com/xSyn.html" - }, - { - "@id": "https://doi.org/10.1177/1176935117728516", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/xtalk/xtalkbioschemas.jsonld b/data/xtalk/xtalkbioschemas.jsonld index cc6ec1ca5213e..cc5d1307c162c 100644 --- a/data/xtalk/xtalkbioschemas.jsonld +++ b/data/xtalk/xtalkbioschemas.jsonld @@ -15,10 +15,10 @@ "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:26400040", { "@id": "https://doi.org/10.1093/BIOINFORMATICS/BTV549" }, - "pubmed:26400040", "pmcid:PMC4907392" ], "sc:description": "Path-based approach for identifying pairs of pathways that may crosstalk.", diff --git a/data/xtalkdb/xtalkdbbioschemas.jsonld b/data/xtalkdb/xtalkdbbioschemas.jsonld index 591672f26f034..dca55eae721de 100644 --- a/data/xtalkdb/xtalkdbbioschemas.jsonld +++ b/data/xtalkdb/xtalkdbbioschemas.jsonld @@ -19,11 +19,11 @@ "biotools:primaryContact": "T. M. Murali", "sc:additionalType": "Database portal", "sc:citation": [ - "pubmed:27899583", "pmcid:PMC5210533", { "@id": "https://doi.org/10.1093/nar/gkw1037" - } + }, + "pubmed:27899583" ], "sc:description": "Curated information for 650 pairs of pathways from over 1600 publications. Report the molecular components (e.g. proteins, hormones, microRNAs) that mediate crosstalk between a pair of pathways and the species and tissue in which the crosstalk was observed.", "sc:featureList": { diff --git a/data/xtandem/xtandembioschemas.jsonld b/data/xtandem/xtandembioschemas.jsonld index ce7e2b5cf550c..ce32f8d026892 100644 --- a/data/xtandem/xtandembioschemas.jsonld +++ b/data/xtandem/xtandembioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Matches tandem mass spectra with peptide sequences.", "sc:name": "XTandem", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://www.thegpm.org/TANDEM/" } \ No newline at end of file diff --git a/data/xtandempipeline/xtandempipelinebioschemas.jsonld b/data/xtandempipeline/xtandempipelinebioschemas.jsonld index 59de2bafade22..bedf9854ef5ff 100644 --- a/data/xtandempipeline/xtandempipelinebioschemas.jsonld +++ b/data/xtandempipeline/xtandempipelinebioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "X!TandemPipeline: Filter, edit and group peptide/protein identifications from X!Tandem (and MASCOT).", "sc:name": "XTandemPipeline", "sc:operatingSystem": [ - "Linux", "Mac", + "Linux", "Windows" ], "sc:url": "http://pappso.inra.fr/bioinfo/xtandempipeline/" diff --git a/data/xtms/xtmsbioschemas.jsonld b/data/xtms/xtmsbioschemas.jsonld index e674917817066..6000cec9df06d 100644 --- a/data/xtms/xtmsbioschemas.jsonld +++ b/data/xtms/xtmsbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:description": "Web-based pathway analysis platform ,which provides full access to the set of pathways that can be imported into a chassis organism such as E. coli through the application of an Extended Metabolic Space modeling framework.", "sc:name": "XTMS", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://xtms.issb.genopole.fr/" diff --git a/data/xtractor/xtractorbioschemas.jsonld b/data/xtractor/xtractorbioschemas.jsonld index b3282f81f7c31..574912eb77ef0 100644 --- a/data/xtractor/xtractorbioschemas.jsonld +++ b/data/xtractor/xtractorbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Extracts pre-defined peaks or regions into a uniform array.", "sc:name": "Xtractor", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://www.ms-utils.org/Xtractor/" } \ No newline at end of file diff --git a/data/xvector/bioconda_xvector.yaml b/data/xvector/bioconda_xvector.yaml index 7c4b734feae6e..e4c82799b2d82 100644 --- a/data/xvector/bioconda_xvector.yaml +++ b/data/xvector/bioconda_xvector.yaml @@ -4,7 +4,6 @@ description: Provides memory efficient S4 classes for storing sequences "externa home: https://bioconductor.org/packages/3.10/bioc/html/XVector.html identifiers: - biotools:xvector -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-xvector summary: Foundation of external vector representation and manipulation in Bioconductor diff --git a/data/xvector/xvectorbioschemas.jsonld b/data/xvector/xvectorbioschemas.jsonld index 1f3d80b508778..1c6169045f01f 100644 --- a/data/xvector/xvectorbioschemas.jsonld +++ b/data/xvector/xvectorbioschemas.jsonld @@ -19,9 +19,9 @@ "sc:license": "Artistic-2.0", "sc:name": "XVector", "sc:operatingSystem": [ - "Linux", + "Mac", "Windows", - "Mac" + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/XVector.html", "sc:version": "0.18.0" diff --git a/data/xwalk/xwalkbioschemas.jsonld b/data/xwalk/xwalkbioschemas.jsonld index 7c1ca595beb25..b30c5ac51eb0f 100644 --- a/data/xwalk/xwalkbioschemas.jsonld +++ b/data/xwalk/xwalkbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "Xwalk", "sc:operatingSystem": [ "Linux", - "Mac", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://www.xwalk.org" } \ No newline at end of file diff --git a/data/xxmotif/xxmotifbioschemas.jsonld b/data/xxmotif/xxmotifbioschemas.jsonld index ce4f94813ebfd..079b515a8115a 100644 --- a/data/xxmotif/xxmotifbioschemas.jsonld +++ b/data/xxmotif/xxmotifbioschemas.jsonld @@ -9,32 +9,32 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/nar/gks602", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/xxmotif", "@type": "sc:SoftwareApplication", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": [ { "@id": "https://doi.org/10.1093/nar/gks602" }, - "pubmed:22990209", "pubmed:22693218", + "pubmed:22990209", "pmcid:PMC3394272" ], "sc:description": "Web server that can discover motifs that are enriched in sets of nucleotide sequences provided by the user. It uses a new approach for finding enriched motifs: It directly optimizes the statistical significance of enrichment for PWMs. It can also score conservation and positional clustering of motifs. In several benchmarks on yeast and metazoan sequences, the underlying XXmotif method showed better sensitivity and produced PWMs of higher quality than state-of-the-art tools.", "sc:name": "XXmotif", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "https://bammmotif.mpibpc.mpg.de/" - }, - { - "@id": "https://doi.org/10.1093/nar/gks602", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/yabi/yabibioschemas.jsonld b/data/yabi/yabibioschemas.jsonld index 597944c9ccce9..7f4acf0f32121 100644 --- a/data/yabi/yabibioschemas.jsonld +++ b/data/yabi/yabibioschemas.jsonld @@ -31,18 +31,18 @@ "@id": "edam:operation_3436" }, { - "@id": "edam:operation_3096" + "@id": "edam:operation_2422" }, { - "@id": "edam:operation_2422" + "@id": "edam:operation_3096" } ], "sc:license": "GPL-3.0", "sc:name": "Yabi", "sc:operatingSystem": [ "Linux", - "Windows", - "Mac" + "Mac", + "Windows" ], "sc:url": "https://github.com/muccg/yabi" } diff --git a/data/yacop/yacopbioschemas.jsonld b/data/yacop/yacopbioschemas.jsonld index 3b33917360c15..c669ca63aa5d4 100644 --- a/data/yacop/yacopbioschemas.jsonld +++ b/data/yacop/yacopbioschemas.jsonld @@ -14,8 +14,8 @@ "sc:description": "Metatool for gene prediction in prokaryotic genomes. The predictions generated by the tool are based on the output of existing gene finding programs.", "sc:name": "YACOP", "sc:operatingSystem": [ - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://gobics.de/tech/yacop.php", "sc:version": "2" diff --git a/data/yagm/yagmbioschemas.jsonld b/data/yagm/yagmbioschemas.jsonld index a284fdd58219f..b98cafc67b5f9 100644 --- a/data/yagm/yagmbioschemas.jsonld +++ b/data/yagm/yagmbioschemas.jsonld @@ -18,15 +18,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Wei-Sheng Wu", - "Meng-Jhun Jhou", - "Chung-Ching Wang" + "Chung-Ching Wang", + "Meng-Jhun Jhou" ], "sc:additionalType": "Web application", "sc:citation": [ + "pubmed:26678566", { "@id": "https://doi.org/10.1186/1752-0509-9-S6-S1" }, - "pubmed:26678566", "pmcid:PMC4674844" ], "sc:description": "A web tool for mining associated genes in yeast based on diverse biological associations.", @@ -36,8 +36,8 @@ "sc:name": "YAGM", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://cosbi3.ee.ncku.edu.tw/yagm/" } diff --git a/data/yakusa/yakusabioschemas.jsonld b/data/yakusa/yakusabioschemas.jsonld index 71bb33ca4577e..85ac085230011 100644 --- a/data/yakusa/yakusabioschemas.jsonld +++ b/data/yakusa/yakusabioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Program devised to rapidly scan a structural database with a query protein structure. It searches for the longest common substructures, called SHSP for “structural high scoring pairs”, between a query structure and every structure in the structural database. It makes use of protein backbone internal coordinates (α angles) in order to describe protein structures as sequences of symbols. It uses a deterministic finite automaton for pattern matching.", "sc:name": "YAKUSA", "sc:operatingSystem": [ - "Linux", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://wwwabi.snv.jussieu.fr/Yakusa/html/help_general.html" } \ No newline at end of file diff --git a/data/yamss/yamssbioschemas.jsonld b/data/yamss/yamssbioschemas.jsonld index e6daa341b8928..5126efd52c240 100644 --- a/data/yamss/yamssbioschemas.jsonld +++ b/data/yamss/yamssbioschemas.jsonld @@ -18,22 +18,22 @@ "Library" ], "sc:citation": [ + "pmcid:PMC5362739", + "pubmed:28221771", { "@id": "https://doi.org/10.1021/acs.analchem.6b04719" - }, - "pmcid:PMC5362739", - "pubmed:28221771" + } ], "sc:description": "Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.", "sc:featureList": [ { - "@id": "edam:operation_3214" + "@id": "edam:operation_3660" }, { - "@id": "edam:operation_2238" + "@id": "edam:operation_3214" }, { - "@id": "edam:operation_3660" + "@id": "edam:operation_2238" }, { "@id": "edam:operation_3694" @@ -43,8 +43,8 @@ "sc:name": "yamss", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/yamss.html", "sc:version": "1.0.2" diff --git a/data/yank/yankbioschemas.jsonld b/data/yank/yankbioschemas.jsonld index a0783ebe73c2e..4f790b082afe2 100644 --- a/data/yank/yankbioschemas.jsonld +++ b/data/yank/yankbioschemas.jsonld @@ -12,10 +12,10 @@ "@type": "sc:SoftwareApplication", "sc:additionalType": "Command-line tool", "sc:contributor": [ - "Wellcome Trust", "EMBOSS Contributors", - "UK MRC", - "UK BBSRC" + "Wellcome Trust", + "UK BBSRC", + "UK MRC" ], "sc:description": "Add a sequence reference (a full USA) to a list file.", "sc:funder": [ diff --git a/data/yapsa/bioconda_yapsa.yaml b/data/yapsa/bioconda_yapsa.yaml index a78230e4148d7..17e50c69df9f9 100644 --- a/data/yapsa/bioconda_yapsa.yaml +++ b/data/yapsa/bioconda_yapsa.yaml @@ -7,7 +7,6 @@ description: This package provides functions and routines useful in the analysis home: https://bioconductor.org/packages/3.10/bioc/html/YAPSA.html identifiers: - biotools:yapsa -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-yapsa diff --git a/data/yapsa/yapsabioschemas.jsonld b/data/yapsa/yapsabioschemas.jsonld index 45d184585d986..556347f19e158 100644 --- a/data/yapsa/yapsabioschemas.jsonld +++ b/data/yapsa/yapsabioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Daniel Huebschmann", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "This package provides functions and routines useful in the analysis of somatic signatures. In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.", "sc:license": "GPL-3.0", diff --git a/data/yaqcaffy/bioconda_yaqcaffy.yaml b/data/yaqcaffy/bioconda_yaqcaffy.yaml index 2b4f570e5e25c..b64027a793a72 100644 --- a/data/yaqcaffy/bioconda_yaqcaffy.yaml +++ b/data/yaqcaffy/bioconda_yaqcaffy.yaml @@ -4,7 +4,6 @@ description: Quality control of Affymetrix GeneChip expression data and reproduc home: https://bioconductor.org/packages/3.10/bioc/html/yaqcaffy.html identifiers: - biotools:yaqcaffy -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-yaqcaffy summary: Affymetrix expression data quality control and reproducibility analysis diff --git a/data/yaqcaffy/yaqcaffybioschemas.jsonld b/data/yaqcaffy/yaqcaffybioschemas.jsonld index 52d3fb4643637..038c7d65eb828 100644 --- a/data/yaqcaffy/yaqcaffybioschemas.jsonld +++ b/data/yaqcaffy/yaqcaffybioschemas.jsonld @@ -12,16 +12,16 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Laurent Gatto", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "The package enables users to do quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.", "sc:license": "Artistic-2.0", "sc:name": "yaqcaffy", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/yaqcaffy.html", "sc:version": "1.38.0" diff --git a/data/yarn/yarnbioschemas.jsonld b/data/yarn/yarnbioschemas.jsonld index d5dcf95e1d75f..dec3e43cb8bc0 100644 --- a/data/yarn/yarnbioschemas.jsonld +++ b/data/yarn/yarnbioschemas.jsonld @@ -12,15 +12,15 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Joseph N Paulson", "sc:additionalType": [ - "Library", - "Command-line tool" + "Command-line tool", + "Library" ], "sc:description": "The package enables users to expedite large RNA-Seq analyses using a combination of previously developed tools. It is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization, leveraging many BioConductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.", "sc:license": "Artistic-2.0", "sc:name": "yarn", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/yarn.html", diff --git a/data/yasara/yasarabioschemas.jsonld b/data/yasara/yasarabioschemas.jsonld index 24d63c52ad13e..33e53c536417a 100644 --- a/data/yasara/yasarabioschemas.jsonld +++ b/data/yasara/yasarabioschemas.jsonld @@ -11,8 +11,8 @@ "@id": "https://bio.tools/yasara", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Contact Form", - "Yasara Support" + "Yasara Support", + "Contact Form" ], "sc:additionalType": "Web application", "sc:description": "YASARA (Yet Another Scientific Artificial Reality Application) is a software package for visualization, simulation and modeling of molecules. It uses Portable Vector Language (PVL) which allows the visualization of very large proteins. YASARA View is available for free, and is primarily a visualization tool.", diff --git a/data/yass/yassbioschemas.jsonld b/data/yass/yassbioschemas.jsonld index d1d7b84ea022b..850c49f6f4041 100644 --- a/data/yass/yassbioschemas.jsonld +++ b/data/yass/yassbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments).", "sc:name": "YASS", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinfo.lifl.fr/yass/" } \ No newline at end of file diff --git a/data/yeast-deletion-library-tools/yeast-deletion-library-toolsbioschemas.jsonld b/data/yeast-deletion-library-tools/yeast-deletion-library-toolsbioschemas.jsonld index 4528a92955f4c..ce296d451b3d2 100644 --- a/data/yeast-deletion-library-tools/yeast-deletion-library-toolsbioschemas.jsonld +++ b/data/yeast-deletion-library-tools/yeast-deletion-library-toolsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "Yeast-Deletion-Library-Tools", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://yeastdb.org" } \ No newline at end of file diff --git a/data/yeast_kid/yeast_kidbioschemas.jsonld b/data/yeast_kid/yeast_kidbioschemas.jsonld index acd937b5d7fae..f92b421a45dca 100644 --- a/data/yeast_kid/yeast_kidbioschemas.jsonld +++ b/data/yeast_kid/yeast_kidbioschemas.jsonld @@ -11,16 +11,16 @@ "@id": "https://bio.tools/yeast_kid", "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ - "Database interface related information", - "Curation information" + "Curation information", + "Database interface related information" ], "sc:additionalType": "Database portal", "sc:citation": "pubmed:21492431", "sc:description": "Contains high- and low-throughput data relevant to phosphorylation events. It includes 6,225 low-throughput and 21,990 high-throughput interactions, from greater than 35,000 experiments.", "sc:name": "Yeast KID", "sc:operatingSystem": [ - "Linux", "Windows", + "Linux", "Mac" ], "sc:url": "http://www.moseslab.csb.utoronto.ca/KID/" diff --git a/data/yeast_metaboliner/yeast_metabolinerbioschemas.jsonld b/data/yeast_metaboliner/yeast_metabolinerbioschemas.jsonld index e3f76758a3500..1c1a7719d78fe 100644 --- a/data/yeast_metaboliner/yeast_metabolinerbioschemas.jsonld +++ b/data/yeast_metaboliner/yeast_metabolinerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Yeast MetaboliNER is a tool to automatically identify metabolite names in the literature, and associate structures where possible, to define the reported yeast metabolome.", "sc:name": "Yeast MetaboliNER", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://nactem7.mib.man.ac.uk/metaboliner/" } \ No newline at end of file diff --git a/data/yeastgfp/yeastgfpbioschemas.jsonld b/data/yeastgfp/yeastgfpbioschemas.jsonld index 6af771c164b65..d254d1654821a 100644 --- a/data/yeastgfp/yeastgfpbioschemas.jsonld +++ b/data/yeastgfp/yeastgfpbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Yeast GFP fusion localization database.", "sc:name": "Yeast GFP fusion localization database (yeastgfp)", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://yeastgfp.yeastgenome.org/" diff --git a/data/yeastract/yeastractbioschemas.jsonld b/data/yeastract/yeastractbioschemas.jsonld index 4c63d3145a1ff..8a65c7b48b9cd 100644 --- a/data/yeastract/yeastractbioschemas.jsonld +++ b/data/yeastract/yeastractbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "The YEAst Search for Transcriptional Regulators And Consensus Tracking is a curated repository of regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae. It includes DISCOVERER and allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor.", "sc:name": "YEASTRACT", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://www.yeastract.com" } \ No newline at end of file diff --git a/data/yeastspotter/yeastspotterbioschemas.jsonld b/data/yeastspotter/yeastspotterbioschemas.jsonld index a69d20a5753f2..b816feea12b2a 100644 --- a/data/yeastspotter/yeastspotterbioschemas.jsonld +++ b/data/yeastspotter/yeastspotterbioschemas.jsonld @@ -20,9 +20,9 @@ "sc:license": "MIT", "sc:name": "YeastSpotter", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "http://yeastspotter.csb.utoronto.ca/" } \ No newline at end of file diff --git a/data/yinoyang/yinoyangbioschemas.jsonld b/data/yinoyang/yinoyangbioschemas.jsonld index 6fb412496a645..3c4240d63c7a2 100644 --- a/data/yinoyang/yinoyangbioschemas.jsonld +++ b/data/yinoyang/yinoyangbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Ramneek Gupta", "sc:additionalType": [ - "Command-line tool", - "Web application" + "Web application", + "Command-line tool" ], "sc:citation": "pubmed:11928486", "sc:description": "Neural network predictions for O-Beta-GlcNAc attachment sites in eukaryotic protein sequences.", diff --git a/data/yloc/ylocbioschemas.jsonld b/data/yloc/ylocbioschemas.jsonld index 1bf5e62286aeb..98678e1b673ea 100644 --- a/data/yloc/ylocbioschemas.jsonld +++ b/data/yloc/ylocbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:license": "GPL-3.0", "sc:name": "YLoc", "sc:operatingSystem": [ + "Linux", "Mac", - "Windows", - "Linux" + "Windows" ], "sc:url": "https://abi-services.informatik.uni-tuebingen.de/yloc/webloc.cgi" } \ No newline at end of file diff --git a/data/yogy/yogybioschemas.jsonld b/data/yogy/yogybioschemas.jsonld index 505bfed28c676..84723ab5ee14d 100644 --- a/data/yogy/yogybioschemas.jsonld +++ b/data/yogy/yogybioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "YOGY", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://www.bahlerlab.info/YOGY/" } \ No newline at end of file diff --git a/data/yosshi/yosshibioschemas.jsonld b/data/yosshi/yosshibioschemas.jsonld index bb3d16f7424fb..42c11a3adcfa2 100644 --- a/data/yosshi/yosshibioschemas.jsonld +++ b/data/yosshi/yosshibioschemas.jsonld @@ -22,19 +22,19 @@ "Web service" ], "sc:citation": [ - "pubmed:31106356", { "@id": "https://doi.org/10.1093/NAR/GKZ385" }, - "pmcid:PMC6602428" + "pmcid:PMC6602428", + "pubmed:31106356" ], "sc:description": "Yosshi (YOur web-server for S-S bond HarvestIng) - web server for disulfide engineering by bioinformatic analysis of diverse protein families.", "sc:featureList": [ { - "@id": "edam:operation_1850" + "@id": "edam:operation_0471" }, { - "@id": "edam:operation_0471" + "@id": "edam:operation_1850" }, { "@id": "edam:operation_0303" @@ -43,9 +43,9 @@ "sc:license": "Unlicense", "sc:name": "Yosshi", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "https://biokinet.belozersky.msu.ru/yosshiserver/" } diff --git a/data/youscope/youscopebioschemas.jsonld b/data/youscope/youscopebioschemas.jsonld index ab9904cece764..5f6bcfcd1c160 100644 --- a/data/youscope/youscopebioschemas.jsonld +++ b/data/youscope/youscopebioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Open-source microscope control software compatible with most present-day automized microscopes. It allows to easily automatize complex microscopy protocols using an user-friendly graphical interface.", "sc:name": "YouScope 1.2 Beta", "sc:operatingSystem": [ - "Windows", "Mac", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://www.youscope.org/" } \ No newline at end of file diff --git a/data/ypa/ypabioschemas.jsonld b/data/ypa/ypabioschemas.jsonld index 9a093c4cadd9e..20b3dbb6bfc4b 100644 --- a/data/ypa/ypabioschemas.jsonld +++ b/data/ypa/ypabioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Database that collects promoter features in Saccharomyces cerevisiae. It integrates nine kinds of promoter features including promoter sequences, genes transcription boundaries-transcription start sites (TSSs), five prime untranslated regions (5’-UTRs) and three prime untranslated regions (3’-UTRs), TATA boxes, transcription factor binding sites (TFBSs), nucleosome occupancy, DNA bendability, transcription factor (TF) binding, TF knockout expression and TF-TF physical interaction.", "sc:name": "YPA", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://ypa.ee.ncku.edu.tw/" } \ No newline at end of file diff --git a/data/yrgate/yrgatebioschemas.jsonld b/data/yrgate/yrgatebioschemas.jsonld index c750ac924782b..e679873193154 100644 --- a/data/yrgate/yrgatebioschemas.jsonld +++ b/data/yrgate/yrgatebioschemas.jsonld @@ -15,10 +15,10 @@ "sc:additionalType": "Web application", "sc:citation": [ "pubmed:16859520", + "pmcid:PMC1779557", { "@id": "https://doi.org/10.1186/gb-2006-7-7-r58" - }, - "pmcid:PMC1779557" + } ], "sc:description": "Web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.", "sc:featureList": { diff --git a/data/yvis/yvisbioschemas.jsonld b/data/yvis/yvisbioschemas.jsonld index 4a5a80a6fd0c8..39f09fe4f4fa9 100644 --- a/data/yvis/yvisbioschemas.jsonld +++ b/data/yvis/yvisbioschemas.jsonld @@ -13,6 +13,10 @@ "@id": "https://doi.org/10.1093/NAR/GKZ387", "@type": "sc:CreativeWork" }, + { + "@id": "https://orcid.org/0000-0001-7776-8446", + "@type": "schema:Person" + }, { "@id": "https://bio.tools/Yvis", "@type": "sc:SoftwareApplication", @@ -23,14 +27,14 @@ "Liza F Felicori" ], "sc:additionalType": [ - "Web application", - "Database portal" + "Database portal", + "Web application" ], "sc:citation": [ - "pubmed:31106372", { "@id": "https://doi.org/10.1093/NAR/GKZ387" }, + "pubmed:31106372", "pmcid:PMC6602444" ], "sc:description": "Antibody high-density alignment visualization and analysis platform with an integrated database.", @@ -45,15 +49,11 @@ "sc:license": "Unlicense", "sc:name": "Yvis", "sc:operatingSystem": [ - "Linux", "Windows", - "Mac" + "Mac", + "Linux" ], "sc:url": "http://bioinfo.icb.ufmg.br/yvis/" - }, - { - "@id": "https://orcid.org/0000-0001-7776-8446", - "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/zcurve/zcurvebioschemas.jsonld b/data/zcurve/zcurvebioschemas.jsonld index 10c1f4745dce8..5e9fc2ccb01a1 100644 --- a/data/zcurve/zcurvebioschemas.jsonld +++ b/data/zcurve/zcurvebioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "New system for recognizing protein coding genes in bacterial and archaeal genomes with highly accurate gene start prediction. The program is based on the Z curve theory of DNA sequence.", "sc:name": "ZCURVE", "sc:operatingSystem": [ - "Mac", "Linux", - "Windows" + "Windows", + "Mac" ], "sc:url": "http://cefg.uestc.edu.cn/zcurve/" } \ No newline at end of file diff --git a/data/zdock/zdockbioschemas.jsonld b/data/zdock/zdockbioschemas.jsonld index e2dc47be528a9..d2814a83eebbf 100644 --- a/data/zdock/zdockbioschemas.jsonld +++ b/data/zdock/zdockbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "The tool performs a full rigid-body search of docking orientations between two proteins, it includes performance optimization and a novel pairwise statistical energy potential.", "sc:name": "ZDOCK", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://zlab.umassmed.edu/zdock/index.shtml" } \ No newline at end of file diff --git a/data/zebrastm/zebrastmbioschemas.jsonld b/data/zebrastm/zebrastmbioschemas.jsonld index 3f022d4c6eccc..7dad32484bdf2 100644 --- a/data/zebrastm/zebrastmbioschemas.jsonld +++ b/data/zebrastm/zebrastmbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:license": "CC-BY-4.0", "sc:name": "ZebraSTM", "sc:operatingSystem": [ - "Mac", "Windows", + "Mac", "Linux" ], "sc:url": "http://lcc.ens.uabc.mx/~zebrastm/" diff --git a/data/zeus/zeusbioschemas.jsonld b/data/zeus/zeusbioschemas.jsonld index f6ae0d62e7f51..f2b56cb63192a 100644 --- a/data/zeus/zeusbioschemas.jsonld +++ b/data/zeus/zeusbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "A molecular visualization tool that supports PDB, MOL, MOL2/SYBYL and XYZ file formats. The rendering engine can output high quality molecular graphics.", "sc:name": "Zeus alpha", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "http://www.al-nasir.com/www/Jamie/Zeus/" } \ No newline at end of file diff --git a/data/zfin/zfinbioschemas.jsonld b/data/zfin/zfinbioschemas.jsonld index 23e04336bb8ae..727f118c96eeb 100644 --- a/data/zfin/zfinbioschemas.jsonld +++ b/data/zfin/zfinbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. It manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. Data formats include text, images and graphical representations.", "sc:name": "ZFIN", "sc:operatingSystem": [ + "Linux", "Windows", - "Mac", - "Linux" + "Mac" ], "sc:url": "http://zfin.org" } \ No newline at end of file diff --git a/data/zfn-scores/zfn-scoresbioschemas.jsonld b/data/zfn-scores/zfn-scoresbioschemas.jsonld index 6061d83f2e412..a9e820db79435 100644 --- a/data/zfn-scores/zfn-scoresbioschemas.jsonld +++ b/data/zfn-scores/zfn-scoresbioschemas.jsonld @@ -14,9 +14,9 @@ "sc:description": "ZFN-Scores searches a DNA sequence for good zinc finger nuclease target sites. The Extended Modular Assembly method has a 40-60% expected success rate", "sc:name": "ZFN-Scores", "sc:operatingSystem": [ - "Windows", + "Mac", "Linux", - "Mac" + "Windows" ], "sc:url": "http://zinc.genomecenter.ucdavis.edu:8080/Plone/zfn-scoresv6", "sc:version": "v6" diff --git a/data/zfpkm/zfpkmbioschemas.jsonld b/data/zfpkm/zfpkmbioschemas.jsonld index 4ff7f1e2a9605..da8487c7f3d6f 100644 --- a/data/zfpkm/zfpkmbioschemas.jsonld +++ b/data/zfpkm/zfpkmbioschemas.jsonld @@ -9,14 +9,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "https://doi.org/10.1186/1471-2164-14-778", - "@type": "sc:CreativeWork" - }, - { - "@id": "http://orcid.org/0000-0002-1880-3341", - "@type": "schema:Person" - }, { "@id": "https://bio.tools/zfpkm", "@type": "sc:SoftwareApplication", @@ -28,11 +20,11 @@ ], "sc:additionalType": "Library", "sc:citation": [ + "pmcid:PMC3870982", + "pubmed:24215113", { "@id": "https://doi.org/10.1186/1471-2164-14-778" - }, - "pmcid:PMC3870982", - "pubmed:24215113" + } ], "sc:description": "This algorithm is based on the publication by Hart et al., 2013. Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.", "sc:featureList": { @@ -41,12 +33,20 @@ "sc:license": "GPL-3.0", "sc:name": "zFPKM", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/zFPKM.html", "sc:version": "1.2.0" + }, + { + "@id": "http://orcid.org/0000-0002-1880-3341", + "@type": "schema:Person" + }, + { + "@id": "https://doi.org/10.1186/1471-2164-14-778", + "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/zifit/zifitbioschemas.jsonld b/data/zifit/zifitbioschemas.jsonld index b1692186d184b..e2051ebf62575 100644 --- a/data/zifit/zifitbioschemas.jsonld +++ b/data/zifit/zifitbioschemas.jsonld @@ -17,8 +17,8 @@ "sc:name": "ZiFiT", "sc:operatingSystem": [ "Mac", - "Linux", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://bindr.gdcb.iastate.edu/ZiFiT/" } \ No newline at end of file diff --git a/data/zinbwave/zinbwavebioschemas.jsonld b/data/zinbwave/zinbwavebioschemas.jsonld index 247b35ee171ce..b4a0fcee5688c 100644 --- a/data/zinbwave/zinbwavebioschemas.jsonld +++ b/data/zinbwave/zinbwavebioschemas.jsonld @@ -16,8 +16,8 @@ "sc:license": "Artistic-2.0", "sc:name": "zinbwave", "sc:operatingSystem": [ - "Windows", "Mac", + "Windows", "Linux" ], "sc:url": "http://bioconductor.org/packages/release/bioc/html/zinbwave.html", diff --git a/data/zinc_finger_tools/zinc_finger_toolsbioschemas.jsonld b/data/zinc_finger_tools/zinc_finger_toolsbioschemas.jsonld index 0dedefbb15554..77957148f8a12 100644 --- a/data/zinc_finger_tools/zinc_finger_toolsbioschemas.jsonld +++ b/data/zinc_finger_tools/zinc_finger_toolsbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "Provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.", "sc:name": "Zinc Finger Tools", "sc:operatingSystem": [ - "Mac", + "Windows", "Linux", - "Windows" + "Mac" ], "sc:url": "http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php" } \ No newline at end of file diff --git a/data/zincbind/zincbindbioschemas.jsonld b/data/zincbind/zincbindbioschemas.jsonld index d4c84e92a2703..cb73db641d294 100644 --- a/data/zincbind/zincbindbioschemas.jsonld +++ b/data/zincbind/zincbindbioschemas.jsonld @@ -9,6 +9,10 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/database/baz006", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/ZincBind", "@type": "sc:SoftwareApplication", @@ -22,8 +26,8 @@ { "@id": "https://doi.org/10.1093/database/baz006" }, - "pubmed:30722040", - "pmcid:PMC6361820" + "pmcid:PMC6361820", + "pubmed:30722040" ], "sc:description": "Database of zinc binding sites.", "sc:featureList": [ @@ -31,10 +35,10 @@ "@id": "edam:operation_0389" }, { - "@id": "edam:operation_2575" + "@id": "edam:operation_0445" }, { - "@id": "edam:operation_0445" + "@id": "edam:operation_2575" } ], "sc:name": "ZincBind", @@ -44,10 +48,6 @@ "Linux" ], "sc:url": "https://zincbind.bioinf.org.uk/" - }, - { - "@id": "https://doi.org/10.1093/database/baz006", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/zincidentifier/zincidentifierbioschemas.jsonld b/data/zincidentifier/zincidentifierbioschemas.jsonld index 4b37fb778d926..9fc6c1a5dd025 100644 --- a/data/zincidentifier/zincidentifierbioschemas.jsonld +++ b/data/zincidentifier/zincidentifierbioschemas.jsonld @@ -15,8 +15,8 @@ "sc:description": "Datasets and scripts used to apply the trained models to predict zinc-binding sites in proteins.", "sc:name": "Zincidentifier", "sc:operatingSystem": [ - "Mac", - "Linux" + "Linux", + "Mac" ], "sc:url": "http://protein.cau.edu.cn/zincidentifier/" } \ No newline at end of file diff --git a/data/zincpharmer/zincpharmerbioschemas.jsonld b/data/zincpharmer/zincpharmerbioschemas.jsonld index 56f2d41cd1d56..852e1209971e3 100644 --- a/data/zincpharmer/zincpharmerbioschemas.jsonld +++ b/data/zincpharmer/zincpharmerbioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "ZINCPharmer is webserver for screening the purchasable subset of the ZINC database (updates occur monthly). ZINCPharmer can import LigandScout and MOE pharmacophore definitions, as well as identify pharmacophore features directly from a molecular structure.", "sc:name": "ZINCPharmer", "sc:operatingSystem": [ - "Linux", + "Windows", "Mac", - "Windows" + "Linux" ], "sc:url": "http://zincpharmer.csb.pitt.edu" } \ No newline at end of file diff --git a/data/zisland_explorer/zisland_explorerbioschemas.jsonld b/data/zisland_explorer/zisland_explorerbioschemas.jsonld index e9a37fe018d4b..494f376ee815b 100644 --- a/data/zisland_explorer/zisland_explorerbioschemas.jsonld +++ b/data/zisland_explorer/zisland_explorerbioschemas.jsonld @@ -16,8 +16,8 @@ "sc:name": "Zisland Explorer", "sc:operatingSystem": [ "Mac", - "Windows", - "Linux" + "Linux", + "Windows" ], "sc:url": "http://cefg.uestc.edu.cn/Zisland_Explorer/" } \ No newline at end of file diff --git a/data/zlibbioc/bioconda_zlibbioc.yaml b/data/zlibbioc/bioconda_zlibbioc.yaml index 433b88d5c0e3d..06e74d4d88b60 100644 --- a/data/zlibbioc/bioconda_zlibbioc.yaml +++ b/data/zlibbioc/bioconda_zlibbioc.yaml @@ -6,7 +6,6 @@ description: This package uses the source code of zlib-1.2.5 to create libraries home: https://bioconductor.org/packages/3.10/bioc/html/zlibbioc.html identifiers: - biotools:zlibbioc -- doi:10.1038/nmeth.3252 license: Artistic-2.0 + file LICENSE license_file: LICENSE name: bioconductor-zlibbioc diff --git a/data/zlibbioc/zlibbiocbioschemas.jsonld b/data/zlibbioc/zlibbiocbioschemas.jsonld index ccd81bfe7af54..fdf5027328196 100644 --- a/data/zlibbioc/zlibbiocbioschemas.jsonld +++ b/data/zlibbioc/zlibbiocbioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": "BioConductor Package Maintainer", "sc:additionalType": [ - "Command-line tool", - "Library" + "Library", + "Command-line tool" ], "sc:description": "This package creates libraries from the source code of zlib-1.2.5 for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package).", "sc:license": "Artistic-2.0", diff --git a/data/zodiac/zodiacbioschemas.jsonld b/data/zodiac/zodiacbioschemas.jsonld index a236297ef3798..9f76c38f57c83 100644 --- a/data/zodiac/zodiacbioschemas.jsonld +++ b/data/zodiac/zodiacbioschemas.jsonld @@ -9,17 +9,21 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ + { + "@id": "https://doi.org/10.1093/JNCI/DJV129", + "@type": "sc:CreativeWork" + }, { "@id": "https://bio.tools/zodiac", "@type": "sc:SoftwareApplication", "biotools:primaryContact": "Support", "sc:additionalType": "Web application", "sc:citation": [ - "pubmed:25956356", { "@id": "https://doi.org/10.1093/JNCI/DJV129" }, - "pmcid:PMC4554190" + "pmcid:PMC4554190", + "pubmed:25956356" ], "sc:description": "A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data.", "sc:featureList": { @@ -27,10 +31,6 @@ }, "sc:name": "Zodiac", "sc:url": "http://www.compgenome.org/zodiac2/" - }, - { - "@id": "https://doi.org/10.1093/JNCI/DJV129", - "@type": "sc:CreativeWork" } ] } \ No newline at end of file diff --git a/data/zooma/zoomabioschemas.jsonld b/data/zooma/zoomabioschemas.jsonld index 3e68021ad25a9..d6849f2ace69d 100644 --- a/data/zooma/zoomabioschemas.jsonld +++ b/data/zooma/zoomabioschemas.jsonld @@ -20,30 +20,30 @@ "@id": "http://orcid.org/0000-0002-2513-5396" }, "sc:citation": [ + "pubmed:21995944", + "pmcid:PMC3194170", { "@id": "https://doi.org/10.1186/2041-1480-2-S5-S3" - }, - "pmcid:PMC3194170", - "pubmed:21995944" + } ], "sc:description": "ZOOMA 2 is a search engine for automatic curation and a repository of annotation knowledge. It facilitates automated data annotation against a variety of ontologies by exploring context and previous annotation efforts as well as lexical matching", "sc:name": "Zooma", "sc:operatingSystem": [ - "Windows", + "Linux", "Mac", - "Linux" + "Windows" ], "sc:provider": "EMBL-EBI", "sc:url": "http://wwwdev.ebi.ac.uk/fgpt/zooma/", "sc:version": "1" }, - { - "@id": "http://orcid.org/0000-0002-2513-5396", - "@type": "schema:Person" - }, { "@id": "https://doi.org/10.1186/2041-1480-2-S5-S3", "@type": "sc:CreativeWork" + }, + { + "@id": "http://orcid.org/0000-0002-2513-5396", + "@type": "schema:Person" } ] } \ No newline at end of file diff --git a/data/zooscatr/zooscatrbioschemas.jsonld b/data/zooscatr/zooscatrbioschemas.jsonld index 2d81ee2b9a98b..68712e7321304 100644 --- a/data/zooscatr/zooscatrbioschemas.jsonld +++ b/data/zooscatr/zooscatrbioschemas.jsonld @@ -17,9 +17,9 @@ "sc:license": "GPL-3.0", "sc:name": "ZooScatR", "sc:operatingSystem": [ + "Mac", "Linux", - "Windows", - "Mac" + "Windows" ], "sc:url": "https://github.com/AustralianAntarcticDivision/ZooScatR" } \ No newline at end of file diff --git a/data/zorro/zorrobioschemas.jsonld b/data/zorro/zorrobioschemas.jsonld index 7ee8bea853e5c..46b7c2c30417a 100644 --- a/data/zorro/zorrobioschemas.jsonld +++ b/data/zorro/zorrobioschemas.jsonld @@ -12,8 +12,8 @@ "@type": "sc:SoftwareApplication", "biotools:primaryContact": [ "Marcelo Carazzole", - "Gustavo Lacerda", - "Ramon Vidal" + "Ramon Vidal", + "Gustavo Lacerda" ], "sc:additionalType": "Script", "sc:description": "ZORRO is an hybrid sequencing technology assembler. It takes to sets of pre-assembled contigs and merge them into a more contiguous and consistent assembly. The main caracteristic of Zorro is the treatment before and after assembly to avoid errors.", diff --git a/data/zpicture_multi/zpicture_multibioschemas.jsonld b/data/zpicture_multi/zpicture_multibioschemas.jsonld index 417c3e86502ee..368cce3b17d5c 100644 --- a/data/zpicture_multi/zpicture_multibioschemas.jsonld +++ b/data/zpicture_multi/zpicture_multibioschemas.jsonld @@ -16,9 +16,9 @@ "sc:description": "zPicture (pairwise alignment) and multi-zPicture (multiple alignment) are web-based sequence alignment tools based on the blastz alignment program. Alignments from zPicture can be automatically submitted to rVista.", "sc:name": "zPicture and multi-zPicture", "sc:operatingSystem": [ - "Linux", "Mac", - "Windows" + "Windows", + "Linux" ], "sc:url": "http://zpicture.dcode.org/" } \ No newline at end of file diff --git a/data/zt/ztbioschemas.jsonld b/data/zt/ztbioschemas.jsonld index cf08b7ca3b35d..4b427aecab79e 100644 --- a/data/zt/ztbioschemas.jsonld +++ b/data/zt/ztbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:license": "GPL-3.0", "sc:name": "ZT", "sc:operatingSystem": [ + "Mac", "Windows", - "Linux", - "Mac" + "Linux" ], "sc:provider": "ugent.be", "sc:url": "http://bioinformatics.psb.ugent.be/software/details/ZT", diff --git a/data/zygprob/zygprobbioschemas.jsonld b/data/zygprob/zygprobbioschemas.jsonld index 72ae18fb10095..43d1da8381a6d 100644 --- a/data/zygprob/zygprobbioschemas.jsonld +++ b/data/zygprob/zygprobbioschemas.jsonld @@ -15,9 +15,9 @@ "sc:description": "Processes convenient and accurate zygosity probability calculation.", "sc:name": "ZygProb", "sc:operatingSystem": [ - "Mac", + "Linux", "Windows", - "Linux" + "Mac" ], "sc:url": "http://neurogenetics.qimrberghofer.edu.au/ZygProb/" } \ No newline at end of file